Liquid-crystal ordering of photo-switchable molecules on a surface [original]

Liquid-Crystal Ordering of

Photo-Switchable Molecules on a

Surface

vorgelegt von

Diplom-Physiker

Raffaele Tavarone

geboren in Benevento, Italien

von der Fakult¨at II - Mathematik und Naturwissenschaften

der Technischen Universit¨at Berlin

zur Erlangung des akademischen Grades

Doktor der Naturwissenschaften (Dr. rer. nat.)

genehmigte

Dissertation

Promotionsausschuss:

Vorsitzender: Prof. Dr. Martin Schoen

Erster Gutachter: Prof. Dr. Holger Stark

Zweiter Gutachter: Dr. habil. Thomas Gruhn

Tag der wissenschaftlichen Aussprache: 27. 05. 2016

Berlin 2016

D83

Abstract

Photo-switchable molecules are chemical compounds that undergo configurational

changes upon photon absorption. In particular, azobenzene-based photo switches possess

two isomeric stable states: an elongated rod-like trans state and a bent-shaped cis isomer.

In this work we consider model molecules whose shape resembles that of azobenzene-based

molecules and investigate their liquid-crystal assembly in two dimensions, mainly using

computer simulations.

The first part of our study, motivated by the recent interest in the self-assembly of

complex structures in two-dimensional systems, consists in examining the influence of

different molecular geometries on the stability of several spontaneously ordered phases.

We perform extensive Monte Carlo simulations of a two-dimensional bent hard-needle

model in both its chiral zig-zag and its achiral bow-shape configurations and present

their phase diagrams. We find evidence for a variety of stable phases: isotropic, quasi-

nematic, smectic-C, anti-ferromorphic smectic-A, and modulated-nematic. This last

phase consists of layers formed by supramolecular arches. They create a modulation

of the molecular polarity whose period is sensitively controlled by molecular geometry.

We identify transition densities using correlation functions together with appropriately

defined order parameters and compare them with predictions from Onsager theory. The

contribution of the molecular excluded area to Onsager theory and simple liquid crystal

phase morphology is discussed. We demonstrate the isotropic–quasi-nematic transition

to be consistent with a Kosterlitz-Thouless disclination unbinding scenario.

The second part of our study is motivated by the growing interest in monolayers of

photo-switchable molecules. They can be used as glassy systems with light-controllable

dynamics. Recent experiments have demonstrated that, in a dense monolayer of photo-

switchable dye Methyl-Red molecules, the relaxation of an initial birefringence follows a

power-law decay, typical for glass-like dynamics. The slow relaxation can efficiently be

controlled and accelerated by illuminating the monolayer with circularly polarized light,

which induces trans-cis isomerization cycles. To elucidate the microscopic mechanism,

we develop a two-dimensional molecular model in which the trans and cis isomers are

represented by straight and bent needles, respectively. As in the experimental system,

the needles are allowed to rotate and to form overlaps but they cannot translate. The

out-of-equilibrium rotational dynamics of the needles is generated using kinetic Monte

Carlo simulations. We demonstrate that, in a regime of high density and low temperature,

the power-law relaxation can be traced to the formation of spatio-temporal correlations

in the rotational dynamics. These correlations correspond to the presence of transient

domains of fast- and slowly-rotating molecules, i.e., dynamic heterogeneity. We also show

that the nearly isotropic cis isomers can prevent dynamic heterogeneities from forming

in the monolayer and that the relaxation then becomes exponential.

Zusammenfassung

Photoschaltbare Molek¨ule sind chemikalische Stoffe, die konfigurative ¨

Anderungen

unter Photonenabsorbtion durchlaufen. Insbesondere Azobenzol-basierte Photoschalter

nehmen zwei isomerische stabile Zust¨ande an: ein l¨anglicher, st¨abchenf¨ormiger

trans-Zustand und ein gekr¨ummter cis-Isomer. In dieser Arbeit untersuchen wir

Modellmolek¨ule, deren Form der Azobenzol-basierten Molek¨ulen ¨ahnelt und untersuchen

ihre Fl¨ussigkristallanordnungen in zwei Dimensionen, wobei wir haupts¨achlich von

Computersimulationen Gebrauch machen.

Der erste Teil unserer Studie, motiviert durch j¨ungst aufkommendes Interesse an

Selbstorganisation von komplexen Strukturen in zweidimensionalen Systemen, besteht

in der Untersuchung des Einflusses von unterschiedlichen, molekularen Geometrien

auf die Stabilit¨at spontan organisierter Zust¨ande. Wir f¨uhren umfangreiche Monte-

Carlo-Simulationen eines zweidimensionalen Modells gekr¨ummter, harter Nadeln

sowohl in einer chiralen Zickzack-, als auch in einer achiralen bogenf¨ormigen

Konfiguration durch und pr¨asentieren Phasendiagramme. Wir finden verschiedene

stabile Zust¨ande: isotrope, quasi-nematische, smektisch-C, anti-ferromorphe smektisch-

A und modulierte, nematische Zust¨ande. Letzterer besteht aus Schichten aus

supramolekularen B¨ogen. Sie kreieren eine neue molekulare Polarit¨at, deren

Periodizit¨at sensibel durch die molekulare Geometrie bestimmt wird. Wir identifizieren

Ubergangswahrscheinlichkeitsdichten mithilfe von Korrelationsfunktionen zusammen mit

geeignet definierten Ordnungsparametern und vergleichen sie mit Voraussagen aus der

Onsager-Theorie. Der Einfluss von molekularer ”excluded area” auf die Onsager-

Theorie und die Morphologie von Fl¨ussigkristallzust¨anden wird diskutiert. We

zeigen, dass der isotrop-quasi-nematische Phasen¨ubergang mit einem Kosterlitz-Thouless

Abl¨osungsszenario konsistent ist.

Der zweite Teile unserer Studie ist durch das ansteigende Interesse an Monoschichten

von photoschaltbaren Molek¨ulen motiviert. Sie k¨onnen als Glassysteme mit

lichtkontollierbarer Dynamik verwendet werden. Neuerliche Experimente haben

aufgezeigt, dass eine initiale Doppelbrechung in einer dichten Monoschicht von

photoschaltbaren methylroten Molek¨ulen einem Potenzgesetz folgend abklingt, so wie

man es aus glas¨ahnlichen Systemen kennt. Die langsame Relaxation kann effizient

durch Bestrahlen mit zirkularpolarisiertem Licht der Monoschicht gesteuert werden,

was zu trans-cis Isomerisierungszyklen f¨uhrt. Um den mikroskopischen Mechanismus

zu beleuchten, entwickeln wir ein zweidimensionales, molekulares Modell, in dem die

trans and cis Isomere von geraden und gekr¨ummten Nadeln repr¨asentiert werden.

Wie in den Experimenten k¨onnen die Nadeln rotieren und ¨uberlappen aber sich nicht

verschieben. Die Nichtgleichgewichtsrotationsdynamik der Nadeln wird mit kinetischen

Mont-Carlo-Simulationen generiert. Wir zeigen, dass in einem Bereich mit hoher

Dichte und geringer Temperatur die Potenzgesetz-Relaxation auf Ort-Zeit-Korrelationen

der Rotationsdynamik zur¨uckgef¨uhrt werden kann. Diese Korrelationen basieren auf

transienten Bereichen von schnell und langsam rotierenden Molek¨ulen, das heißt auf

dynamischer Heterogenit¨at. Wir zeigen auch, dass die fast isotropen cis Isomere

dynamische Heterogenit¨aten in der Monoschicht verhindern k¨onnen und in diesem Fall

die Relaxation exponentiell verl¨auft.

Contents

Abstract iii

Zusammenfassung v

Contents vii

1 Introduction 1

2 Liquid-Crystalline Order 5

2.1 Introduction to liquid crystals . . . . . . . . . . . . . . . . . . . . . . . . 5

2.2 Nematicorder................................. 7

2.2.1 Onsager theory: heuristic approach . . . . . . . . . . . . . . . . . 9

2.2.2 Frank-Oseen-Zocher elastic theory . . . . . . . . . . . . . . . . . . 11

2.2.3 Optical birefringence . . . . . . . . . . . . . . . . . . . . . . . . . 12

2.2.4 Topological defects . . . . . . . . . . . . . . . . . . . . . . . . . . 14

2.3 Nematic order in two dimensions . . . . . . . . . . . . . . . . . . . . . . 17

2.3.1 Quasi-long-range orientational order . . . . . . . . . . . . . . . . 17

2.3.2 Disclination unbinding . . . . . . . . . . . . . . . . . . . . . . . . 20

2.4 Smecticorder ................................. 21

2.4.1 Smectic order in three dimensions . . . . . . . . . . . . . . . . . . 21

2.4.2 Smectic order in two dimensions . . . . . . . . . . . . . . . . . . 23

2.4.3 Polar smectic phases . . . . . . . . . . . . . . . . . . . . . . . . . 25

2.5 Distorted nematic phases . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

2.6 Onsagertheory ................................ 27

2.6.1 Virialexpansion............................ 27

2.6.2 Application to non-spherical hard-core particles . . . . . . . . . . 29

2.6.3 Numerical evaluation of the excluded area . . . . . . . . . . . . . 32

2.7 Orderparameters............................... 33

3 Photo-Switchable Molecules and Applications 37

3.1 Introduction to photo-switchable molecules . . . . . . . . . . . . . . . . . 37

3.2 Photochemical properties of azobenzene . . . . . . . . . . . . . . . . . . 38

3.3 Light-induced orientational order . . . . . . . . . . . . . . . . . . . . . . 40

3.4 Light-control of the birefringence relaxation . . . . . . . . . . . . . . . . 42

3.4.1 Rotational dynamics . . . . . . . . . . . . . . . . . . . . . . . . . 44

vii

Contents viii

3.4.2 Non-exponential relaxation processes . . . . . . . . . . . . . . . . 45

4 Numerical Methods 49

4.1 MonteCarlosimulation............................ 49

4.1.1 NV T Monte Carlo simulation . . . . . . . . . . . . . . . . . . . . 51

4.1.2 NPT Monte Carlo simulation . . . . . . . . . . . . . . . . . . . . 52

4.2 Optimization techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

4.2.1 Anisotropic neighbor list . . . . . . . . . . . . . . . . . . . . . . . 53

4.2.2 Clustermoves............................. 54

4.3 Kinetic Monte Carlo simulation . . . . . . . . . . . . . . . . . . . . . . . 56

5 Phase Behavior of the Bent Hard-Needle Model 59

5.1 Bent hard-needle model . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

5.2 Details of the Monte Carlo simulation . . . . . . . . . . . . . . . . . . . . 60

5.3 Isotropic–quasi-nematic transition . . . . . . . . . . . . . . . . . . . . . . 61

5.4 Quasi-nematic–smectic transition . . . . . . . . . . . . . . . . . . . . . . 63

5.5 Modulated-nematic phase . . . . . . . . . . . . . . . . . . . . . . . . . . 65

5.6 Phasediagram ................................ 68

5.7 Summary ................................... 69

6 Birefringence Relaxation of Photo-Switchable Molecules on a Surface 71

6.1 Molecularmodel ............................... 72

6.2 Details of kinetic Monte Carlo simulations . . . . . . . . . . . . . . . . . 73

6.3 Birefringence relaxation . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

6.4 Relaxation dynamics in a pure trans system ................ 76

6.5 Relaxation dynamics during isomerization . . . . . . . . . . . . . . . . . 81

6.5.1 Thermalerasure............................ 81

6.5.2 CPerasure .............................. 83

6.5.3 Comparison between thermal and CP erasure . . . . . . . . . . . 86

6.6 Summary ................................... 87

7 Conclusion 89

A Power-law birefringence relaxation 93

List of Publications 97

Bibliography 99

Acknowledgements 115

Chapter 1

Introduction

The possibility to control organic and inorganic materials at the molecular, nanoscale level

is crucial for a large variety of advanced applications and for a deeper understanding

of matter [1–8]. In particular, interest in two-dimensional and quasi-two-dimensional

structures in thin films has grown tremendously in recent years [9–11]. Molecular order

can be fine tuned in thin films, which makes them suitable for myriad of technological

applications [12], ranging from electronics [13] and optics [14] to biology [15].

Control over molecular ordering is achieved, on the one hand, by understanding how

the characteristics of a single molecule influence the spontaneous self-assembly of large

aggregate, and, on the other hand, by studying how the molecules responds to external

stimuli, which can be employed to control the formation of peculiar structures. In the first

case, investigating how molecular geometry determines the characteristics of aggregates is

certainly crucial. A common starting point for studying this relation are hard-core models,

which capture the static and dynamical properties of a wide range of phenomena, from

the hard-sphere-like freezing of atomic liquids [16] to quasicrystal formation [17]. In the

second case, among possible tools for molecular control, light is one of the most promising.

Some of the appealing applications include: illuminating the metallic tip of a scanning

force microscopy to precisely control the position of single molecules [2], using nanowires

to build miniaturized photonic devices [4], and inscribing nano-sized geometrical patterns

on a surface by photolithography [18].

Photochromic molecular switches, molecules that undergo configurational changes

between two (or even more) isomeric states when irradiated by light [19], offer yet another

appealing way to control material properties with light. Photo-switchable molecules

are attracting huge interest because, when incorporated into a monolayer, illumination

with light of proper wavelength results in a drastic change of the monolayer macroscopic

properties. These systems belong to the class of functional monolayers. To give a few

examples, one can control the surface wettability [20], induce deterministic nanotexturing

[21], encode information [22], and tune the electrical conductivity of the monolayer [23].

In this Thesis we investigate the formation and the control of liquid-crystal order in two

dimensions – both by self-assembly and by illumination with light – using model molecules

whose shape resembles that of the azobenzene, an important photo-switchable compound.

Indeed, the self-organized formation of liquid-crystal phases on two-dimensional surfaces

is key to various nanotechnological applications [24–26], but it is also possible to employ

photo-switchable molecules to reorient a nematic liquid crystal or directly control both

the formation and relaxation of orientational order in a monolayer [1, 27–31].

In applications involving liquid-crystal materials, azobenzene is the most commonly

used photo-switch [32]. It possesses two stable states, a trans and a cis isomer, whose

Chapter 1. Introduction 2

zig-zag bow-shaped

Model trans Model cis

NNN

Azobenzene

trans

Azobenzene

cis

Figure 1.1: (a) Structures of trans and cis isomers of azobenzene. (b) The two isomers are

modeled by an infinitely thin needle for the trans configuration and a bent version for the cis

molecule. (c) Bent-needle model molecule in chiral zig-zag (left) and achiral bow-shaped (right)

configurations.

structure is shown in Fig. 1.1(a). In the trans form, azobenzene is elongated and rod-

like while the cis isomer has a bent shape. Inspired by the conformational switch

of azobenzene-based molecules upon isomerization, we build a simple model for these

compounds. The model allows us to study the consequences of a basic morphological

change of the molecules on their equilibrium and out-of-equilibrium assembly in two

dimensions. Our study mainly consists of two parts. In the first part, we consider how

different molecular shapes influence the equilibrium self-assembly properties of the system.

In a second part, inspired by recent experimental results of Fang et al. [1], we study how

the isomerization process influences the out-of-equilibrium dynamics of a self-assembled

monolayer.

The first part of our study is motivated by recent interest in controlling the self-

assembly of two-dimensional structures. Indeed, nowadays it is possible to obtain thin

aggregates with quasicrystalline [33–36], hexagonal [37], crystalline [38], and liquid-

crystalline [39–41] order. Because hard-core models are known to reproduce the rich

two-dimensional liquid-crystal ordering of objects with high aspect ratios such as rods

[42–44], rectangles [45, 46], spherocylinders [47, 48], and ellipsoids [49, 50], we consider

the two-dimensional phase behavior of a bent hard-needle model in both its chiral zig-

zag and achiral bow-shaped configurations [Fig. 1.1(c)]. These two versions display

significantly different mesophases, for which we map out complete phase diagrams.

Zig-zag molecules are known to assemble in either a nematic or a smectic-C phase

depending on the packing density ρ[51, 52], and bow-shaped molecules have been

found to display tetradic and nematic order [53]. Yet these studies did not clarify

Chapter 1. Introduction 3

the role of topological defects and of thermal fluctuations on the long-range stability

of the mesophases, which are of fundamental physical interest [54–56]. The relatively

coarse sampling of configuration space in previous studies left open the possibility that

qualitative features of the molecular ordering have been missed. Indeed, we find that,

in addition to forming quasi-nematic and smectic phases, bow-shaped molecules assume

a stable modulated-nematic phase, comparable to what was previously predicted [57]

and observed [58, 59] in three-dimensional systems. Our improved results are not only

made possible by the use of specialized Monte Carlo simulations of large systems, but

also by the definition of appropriate order parameters and correlation functions. Our

analysis thence extends investigations of two-dimensional systems of hard needles [44,

60, 61], hard spherocylinders [42, 48], and spherocylinders with a polar head [62]. These

improved numerical results on two-dimensional liquid crystal formation are also compared

to predictions from Onsager theory [63].

In the second part of this study we consider a self-assembled monolayer of light-

switchable molecules tethered to a surface. We perform kinetic Monte Carlo simulations

for a molecular model, where we approximate the two isomeric states, trans and cis, by a

straight and a bent needle, respectively [Fig. 1.1(b)]. The simplicity of the model allows

us to study the long-time collective dynamics of a statistical ensemble consisting of 10,000

molecules [64], much more than atomistic molecular dynamics simulations can handle.

As mentioned before, our work is motivated by a recent experimental study of Fang

et al. [1] on the glasslike orientational dynamics of a self-assembled monolayer of photo-

switching molecules. After aligning the molecules with light, the authors observed the

decay of orientational order (or birefringence) under either thermal erasure or erasure with

circularly polarized (CP) light. In both cases they find that the relaxation of birefringence

follows a power law, which is typical for glasslike dynamics. Within our relatively simple

model we can reproduce this feature in a system containing straight needles alone (trans

molecules), if the density is sufficiently high and temperature is low. We demonstrate

that the needles, when randomizing their orientations, develop dynamic heterogeneities in

space and time [65, 66], which ultimately cause the power-law decay. The presence of cis

molecules, which have a rather isotropic shape, can prevent the formation of such spatio-

temporal variations in the local structure and the birefringence relaxation then becomes

exponential. In the following, we clarify under which conditions our model reproduces

the experimental observation of a power-law decay by tuning isomerization probabilities.

This Thesis is organized as follows. In Chapter 2 we introduce the liquid-crystal

order, with particular focus on the liquid-crystal phases observed in the bent hard-

needle model. In Chapter 3 we detail the photo-chemical properties of photo-switchable

molecules and review some of their most appealing applications. Additionally, we describe

the experiments presented in Ref. [1], which motivate part of our theoretical study. In

Chapter 4 we introduce the numerical methods relevant for our work. In Chapter 5 we

present the complete phase diagram of the bent hard-needle model. In Chapter 6 we

detail our model for the self-assembled monolayer of light-switchable molecules of Ref. [1]

and we discuss the related dynamics, as generated by kinetic Monte Carlo simulations.

In Chapter 7 we conclude our investigation and we give an outlook of the possible future

directions of our research.

Part of this work has been published in Refs. [A] and [B].

A. Tavarone, R., Charbonneau, P. & Stark, H. Phase ordering of zig-zag and bow-

shaped hard needles in two dimensions. J. Chem. Phys. 143, 114505 (2015).

Chapter 1. Introduction 4

B. Tavarone, R., Charbonneau, P. & Stark, H. Kinetic Monte Carlo simulations for

birefringence relaxation of photo-switchable molecules on a surface. J. Chem. Phys.

144, 104703 (2016).

Chapter 2

Liquid-Crystalline Order

In this Chapter we discuss the liquid-crystalline state of matter, with particular focus on

the liquid-crystal phases identified in the bent hard-needle model [Fig. 1.1(c)]. In Sec.

2.1 we introduce liquid crystals and some terminology and we give a short overview of

this enormous, very intriguing, and constantly growing research field. Two fundamental

liquid-crystalline phases (nematic and smectic) are discussed more deeply in Sections

2.2, 2.3 and 2.4. In Section 2.5 we discuss a nematic phase with energetically stable

deformations, the modulated-nematic phase, which is currently attracting interest and

that is relevant for the following discussion. Because we are interested in the phases

formed by bent needles on a two-dimensional surface, we also clarify how the system low

dimensionality influences the long-range stability of these phases. In Sec. 2.6 we discuss

the Onsager theory and its application to the phase behavior of hard-core molecular

liquids. Finally, in Sec. 2.7 we summarize and detail our definition of the order parameters

and associated correlation functions used to study the phase ordering of the bent-needle

model.

2.1 Introduction to liquid crystals

Liquid crystals (LC) are materials characterized by a degree of molecular ordering, which

is intermediate between the lack of structure of a liquid and the perfect ordering of a

crystal [67–69]. A phase with such a partial ordering is called a mesophase, and molecules

able to arrange in a mesophase are called mesogens. In a mesophase, some macroscopic

properties of the material, as light propagation or viscosity, typically are anisotropic.

The investigation of liquid crystals dates back to 1888, when the Austrian botanic

Friedrich Reinitzer discovered the first example of a material which belongs to the class

of what are now called cholesteric liquid crystals [70]. Since then, a large variety of

different mesophases have been identified. Here, we give a overview of the fundamental

classifications of these materials and refer the interest reader to more detailed texts.

Classically, liquid crystals are divided into thermotropic [68, 71], lyotropic [68] and

polymeric [72]. In thermotropic LCs the state of the material is fully determined by

the temperature of the system, while lyotropic LCs consist of a combination of aqueous

solutions and amphiphilic substances whose concentration also determines the state of

the system. Above a certain concentration, amphiphile molecules form micelles. Further

increase of the concentration eventually leads to formation of micellar aggregates with

liquid-crystalline properties. In polymeric liquid crystals, polymers act as mesogens.

Chapter 2. Liquid crystals 6

Nematic Columnar Smectic-A Smectic-C

Figure 2.1: Schematic illustration of some fundamental mesophases formed by calamitic and

discotic mesogens.

The macroscopic anisotropy of thermotropic LC is a consequence of the anisotropy

of the constituent mesogens. Classically, such mesogens are classified according to their

shape: rod-like molecules are called calamitic and plate-like molecules are called discotic

[73]. Figure 2.1 schematically illustrates four fundamental liquid-crystal phases: calamitic

mesogens arrange in nematic and smectic phases while discotic mesogens arrange in

nematic and columnar phases. These phases typically occur in the sequence isotropic

→nematic →smectic or isotropic →nematic →columnar with decreasing temperature.

The discotic columnar phase consists of molecules stacked in columns. The positions

of the molecules along a column are liquid-like, but the columns themselves form a two-

dimensional lattice of various symmetries. In the nematic phase molecules are aligned

along one spatial direction (the nematic director) but their positions are randomly

distributed. Nematic liquid crystals are discussed in more detail in Secs. 2.2 and 2.3.

In addition to orientational order, the smectic phase possesses positional order along one

spatial direction, because molecules are arranged in layers. More details on the smectic

phase are given in Section 2.4. For now, we note that the smectic phase is further sub-

divided into smectic A, B, C, I, F, L [40, 74]. In the smectic A phase molecules are oriented

along the layer normal while in the smectic C phase the orientation of the molecules is

tilted with respect to the layer normal by a fixed angle. In both cases the positions of

the molecules within each layer are liquid-like. By further lowering temperature, one can

eventually access the hexatic smectic phases B, I, L and F in which molecular positions

possess a sixfold rotational symmetry within each layer (hexatic order).

Chiral molecules (chemical groups that cannot be superimposed to their mirror

images) are a special class of mesogens [75, 76]. These compounds can form special

macroscopic structures, since the chirality of the mesogens induces chirality in the related

mesophase. For example, a chiral nematic phase (called cholesteric for historical reasons)

is a nematic phase in which the nematic director slowly rotates around one axis, thus

forming an helix. Frustrated chiral phases are more complicated structures that are

usually found in a narrow range of temperature. Some examples are the blue phases [77]

or the twist-grain boundary phase [78, 79].

Another important class of liquid crystal formers are bent-core or banana-shaped

molecules [80, 81]. The mesogenic properties of these molecules have been recognized

relatively recently, starting from the pioneering work of Matsunaga and Matsuzaki [82]

and Cladis and Brand [83] in 1993. It was, however, after the publication of the work

by Takezoe and collaborators in 1996 [84] that the interest in the field exploded, since

Chapter 2. Liquid crystals 7

banana-shaped molecules where recognized as the first achiral molecules able to arrange

in ferroelectric and antiferroelectric structures.

Liquid crystals based on bent-core molecules have astonishing properties: they can

form at least 7 different mesophases [80], characterized by highly non-linear optic effects

[85]. Even more recently, in 2001, Dozov proposed that the achiral shape of a bent-core

mesogen can induce a spontaneous local bending of the nematic director that can result

in splay-bend oscillations or conical twist-bend helix [57]. The existence of the latter

phase has been later demonstrated experimentally by Noel Clark and coworkers in 2013

[86]. We discuss more deeply the stable deformations of the nematic director field in

Section 2.5.

Liquid-crystal materials can also be photoresponsive: anisotropic order can be induced

or modified by illumination of the sample with light [27, 87, 88]. This property is

achieved by incorporating in the LC material light-absorbing molecules, which are able

to switch between different stable configurations upon irradiation. The light-absorbing

molecules can be either dispersed in a host liquid-crystal matrix or they can be directly

used as mesogens. In both cases, the modification induced by light at the microscopic

level are reflected in a sensitive change in the macroscopic properties of the material.

Photoresponsive liquid crystal are not simply thermotropic since illumination does not

necessarily induce significant heating. Because of the importance that photoresponsive

LC have for this work, we discuss the subject more extensively in Chap. 3.

Before concluding this short overview, we note that one of the most promising research

direction in the liquid-crystal field is nowadays represented by the possibility to obtain

non-equilibrium mesophases using active matter [89]. The individual components of an

active system dissipate energy and move in a collective fashion. When these individual

components are elongated objects they can form liquid-crystalline states with surprising

out-of-equilibrium dynamical and rheological properties [90, 91].

Finally, we refer the interested reader to Ref. [68] and Ref. [72] for a discussion on

lyotropic and polymeric liquid crystal, respectively.

2.2 Nematic order

In a nematic phase mesogens tend to be aligned along one common axis, identified by a

unit vector ncalled the director. This phase is characterized by the following properties

[67]:

1) The correlation between the mesogens positions is only short-ranged, resembling

that of a liquid.

2) Two states characterized by nand −nare by all means indistinguishable.

3) A nematic liquid crystal has full cylindrical symmetry around n.

From the molecular point of view, a nematic phase can be described by an orientational

distribution function peaked around an arbitrary direction (all the directions of nare

equivalent). Let us consider a rod as a simple mesogen able to form a nematic phase.

The orientation of the rod is defined by a vector u. In three dimensions ucan be expressed

in terms of the polar angles (θ, ϕ) as

ux= sin θcos ϕ , uy= sin θsin ϕ , uz= cos θ . (2.1)

The orientation of the system is therefore characterized by a distribution function f(θ, ϕ),

where f(θ, ϕ)dΩ gives the probability to find a rod in the solid angle dΩ = sin θ dθ dϕ

Chapter 2. Liquid crystals 8

around (θ, ϕ). If we assume that the nematic director is oriented along z, because of

property 3, f(θ, ϕ) is independent of ϕ(cylindrical symmetry). We can now look for a

quantity which characterizes the degree of alignment in the system. Because there is no

polar order in the system, the quantity

⟨cos θ⟩=f(θ) cos θ dθ , (2.2)

vanishes (⟨cos θ⟩= 0) and one has to look at higher-order quantities. One possibility is

to use

S=1

2⟨3 cos2θ−1⟩=1

2f(θ)[3 cos2θ−1] dθ , (2.3)

which gives S= 1 if f(θ) is peaked around θ= 0 or θ=π, and S= 0 if f(θ) is uniform

(⟨cos2θ⟩= 1/3). Therefore, Sis a good measure of the degree of alignment of a nematic

liquid crystal and it is called the Maier-Saupe order parameter.

In other words, because of the symmetry properties of the nematic phase, it is not

possible to define a vector order parameter, and a nematic LC needs to be described

by tensorial quantities. Indeed, if we consider a system of Nmolecules, in which the

orientation of a single molecules is described by a unit vector u(i), a natural generalization

of Eq. (2.3) is

Qαβ =1

2N⟨



i=1 3u(i)

αu(i)

β−δαβ⟩,(2.4)

where δis the Kronecker symbol and α, β =x, y, z. The tensor Qis called the tensor

order parameter, it is symmetric and of zero trace. To demonstrate the properties of Q,

it is convenient to express u(i)in spherical coordinates as in Eq. (2.1). In this way

Qαβ =1

22π

dϕ π

sin θ dθ f(θ, ϕ)3uαuβ−δαβ.(2.5)

In the isotropic phase the distribution function is independent of the molecular

orientation. The normalization condition

2π

dϕ π

sin θdθ f(θ, ϕ)=1,(2.6)

gives fiso = 1/4π. Using fiso together with Eqs. (2.1) in Eq. (2.5) gives, for example,

Qxx =1

2fiso 2π

dϕ π

sin θdθ (3 cos2ϕsin2θ−1) = 0 .(2.7)

Similar calculations for the other components show that, in the isotropic phase, Q= 0.

In a perfectly aligned uniaxial nematic phase, assuming that molecules are oriented

along the zaxis, it is sufficient to evaluate Qzz = (3uzuz−1)/2 = 1 and the other

components are immediatly obtained considering that Qis symmetric and of zero trace:

Q=

−1/200

0−1/2 0

0 0 1

.(2.8)

Chapter 2. Liquid crystals 9

The tensor order parameter is a good quantity to characterize nematic order. In many

situations however, it is convenient to use some simple quantity, like Sin Eq. (2.3), to

quantify the degree of alignment more directly. This is usually done by writing the tensor

order parameter in a coordinate system where it is diagonal. Because the tensor order

parameter is a 3 ×3 symmetric matrix, the diagonalization gives three real eigenvalues.

The eigenvector corresponding to the eigenvalue with the largest absolute value indicates

the direction along which molecules are more strongly aligned, and it is therefore the

natural candidate for the nematic director n. The largest eigenvalue quantifies the degree

of alignment along the correspondent direction and it is therefore identified with S. For

an uniaxial nematic phase the tensor order parameter can thus be written as

Qαβ =S

2(3nαnβ−δαβ).(2.9)

Having identified a proper order parameter for the nematic phase, we can now

discuss some of the approaches used to study the transition between an isotropic phase

(uniform distribution of molecular alignment) and a nematic phase with a well-defined

average orientation. This is the isotropic–nematic transition and it is one of the most

extensively studied phase transition in the LC literature. Therefore, in the following we

just summarize the basic features of the main approaches to this problem, with a special

attention to those having relevance in the following Chapters of this thesis.

2.2.1 Onsager theory: heuristic approach

The simplest microscopic picture of a nematic phase is given by the Onsager theory. In

his seminal work [92], Onsager assumed that the nematic mesogens are rods of length L

and diameter D. The rods feel an hard-core repulsion, i.e., they cannot interpenetrate

each other. In theory, a nematic liquid crystal is thus treated as an extension of a fluid

of hard spheres [93], with the only exception that the molecules have now an highly

anisotropic shape. The shape anisotropy is responsible for the formation of a nematic

phase at high density. The theory, based on an expansion of the free energy in powers of

the orientational density, is detailed in Sec. 2.6. In this section we provide an heuristic

argument, which demonstrates the isotropic-nematic transition in a system of elongated

hard molecules.

A central concept in the Onsager theory is the excluded volume. Given two rods with

orientation defined, respectively, by u(1) and u(2), the excluded volume, Vexl(u(1),u(2)), is

the portion of space not accessible to rod 2 because it will result in an overlap with rod

1 (see Fig. 2.2). For very long rods (L≫D) one shows that

Vexl(u(1),u(2))∼2L2Dsin γ , (2.10)

where γis the angle between u(1) and u(2).

At constant temperature and density, the internal energy of hard-core systems is fixed.

Hence, according to the second law of thermodynamics, if the system orders it can only do

so by increasing its entropy. This counter-intuitive picture (an ordered system with higher

entropy than a disordered one) is indeed the correct explanation for the isotropic-nematic

transition in the Onsager theory: at sufficiently high density, the loss in orientational

entropy is compensated by an increase in translational entropy.

This statement can be made quantitative by using the Boltzmann entropy of an

isolated system of Nmolecules in a volume Vin order to evaluate the difference in

Chapter 2. Liquid crystals 10

a) b)

Figure 2.2: The light-grey region represents the excluded area for two rods with orientation

defined by u(1) and u(2). The angle between the two orientations is γ. In (a) we give a side

view of the excluded area while in (b) the view is from the top.

the entropy in the isotropic and the nematic phase. The translational entropy can be

estimated by considering the amount of free volume available. Using Eq. (2.10) and

assuming that the excluded volume in the nematic phase is approximately zero,

∆Stranslation =Snematic −Sisotropic =kBln( V

V−NVexl

)≈kBρL2D , (2.11)

where ρ=N/V is the number density. The orientational entropy is proportional to the

number of accessible orientational states Ω,

∆Sorientation =Snematic −Sisotropic =kBln Ωnematic

Ωisotropic ∝ −kB,(2.12)

where the proportionality is up to a positive constant because Ωnematic <Ωisotropic. At the

isotropic-nematic transition the two contribution are balanced

∆Stranslation + ∆Sorientation = 0 ,(2.13)

which gives a good estimate for the transition density ρI−N∝1/L2D,i.e., longer rods

form a nematic phase at lower density. The result can also be expressed in terms of rod

volume concentration Φ:

ΦI−N=Vrods

VI−N∝NLD2

NL2D=D

L.(2.14)

A more precise calculation shows that, at the transition point, the nematic and the

isotropic phase coexists, with ΦN= 4.5D/L for the nematic phase and ΦI= 3.3D/L in the

isotropic phase. In the nematic phase the order parameter is S≈0.8 [67]. Onsager theory

predicts therefore a first order transition between a disordered and an highly ordered phase

separated by a sudden jump in density. Also, due to the hard-core interaction potential

the transition point is independent of temperature.

In order to overcome these limitations, a mean-field theory has been proposed in 1958

by Maier and Saupe [94]. In their theory two mesogens with orientations respectively

defined by the unit vectors uand u′interact via a pair potential which favors molecular

Chapter 2. Liquid crystals 11

alignment, V(u,u′)∝P2(u·u′) where P2is the second Legendre polynomial. The Maier-

Saupe theory predicts a first-order isotropic–nematic phase transition with decreasing

temperature [67].

2.2.2 Frank-Oseen-Zocher elastic theory

Once a proper order parameter has been defined, as we did in Eq. (2.4), Landau theory

allows us to express the free energy density of the system as an analytic function of it.

In the Landau-de Gennes approach, the free energy density of a nematic liquid crystal

is expanded in power series of the tensor order parameter Qdefined in Eq. (2.4). The

expansion must contain all the possible combinations of Qthat are invariant under rigid

rotation of the axes. Up to the fourth order (summation over repeated indices is implied)

the free energy density reads

F=Fi+1

2AQαβQαβ −1

3BQαβQβγQγα +1

4CQαβQαβQγδQγδ ,(2.15)

where Fiis the free energy density of the isotropic phase and A,Band Care temperature-

dependent coefficients. The third-order term in Eq. (2.15) is absent in the Landau free

energy of magnetic systems due to their vectorial symmetry, but it is present in Eq.

(2.15) due to the equivalence between nand −n. It is because of this term that the

isotropic–nematic phase transition is first order [67].

A free energy density of the type of Eq. (2.15) implies that the tensor order

parameter is spatially uniform. In reality, a nematic liquid crystal shows spatial variation

of the orientational order. Hence, the next natural step in the development of a

continuous theory consists in introducing an explicit spatial dependence of the tensor

order parameter.

Because we want the theory to be continuous, we shall assume that the molecular

orientation varies slowly relative to the molecular length. Under this assumption, a

spatially dependent tensor order parameter can be properly defined by making the

nematic director dependent on its spatial coordinates, i.e.,n→n(r) [see Eq. (2.9)].

With this definition we can now write the free energy density, Fd, associated with the

distortion of the nematic director. Fdhas to be a function of all the combinations of the

spatial derivatives of n(r) that are compatible with the symmetry of the nematic phase.

The usual approach is to retain only first and second order terms in the derivatives of the

local nematic director, ∇αnβ(r), and to impose uniaxial symmetry [95, 96].

The evaluation of all these terms is a rather tedious operation, and we refer the

reader to Ref. [95] for a complete discussion. After some algebra the distortion free

energy density of an uniaxial, centrosymmetric (non-cholesteric) nematic liquid crystal in

the bulk is conveniently written as

Fd=1

2K1(∇·n)2+1

2K2(n·(∇×n))2+1

2K3(n×(∇×n))2(2.16)

where K1,K2and K3are three positive constant with the dimension of energy/length.

Equation (2.16) is the Frank-Oseen-Zocher (FOZ) elastic free energy density for a

nematic liquid crystal in the bulk [96–98]. It tells us that the ground state of a nematic

material is the spatially uniform orientation, and each distortion costs elastic energy. The

terms in the FOZ free energy density have a well defined physical interpretation: they

evaluate, respectively, splay, twist and bend deformations. These elastic deformations are

Chapter 2. Liquid crystals 12

splay twist bend

Figure 2.3: Schematic illustration of the splay, twist and bend elastic deformation of a nematic

liquid crystal. Each term in Equation (2.16) is associated with one of these deformations.

illustrated in Fig. 2.3. Calamitic liquid crystals usually have K3≥K1> K2(bending

costs much more energy than twisting) while discotic liquid crystals have K2≥K1> K3

[99].

A summary of the theoretical approaches to the calculation of the elastic constants

of uniaxial nematic LC can be found in Ref. [100]. They can also be determined in

computer experiments using the orientational fluctuation of the tensor order parameter

as a function of a wave vector [101–103].

Due to the complexity of Eq. (2.16), it is very common to treat the FOZ free energy

using the so called one-constant approximation, which consists in setting K1=K2=

K3=K. In this way all the effects of the anisotropic elasticity are neglected, but it is

easier to understand some qualitative features of the distorted nematic phase since Eq.

(2.16) reduces to

Fd=K

2[(∇·n)2+ (∇×n)2],(2.17)

which is much easier to treat both numerically and analytically. We use the one-constant

approximation in Sec. 2.3.1 to discuss the stability of nematic order in two-dimensional

systems.

2.2.3 Optical birefringence

Because of their complex anisotropic structures, liquid crystals possess astonishing optical

properties [104]. Among those, birefringence is a fundamental aspects of the liquid-

crystalline structures. Additionally, the birefringence of a nematic monolayer is a central

concept in Chapters 3 and 6. In this section we define the birefringence and shortly

discuss its connection to the microscopic structure of nematic liquid crystals. We warn

the reader that only in this section the symbol nidenotes refractive indexes and not the

spatial components of the nematic director.

The electric permittivity, ϵ, of an anisotropic medium is a second-rank tensor [105].

Since ϵis symmetric, it is possible to identify a coordinate system, in which all the off-

diagonal element of ϵvanish. This coordinate system defines the principal axes of the

anisotropic medium. The permeability of non-ferroelectric material at optical frequencies

is close to unity. Hence, the permittivities along the principal axes correspond to a set of

refractive indexes,

ni=ϵi

ϵ01/2,(2.18)

where ϵ0is the vacuum permittivity. Consider a linearly polarized wave propagating

along one of the principal axes of the material with the polarization direction having

components along the two remaining axes. The two components will travel at different

Chapter 2. Liquid crystals 13

velocities, e.g.,c0/n1and c0/n2. When recombined at the exit of the material, they will

thus experience a phase shift ∆ϕ∝(n2−n1). The resulting wave will be elliptically

polarized and the material act as a wave retarder.

If two of the principal refractive indexes are equal, the material is called uniaxial,

while if the niare all different the material is called biaxial. For an uniaxial material, the

ordinary and extraordinary refractive indexes are defined, respectively, by no=n1=n2

and ne=n3. The difference ∆n=ne−nois called birefringence. Uniaxial materials also

possess a special axis called the optic axis [105]. A ray propagating along the optic axis

shows no sign of birefringence. In uniaxial nematic liquid crystals the nematic director

coincides with the optic axis.

In isotropic systems, the connection between the macroscopic and microscopic

properties of a material is described by the Lorentz-Lorentz equation, which gives the

refractive index nas a function of the molecular polarizability α,

n2−1

n2+ 2 =N

3ϵ0

α , (2.19)

where Nis the number of molecules per unit volume.

For anisotropic molecules, the polarizability αis a tensor. Let us assume that, in the

reference frame defined by the main molecular axes, the tensor is diagonal, i.e.,

α=



αo0 0

0αo0

0 0 αe

,(2.20)

where we also assumed that αhas cylindrical symmetry around one molecular axis. The

Lorentz-Lorentz relation of Eq. (2.19) is thus generalized as

i−1

n2+ 2 =N⟨αii⟩

3ϵ0

,(2.21)

where ⟨αii⟩is the mean molecular polarizability along the direction of a principal axis

and n= (ne+ 2no)/3 [104].

It is important to note that the average values of α, expressed in a reference frame

coincident with the principal axes, depend on the degree of nematic order in the system

[104]. Also, due to the equivalence of the nematic director and the optic axis one has

no=n⊥and ne=n∥, where the subscript ”∥” (”⊥”) denotes components parallel

(perpendicular) to the nematic director. It can thus be shown (see for instance Ref.

[106]) that Eq. (2.21) leads to

S∆α

α=n2

∥−n2

⊥

⊥n2

∥+n2

⊥−2=(n∥−n⊥)(n∥+n⊥)

⊥n2

∥+n2

⊥−2,(2.22)

where ∆α=αe−αois the polarizability anisotropy and α= (αe+ 2αo)/3 is the mean

molecular polarizability.

When the birefringence ∆n=n∥−n⊥is small, Eq. (2.22) can be written as

S∆α

α=2n∥∆n

(n2

∥−1)(n2

∥+ 2) .(2.23)

Chapter 2. Liquid crystals 14

linear

polarizer

linear

polarizer

nematic

cell

unpolarized

light

source

Figure 2.4: (a) Schematic illustration of a nematic film placed between crossed polarizers.

The polarization direction of the two polarizers is indicated by the blue arrows, which are

perpendicular. Unpolarized light is emitted from a source (blue circle) and linearly polarized

by the first polarizer. Due to the birefringence of nematic materials, the polarization of light

acquires an additional component in a perpendicular direction. Hence, a light signal can be

recorded after the second polarizer, which eventually results in a Schlieren texture. (b) Typical

example of a Schlieren texture, from Ref. [107]. The circle surrounds a disclination while the

square surrounds an hedgehog.

By defining ∆nmax as the maximum value of the birefringence for a perfectly aligned

sample with S= 1, Eq. (2.23) gives

S=∆n

∆nmax

,(2.24)

which demonstrates that the birefringence of a fully uniaxial system is proportional to

the nematic order parameter. In the next Section we give an example of how the local

structure of the director in a nematic film can be inferred from its optical properties.

2.2.4 Topological defects

A purely continuous picture as in the FOZ theory cannot describe some fundamental

properties of nematic LC. The limitations of a continuous approach become clear when

a thin nematic film is placed between crossed polarizers as in Fig. 2.4(a). The term

”nematic” (from the greek ν˜ηµα, ”thread”) comes from the peculiar texture that a

nematic liquid crystal shows in this condition, because some dark filaments (also called

Chapter 2. Liquid crystals 15

brushes) are visible in the sample [69] (see Fig. 2.4(b)). These brushes corresponds to

the places in the sample where the nematic director is either parallel or perpendicular

to the entering light, which therefore acquires no additional polarization component (the

birefringence vanishes when light is linearly polarized along one of the principal axes).

Indeed, when rotating the crossed polarizer keeping the nematic film fixed, the brushes

also rotate. These brushes can also meet in a single point. The resulting texture is

called Schlieren texture [108] (see Fig. 2.4(b)). The points where the brushes meet are

singularities of the director field, i.e. places where the nematic director is not defined, and

are called defects. Because it is not possible to make a defect disappear with a continuous

deformation of the order parameter at finite, arbitrary distance from the core, defects are

more properly called topological defects.

From the Schlieren texture one can already senses that defects can be of different

types. For example, typically there are points where either two (circle in Fig. 2.4(b))

or four (square in Fig. 2.4(b)) brushes meet. Also, when rotating the crossed polarizers

clockwise, the brushes surrounding one defect can rotate either clockwise or counter-

clockwise. The rigorous tool for the classification of defects is provided by homotopy

theory, a theoretical framework which allows to group objects depending on their

topological properties [109–113]. A formal understanding of topology requires the

knowledge of specialized mathematical tools. Our aim here, rather than proceeding

rigorously, is to provide the reader with a basic understanding of the physics behind

topological defects in liquid crystals. Several reviews provide a much more extensive

treatment of the topic [109, 113–116].

A crude, yet efficient, classification of the defects in nematic LC can be directly built

from a Schlieren texture [108]. Let us associate to each defect a number, w, which counts

the number of brushes that meet at the defect core. The absolute value of wis defined

as |w|= number of brushes/4. Let us also assign a positive sign to wif the brushes

surrounding a defect rotate according to the crossed polarizer and a negative sign vice

versa. The number wis called the winding number of the defect.

One can relate the winding number to the properties of the director field surrounding

a defect. First of all, we should say that because of the inversion symmetry (n=−n) the

nematic director field is a line field rather than a vector field. Therefore the conformation

of the field around a defect can be represented by the black lines in Fig. 2.5, where

we depicted defects with winding number w=±1/2,±1. Consider a circle centered at

the defect core with a radius sufficiently large that the field along the circle contour is

continuous. Because n(r) is continuous along the circle, the angular variation, ∆θ, of

the nematic director with respect to a fixed orientation must be a multiple of π. The

proportionality factor between ∆θand 2π(when crossing the circle counter-clockwise and

counting counter-clockwise angle increments as positive) is exactly the winding number

of the defect, hence ∆θ= 2wπ. Defects with w=±1/2 are are called disclination and

defects with w=±1 are called hedgehog. Disclinations cannot exist in a vector field,

therefore their presence in nematic LCs is a consequence of the symmetry n=−n.

The topological stability of a defect is a different concept from its physical stability.

It depends from the spatial dimension d, the dimensionality nof the order parameter and

that of the defect core ds. A defect is unstable if n > d −ds. For example, in a system of

three dimensional vectors (n= 3) on a plane (d= 2), a point defect (ds= 0) is unstable.

If the vectors surrounding a vortex as in Fig. 2.5(a) are allowed to rotate outside of the

figure plane, the topological defect can be continuously deformed into a uniform state,

Chapter 2. Liquid crystals 16

Figure 2.5: Topological defects in a nematic liquid crystal with winding numbers (a) w= +1,

(b) w=−1, (c) w= +1/2 and (d) w=−1/2. The black lines represent the nematic director

filed as obtained from the schematic molecular configurations shown in light gray. The red

circles represent possible contours surrounding the defect cores along which the rotation of the

nematic director (red double arrows) can be evaluated.

a mechanism called escape to the third dimensions. On the contrary, a point defect of a

two-dimensional order parameter in two dimensions is stable because n=d−ds.

If the circular path surrounding one defect is extended in such a way that it encloses

two defects of opposite winding number, the net variation of ∆θalong the circular

contour is zero. This simple argument reflects the fact that at distances larger than the

separation between two defects with opposite winding number, the surrounding field can

be continuously distorted into an uniform configuration. Therefore, when coming close,

two opposite defects can annihilate each other, which also means that pairs of opposite

defects can be created relatively easily. This circumstance is particularly important in

two-dimensional systems with the symmetry properties of the xy-model, which we discuss

in more details in Sec. 2.3.

To conclude, we remark that topological defects are a general consequence of

spontaneous symmetry breaking [117] and therefore they are important in a large variety

of phenomena. They play an essential role in the phase transitions of two-dimensional

models [118, 119], in the Abrikosov vortices of super-conductive materials [120], in the

twist-grain boundary phase of liquid-crystal systems [121], and in super-fluid helium [122,

123]. Additionally, defects allow to control the assembly of colloidal particles dispersed in

nematic suspensions [41, 99], are useful to understand the structure of biological materials

[124], and they even allow to test cosmological models using condensed matter systems

[125–127].

Chapter 2. Liquid crystals 17

2.3 Nematic order in two dimensions

In the previous Section we noticed that, due to the non-polar symmetry of the nematic

phase, the Landau-de Gennes theory predicts a first-order isotropic-to-nematic transition.

Some experimental observations indicate that the transition is only weakly first order [67],

which suggest that the third-order coefficient in Eq. (2.15) could be anomalously small.

The situation in two dimensions is more complicated. On the one hand, the Mermin

and Wagner theorem states that the spontaneous symmetry breaking of a continuous

order parameter is always suppressed by fluctuations in dimensions d≤2 for systems

with sufficiently short-ranged interactions [128, 129]. The theorem readily applies to the

standard two-dimensional xy-model [130] and, more recently, Bruno rigorously extended

the conclusions of the theorem to xy-systems with long range interaction [131]. On the

other hand, the two-dimensional analogous of the Onsager theory for nematic LC (in

which the interaction range is of the order of the molecular length) predicts a transition

between a disordered isotropic phase and an orientationally ordered nematic phase [132].

This transition is found to be continuous when solved either by a scaled-particle method

[133] or by bifurcation analysis [134], but no definitive conclusion can be made on the

stability of the ordered phase.

The long-range stability of a nematic liquid crystal in two dimensions cannot be ruled

out a priori because, as demonstrated by Straley in 1971 [132], the Mermin and Wagner

theorem does not necessarily hold if the interaction between particles is not separable into

orientation- and position-dependent terms, which is the case for the hard-core interaction

of non-spherical objects. Thus, the possibility for a specific two-dimensional liquid-crystal

system to belong to the universality class of the xy-model is model dependent and has to

be directly investigated in each specific case.

In the xy-model, the existence of long-range order is forbidden by the Mermin and

Wagner theorem [128, 129]. In 1973, however, Kosterlitz and Thouless (KT) first realized

that a transition is still possible between, on the one hand, a disordered phase wherein

the correlation function of the orientational order parameter decays exponentially and

thereby only exhibits short-range order, and, on the other hand, a phase with quasi-

long-range order wherein the correlation function decays as a power law in distance r

[118]. In this transition, the topological defects introduced previously play a fundamental

role. Because the KT transition is important in the following Chapters of this Thesis, we

review its main results in the following.

2.3.1 Quasi-long-range orientational order

We start our review of the KT transition by demonstrating that the correlation function

of a properly defined order parameter can decay as a power-law in the distance runder

certain conditions. Here, we focus on a two-dimensional system with the symmetry

properties of a nematic liquid crystal. A nematic phase with quasi-long-range order is

called a quasi-nematic phase.

Algebraic order is expected if the free energy associated with the distortion of a

director field is of the form

Fd=K

2[∇θ(r)]2dr,(2.25)

Chapter 2. Liquid crystals 18

where θis the angle between the local nematic director n(r) and a fixed axis, and Kis the

Frank elastic constant. Eq. (2.25) is the two-dimensional analogous of the Frank-Oseen-

Zocher elastic energy introduced in Sec. 2.2.2, under the one-constant approximation. In a

more general theory, Eq. (2.25) should include two different elastic constants, one for splay

and one for bend deformations, but on sufficiently large length scales they renormalize

to the same value [135]. A free energy of the type of Eq. (2.25) is also equivalent to a

two-dimensional xy-model in the spin-wave approximation [130] and it is the simplest

free energy analytic in ∇θand with an uniform state as a minimum.

We demonstrate now that the free energy of Eq. (2.25) leads to a power-law decay of

the correlation function of the nematic order parameter. The two-dimensional analogous

of the nematic order parameter defined in Eq. (2.3) is

S=⟨cos(2θ)⟩.(2.26)

where ⟨. . . ⟩denotes average over thermal fluctuations. For a system described by Eq.

(2.25), true long-range order is forbidden by the Mermin-Wagner theorem [128], therefore

S= 0 in the thermodynamic limit, N→ ∞. In order to characterize orientational order

in the quasi-nematic phase, we resort to the orientational correlation function

G(r) = ⟨cos[2(θ(r)−θ(0))]⟩,(2.27)

which monitors the spatial decay of orientational correlations.

To proceed with the evaluation of Eq. (2.27), we Fourier transform θ(r) as

θ(r) = 

θkeik·r,(2.28)

and Eq. (2.25) becomes

Fd=1

2KΩ

k2|θk|2.(2.29)

where Ω is the area of the system. The correlation function in Eq. (2.27) can now be

evaluated using the Boltzmann distribution with the free energy from Eq. (2.29), i.e.,

G(r) = Re1

ZD θ exp −

k1

2βKΩk2|θq|2−2iθk(eik·r−1),(2.30)

where β= 1/kBTand

Z=D θ exp −

2βKΩk2|θk|2,(2.31)

is the partition function of the system and the integral is performed over all the possible

configurations of θ(r).

It is convenient to separate θkin its real and imaginary parts as

θk=Ak+iBk,(2.32)

where, since θ(r) is real, Akis even and Bkis odd in k. Substituting Eq. (2.32) into Eq.

(2.30) the argument of the exponential function in Eq. (2.30) becomes

Chapter 2. Liquid crystals 19



k1

2βKΩk2|θk|2−2iθk(eik·r−1) =



k1

2βKΩk2(A2

k+B2

k)−2iAkcos(k·r)+2iAk+ 2iBksin(k·r)(2.33)

where we left out all the odd terms in k, which cancel because of the summation over k

and −k. Completing the squares, Eq. (2.33) can be written as



k··· =

2βKΩk2Ak−2icos(k·r)−1

βKk22+Bk+ 2isin(k·r)

βKk22+

+

βKΩk2(1 −cos(k·r)) .(2.34)

The contribution to G(x) coming from the first term on the right hand side of Eq. (2.34)

cancels with the partition function in the denominator of Eq. (2.30) (it corresponds to

the same gaussian integral as in Z, but shifted) and therefore we are left with

G(r) = e−h(r)(2.35)

where

h(r) = 4

βKΩ

1−cos(k·r)

k2.(2.36)

Eq. (2.36) can be evaluated using the substitution



k→Ω

(2π)2dk,(2.37)

which gives

h(r) = 2

βKπ Λ

2π2π

dϕ[1 −cos(k|x|cos ϕ)] = 2

βKπ Λ

1−J0(k|r|)

kdk , (2.38)

where ϕis the angle between kand r, Λ is an ultraviolet cutoff and J0(k|r|) is a Bessel

function. For large |r|, Eq. (2.38) behaves as [130]

h(r) = 2

βKπ ln(c|r|),(2.39)

with csome constant. The asymptotic behavior of the correlation function is therefore

G(r)∝ |r|−η(2.40)

with

η=2kBT

πK .(2.41)

Usually, a power-law decay of the correlation function is expected when the temperature

of a system is close to the critical temperature of a continuous phase transition. In the

quasi-nematic phase, the correlation function decays algebraically over the whole range of

Chapter 2. Liquid crystals 20

temperatures, where Eq. (2.25) holds, with an exponent that increases with temperature

and decreases with increasing elastic constant.

Clearly, Eq. (2.25) is valid as long as the spatial variations of θ(r) are continuous,

i.e., as long as the presence of topological defects can be neglected. Indeed, the quasi-

nematic phase is destroyed when the temperature is high enough for topological defects to

proliferate, which makes the orientational correlation function decay exponentially. The

transition between a phase with proliferating defects (short-range order) and a phase

with quasi-long-range order is the KT transition. In the following we discuss an heuristic

argument to estimate the conditions under which the free energy in Eq. (2.25) provides

a correct description of the system.

2.3.2 Disclination unbinding

As anticipated in the previous section, the KT transition is between a disordered phase

with exponentially decaying orientational correlation function and a phase, in which the

correlation function decays algebraically. A quasi-nematic phase with algebraic order is

expected as long as the elastic free energy of Eq. (2.25) provides a correct description of

the system, that is as long as topological defects do not proliferate.

To estimate the range of validity of a continuous picture, we start with the evaluation

of the energy cost associated with the creation of a topological defect. As discussed in

Sec. 2.2.4, the total angular variation along a contour surrounding the defect must be a

multiple of π,i.e.,∇θ(r)·dl= 2πw , (2.42)

where wis again the winding number of the defect. From Eq. (2.42) it follows that

|∇θ|=w/r, which can be used in Eq. (2.25) to evaluate the elastic energy of a topological

defect

Etd =πKw2R

r=πKw2ln(R

a),(2.43)

where Ris the linear size of the system and ais a small cut-off which corresponds to

the size of the defect core. Eq. (2.43) tells us that the energy required to create a defect

diverges logarithmically with the system size.

Since a defect can be anywhere in the sample, its entropy can be estimated by counting

how many defects with core of size acan be placed in a two-dimensional sample of linear

extension R,i.e.

Std =kBln(R2

a2),(2.44)

which also diverges logarithmically with the system size. From Eqs. (2.43) and (2.44),

the free energy of a sample with a topological defect becomes:

F=Etd −TStd = (πKw2−2kBT) ln(R/a).(2.45)

According to Kosterlitz and Thouless, a transition results from the competition

between the elastic energy needed to create topological defects and the entropy gained

when these defects unbind and are thus free to move [130]. In a nematic liquid crystal,

defects with the lowest energy have w=±1/2 (disclination). Therefore, disclination

Chapter 2. Liquid crystals 21

unbinding takes place at the critical value of the Frank elastic constant [42],

πKc

8kBT= 1 .(2.46)

If K < Kc, isolated disclinations are found, which leads to an overall isotropic state

characterized by an exponential decay of the orientational correlation function. If

K > Kc, disclinations can still be found, but they are bound in pairs [118] and the

orientational correlation function is thus expected to decay algebraically. The critical

value, Kc, is the result of a balance between the disclination energy and entropy, and in

two dimensions both have the same logarithmic dependence on system size. Hence, Kcis

a scale-free quantity that locates the transition between short-range and quasi-long-range

nematic order in the thermodynamic limit [42].

The KT transition is an important phenomenon found in a large variety of situations:

in superconductive two-dimensional array of Josephson junctions [136, 137], in superfluid

helium films [138], in two-dimensional arrays of Bose-Einstein condensate [139], in

harmonically trapped atomic gases [140], and where a two-dimensional solid melts through

the intermediate hexatic phase [56, 141].

In their seminal work, Frenkel and Eppenga where the first to demonstrate that a

two-dimensional fluid of hard-needles undergoes an isotropic–quasi-nematic transition

via disclination unbinding [60]. More recently, an isotropic–quasi-nematic transition

compatible with the KT scenario has been identified in numerical simulations of various

two-dimensional liquid-crystal systems [42, 47, 61, 62, 142]. We demonstrate in Sec. 5.3

that the isotropic–quasi-nematic transition in the bent hard-needle model [introduced

in Fig. 1.1(c)] is consistent with the KT picture. Examples of the isotropic and quasi-

nematic phases of the bent-needle model in the zig-zag and bow-shaped configuration are

shown in Fig. 2.6.

Before concluding this section, we note that the isotropic–quasi-nematic transition is

continuous for two-dimensional systems described by the elastic free energy in Eq. (2.25)

[111]. However, recent investigation showed that the transition can be made first-order by

a formally simple generalization of the interaction energy [143–145]. This result further

highlights the rich phenomenology of two-dimensional systems.

2.4 Smectic order

2.4.1 Smectic order in three dimensions

In the smectic mesophase molecules are organized in layers. Therefore they possess, in

addition to orientational order, translational order along the layer normal. Positional

order is only short-ranged within each layer. Usually, smectic phases occur at lower

temperature than nematic. In smectic systems thermal fluctuations prevent the formation

of long-range translational order already in three dimensions. This follows when

investigating the local displacement v(r) of the layer from its equilibrium position (see

Fig. 2.7).

The elastic free energy of a smectic system is obtained by symmetry considerations

(see Ref. [130] and Ref. [67]). Assuming that the layers are perpendicular to the z-axis,

Chapter 2. Liquid crystals 22

a) b)

c) d)

Figure 2.6: Molecular configurations obtained from Monte Carlo simulation for both zig-zag

and bow-shaped molecules at different values of the density ρ. To ease the identification of

the mesophase, only a portion of the simulation box is shown, with fixed later size 5 times

larger than the total molecular length. (a) Isotropic phase of zig-zag molecules with a= 0.25,

α=π/3 and ρ= 7. (b) Quasi-nematic phase of zig-zag molecules with a= 0.25, α=π/3 and

ρ= 14. (c) Isotropic phase of bow-shaped molecules with a= 0.35, α=π/25 and ρ= 4. (d)

Quasi-nematic phase of bow-shaped molecules with a= 0.35, α=π/25 and ρ= 10. The red

arrows in (c) and (d) give the nematic director.

it reads

Fsm =1

2drB1∂v(r)

∂z 2+B2∂2v(r)

∂x2+∂2v(r)

∂y22,(2.47)

where B1is the elastic constant associated to stretching and compressing the layers and

B2is the elastic constant associated with splay distortions. The Fourier transform of Eq.

(2.47) is

Fsm =1

2(2π)3d3qB1q2

z+B2q4

⊥|v(q)|2,(2.48)

Chapter 2. Liquid crystals 23

a) b)

Figure 2.7: Elastic deformations in a smectic liquid crystal. The dashed red lines indicate

the equilibrium positions of the layers. (a) Splay deformation that keep the inter-layer distance

dfixed. The local displacement of the layers from their equilibrium position is given by v(r).

(b) Deformation associated with stretching and compressing the layers.

where qzand q⊥are defined in Fig. 2.7. Using the equipartition theorem one finds that

⟨v2(r)⟩ ∝ ln(R

d),(2.49)

where Ris the system size and dthe equilibrium layer spacing. The mean square

fluctuations of the layer displacement logarithmically diverge with the system size,

an effect called Landau-Peierls instability. Thus, in analogy to the two-dimensional

case of the xy-model described in Sec. 2.3.1, the correlation function ⟨v(0)v(r)⟩decays

algebraically in three dimensions. The quasi-long-range order in the layers periodicity

manifests itself in the power-law singularities of the Bragg peak when performing X-ray

analysis [40].

As for the nematic phase, a continuum approach has to be combined with the

description of singularities in the displacement field. Topological defects of a periodic

structure are called dislocations and they can be of two types: screw and edge dislocations.

One can think of a screw dislocation as a spiral staircase: the dislocation line is the axis

of the spiral along which each layer changes height by half of the layer spacing in half

circuit of the core. An edge dislocation can be thought of as resulting from the insertion

of additional layers from one side of the defect core. The unbinding of dislocation loops is

responsible for the nematic–smectic-A transition [146, 147] and the smectic-A–cholesteric

transition in lyotropic systems [148]. Also, screw-dislocation are an essential component

of the twist-grain-boundary phase [78, 121].

2.4.2 Smectic order in two dimensions

Bound pairs of dislocations play a fundamental role in the melting of two-dimensional

solids, which possess only quasi-long-range translational order but true-long-range order

in the orientation of nearest-neighbor bonds [119, 141]. Starting from a two-dimensional

solid, the unbinding of dislocation pairs produces a fluid with short-range translational

order but algebraic decay of bond-angle correlation (the hexatic phase). A second

transition is necessary to reach the liquid state. Using Monte Carlo simulation, it

has recently been demonstrated that the solid-hexatic transition is continuous while the

hexatic-liquid transition is of first order [56].

Two-dimensional layered systems are expected to show an analogous two-steps

transition. The scenario is discussed in detail in Ref. [149]. In this section, we give a short

Chapter 2. Liquid crystals 24

a) b)

Figure 2.8: (a) Schematic picture of the nematic-like structure expected in two-dimensional

layered system, from Ref. [149]. The system is divided into smectic islands whose size is

controlled by the average separation between dislocations. (b) A snapshot of a portion of the

Monte Carlo simulation box illustrates the smectic-C phase formed by zig-zag molecules with

a= 0.25, α=π/3 at density ρ= 30 in two dimensions. The red arrow indicates the nematic

director while the blue arrow is normal to the layers.

summary of the main conclusions of this study. Since layered systems are characterized

by a one-dimensional density wave, the translational order parameter Φ(r) is usually

defined as the amplitude of the first harmonic of this wave. In two-dimensional smectics,

due to phonon fluctuations, the correlation of the translational order parameter decays

exponentially with the distance r,i.e. ⟨Φ(r)Φ(0)⟩ ∼ exp(−r), at any finite temperature.

These fluctuations are not as effective in decorrelating the layers orientations, which

should maintain long-range order [149].

The scenario changes drastically upon considering the effect of a finite density of

dislocations. The mean separation between two thermally induced dislocations is

ξd≈aexp( Ed

2kBT),(2.50)

where ais the size of the defect core and Edis the energy of the dislocation. The length

scale over which the layer orientations are correlated is fixed by ξd. One thus expects to

find the system divided into ”islands” of linear size ∼ξd, as illustrated in Fig. 2.8(a).

Within each island, translational order is decorrelated by phonon fluctuations, but the

layer orientations are strongly correlated. For distances much larger than ξdthe properties

of a two-dimensional layered system are instead those of a quasi-nematic phase, with the

correlations between the layer orientations following a power-law decay.

The snapshot of a Monte Carlo simulation shown in Fig. 2.8(b) gives an example of the

smectic-C phase formed by zig-zag molecules at high packing density. As the area in the

snapshot is approximately 40% of the total simulation area, one can already senses that

the smectic phase is well stabilized in our numerical simulations. Indeed, we anticipate

that we were unable to test the expected scenario, depicted in Fig. 2.8(a), due to the

limitation imposed by the finite size of the system. Details on the smectic phase formed

by zig-zag molecules are given in Sec. 5.4.

Chapter 2. Liquid crystals 25

Figure 2.9: The anti-ferromorphic smectic-A phase of bow-shaped molecules with a= 0.35,

α= 2π/5 at density ρ= 30 from a snapshot of a portion of the Monte Carlo simulation box.

The blue arrow indicates the direction normal to the layers. It can be seen that molecules have

opposite orientation in adjacent layers.

2.4.3 Polar smectic phases

Another relevant topic for our molecular model is the existence of polar smectic phases,

which possess ferro- or antiferro-electric properties. The first polar smectic phases were

chiral phases of the smectic-C type formed by chiral mesogens, which carry an an electric

dipole moment [150]. It was soon realized that such phases can also be obtained by

dispersing few chiral molecules in a non-chiral smectic-C liquid-crystal host [151]. In

these mesophases, the chirality results from the tilt with respect to the layer normal and

the polarity from the intra-layer ordering.

The possibility to obtain a chiral phase by employing achiral mesogens has been

a subject of debate for long time, until it was found in 1997 that achiral, bent-core

mesogens were indeed able to spontaneously assemble in chiral smectic phases [152]. At

approximately the same time, in 1996, an achiral (not twisted) and polar smectic phase,

also formed by bent-core molecules, was discovered [84]. Since then, interest in bent-core

or banana-shaped molecules has grown enormously. Such mesogens are able to form a

large variety of mesophases (denoted with the letter B) [80, 81] and they even provided

the first experimental evidence for a thermotropic biaxial nematic phase [153].

Polar smectic phases can exhibit ferro- or antiferro-electric properties depending on

the relative orientation of polarization in adjacent layers. In these systems, due to the

high packing density within each layer, the molecular dipoles are aligned in a direction

perpendicular to the layer normal. If the dipoles have the same orientation in each layer,

the material possesses ferro-electric properties, as in Ref. [84]. This configuration is thus

called ferromorphic. In Ref. [154] instead, the orientation of the dipoles alternates from

layer to layer, which results in anti-ferroelectric properties. This configuration is called

anti-ferromorphic.

The possibility to obtain such structures in three dimensions by only considering

molecular steric interactions has been studied in Refs. [155] and [156] using Monte Carlo

simulation. The hard-core spherocylinder dimers considered in Ref. [156] only showed

evidence for an anti-ferromorphic smectic-A phase. Quantitative free-energy calculations

Chapter 2. Liquid crystals 26

a) b) c)

Figure 2.10: The spontaneous, stable deformation of the nematic director in banana-shaped

molecular systems are schematically illustrated in (a) and (b) (adapted from [57]). In (a) the

nematic director forms spontaneous splay-bend deformation while in (b) the deformation gives

rise to a conical twist-bend helix. (c) A snapshot of the simulation box from a Monte Carlo

simulation of bow-shaped molecules with a= 0.35, α=π/8 at density ρ= 20 illustrating the

two-dimensional modulated nematic phase. To ease the identification of the mesophase, only a

portion of the simulation box is shown.

demonstrated that the anti-ferromorphic arrangement is energetically favoured over the

ferromorphic [156].

Bow-shaped molecules [see Fig. 1.1(c)] also arrange in an anti-ferromorphic smectic-A

phase if the angle between the central and the external segments is sufficiently high and

if very closely packed. This can be clearly seen in the molecular configuration obtained

from the Monte Carlo simulation shown in Fig. 2.9. We discuss the possible reasons

behind this rather unusual ordering in Sec. 5.4.

2.5 Distorted nematic phases

The striking features of bent-core or banana-shaped compounds are not limited to the

wide variety of smectic phases that they can form. Meyer was the first, in 1969, to suggest

that flexoelectricity (the ability to generate a spontaneous polarization in response to a

distortion of the nematic director) should be favored by a mesogen shaped like a banana

[157]. The predicted effect was experimentally confirmed only very recently [158].

Three decades after the prediction by Meyer, Dozov suggested that bent-core mesogens

could give rise to a whole new class of nematic phases [57]. In Ref. [57], the possible

occurrence of a nematic phase with stable splay-bend or twist-bend deformations is

discussed as resulting from pathological elasticity, i.e., from negative-valued elastic

constants. Starting from a Frank-Oseen-Zocher elastic free-energy as in Eq. (2.16),

spontaneous bend deformations of the nematic director can be obtained by using a

negative K3. Indeed, nothing prevents the Frank elastic constant to be negative besides

the requirement of a uniform ground state. To stabilize the resulting phase and to limit

the free energy, fourth-order elastic terms in ∇αnβneed to be taken into account.

Chapter 2. Liquid crystals 27

Assuming for simplicity that the nematic director nis uniform in the xy-plane and

that it only depends on z, there are only three fourth-order terms compatible with the

nematic symmetry. The free energy then reads [57]

F=Fd+1

4C1d2nαnβ

dz22+ 2C2d2nznβ

dz22+C3d2n2

dz22,(2.51)

where nzis the z-component of n,Fdis as in Eq. (2.16), the Ci>0 are additional elastic

constants, and summation over repeated indexes is assumed. Equation (2.51) admits two

stable solutions, illustrated in Figs. 2.10(a) and 2.10(b): a modulated nematic phase with

splay-bend deformations and a conical twist-bend helix phase.

In 2002, the twist-bend nematic phase has been observed in three-dimensional

molecular computer simulation using banana-shaped molecules interacting through a

Gay-Berne potential [59]. Experimentally, the helical twist-bend nematic phase predicted

by Dozov was first discovered in 2013 by Noel Clark and collaborators [86]. Using achiral

dimer molecules (cyanobiphenyl-(CH2)7-cyanobiphenyl) they realized a stable modulated

nematic phase with a pitch of few molecular lengths. The phase is not smectic since it

shows no modulations in the molecular density. Further investigations demonstrated that

in this phase the bend elastic constant K3is, as expected, anomalously small [58].

In Sec. 5.5 we demonstrate that bow-shaped molecules in two dimensions arrange in

a modulated nematic phase with splay-bend deformation. This phase consists of layers

made up of arches formed by several molecules. Our results represent the first evidence

for a modulated-nematic phase in two dimensions, and additionally demonstrate for the

first time that such a phase can be stabilized by only considering steric interactions. A

snapshot showing the bow-shaped molecules in the modulated-nematic phase is shown in

Fig. 2.10(c).

2.6 Onsager theory

In Sec. 2.2.1 we introduced the Onsager theory [92] for a system of hard rods. We

showed that, at sufficiently high density, nematic order is favored since the decrease

of orientational entropy is compensated by the increase in translational entropy. A

generalization of the theory allows for the determination of the phase behavior of fluids

composed of anisotropic molecules of more complex shapes [46, 63]. Indeed, in Sec. 5.6

we use Onsager theory as an alternative method for calculating the phase diagrams of the

bent-needle model. Part of the work presented in Secs. 2.6.2 and 2.6.3 has been published

in Ref. [A].

2.6.1 Virial expansion

We start by shortly discussing the simple case of a monoatomic gas of Nidentical particles

of mass min a volume Vat temperature T, which is very useful to illustrate the main

assumption behind the Onsager approach. We are interested in obtaining the free energy,

F, which in the canonical ensemble is given by

βF =−ln Z , (2.52)

Chapter 2. Liquid crystals 28

where Zis the partition function

Z=1

h3Nd3q1···d3qNd3p1. . . d3pNe−βH(p1,...,pN,q1,...,qN).(2.53)

Here his the Planck constant, the qiare the particle positions, the pithe conjugate

momenta, β= 1/kBT, and His the Hamiltonian. In classical systems

H(p1, . . . , pN, q1, . . . , qN) =



i=1

2m+U(q1, . . . , qN),(2.54)

therefore the partition function splits up into a product of an integral over the momenta

and an integral over the coordinates. Because for an ideal gas of non-interacting particles

(U= 0) one has

Zig =1

h3NV

λ3

th N,(2.55)

where λth =h/√2πmkBTis the thermal de Broglie wavelength, it is convenient to rewrite

Eq. (2.53) as

Z=ZigQN,(2.56)

where

QN=1

VNd3q1. . . d3qNe−βU(q1,...,qN),(2.57)

is the contribution of the interaction potential to the partition function. In this way the

free energy Fin Eq. (2.52) can be expressed as the sum of the free energy of an ideal gas,

βFig =−ln Zig, and a term, which takes into account the molecular interactions, i.e.,

βF =βFig −ln QN.(2.58)

To evaluate QN, it is useful to rewrite Eq. (2.57) as

QN=1

VNd3q1. . . d3qNe−βU(q1,...,qN)−1+ 1 ,(2.59)

and to consider that the interaction between particles becomes relevant only when

particles are very close to each other, i.e., when they nearly collide. If the gas is sufficiently

dilute, we can assume that only isolated binary interactions take place and, since there

are N(N−1)/2 ways of choosing a pair of particles in our system, we can write

VNd3q1. . . d3qNe−βU(q1,...,qN)−1

N(N−1)

2d3q1. . . d3qNe−βU12 −1

N(N−1)

2VN−2d3q1d3q2e−βU12 −1

≈1

Vd3qe−βU12 −1,(2.60)

where U12 is the interaction potential between two particles, we used N(N−1) ≈N2

and, in the last step, we evaluated the integral over the coordinates qof the center of

Chapter 2. Liquid crystals 29

gravity of the two particles (assuming that U12 only depends on their mutual distance).

By defining

B2=1

2d3qe−βU12 −1,(2.61)

and using ln(1 + x)≈xfor x≪1 we can finally write

ln QN= ln 1

VNd3q1. . . d3qNe−βU(q1,...,qN)≈N2

VB2(2.62)

which, substituted in Eq. (2.58), gives the lowest order correction to the free energy of

an ideal gas.

Higher-order terms can be obtained by progressively considering interactions between

three, four, etc. particles. They correspond respectively to additional coefficients B3,

B4, etc [159], which are called virial coefficients and depend on the specific interaction

potential.

2.6.2 Application to non-spherical hard-core particles

In Ref. [63], the Onsager theory was used to determine the phase behavior of zig-zag

molecules. In the following, we summarize and extend the results of this Onsager theory.

The conclusions of the previous Section can be easily applied to the hard-core,

orientation-dependent interaction of bent needles. The differential volume d3qin Eq.

(2.53) has to be replaced by a differential volume over the spatial positions, r, of the

particles and a differential volume over their orientation, defined by some unit vector ω.

Indeed, the integration over the positions gives the volume V, while the integral over the

angles only gives a constant that can always be normalized to unity [159].

Since the pair potential for hard-core particles is

U12(r1,r2,ω1,ω2) = ∞if particles overlap (2.63)

U12(r1,r2,ω1,ω2) = 0 otherwise ,

it is convenient to introduce the Mayer function of the pair potential

fM=e−βU12 −1,(2.64)

which is zero except when particles overlap, where fM=−1. Up to a second-order virial

expansion, the Onsager free energy functional is thus

βF =drdωρ(r,ω)ln ρ(r,ω)−1

−1

2dr1dω1ρ(r1,ω1)dr2dω2ρ(r2,ω2)fM(r12,ω1,ω2),(2.65)

where ρ(r,ω) is the local number density at position rand orientation ω, normalized

such that

N=drdωρ(r,ω).(2.66)

Our stategy now is to simplify Eq. (2.65) in order to minimize the free energy and to

obtain transition densities between different mesophases.

Chapter 2. Liquid crystals 30

In the isotropic and nematic phases, positional order does not exist and one has

ρ(r, ω) = ρf(ω) that substituted in Eq. (2.66) gives

dωf(ω)=1,(2.67)

where we used ρ=N/V . The domain of definition of f(ω) depends on the symmetry

properties of the molecules. Since our molecules are constrained to a two-dimensional

surface, zig-zag molecules are symmetric with respect to rotation by πwhile bow-shaped

molecules are symmetric with respect to rotation by 2π. Therefore, Eq. (2.67) becomes

mπ

dθf(θ) = 1 ,(2.68)

where we introduced an index m= 1 for zig-zag molecules and m= 2 for bow-shaped

molecules.

Integration of Eq. (2.65) over rgives

βF

A=ρln ρ−ρ+ρmπ

dθf(θ) ln(mπf(θ))

2ρ2mπ

dθ1mπ

dθ2f(θ1)f(θ2)Aexl(∆θ),(2.69)

where Ais the area of the system (we are now explicitly in two dimensions), Aexl(∆θ) is

the excluded area in terms of the angle ∆θbetween two molecular orientations. We also

added a term ln(mπ)for later convenience, which does not change the phase behavior.

Before proceeding to the minimization, it is convenient to Fourier transform the

orientational distribution function and the excluded area. They are both even functions,

thus

f(θ) =



i=0

ficos(2iθ/m) and Aexl(∆θ) =



i=0

Aicos(2i∆θ/m),(2.70)

where f0= 1/mπ is fixed by Eq. (2.68). The free energy in Eq. (2.65) is evaluated by

substituting Aexl(∆θ) and f(θ) with the respective Fourier transforms and by using the

orthogonal properties of trigonometric functions

Λ

dθ cos(n2π

Λθ) cos(n′2π

Λθ) = 









Λn=n′= 0

2n=n′= 0

0n=n′

(2.71)

and Λ

dθ cos(n2π

Λθ) sin(n′2π

Λθ) = 0 ,(2.72)

together with the cosine addition formula for cos(∆θ) = cos(θ1−θ2).

Chapter 2. Liquid crystals 31

After some algebra we obtain

βF

A=ρln ρ−ρ+ρ



i=0

fimπ

dθ cos(2iθ/m) ln 1 + mπ



j=1

fjcos(2jθ/m)

2ρ2A0+ρ2mπ

22n



i=0

iAi.(2.73)

Minimization with respect to the Fourier amplitude fiof f(θ) gives

mπ

dθ cos(2iθ/m) ln 1 + mπ



j=1

fjcos(2jθ/m)+ρmπ

22fiAi= 0 ,(2.74)

and using ln(1 + x)≈x, we obtain

mπ



j=1

fjmπ

dθ cos(2iθ/m) cos(2jθ/m) + ρmπ

22fiAi= 0 .(2.75)

By using again the orthogonal properties of trigonometric functions, Eq. (2.75) gives

the values of the densities which minimize the Onsager free energy, i.e.

ρ(i)

B=−2

.(2.76)

We interpret the ρ(i)

Bas a series of possible bifurcation densities. In particular, we choose

the lowest positive value of ρ(i)

Bas the isotropic-nematic transition density ρIN, which

is realized at i= 1 for zig-zag molecules and at i= 2 for bow-shaped molecules. The

resulting transition lines are plotted as red dashed lines in the phase diagrams of Fig.

5.9 in Chapter 5. We determine the Fourier coefficients Ainumerically by means of the

Monte Carlo integration technique described in the following section.

To determine the nematic–smectic transition density ρNS, we choose a periodic

modulation of the density along the zaxis, ρ(r) = ρ(z) = ρ(z+d), and assume perfect

alignment of the molecules as in Ref. [63], because the nematic order in the smectic

phase is typically very high. The evaluation of the free energy functional now involves

an excluded distance dexl(z, θ), where θis the orientation angle of the central molecular

segment with respect to the smectic layer normal. The excluded distance is related to the

excluded area by Aexl =dz dexl(z, θ). Taking into account only the first Fourier mode

of the density modulation in the free energy and minimizing with respect to the Fourier

amplitude, we obtain an equation for the nematic–smectic transition density ρNS,

1 + ρNS cos(2πz/d)dexl(z, θ)dz = 0 ,(2.77)

where dis the smectic period. The tilt angle θand the period dare also determined by

minimizing the free energy functional. For details of the calculation, we refer the reader to

the work of Varga et al. [63]. Note that we were only able to calculate a nematic–smectic

transition line for zig-zag molecules. It is plotted in the phase diagram of Fig. 5.9(a) as

blue dotted line.

Chapter 2. Liquid crystals 32

Figure 2.11: Illustration of the calculation of the excluded area for bow-shaped molecules with

α= 57.3◦,a= 0.35 and the same orientation. The excluded area is obtained by repeatedly

inserting the second molecule inside the box and checking for overlaps. The shaded region is

obtained by placing a dot at the position of the center of mass of a randomly inserted particle

if it overlaps with the fixed particle.

2.6.3 Numerical evaluation of the excluded area

The determination of the bifurcation densities in Eq. (2.76) requires the determination

of the Fourier amplitudes of the excluded area Aexl(∆θ), which we obtain numerically.

As anticipated in Sec. 2.2.1, given two molecules with a fixed relative orientation ∆θ,

then the excluded area Aexl(∆θ) is defined as the portion of the plane surrounding a

molecule that is not accessible to the other. If the center of the second molecule is inside

the area excluded by the first, then the molecules overlap. Figure 2.11 shows an example

of the shape of the excluded area for two bow-shaped molecules with the same orientation

(∆θ= 0). As clearly shown by Eq. (2.65) for hard-core potentials, the excluded area is

proportional to the second virial coefficient in an expansion of the free energy in powers of

density. Hence, Aexl provides a microscopic description of the balance between positional

and orientational entropy.

We evaluate the excluded area by Monte Carlo integration. One molecule is fixed at

the center of a box of area Abox. The size of the box is chosen such that it is impossible

for a molecule outside the box to overlap with the fixed molecule. Another molecule

with fixed relative orientation ∆θis then inserted at random in the box. The process is

repeated Ntrial times, keeping track of the number of overlaps Noverlap that occur during

the whole process. In the end, the excluded area is Aexl(∆θ) = Abox(Noverlap/Ntrial). The

Fourier amplitudes, Ai, who appear in Eq. (2.76) are then obtained via

Ai=2

mπ

0

Aexl(x) cos 2ix

mdx , (2.78)

where, again, we used m= 1 for zig-zag molecules and m= 2 for bow-shaped molecules.

Chapter 2. Liquid crystals 33

2.7 Order parameters

In the previous Sections we showed that zig-zag molecules arrange in isotropic [Fig.

2.6(a)], quasi-nematic [Fig. 2.6(b)], and smectic-C [Fig. 2.8(b)] phases, while bow-

shaped molecules arrange in isotropic [Fig. 2.6(c)], quasi-nematic [Fig. 2.6(d)], modulated-

nematic [Fig. 2.10(c)], and anti-ferromorphic smectic-A [Fig. 2.9] phases. In this section

we summarize and detail the definition of the order parameters and the related correlation

functions used to map out the phase diagram of the bent-needle model.

We define the two-dimensional nematic order parameter Sby first introducing the

two-dimensional tensor order parameter Q:

Qαβ =⟨N−1



i=1

(2ui

αui

β−δαβ)⟩,(2.79)

where ui

αis the α-th Cartesian coordinate of the unit vector pointing along the central

segment of the i-th of Nmolecules [see Fig. 1.1(c)] and ⟨. . .⟩denotes the ensemble

average. The positive eigenvalue and corresponding eigenvector of Qgive Sand the

nematic director n, respectively. As discussed in Sec. 2.3, in two dimensions only quasi-

long-range orientational, i.e., quasi-nematic, order can exist, and hence we resort to the

orientational correlation function to characterize orientational order in the quasi-nematic

phase,

g2(r) = ⟨cos[2(θ(0) −θ(r))]⟩,(2.80)

where θis the angle between the central molecular segment along ˆ

uand a fixed axis, and

ris the distance between the centers of two molecules. The function g2(r) thus monitors

the spatial decay of orientational correlations. Note that because we work under periodic

boundary conditions, correlation functions are radially truncated at half the edge length

of the simulation box.

A smectic liquid crystal can be thought of as a stack of parallel molecular layers of

thickness d. It is therefore possible to identify a density wave along the normal to the

layers. The smectic order parameter Λsm is then the amplitude of this density wave. To

determine Λsm, we calculate the Fourier transform of the normalized density [160],

Λ(ˆ

k, d) = 1

N



j=1

eik·rj,(2.81)

where rjis the position of the j-th particle, and k= (2π/d)ˆ

kis the wave vector with

wavelength dand unit vector ˆ

k. To determine the actual distance dbetween smectic layers

and the layer orientation ˆ

k, we calculate Λ(ˆ

k, d) for different values of dand directions ˆ

and take its maximum Λsm as the smectic order parameter[51]. Figure 2.12(a) illustrates

this optimization procedure.

Bow-shaped molecules are able to display polar order, which we quantify by

introducing the global polar order parameter

Pg=



i=1

vi

,(2.82)

Chapter 2. Liquid crystals 34

Figure 2.12: Illustration of the maximization procedure for determining the smectic (a)

and modulated-nematic (b) order parameter. (a) Fourier transform of the density, Λ(ˆ

k, d),

plotted versus orientation angle ϕ1and wavelength dof the wave vector k= (2π/d)ˆ

kwith

k= [cos ϕ1,sin ϕ1]. The data refer to zig-zag molecules with a= 0.25, α=π/2, and ρ= 30.

The maximization gives Λsm = 0.83. (b) Fourier transform of the polar order parameter,

Ψ(ˆ

h, λ), plotted versus orientation angle ϕ2and wavelength λof the wave vector h= (2π/λ)ˆ

with ˆ

h= [cos ϕ2,sin ϕ2]. The data refer to bow-shaped molecules with a= 0.35, α=π/13,

ρ= 24. The maximization gives Ψm= 0.62. In both cases the procedure gives rise to a clear

maximum, which is used for further analysis. Note that only a portion of the domain explored

during the optimization procedure is displayed here.

where ˆ

viis a unit vector perpendicular to the molecular axis ˆ

ui(see Fig. 1.1(c)). Since

Pgcannot distinguish between isotropic and anti-polar order – in both cases Pg= 0 –,

other order parameters are needed to characterize an anti-polar state. In the modulated-

nematic phase [introduced in Sec. 2.5 and in Fig. 2.10(c) and discussed in detail in Sec.

5.5], molecules form arches, where the orientation of the molecules’ central segments –

and thus also the polar vector ˆ

v(see Fig. 1.1(c)) – are periodically modulated along

one particular spatial direction. To quantifiy this spatial modulation, we introduce

its amplitude as an order parameter Ψm, which we determine in full analogy to the

definition of the smectic order parameter Λsm. We define the spatially dependent polarity,

Pl(r) = N

j=1 eiθjδ(r−rj), and introduce the absolute value of its Fourier transform

Ψ(ˆ

h, λ) = 1

N



j=1

eiθjeih·rj,(2.83)

Chapter 2. Liquid crystals 35

where h= (2π/λ)ˆ

his the wave vector with wavelength λand unit vector ˆ

h. Note that

because θ+π/2 quantifies the orientation of ˆ

v, Ψ describes periodic variations in ˆ

v. We

evaluate Ψ(ˆ

h, λ) for different values of λand directions ˆ

hand take the maximum Ψm

as the order parameter for the modulated-nematic phase. The optimization procedure is

illustrated in Fig. 2.12(b).

In order to have additional information on the structural properties of the modulated-

nematic phase, we monitor polar correlations along the optimal direction ˆ

hmusing the

polar correlation function

g||

1(r) = 1



i=1 

j=i

vi·ˆ

vjδr||

ij −r.(2.84)

Here, r||

ij =|ri−rj| · ˆ

hmis the projection of the vector joining the centers of the i-th

and j-th molecules onto the direction of ˆ

hm. Order parameters and correlation functions

defined in this Section are used to map out the complete phase diagram of zig-zag and

bow-shaped molecules. The results are presented in Chap. 5.

Chapter 3

Photo-Switchable Molecules and

Applications

In this Chapter we discuss photo-switchable molecules and we give an overview over their

most recent technological applications, with particular focus on a series of experiments

performed by Fang et al. in 2013. In Sec. 3.1 we introduce the photo-switching molecules

and we give an overview of their most appealing technological applications. In Sec. 3.2

we discuss the chemical properties of azobenzene, one of the most important photo-

switchable compounds. In Sec. 3.3 the effect of light on the orientation of liquid crystals

that contain light-absorbing molecules is reviewed. Finally, in Sec. 3.4 we explain a series

of experiments performed by Fang et al. [1]. A detailed description of these experiments

is important since they strongly inspired the molecular model discussed in Chap. 6.

3.1 Introduction to photo-switchable molecules

Photo-switchable molecules are chemical compounds that received much attention in the

last years. These molecules can switch between two (or even more) stable states when

irradiated by light. When photo-switchable molecules are incorporated into a surrounding

media, the conformational changes induced by light at the molecular level can result in a

drastic change in the macroscopic properties of the material.

There are different types of photo-switchable compounds. Examples are spiropyrans,

azobenzenes, dithienylethenes, and alkenes [161]. Illumination of a photo-switchable

molecule with light of a proper wavelength can result in dramatic changes of the molecular

properties. In case of light-induced trans-cis isomerization, photon absorption leads to a

spatial rearrangement of the molecule that eventually affects the surrounding structure.

Since the switching mechanism is highly efficient, precisely controllable, and completely

reversible, its central role in many advanced applications is not surprising. The research

activity in this field is nowadays very vital [32, 162].

Photo-switchable molecules can be used to build simple molecular machines [163],

to control the electron transfer in molecular electronic switches [164] or to control

the stability of liquid-crystal systems [87]. When incorporated into micelles, light-

switches can be used to disaggregate the micellar structure upon illumination [165]. This

mechanism has been used to design light-controlled drug-delivery systems [166].

Further interesting applications concern the control of both the structures and the

functions of biological systems [167]. There are many fascinating examples: incorporation

of light-controlled molecules on the backbone of a protein allows for the precise control

Chapter 3. Photo-switchable molecules 38

of the folding-unfolding process [168], conjugation of a protein ligand with a photo-active

molecule changes the ligand-protein binding properties [169], integration of light-switching

molecules in lipid membranes alters the membrane permeability [170], etc.

Another promising direction for exploring how light can be used to control material

properties are light-switchable sufactants [171–174]. They accumulate at fluid interfaces.

By switching locally between the two isomeric states, the surface tension changes, and its

gradient drives Marangoni flow. This moves emulsion droplets along a surface or in bulk

with interesting non-linear dynamics [175, 176].

Other technological applications are functionalized surfaces, monolayers covered by

photo-switchable molecules. Illumination modifies the monolayer wettability [177],

controls the motion of a flat molecular rotary motor [178], the rate of electron transfer

between the monolayer surface and its environment [23] or the conductance in a molecular-

scale electronic device [179]. It is also possible to inscribe nano-sized patterns on the

monolayer by photo-lithography because of a mechanism called surface relief gratings

[180, 181].

Very importantly for our purpose, photo-switchable molecules can be embedded in a

liquid-crystal host matrix [182] or they can act as mesogens themselves [27, 183]. In both

cases, light absorption controls both the phase stability and the alignment of the liquid

crystal. Illumination can trigger an isothermal transition between different liquid-crystal

phases [87] or reorient the director in the nematic phase [184].

In Chap. 6 we present a molecular model for the relaxation dynamics of orientational

order in a monolayer of photo-switchable molecules. Our model is strongly inspired by a

series of experiments performed by Fang et al. [1]. These experiments demonstrate how,

in a self-assembled monolayer of azobenzene-based molecules, orientational order can be

precisely controlled by illumination with light. In Sec. 3.2 we summarize the chemical

properties of azobenzene and how they couple to light. It will become clear that many

fundamental properties of azobenzene can be substantially different depending on the

experimental conditions.

3.2 Photochemical properties of azobenzene

In the context of liquid crystals, the most widely used photo-switchable molecule certainly

is azobenzene [32]. Azobenzene is a molecule composed of two phenyl rings separated

by an azo group. It can be found in two configurations, the trans and the cis isomers,

schematically illustrated in Fig. 3.1(a).

The trans isomer is nearly planar and rod-like with a nearly absent dipole moment.

In the cis isomer the two phenyl rings are twisted and out of plane. In the trans

configuration, the distance between the two ends of the molecule is ≈0.99nm, while

in the cis state it reduces to ≈0.5nm [186]. Consequently, the cis isomer acquires a

dipole moment of nearly 3 Debye. The free-volume of the cis isomer is also larger than

that of the trans configuration [187].

The transition between the two isomers happens either by thermal excitation or by

photon absorption with high efficiency. The quantum yield of the isomerization is close to

unity. The trans configuration is the lower-energy state of the molecule. Therefore, when

azobenzenes are left in the dark (or in typical ambient conditions) nearly all of them are

found in the trans state.

A fundamental characteristic of the azobenzene is the strong electronic absorption

of its π-bonds system. In the azobenzene molecule, cis and trans isomers have distinct

Chapter 3. Photo-switchable molecules 39

a) b)

NNN

azo-based

trans

azo-based

cis

Figure 3.1: a) Example of an azobenzene-based photo-switchable molecule in the trans (left)

and cis (right) configuration. The azobenzene molecule (two benzene rings connected by the

azo bond) is responsible for the light-switching properties, but other chemical groups can be

attached in the positions denoted by Rand R′. (b) Absorption spectra of trans azobenzene

in dilute tetrahydrofuran solution. The three curves refer to azobenzenes with different ring-

substitution patterns: azobenzene (black), amino-azobenzene (blue) and pseudo-stilbene (red).

From [185].

absorption spectra, only weakly overlapping. The absorption spectra can, however, be

tuned to lie in a large range of the electromagnetic spectrum by adding proper chemical

groups to the phenyl rings (ring substitution patterns, indicated with the letters R and

R’ in Fig. 3.1(a)) [185]. In Fig. 3.1(b) the absorption spectra of a trans azobenzene with

different ring substitution patters are shown. Depending on the location of the absorption

peak, the azo-based molecules are divided into three fundamental categories: azobenzene,

amino-azobenzene and pseudo-stilbene. The absorption spectrum of the cis isomers is

affected by the substitution patterns as well. Especially in the case of pseudo-stilbene,

where the absorption peak is strongly shifted towards the red, the overlap of the trans

and cis absorption spectra can be very significant. Thus, it is possible to excite both the

cis-to-trans and the trans-to-cis transitions by using light of the same wavelength, and

the molecule cycle between trans and cis configurations.

The ring substitution patterns also strongly influence the average life time of the

isomers. In different experimental conditions, the thermal conversion time from cis

to trans can range from milliseconds to hours or even days [185]. Consequently,

under illumination a sample containing azobenzene-based molecules is characterized by

a relative concentration of the two isomers that is depends on a large variety of factors:

light intensity and wavelength, the quantum yield of the isomerization, temperature, the

characteristic times of both the light-induced and the spontaneous thermal isomerization

as well as the molecular environment.

The isomerization of azobenzene is a complicated process and, indeed, the precise

pathway followed by the molecule during the conformational change is still discussed

[188]. Wang et al. [189] described the isomerization in terms of subsequent transitions

between molecular electronic levels, as schematically illustrated in Fig. 3.2. Upon photon

absorption, a molecule in the singlet trans state S0is exited to the trans state S1, from

which it decays to the triplet state T1. From here the molecule can back-isomerize to S0

or reach the exited triplet state of the cis isomer T′

1. In the latter case, the trans-to-cis

isomerization (T′

1→S′

0) is completed with much higher probability than the back T′

1→S0

transition [189]. A similar, reverse path is followed during cis-to-trans isomerization. The

Chapter 3. Photo-switchable molecules 40

Figure 3.2: Diagram of the energetic levels of a pseudo-stilbene molecule. From [190].

energy difference between the trans ground state and the cis ground state (S0and S′

0in

Fig. 3.2, respectively) is approximately 50kJ/mol [187].

Atomistic molecular dynamics simulations can reconstruct the spatial configuration

of the azobenzene at each step of the isomerization [188]. This process is even more

complicated in the presence of a solvent, mainly because the transition can be hindered

by the surrounding molecules [191]. Either in vacuum or in the presence of a crowded

environment, isomerization is an extremely fast process which happens on the time scale

of picoseconds [185, 191]. As explained in Sec. 6.1, this remarkably small time scale

allows us to model the isomerization of azobenzene as a drastically simplified process: an

instantaneous transition in a system which only comprises the trans and the cis ground

states S0and S′

3.3 Light-induced orientational order

The phenomenology of the interaction between light and nematic liquid crystals is very

rich [192]. The basic effect results from the coupling between the dipole moment of the

mesogens and the electric field of the electromagnetic wave, which generates an optical

torque. If the intensity of the electromagnetic wave exceeds a threshold value, the torque

overcomes elastic and viscous forces and the nematic director rotates and eventually aligns

with the electric field. The effect is analogous to the Freedericksz transition [193] induced

by a static electric field in nematic liquid crystals (here the director aligns with the field

above a certain field strength) and is thus called optical Freedericksz transition [192].

In 1990 Janossy et al. discovered that by dispersing a small amount of light-absorbing

molecules (≈1%) in a nematic liquid crystal, the threshold of the optical Freedericksz

transition can be reduced by up to three orders of magnitute [194]. The effect was later

explained by the interaction between the exited state of the light-absorbing molecules

and the nematic liquid crystal host [195–198].

The situation changes if the light-absorbing molecules are also photo-switches, i.e., if

they undergo significant conformational changes upon photon absorption. In this case,

the molecular alignment results from a process called angular hole burning, rather than

from a torque [199]. To illustrate the phenomena, we consider the illumination of a liquid

crystal entirely made of azo-based molecules by linearly polarized light. In most cases,

trans isomers act as good mesogens while cis isomers do not show relevant mesogenic

properties [32, 200].

The probability for a molecule to absorb a photon and isomerize depends on its

transition moment, a vector whose direction defines the polarization of the cis-trans

transition. We assume that the transition moment of the molecule is oriented along the

Chapter 3. Photo-switchable molecules 41

a) b)

Figure 3.3: (a) Trans (blue) and cis (red) model azo-isomers under illumination with light

linearly polarized along e. The isomerization probability is proportional to the cosine square

of the angle between the light polarization and the transition moment of the molecule (along

the main molecular axis). (b) Schematic illustration of the angular hole-burning process. Azo-

molecules are in the ground state trans configuration at ambient conditions. Under illumination

with linearly polarized light, a series of consecutive angular-dependent isomerizations lead to a

steady state in which trans isomers are oriented perpendicularly to the light polarization.

main molecular axis, defined by the unit vector s. When light is polarized along the

transition moment, the isomerization probability is maximized. More specifically, the

probability for azobenzene to absorb a photon is proportional to the cosine square of

the angle between the direction of polarization of light and s. Molecules are repeatedly

isomerized under illumination, and after isomerization they assume random orientation

[201, 202]. The distribution of molecular orientations thus reaches a steady state, wherein

the transition moments of the molecules are aligned. The alignment is in the direction

along which molecules are less likely to be further isomerized. In this way, the mesogenic

trans molecules form nematic order perpendicular to the light polarization. The process

is illustrated in Fig. 3.3.

In theory, angular hole burning is described by Fokker-Plank equations for the

respective molecular orientation distribution functions, ft(s, t) and fc(s, t), for the trans

and cis isomers at time t[184]. In the most general case the dynamics reads

∂ft(s, t)

∂t +∇RJt=−pt(s)ft(s, t) + ds′pc(s′)fc(s′, t) + 1

τc

fc(t) (3.1a)

∂fc(s, t)

∂t +∇RJc=−pc(s)fc(s, t) + ds′pt(s′)ft(s′, t)−1

τc

fc(t),(3.1b)

where ∇Ris the the angular part of the usual nabla operator, Jtand Jcare rotational

currents (defined below), pc(s) and pt(s) are the angular-dependent isomerization rates

(cis-to-trans and trans-to-cis, respectively) and the last terms on the right-hand side

account for the cis-to-trans spontaneous thermal relaxation with characteristic time τc.

Equations (3.1) must be solved with the normalization condition

dsfα(s, t) = ¯

fα(t),(3.2)

Chapter 3. Photo-switchable molecules 42

where we introduced the subscript α=c, t and ¯

ft(t) [ ¯

fc(t)] is the fractional population of

trans [cis] isomers at time t. Since the total number of molecules is conserved, we have

fc(t) + ¯

ft(t) = 1 at any time.

The isomerization rates are given by

pα(s) = Iσα(s·e)2,(3.3)

where Iis the light intensity, σαis a molecular parameter (it contains the cross section

for photon absorption, the quantum yield of the process, and the dependence on the light

wavelength) and eis a unit vector defining the orientation of the optical electric field.

Due to the nearly isotropic shape of cis isomers, it is common to assume that pc(s) is

constant, i.e., that the cis photon absorption does not depend on the isomer orientation.

The rotational currents are the sum of a diffusion and a drift term

Jα=−Dα∇Rfα(s, t)−Dα

kBT(∇RUα)fα(s, t),(3.4)

where the Dαare rotational diffusion constants (in principle different for the trans and cis

isomers) and Uαis the potential describing intermolecular interactions and the potential

energy in external fields. In previous studies, the interaction potential is assumed to be

of the Maier-Saupe type and the model is studied in mean-field approximation [184, 197].

In the following section we discuss a set of experiments reported by Fang et al. in Ref.

[1]. The rotational dynamics of the molecules is described using Eqs. (3.1). Furthermore,

we discuss the limitation of a mean-field approach and how the dynamical model in Eqs.

(3.1) inspired the kinetic Monte Carlo simulations described in Chapter 6.

3.4 Light-control of the birefringence relaxation

The recent experiments of Fang et al. [1], which have attracted considerable attention,

motivated the kinetic Monte Carlo simulations presented in Chapter 6. In this section

we summarize the experimental results.

A self-assembled monolayer (SAM) with glasslike properties is realized by covering a

glass surface with dye Methyl-Red (dMR) molecules at high in-plane density and tethering

them with covalent bonds at random positions [see Fig. 3.4(a)]. The molecules are free

to rotate but their translational freedom is constrained to ≈1nm displacements. In

the ground state dMR molecules assume a rod-like trans configuration with anisotropic

optical properties. The light-induced cis configuration has a bent-core shape and is

nearly isotropic. Because of the photo-switchable core, isomerization between the two

configurations can efficiently be induced by illumination with light at a 514nm wavelength.

The absorption spectra of the cis and trans isomers partially overlap and illumination

with light of this wavelength induces both cis-to-trans and trans-to-cis transitions.

In Ref. [1] the initial orientation of the molecules in the SAM was random. Under

illumination with linearly polarized light (writing process), trans molecules form nematic

order perpendicular to the light polarization via angular hole-burning [201–203], as

illustrated in Fig. 3.4(b). Thus the monolayer exhibits some birefringence Q(t). Since

light also induces the reverse, cis-to-trans transition, in steady state a mixture of both

isomers exists at a relative concentration that depends on the light intensity, the density

of the monolayer and other factors.

Chapter 3. Photo-switchable molecules 43

a) b)

Figure 3.4: (a) Dye Methyl-Red molecule tethered to a glass surface via covalent bond. The

transition moment t(blue arrow) is mainly determined by the orientation of the azo-core and

is nearly parallel to the glass surface (Ψ ≈25◦). The dipole moment of the dMR, d, is given

by the pink arrow. From [1]. (b) Arrangement of trans molecules after illumination of the

monolayer with light linearly polarized along e. The isomers are aligned perpendicularly to the

light polarization. (c) Isotropic configuration of trans molecules after thermal or CP erasure

(details in the text). The experimental in-plane density of dMR on the monolayer is higher

than in the figures [1]. In order to randomize their orientations, molecules have to pass over

each other.

Reference [1] investigated the relaxation of the birefringence under two different

illumination conditions following the writing process:

1) The SAM is left in the dark, resulting in relaxation driven by thermal fluctuations only

(thermal erasure). At room temperature all molecules in the cis configuration relax back

to the trans form after a characteristic time [204]. They assume random orientations and

the nematic order is lost.

2) The SAM, immediately after the end of the writing process, is illuminated with

circularly polarized (CP) light at 514nm, which makes the molecules cycle between

the trans and cis configurations and speeds up the relaxation of the birefringence (CP

erasure). A schematic picture of the trans isomers in the monolayer after thermal erasure

or CP erasure is shown in Fig. 3.4(c).

A schematic of the typical experimental results is given in Fig. 3.5, where the temporal

evolution of the birefringence Q(t) is shown for both thermal and CP erasure processes.

Fang et al. [1] showed that the relaxation of the birefringence is non-exponential, and is

instead accurately described by a functional form of the type

Q(t) = [1 + (t/τt)]−η.(3.5)

An asymptotic power-law relaxation starts at t≈τtand proceeds as Q(t)≈(t/τt)−ηfor

t > τt.

Non-exponential relaxations are characteristic of a glassy state, i.e., of systems

sampling a rugged free-energy landscape [205–208]. Here, the underlying dynamics

does not possess a single characteristic time scale, but rather a distribution of them.

It has been suggested [1, 29] that a distribution of energetic barrier that leads to the

Chapter 3. Photo-switchable molecules 44

Figure 3.5: Schematic representation of the relaxation of the birefringence, Q(t), obtained

in the experiment discussed in Ref. [1]. The birefringence inscribed in the monolayer by

illuminating it with linearly polarized light can be erased either by thermal fluctuations at

room temperature (thermal erasure) or by illumination with circularly polarized light (CP

erasure). In both cases the relaxation is well described by the long-time power law decay of

Eq. (3.5). Parameters τtare shown as a diamond marker. Other parameters are η= 0.25 for

the thermal erasure curve and η= 0.63 for the CP erasure curve.

power-law relaxation in the SAM originates from i) the high packing density and ii)

the molecular rotations proceeding in discrete jumps as molecules pass each other by

stretching or squeezing the covalent bonds which tether them to the surface. We discuss

non-exponential relaxation processes more extensively in Sec. 3.4.2.

3.4.1 Rotational dynamics

The erasure processes 1) and 2) can be modeled by defining a rotational dynamics for

the orientational distribution functions of the isomers through the formalism introduced

in Sec. 3.3. As the dMR molecules in the cis state are nearly isotropic, we assume

pc(s) = piso

c. Also, since the transition moment of the molecules is approximately parallel

to the glass substrate, we treat the system as purely two-dimensional. The molecular

orientation sin Eqs. (3.1) is thus fully determined by an angle θ. With these conditions,

Eqs. (3.1) become

∂ft(θ, t)

∂t +∇RJt=−pt(θ)ft(θ, t) + piso

c¯

fc(t) + 1

τc

fc(t) (3.6a)

∂fc(θ, t)

∂t +∇RJc=−piso

cfc(θ, t) + 2π

dθ′pt(θ′)ft(θ′, t)−1

τc

fc(t).(3.6b)

We recall that ft(θ, t) and fc(θ, t) are the orientational distribution functions for trans

and cis isomers, respectively. The light-induced isomerization rates, p, and the rotational

currents, J, have been defined in Eq. (3.3) and Eq. (3.4), respectively.

Chapter 3. Photo-switchable molecules 45

During thermal erasure the monolayer is left in the dark, therefore, there are no

light-induced isomerizations: piso

c= 0 and pt(θ) = 0. Eqs. (3.6) hence become

∂ft(θ, t)

∂t +∇RJt= + 1

τc

fc(t) (3.7a)

∂fc(θ, t)

∂t +∇RJc=−1

τc

fc(t).(3.7b)

During CP erasure the isomerization of trans isomers is not angular dependent, hence

pt(θ) = piso

t. Additionally, the characteristic times of light-induced isomerizations are

several orders of magnitude smaller than that of the spontaneous cis-to-trans thermal

relaxation. Therefore, the last terms on the right-hand side of Eqs. (3.6) can be neglected.

With these conditions Eqs. (3.6) become

∂ft(θ, t)

∂t +∇RJt=−piso

tft(θ, t) + piso

c¯

fc(t) (3.8a)

∂fc(θ, t)

∂t +∇RJc=−piso

cfc(θ, t) + piso

t¯

ft(t).(3.8b)

In Ref. [1], Eqs. (3.7) and (3.8) are solved numerically in order to obtain the temporal

evolution of the orientational distribution functions. Solutions are obtained under the

assumption that the rotational diffusion constants of the two isomers are the same, i.e.

Dt=Dc, and neglecting molecular interactions, i.e.,Ut=Uc= 0.

In general, the temporal relaxation of birefringence obtained with this procedure

is exponential [1]. The experimental power-law decay of Q(t) [as in Eq. (3.5)] can

only be reproduced by combining the results of several sets of equations (at least 7)

each with different values of the characterizing parameters [1]. We find this procedure

quite unsatisfying, as it requires the fine tuning of a large number of free parameters

whose values are, ultimately, rather arbitrary. Nevertheless, the analysis suggests a

multi-domain structure of the monolayer, with different areas characterized by different

relaxation dynamics, which in turn generates the distribution of characteristic times

required for the power-law relaxation.

In Chapter 6 we discuss a molecular model inspired by Eqs. (3.7) and (3.8) for

the relaxation of the birefringence during both thermal and CP erasure. However,

we do not focus on the orientational distribution functions but instead we solve the

rotational dynamics for each single molecule in the system using kinetic Monte Carlo

simulations. Furthermore, we take into account the molecular conformational changes

upon isomerization, the effect of the molecular environment, and the energetic cost for

each molecule to overlap with its neighbors by stretching the tethers. With this approach

we are able to capture the essential physics of the system and reproduce the experimental

results.

3.4.2 Non-exponential relaxation processes

A simple relaxation process follows an exponential form ϕ(t) = exp(−t/τ) (a Maxwell-

Debye relaxation) and its dynamics is thus fully characterized by a single time scale τ. In

many systems however, the relaxation deviates from a simple exponential and is instead

Chapter 3. Photo-switchable molecules 46

described by a stretched-exponential ϕ(t) = exp −(t/τ)βwith 0 < β < 1 or an asymptotic

power-law as in Eq. (3.5) [205, 207, 209].

Non-exponential relaxations were first observed in 1847 by Kohlrausch [210] and have

been found in many contexts: in the relaxation of dipole moments in a viscous fluid [211],

in the strain recovery of a polymeric glass [212], in the dynamics of supercooled colloidal

systems [213], and in the growth of interfaces [214]. Deviations from a Maxwell-Debye

relaxation are normally ascribed to heterogeneity in the system structure or dynamics

[215].

The underlying idea is that a system is divided into multiple regions. Each region

relaxes exponentially with its own characteristic time and the overall non-exponential

relaxation results from an average over these different domains. The presence of spatial

correlations in the local dynamics, which correspond to transient regions of fast- and

slowly-moving molecules, is called dynamic heterogeneity [66], a collective feature of

glasslike systems especially studied in the context of supercooled liquids [216].

Following this interpretation, Fang et al. proposed that the power-law relaxation of

the birefringence in Ref. [1] should be considered as an activation process that takes place

with a distribution of energetic barriers f(U), which results in a distribution of relaxation

times. The birefringence Q(t) is thus defined as

Q(t) = ∞

exp[−t/τ(U)]f(U)dU , (3.9)

where the relaxation times τ(U) are governed by the Arrhenius law

τ(U) = τtexp(U/kBT),(3.10)

and τtis the characteristic time scale of molecular fluctuations. The energy barriers are

distributed according to a generalized Gumbel distribution [217]

f(U) = γ

UmΓ(1/γ)exp −U/Um−exp(−γ(U/Um)),(3.11)

where Umand γare distribution parameters and Γ is the Euler gamma function.

Substituting Eq. (3.11) into Eq. (3.9) using Eq. (3.10) gives a power-law decay of Q(t)

exactly as in Eq. (3.5). The calculation is detailed in Appendix A.

The Gumbel distribution is one of the only three possible limit distributions for the

extremal values of a sequence of properly scaled, identically distributed and independent

random variables [217]. There is no fundamental reason for the energy barriers to be

distributed according to Eq. (3.11), but a generalized Gumbel distribution is often used

in the studies of correlated systems as a convenient fitting function, a procedure that

generated speculations about the role of extreme-value statistics in correlated systems

[218, 219]. The basic argument is as follows: in highly-correlated systems, there are

mesoscopic regions that are not statistically independent and, as a result, spatially

averaged quantities do not necessarily satisfy the fundamental assumptions of the central

limit theorem. Hence, the related probability distribution functions are not Gaussian

[219].

Besides non-exponential relaxation processes, other features such as a subdiffusive

regime at intermediate times or a non-Gaussian distribution of single-particle

displacements are considered universal signatures of glasslike dynamics [220]. The

subdiffusive regime is often related to the presence of low-mobility particles, whose

Chapter 3. Photo-switchable molecules 47

displacements are hindered by their neighbors [221, 222]. The non-Gaussian distribution

of particle displacements is interpreted as a manifestation of heterogeneous dynamics

[223]. Indeed, the distribution of particle displacements is expected to be Gaussian in

a purely random diffusion process. For example, in a continuous time random walk,

the Gaussian distribution of the displacements is essentially a consequence of the central

limit theorem, since subsequent steps are assumed to be independent and identically

distributed stochastic variables. Hence, deviations from a Gaussian distribution can

be ascribed to non-identically distributed or eventually correlated steps. Additionally,

heterogeneous dynamics has been connected to a violation of the Stokes-Einstein relation,

which predicts a linear dependence of the diffusion coefficient on temperature [222, 224,

225]. In Chapter 6 we demonstrate that universal signatures of glasslike dynamics can be

observed in our molecular model in a proper region of the parameters space, where the

simulated birefringence relaxes non-exponentially.

The direct observation of dynamic heterogeneity requires the precise resolution

of single-molecule motion, which allows to extract information about fluctuations.

Furthermore, even if dynamic heterogeneity is a transient phenomena (in non-crystalline

structures molecules are constantly moving and rearranging), spatial correlations in the

molecular dynamics can last for several time decades, in during which the molecular

motion must be tracked. Such challenging measurements have successfully been

performed only recently on some colloidal glasses [226–228].

The common route to the direct identification of dynamic heterogeneity in a

translationally invariant system at equilibrium is well described in Ref. [65]. It starts

with the definition of the molecular mobility c(r;t, 0), that measures how much a particle,

located at position rat time 0, has moved between time tand time 0. For example, one

can define

c(r;t, 0) =



i=1

exp(−|ri(t)−ri(0)|2)δ(r−ri(0)) ,(3.12)

where Nis the number of molecules and ri(t) is the position of the i-th molecule at time

t. The next step is to define a correlation function, which measures the degree of spatial

correlation between molecules with a similar dynamics,

G4(r;t) = ⟨c(r;t, 0)c(0;t, 0)⟩−⟨c(r;t, 0)⟩2,(3.13)

where ⟨. . . ⟩denotes ensemble average and where r=|r|. If the molecule dynamics are

spatially correlated at time t, the correlation function G4(r;t) is expected to decay to

zero at a certain distance r0, which is an estimate for the size of correlated regions. Thus,

the integral of the correlation function also increases with the size of dynamical domains

and can be taken as a measure of the extension of dynamic heterogeneity in the system.

This integral is defined as

χ4(t) = drG4(r;t),(3.14)

and is called dynamical susceptibility because it shows several qualitative analogies with

the susceptibility of critical systems.

As mentioned before, the procedure just described works for a system at equilibrium

and, hence, cannot be immediately applied to the relaxation of the birefringence Q(t)

studied in Ref. [1]. Indeed, the system is out of equilibrium in the course of the relaxation

towards an equilibrium state. During this transient regime, it is not possible to perform

ensemble averages as in Eq. (3.13). Nevertheless, inspired by the procedure just described,

Chapter 3. Photo-switchable molecules 48

in Sec. 6.4 we provide a direct measure of the extension of spatio-temporal correlated

domains during a relaxation process. In this way we can unambiguously demonstrate

the presence of dynamical heterogeneity and their connection with a non-exponential

relaxation dynamics.

Chapter 4

Numerical Methods

In this Chapter we explain the numerical methods used to solve our molecular models.

Monte Carlo simulations are at the base of the studies presented in Chapter 5, where

we map out the phase behavior of the bent-needle model. Monte Carlo methods are

discussed in Sec. 4.1, with particular attention to implementation of the Monte Carlo

technique in the Canonical and in the Isobaric-Isothermal ensemble. In Sec. 4.2 we discuss

the specialized optimization techniques used to save computational time. Kinetic Monte

Carlo simulations are used to generate the rotational dynamics of the model presented in

Chapter 6. Therefore we detail this special kinetic implementation in Sec. 4.3.

4.1 Monte Carlo simulation

When a certain molecular model is proposed, it is essential to test it against real

experimental data. Because not all the properties of a system are easily accessible in

real-life experiments, the main sources of informations are typically averaged quantities.

It follows that, in order to test a model, one has to compare the predicted average values

of certain observables with the experimental ones. In the context of statistical mechanics,

the average value of an observable Ois defined in the canonical ensemble as

⟨O⟩=dNpdNqe−βH(q1,...,qN,p1,...,pN)O(q1,...,qN,p1,...,pN)

dNpdNqe−βH(q1,...,qN,p1,...,pN),(4.1)

where the qiare the particles positions, the pithe conjugate momenta, β= 1/kBT,His

the Hamiltonian of the system and Nis the number of particles. As in many cases both

the observable Oand the potential energy are independent on the conjugate momenta,

the kinetic terms in Eq. (4.1) are integrated out and one is left with the configurational

part

⟨O⟩=dNqe−βU(q1,...,qN)O(q1,...,qN)

dNqe−βU(q1,...,qN),(4.2)

where Uis the potential energy, which only depends on the particles coordinates.

On the one hand, Eq. (4.2) can be evaluated analytically only in a few simple cases,

therefore is natural to look for numerical methods. On the other hand, standard numerical

methods are difficult to apply given the high dimensionality of the problem. For example,

one can think of evaluating Eq. (4.2) using quadrature methods over cpoints on each

coordinate axis. In this case, the total number of points would be cdN where dis the

dimensionality of the system. Using 100 particles in three dimensions means that the

Chapter 4. Numerical methods 50

integral has to be evaluated on c300 points, a huge number already for small values of c

[229]. Is clear that more sophisticated techniques must be used.

The Monte Carlo method is essentially a technique to evaluate high-dimensional

integrals. The main idea behind the Monte Carlo integration is that only a small subset

of configurations significantly contribute to the integral in Eq. (4.2). Indeed, Eq. (4.2)

can be rewritten as

⟨O⟩=dNqD(q1,...,qN)O(q1,...,qN),(4.3)

where

D(q1,...,qN) = e−βU(q1,...,qN)

dNqe−βU(q1,...,qN),(4.4)

is the probability density of finding the system in a configuration specified by (q1,...,qN).

If we are only interested in the relative and not in the absolute probability of finding the

system in a particular configuration, we can generate points in the space of configurations

with a probability proportional to D. In this case there would be no need to evaluate the

integral in the denominator of Eq. (4.4).

In practice, the Monte Carlo technique consists in starting with a certain configuration

of the system, which we denote with o(old), and comparing it with another trial

configuration denoted with n(new). The configuration nwill be accepted according to

its relative probability with respect to the configuration o. The most important condition

to impose in defining this sampling process is to ensure that an equilibrium configuration

is not destroyed once it is reached. At equilibrium, the probability to leave state ofor

another state nmust be equal to the probability of reaching state ostarting from n. If

we denote with W(o→n) the probability to go from configuration oto configuration n,

this condition reads

D(o)W(o→n) = D(n)W(n→o),(4.5)

and is called condition of detailed balance.

There exist several forms of Wthat satisfy Eq. (4.5) [230]. In the following we discuss

the Metropolis scheme [231]. The probability to go from oto ncan be expressed as

W(o→n) = α(o→n)γ(o→n),(4.6)

where α(o→n) is the probability to generate nstarting from oand γ(o→n) is the

probability to accept the move from oto n. In the Metropolis scheme [231] α(o→n) is

symmetric [α(o→n) = α(n→o)], thence Eq. (4.5) becomes

γ(o→n)

γ(n→o)=D(n)

D(o)= exp[−β(U(n)−U(o))] ,(4.7)

and a natural choice for γ(o→n) is

γ(o→n) = 





D(n)

D(o)if U(n)> U(o)

1 if U(n)≤U(o)

.(4.8)

Eq. (4.8) means that the trial move from oto nis accepted with probability

exp[−β(U(n)−U(o))] <1 if the move brings the system in a configuration with higher

Chapter 4. Numerical methods 51

energy than before, or is accepted with certainty if the new configuration has lower energy

than the old one.

In practice, the condition given by Eq. (4.8) is implemented in the following way: if

U(n)≤U(o) the new configuration is immediately accepted. If U(n)> U(o), a random

number rand ∈[0,1] is extracted from an uniform distribution. The trial move is accepted

if rand < exp[−β(U(n)−U(o))] and rejected otherwise.

The average values of interest can be measured after any trial move. One of the

basic route to test for the system equilibration is to start the Monte Carlo simulation

from several different initial configurations and to keep track of the evolution of the

relevant average quantities. When the same averaged quantities (measured in simulations

initialized with different initial conditions) converge to a common value, one can assume

that an equilibrium state has been reached.

Modern computer technologies typically allow for the simulation of systems with

several thousands of molecules, a large number which is nevertheless far from the

thermodynamic limit. Thus, to simulate the properties of a system in the bulk, it is

common practice to employ periodic boundary conditions, as we do in Chapters 5 and

6. Under periodic boundary conditions, the system is considered as the primitive cell

of an infinite periodic structure of identical cells. If the distance of a molecule from the

cell border is smaller than the inter-molecular interaction range, the interaction with

molecules at the opposite side of the cell must be taken into account. Additionally, when

a translational move brings the molecule outside the cell, the molecule will reenter the

cell from the opposite side.

In Secs. 4.1.1 and 4.1.2 we explain how the Metropolis scheme is implemented in two

typical situations: a canonical or a isothermal-isobaric ensemble.

4.1.1 NV T Monte Carlo simulation

In the canonical ensemble a system can only exchange heat with its surrounding. The

number of particles N, the system volume Vand the temperature Tare therefore fixed.

In order to generate a new configuration of the system from an old one, molecules have to

change their positions and, eventually, their orientations. In the following we summarize

the implementation of a Metropolis Monte Carlo simulation assuming that we are in two

dimensions, where the orientation of a molecule is fully specified by an angle.

The starting configuration of a system is in principle arbitrary but an educated choice

can reduce the time needed to reach an equilibrated state. From the starting configuration

(o), a molecule is selected at random and translated or rotated with equal probability. Let

us denote with (xo, yo) the spatial coordinates of a molecule in the starting configuration

and let us assume that in this configuration the orientation of the molecule is given by an

angle θo. The trial move brings the molecule in a new configuration n. If a translational

move is selected, the new coordinates are obtained via the following substitution

xo→xo+ ∆Tξ1

yo→yo+ ∆Tξ2,(4.9)

where ξ1and ξ2are two random numbers extracted from a uniform distribution between

−0.5 and 0.5 and ∆Tis the maximum translational displacement. If a rotational move is

selected, the new orientation is given by

θo→θo+ ∆Rξ3,(4.10)

Chapter 4. Numerical methods 52

where ξ3is again a random number uniformly distributed between −0.5 and 0.5 and ∆R

is the maximum rotational displacement.

The trial move is then accepted according to Eq. (4.8), i.e., with probability γ(o→

n) = min[1,exp[−β(U(n)−U(o))]], and the whole process is repeated again. A cycle of

Nindependent trial displacements is called a Monte Carlo sweep. It is common practice

to evaluate the relevant average quantities at least after a complete Monte Carlo sweep.

The variables ∆Tand ∆Rare in principle arbitrary, but too large displacements will

result in most of the new trial configurations being rejected, while too small maximum

displacements cannot guarantee a full exploration of the configurational space in a

reasonable time. In practice, it is convenient to fix the average acceptance rate of a

displacement move to be around 50% of the total attempts, and to adjust the maximum

displacement accordingly.

The new position of the molecule can be anywhere (with finite probability) inside a

square of lateral size ∆Tcentered in (xo, yo). Also, the new orientation is defined by an

agle that can be anywhere (with finite probability) in the interval (−∆R/2,∆R/2) around

θo. The method is therefore clearly ergodic.

4.1.2 NPT Monte Carlo simulation

In most experimental situations the control variable is pressure rather than volume

of the system. It is therefore convenient to introduce an ensemble, where the fixed

thermodynamic parameters are the temperature T, the number of molecules N, and the

pressure P. In order to keep the pressure fixed, the volume Vmust fluctuate. Indeed, a

constant pressure system is coupled to an isotropic piston, which expands or compresses in

order to keep the internal pressure equal to the external applied pressure. If such a system

is also allowed to exchange heat with a surrounding heat bath, then its temperature will

also stay constant.

In the isothermal-isobaric ensemble, the partition function of a system is essentially

a canonical partition function with an additional volume integration, where a PV term

has been added to the Hamiltonian. In two dimensions it reads

Q(N, P, T) = βP

λ2N

th N!dV V Ne(−βP V )dNse(−βU(s1,...,sN;L)) ,(4.11)

where λth is the thermal de Broglie wavelength and we expressed the molecular position

in terms of the scaled variables si=qi/L (L=√Vas the system is assumed to be in a

square box) for later convenience, but the presence of Las an argument of Uindicates

that the interaction energy depends on the real distance between molecules.

In complete analogy with Eq. (4.4), the probability density to find the system in a

configuration defined by (s1,...,sN) and with volume Vis

D(s1,...,sN;V)∝VNe(−βP V )e(−βU(s1,...,sN;L)) .(4.12)

In practice, in the isothermal-isobaric ensemble, a Monte Carlo attempt to change the

system volume has to be defined in addition to the moves for the molecular displacements.

To ensure that the condition of detailed balance is satisfied, an attempt to change the

volume has to be made on average every Ntrial molecular displacements. Denoting with

Vo(Vn) the volume of the old (new) configuration o(n), the new volume is obtained via

Vn=Vo+ ∆VξV,(4.13)

Chapter 4. Numerical methods 53

where ∆Vis the maximum volume displacement and ξVis a random number uniformly

distributed between −0.5 and 0.5. Subsequently, the coordinates (x, y) of the center of

mass of all the molecules in the system have to be scaled according to

x→xLn

y→yLn

,(4.14)

where Ln=√Vnand Lo=√Vo. The energy of the new configuration U(n) is evaluated

and the volume move is accepted with probability

γ(o→n) = min[1,exp{−β[(U(n)−U(o)) + P(Vn−Vo)] + Nln(Vn

)}].(4.15)

Clearly, since after a trial volume change all the inter-molecular interactions must be

evaluated again, a volume change is computationally more costly then a molecular

displacement.

4.2 Optimization techniques

In this Section we explain the numerical optimization techniques used to save

computational time in our implementation of the Monte Carlo simulation. In Sec. 4.2.1 we

describe a specialized implementation of the basic isotropic Verlet list [229], which takes

advantage of the highly anisotropic shape of the bent-needle molecules. In Sec. 4.2.2 we

detail a cluster algorithm, which is used to displace a group of several molecules in a

single Monte Carlo move in order to efficiently unlock kinetically trapped configurations.

4.2.1 Anisotropic neighbor list

If the interactions in the simulated model are pairwise additive and if the interaction

range of the molecules is smaller than the simulation box, several techniques can be used

to avoid the calculation of all the N(N−1)/2 pair interactions after each molecular

displacement.

The simplest possibility is to use a linked list. The linked list is built by using a

square decomposition of the simulation box. The simulation box is divided into smaller

sub-boxes of a side length equal or larger than the intermolecular interaction range rI.

Hence, each molecule only interacts with other molecules in the same sub-box or in the

other eight neighboring sub-boxes (in two dimensions).

The Verlet list is another method of reducing the number of pair interactions that must

be evaluated after each Monte Carlo trial displacement. In its basic implementation, one

introduces a cutoff radius rC=rS+rI(larger than the interaction range), where the

distance rSis called skin radius [see Fig. 4.1(a)]. A list of all the molecules within a

distance rCis then built for each molecule. After a trial displacement of a molecule,

the interaction energy has to be evaluated only within the molecules that belong to the

Verlet list, but the list has to be updated if a translational displacement brings the

molecule under consideration at a distance larger than rSfrom its initial position [229].

A large value of rsreduces the update frequency of the list, but increases the number of

neighboring molecules within the list.

Chapter 4. Numerical methods 54

rS1

a) b)

Figure 4.1: a) The isotropic Verlet list of particle icontains all the particles that are within a

range rI+rsfrom it, where rIis the particle interaction range and rSis the skin radius. b) The

anisotropic Verlet list for bent hard needles is built by wrapping a bent spherocylinder around

each molecule. Molecule ibelongs to the Verlet list of molecule jif their spherocylinders overlap.

In the figure, molecule 2 is in the Verlet list of molecule 1 (and vice versa) while molecule 3 is

not.

In our specialized implementation, we rely on the fact that bent needles have

anisotropic shape and that they interact through a hard-core potential, which does

not allow the needles to overlap. Thus, we use an anisotropic shape to build the list

instead of simply checking for radial distances. Our Verlet list is built by wrapping a

spherocylinder body around each molecule. This non-trivial shape is obtained by gluing

together three spherocylinders, one for each molecular segment. The Verlet list is then

filled with the neighboring molecules whose bent spherocylinders overlap with the one

under consideration. The bent spherocylinder of a molecule remains fixed for many

Monte Carlo steps, but has to be reconstructed when a rotational or a translational

Monte Carlo move brings the molecule out of its bent spherocylinder. Shrinking the

spherocylinder radius for the Verlet list considerably reduces the time needed to detect

potential overlaps, but increases the rate at which the lists need to be updated [229].

Before starting a Monte Carlo simulation, we thus first determine the spherocylinder

radius that optimizes algorithmic performance.

Because we use a combination of linked list and Verlet list, the lateral extension of

the linked list cells is roughly given by the particle length plus the spherocylinder radius

of the Verlet list. The Verlet list in a given sub-box can then be built by only considering

molecules within that same sub-box as well as within the eight neighboring sub-boxes.

4.2.2 Cluster moves

In Chapter 5 we employ Monte Carlo simulations to map out the phase diagram of

the bent hard-needle model, which shows a variety of transitions between liquid-crystal

phases. Especially in the vicinity of the isotropic–quasi-nematic transition (see Fig. 2.6),

small clusters of very close and well aligned molecules develop in the isotropic phase. Once

these relatively small but highly packed clusters of particles form, molecule orientations

can get kinetically locked. Equilibration, however, requires overcoming the high free-

energy barriers associated with aligning these clusters, which considerably slows down

equilibration. A way to alleviate this problem is to rely on the fact that Monte Carlo

simulations need not be tied to a local and thus physical dynamics. Instead of moving

Chapter 4. Numerical methods 55

Figure 4.2: Example of a cluster (blue colored molecules) for zig-zag molecules with a= 0.25

and α=π/2. The parameters of the artificial potential in Eq. (4.16) are ϵ= 1.0, ∆rmax = 0.3

and ∆θmax = 6.0◦. To ease the identification of the cluster, we only show a portion of the

simulation box. The system density, in units of the molecular length, is ρ= 14, thus the system

is in the vicinity of the isotropic–quasi-nematic transition (see the phase diagram in Fig. 5.9(a)).

particles one at a time, one can define collective moves that identify groups of correlated

particles and then move them as a single object [232, 233]. However, in order to satisfy

detailed balance and ensure that reverse displacements are also possible, the operation

must be done in a probabilistic way.

Here, we build clusters of particles by introducing an artificial attractive potential

uf(ϵij) that links particles together [234, 235]. The potential form is arbitrary, but is

most successful if it captures the nature of correlations within a cluster. Our choice is

uf(ϵij) = −ϵH(∆θmax −∆θij)H(∆rmax −∆rij),(4.16)

where H is the Heaviside step function, and ∆rmax and ∆θmax are tunable thresholds.

Typical values are ϵ= 1.0, ∆rmax = 0.3 and ∆θmax = 6.0◦. For a given configuration, the

linking probability between particles iand jis

pij = max[0,1−exp(βuf(ϵij))] .(4.17)

Molecules that are close and well aligned are thus linked with high probability, whereas

molecules outside the range of ∆rmax and ∆θmax are not linked at all. A cluster is built

by choosing a particle iat random and by attempting to build links with its neighbors.

If a link between iand jis formed, jbecomes a member of the cluster formed around

molecule i. An example of a cluster built with this procedure for zig-zag molecules in the

vicinity of the isotropic–quasi-nematic transition is shown in Fig. 4.2.

Once the cluster has been formed, we perform a trial move by translating or by rotating

it around its center of mass. If the trial move generates overlaps, it is immediately rejected.

If not, it is accepted with probability

W(old →new) = min[1,exp(β(Unew −Uold))] ,(4.18)

where Uν=i,j∈Iνuf(ϵij) is the artificial interaction energy between the cluster and

its environment in either the ν=old or new state. The interface Iνis defined by all

the particles iinside and the particles joutside the cluster that contribute to Uν. As

for standard Monte Carlo simulations, the results are valited by checking that different

Chapter 4. Numerical methods 56

initial conditions for both constant-NV T and constant-NPT simulations give the same

outcome.

4.3 Kinetic Monte Carlo simulation

In the previous Sections of this Chapter we described the Monte Carlo technique as a

method for solving high-dimensional integral through a random walk in the space of

configurations. In this regard, the Monte Carlo evolution of a system is completely

unrelated to its physical time evolution. In this section we explain how, by employing

some special precautions, a reliable dynamics can be obtained using a Monte Carlo

simulation scheme. This numerical technique is called kinetic Monte Carlo simulation

[64, 236].

In general, the kinetic Monte Carlo simulation is a numerical technique well suited

to study phenomena, whose dynamics lies on a time scale several order of magnitude

larger than the time scale of atomic vibrations, but for which microscopic details are

still essential. For instance, typical molecular dynamic simulations (which incorporate

detailed inter-atomic potentials) cannot span time scales larger than microseconds and

cannot track the dynamics of a statistically significant ensemble of interacting molecules.

In kinetic Monte Carlo simulations atomic details are course-grained, which enables the

exploration of the long-time collective behavior of complex systems.

In the kinetic Monte Carlo method, each simulated process is associated with a certain

rate, which defines the average frequency of occurrence of the process in a sequence of

random transitions. Clearly, unphysical moves like the cluster moves described in Sec.

4.2.2 must be avoided. Also, an event should almost always be realized after any Monte

Carlo move, which means that the acceptance rates of the moves must be very close to 1.

As the probability of accepting a Monte Carlo move is in general inversely proportional

to the related maximum displacement, very small displacements should be used, which

also make the moves local.

Most importantly, a unique Monte Carlo time scale must be defined independently

from the acceptance rate of the Monte Carlo moves. This unique time scale defines the

time unit to which the rates of different processes can be compared. To understand how

this time scale is introduced, we follow the discussion in Ref. [237].

Let us assume that we are simulating a system with mdegrees of freedom. In a

Monte Carlo move a particle is displaced from its initial position by an amount included

in the interval [−δi, δi], where δiis the maximum displacement for the i-th degree of

freedom (i= 1, . . . , m). If the probability of accepting a move Ais independent from the

maximum displacement (i.e. for an infinitely dilute system or if we only consider small

maximum displacements), the probability density of a successful move is p=A/2δi. The

mean square displacement of the variable xiassociated with the i-th degree of freedom is

thus given by

⟨x2

i⟩=

δi



−δi

px2

idxi=A(δi)2

3.(4.19)

If the Monte Carlo moves are statistically independent, one has

δ2

i= 2Didt ,(4.20)

Chapter 4. Numerical methods 57

where Diis the self-diffusion constant for the i-th degree of freedom and dt is a Monte

Carlo time scale. Substituting Eq. (4.20) into Eq. (4.19) gives

⟨x2

i⟩=2ADidt

3,(4.21)

which establishes a direct connection between the kinetic Monte Carlo simulation and

the diffusivity in Einstein’s theory of Brownian motion.

In a Brownian dynamics simulation one has

⟨x2

i⟩= 2DitBD ,(4.22)

where tBD is the Brownian dynamics time unit. Substituting Eq. (4.22) into Eq. (4.21)

gives

tBD =Adt

3.(4.23)

Eq. (4.23) means that it is possible to simulate the same process in several kinetic Monte

Carlo simulations using different values of dt. The resulting time dependent quantities

collapse in a single master curve when dt is scaled with the corresponding A, which

demonstrates the existence of a unique Monte Carlo time scale [237] equal to the Brownian

dynamics time scale.

Kinetic Monte Carlo simulations have been used in several contexts: in liquid crystals

[238, 239], in glass-forming systems [240, 241], to study the nucleation rate in a suspension

of hard spheres [242], the mobility of rods in a quasicrystalline potential [48], the transport

dynamics of polymers [243], the formation of vesicles [244], the growth of crystals

[245], and the dynamics of thin film deposition [246, 247]. In Sec. 6.2 we detail our

implementation of the kinetic Monte Carlo simulation scheme for a molecular model of

the experiments described in Sec. 3.4. The results of the simulation are discussed in

Chapter 6.

Chapter 5

Phase Behavior of the Bent

Hard-Needle Model

In this Chapter we study the two-dimensional phase behavior of the bent-needle model

introduced in Fig. 1.1(c) using Monte Carlo simulation. The model has two configurations,

a chiral zig-zag shape and an achiral bow-shaped shape, which show significant differences

in their self-assembly properties. In Chapter 2 we already anticipated the mesophases

identified in this model, described their qualitative features, and showed their structures

through snapshots of the simulation box. Here, the complete phase diagram of the bent-

needle model is obtained by using the order parameters and the correlation functions

defined in Sec. 2.7. The mesophases identified in the model are summarized in Fig. 5.1.

We find that zig-zag molecules assemble in a quasi-nematic and a smectic-C phase [(Fig.

5.1(a)], while bow-shaped molecules assemble in a quasi-nematic, an anti-ferromorphic

smectic-A, and a modulated-nematic phase [Fig. 5.1(b)].

The Chapter is structured as follow. In Sec. 5.1 we detail the model and in Sec. 5.2 we

specify the numerical simulation scheme. In Secs. 5.3 and 5.4 we identify the isotropic–

quasi-nematic and the quasi-nematic–smectic transition densities, respectively. In Sec.

5.5 the modulated-nematic phase of bow-shaped needles is described in detail. Finally,

in Sec. 5.6 we present the complete phase diagram of the bent hard-needle model.

This Chapter is essentially based on the material in Ref. [A].

5.1 Bent hard-needle model

Our bent hard-needle model consists of a central line segment of length bto which two

terminal line segments of equal length aare attached at a fixed angle α[Fig. 1.1(c)]. The

molecules can adopt a chiral zig-zag or an achiral bow-shape configuration, depending

on whether αis defined on the same or on opposite sides of the central segment. Note,

however, that we only consider enantiomerically pure systems in order to avoid chiral

segregation [248]. Pairs of molecules interact via a hard-core exclusion potential but are

infinitely thin, i.e., they can be infinitely close to one another but cannot overlap. Since

the hard-core interaction potential is athermal, we set to unity the product of Boltzmann’s

constant and temperature, kBT= 1/β = 1, without loss of generality. The total length of

the molecule, L= 2a+b= 1, is used as the unit of length, also without loss of generality.

Each model is thus completely determined by two parameters: aand α. In the following

we let αvary from 0 to π/2 (at α= 0 both models are equivalent), but we fix a= 0.25

for zig-zag molecules and a= 0.35 for bow-shaped molecules. This choice maximizes

Chapter 5. Bent hard-needle model 60

b) Quasi-nematic Smectic-A Modulated-Nematic

Quasi-nematic Smectic-C

Figure 5.1: Snapshots of the main mesophases identified in Monte Carlo simulations: (a)

zig-zag molecules with a= 0.25, α=π/3 in both the quasi-nematic (ρ= 14) and the

smectic (ρ= 30) phases, and (b) bow-shaped molecules with a= 0.35, α=π/16, ρ= 20

in the quasi-nematic, with a= 0.35, α=π/3, ρ= 30 in the smectic, and with a= 0.35,

α=π/6, ρ= 26 in the modulated-nematic phases. The nematic director, the smectic surface

normal and the modulated-nematic layers normal are indicated as red, blue, and green arrows,

respectively. Note that in order to clearly illustrate the mesophase morphology, only a portion

of the simulation box is displayed.

the excluded area, and thus pushes down the isotropic–mesophase transition densities,

making them computationally less costly to study.

5.2 Details of the Monte Carlo simulation

In order to study the phase behavior of the zig-zag and bow-shaped models, we perform

Monte Carlo simulations mostly in the constant-NV T but also in the constant-NPT

ensemble. The Monte Carlo simulation scheme in the constant volume and constant

pressure ensemble has been introduced in Sec. 4.1. In this section we detail our

implementation for the bent hard-needle model. Most simulations have N= 2000 in

a square box of area Vunder periodic boundary conditions.

Constant-NV T simulations are performed at fixed reduced density ρ=N/V and

consist of up to 3.0×107sweeps, where a Monte Carlo sweep comprises Nindependent

trial displacements. The basic Monte Carlo move in the NV T ensemble consists of

either translating or rotating (randomly chosen with equal probability) a randomly chosen

molecule. The maximum attempted displacement is preliminarily adjusted in such a way

that an acceptance rate of approximately 50% is achieved, but during the production runs

the maximum step sizes are fixed – dynamical adjustments would violate detailed balance

Chapter 5. Bent hard-needle model 61

[249]. The hard-core nature of the pair interaction simplifies the Metropolis acceptance

rule in Eq. (4.8): the displacement of a molecule is accepted if it does not generate an

overlap, and is rejected otherwise. In order to check that the sampled configurations

correspond to equilibrium (and not metastable) states, different initial configurations –

including isotropic, perfect polar and anti-polar nematic, as well as perfect smectic states

– are used. Note that reaching equilibrium and properly sampling states sometimes

require up to several million Monte Carlo sweeps, leading to computational times of up

to four weeks on a single-thread of an Intel Xeon X5550 machine with a 2.66 GHz CPU.

The minimum simulation time was about one week.

Constant-NPT simulations also include changes in Vin order to keep the system

pressure Pconstant (see Sec. 4.1.2). A Monte Carlo sweep then comprises an average

of Nindependent single-molecule trial displacements and one trial volume change. In a

trial volume change, Vis modified by an amount ∆ ln Vand all the molecule positions

are rescaled accordingly. Since we perform the random walk in ln Vrather than in V(the

former is known to be computationally more efficient [229]), the acceptance probability

of a trial volume change given by Eq. 4.15 must be slightly modified. If no overlap occurs

in the resulting configuration, the move is accepted with probability

p(V→V+ ∆V) = exp[−P∆V+ (N+ 1) ln(1 + ∆V/V )],(5.1)

and is rejected otherwise (note the (N+ 1) prefactor of the ln term).

For the bow-shaped molecules with intermediate α, constant-NV T simulations

either result in ferromorphic or in anti-ferromorphic states, depending on the initial

configuration. In order to identify the equilibrium ground state, we thus also performed a

slow pressure annealing. This process was achieved through a sequence of constant-NPT

simulations starting from the isotropic regime and increasing Pin steps of 10-20%. At

each step ρwas equilibrated for at least 2.0×106sweeps. The reverse procedure was

used to check for hysteresis. This study revealed that the anti-ferromorphic phase is the

equilibrium state, as we discuss in Sec. 5.5.

The optimization techniques described in Sec. 4.2 are employed to save computational

time. In particular, we use both the anisotropic neighbor list and the cluster algorithm

introduced in Sec. 4.2.2 in constant-NV T simulations. In constant-NPT simulations we

only use a linked list because each volume change forces the anisotropic neighbor list to

be updated, which is a computationally expensive procedure.

5.3 Isotropic–quasi-nematic transition

Upon increasing density, both zig-zag and bow-shaped molecules form a quasi-nematic

phase with quasi-long-range orientational order. As per the discussion in Sec. 2.3, the

quasi-nematic phase and the isotropic–quasi-nematic phase transition via disclination

unbinding are evidenced by the transition from an exponential decay of g2(r) at low ρ

to a power-law decay, g2(r)∝r−η, as ρincreases (see Fig. 5.2). From Eq. (2.46) follows

that the quasi-nematic phase is expected to be stable against spontaneous disclination

unbinding when πK/(8kBT)>1. We obtain the Frank elastic constants from the relation

η= 2kBT/πK, where the power-law decay of g2(r) is obtained from a linear fit of ln g2(r)

versus ln rover the range 0.5≤r≤4.0. Note that the lower threshold is necessary

because g2(r) deviates from the power law at small r, while the higher threshold is chosen

so as to exclude correlations resulting from the use of periodic boundary conditions. Note

Chapter 5. Bent hard-needle model 62

a) b)

Figure 5.2: (a) Radial dependence of the orientational correlation function for several densities

for (a) zig-zag molecules with α=π/3 and a= 0.25, and (b) bow-shaped molecules with

α= 2π/5 and a= 0.35. Dashed lines in (b) show the fits to an exponential function for ρ= 15

and 16 and to g2(r)∝r−ηfor ρ= 18, 20, and 23. Fit exponents are given in Fig. 5.3. The inset

in (a) shows a portion of the simulation box at ρ= 11, close to the isotropic–quasi-nematic

transition. The inset in (b) details the local packing of molecules, which results in oscillations

of g2(r).

a) b)

Figure 5.3: Density evolution of the reduced Frank elastic constant Kobtained from the

power-law decay of g2(r) for (a) zig-zag molecules with a= 0.25 and (b) bow-shaped molecules

with a= 0.35. The isotropic–quasi-nematic transition densities, ρIN are obtained from the

intersections of the linear fits to the numerical results with the line πK/8kBT= 1. For each

point, error bars are obtained by propagating the standard errors of the power-law exponents

ηobtained from the least squares fits of g2(r). Where not shown, error bars are smaller than

the symbols.

also that bow-shaped molecules display correlation functions with fairly large oscillations

as a result of the local packing structures, which do not exist for straight needles [see

inset in Fig. 5.2(b)].

The results for the reduced Frank elastic constant πK/(8kBT) are plotted in Fig. 5.3

for both molecule types. Since the results scale nearly linearly with ρ, we identify the

isotropic–quasi-nematic transition densities ρIN as the intersection between linear fits to

data the points and πKc/(8kBT) = 1, as explained in Sec. 2.3.2.

For zig-zag molecules, the quasi-nematic phase is systematically destabilized by

bending the terminal segments [Fig. 5.3(a)]. As the central-to-tail angle αincreases,

Chapter 5. Bent hard-needle model 63

Figure 5.4: Excluded area versus central-to-tail angle αfor parallel zig-zag (black line) and

bow-shaped (red line) molecules.

the transition is thus pushed to higher densities. Bow-shaped molecules, however, show

a non-monotonic trend of the transition density ρIN with α[Fig. 5.3(b)]. For small αthe

transition density increases with α, while for α≥π/3 the trend is inverted. In the range

π/13 ≲α≲π/3 the quasi-nematic phase is unstable with respect to the modulated-

nematic phase, and the power-law scaling analysis is then inapplicable (see Secs. 5.5 and

5.6).

We try to understand the difference in the two molecular geometries by examining

the size Aexl of the excluded area for perfectly parallel molecules (see Fig. 5.4). Like

ρIN, it monotonically increases with αfor zig-zag molecules, but reaches a maximum at

α≈π/3 and then decreases for bow-shaped molecules. Large values of Aexl suggest that

parallel molecules have to pack locally to come close to one another, as evidenced by

the undulations of g2(r) in Fig. 5.2(b). This packing constraints translational freedom,

and thus reduces the translational contribution to the entropy. Because the translational

contribution normally compensates for the loss of orientational freedom in the nematic

phase, higher ρthan usual are needed for this effect to be significant, and as a result ρIN

increases.

5.4 Quasi-nematic–smectic transition

Smectic order consists of a periodic arrangement of particle positions along one direction,

which leads to a well-defined density wave along the corresponding wave vector. Within

smectic layers, however, translational order is absent. In Sec. 2.4.2 we discussed how long-

range translational order is not expected in the thermodynamic limit of two-dimensional

systems. Nevertheless, smectic order is obervable on sufficiently small length scales. For

now, we consider the smectic order parameter defined in Eq. (2.81) as a function of density

for both the zig-zag and bow-shaped molecules in Fig. 5.5. The Monte Carlo simulation

data are fitted with

f(ρ) = 1/2 + arctan[h(ρ−ρNS)]/π, (5.2)

where ρNS and hare fit parameters. Hence, the quasi-nematic–smectic transition density

ρNS is defined as the point of maximum slope of f(ρ). The smectic order parameter

for bow-shaped molecules does not assume large values even at the highest densities

Chapter 5. Bent hard-needle model 64

a) b)

Figure 5.5: Smectic order parameter Λsm plotted versus density ρat several central-to-tail

angles αfor (a) zig-zag molecules with a= 0.25 and (b) bow-shaped molecules with a= 0.35.

Data points are obtained from Monte Carlo simulations. Error bars indicate the standard

deviations of Λsm over equilibrated samples. Lines are a fit of Eq. (5.2) to the data using the

transition density ρNS and has fitting parameters (see phase diagrams of Fig. 5.9 for results on

ρNS).

simulated, which is likely the result of out-of-layer fluctuations and of the instability

of two-dimensional smectic order described. Fits to the simulation results nonetheless

provide an estimate for ρNS. Note that the values of the transition densities identified in

this way are close to the highest values of the densities explored in our simulation.

As could be seen in Figs. 2.8(b) and 5.1(a) and as was previously noted in Ref.

[51], zig-zag molecules form a smectic-C phase, wherein the nematic director is tilted

with respect to the layer normal. Bow-shaped molecules instead arrange in an anti-

ferromorphic smectic-A structure [see Figs. 2.9 and 5.1(b)], wherein the polar vector

vadopts an opposite orientation in adjacent layers. This unusual ordering can be

rationalized by extending a packing argument developed for the anti-ferroelectric ordering

of V-shaped molecules [53, 250], i.e., for b= 0 [251]. Because the excluded area of two

molecules is smaller in the anti-parallel (ˆ

v(i)=−ˆ

v(j)) than in the parallel (ˆ

v(i)=ˆ

v(j))

arrangement, the former is entropically favored. Molecules can also more easily penetrate

into neighboring layers in the anti-ferromorphic smectic phase than in the ferromorphic

smectic phase. This effect enhances out-of-layer fluctuations and thus entropically favors

anti-ferromorphic smectic ordering as well. This behavior is similar to that of three-

dimensional bent-core molecules [156].

No significant smectic ordering is found for values of αsmaller than those given in

Figs. 5.5(a) and (b). For zig-zag molecules at even smaller α, we extrapolate the quasi-

nematic–smectic transition to take place at ρNS that are inaccessible within a reasonable

computational time; for bow-shaped molecules, however, the existence of a smectic phase

at α < π/3, even for large ρ, is unclear.

As already discussed in Sec. 2.4.2, two-dimensional long-range smectic order should

not be thermodynamically stable. One expects instead the scenario illustrated in Fig.

2.8(a). At a given ρ, dislocations destroy translational order on length scales larger

than the mean distance between thermally induced dislocations, but correlations in

the layer orientations persist and exhibit a long-range algebraic decay. Although this

Chapter 5. Bent hard-needle model 65

a) b)

Figure 5.6: (a) Snapshot of bow-shaped molecules in the modulated-nematic phase for

α=π/8, a= 0.35, and ρ= 20. The complete simulation box with N= 2000 molecules is

shown. The red arrows indicate the polar vector ˆ

vperpendicular to the molecular orientation

in the center of the layers. The blue arrow indicates the direction of the optimal wave vector

hm. The radius of the blue circle is half the optimal wavelength λmas defined in Eq. (2.83) and

obtained from the maximization procedure illustrated in Fig. 2.12(b). For this configuration

Ψm≈0.25. (b) The orientational correlation function g2(r) for bow-shaped molecules with

α=π/13 decays exponentially at ρ= 6, algebraically at ρ= 11, and exponentially again at

ρ= 13 due to the appearance of the modulated-nematic phase.

scenario is physically reasonable and may explain the weak smectic ordering of bow-

shaped molecules, we were unable to test it against our simulation data because of the

limited range of computationally accessible N. Instead, we find smectic order to be fully

stabilized in our simulations.

5.5 Modulated-nematic phase

Although at small αand for α≳π/3 bow-shaped molecules form a quasi-nematic phase

[Fig. 2.6(d)], for intermediate α, they also equilibrate in a modulated-nematic phase,

which we introduced in Sec. 2.5. In this phase no overall orientational or positional order

exists [Fig. 5.6(a)]. Instead, it shows a different kind of supramolecular arrangement,

wherein the orientation of a series of molecules varies gradually along arches that form

approximate half-circles, and these arches themselves form layers. Periodic order exists

along the layer normal but the mean polar vector ⟨ˆ

v⟩in one layer is antiparallel to that of

a neighboring layer (see Fig. 1.1(b) for the definition of v). This arrangement destabilizes

the quasi-nematic phase and its algebraic orientational order. As shown in Fig. 5.6(b),

the occurrence of the modulated-nematic phase can even result in a reentrant exponential

decay of g2(r) with increasing ρ. For π/13 ≲α≲π/3, however, we found no evidence for

a power-law decay of g2(r) in the whole range of explored densities. A direct transition

from the isotropic to modulated-nematic phase occurs instead.

In Fig. 5.7(a) the modulated-nematic order parameter Ψmdefined in Eq. (2.83) is

shown as a function of density for several values of α. In analogy with the treatment

Chapter 5. Bent hard-needle model 66

a) b)

Figure 5.7: (a) Modulated-nematic order parameter Ψmplotted versus ρfor bow-shaped

molecules at several values of α. The Monte Carlo simulation results are fitted with Eq. (5.3).

Error bars give the standard deviation of Ψmover equilibrated samples. From the fit we obtain

ρm= 29.95, 19.97, 18.71, 21.42, 23.38, and 45.57 for α=π/25, π/16, π/13, π/10, π/8, π/6,

and π/4, respectively. (b) Polar correlation function g||

1(r) for α=π/10 and several values of

ρ. As density increases, the amplitude of the modulation of g||

1(r) increases, which we take to

be a signature of the modulated-nematic phase.

for the identification of smectic order in Sec. 5.4, we fit Ψm(as obtained from the Monte

Carlo simulation data) with a trial function similar to Eq. (5.2),

f(ρ) = 1/2 + arctan[l(ρ−ρm)]/π (5.3)

where land ρmare fit parameters. In order to clarify the structural properties of the

modulated-nematic phase, we consider the polar correlation function g||

1(r) as defined in

Eq. (2.84). Because of the periodic modulation in the molecular polar vector ˆ

valong

the layer normal, g||

1(r) becomes a periodic function when the layered structure is well

established. In particular, since molecules in adjacent layers have opposite polarization,

g||

1(r) shows a minimum at a distance corresponding to the layer thickness followed by a

maximum, which results from correlations with the next-nearest-neighbor layer. In Fig.

5.7(b) we show g||

1(r) for α=π/10 and several values of ρ. As expected, the periodic

modulation of g||

1(r) becomes stronger with increasing density, indicating the progressive

development of layers. This behavior is also observed for all other values of α.

Our Monte Carlo data show that modulations in g||

1(r) are already present at relatively

small ρ, whereas the order parameter Ψmhas not yet increased much. For instance, for

α=π/10 it can be seen in Fig. 5.7(b) that g||

1(r) is already weakly modulated at ρ= 14,

while the corresponding order parameter is only Ψm≈0.2. Similarly, we find Ψm≈0.25

for the configuration shown in Fig. 5.6(a), even though a remarkable degree of layering

is already clearly established. In other words, the layered structure of the modulated-

nematic phase is established continuously, which makes it difficult to clearly define a

transition density. For this reason, we approximate the transition density ¯ρminto the

modulated-nematic phase by using a threshold, Ψm= 0.2, on the order parameter. The

Chapter 5. Bent hard-needle model 67

Figure 5.8: Distance between two adjacent layers, λm/2, plotted versus α(points). The results

for λmare obtained at ρ > ¯ρm, but are observed to be fairly insensitive to changes in ρ[inset

(3)]. Error bars give the standard deviation. The continuous red line is the projected length of

the molecule onto a direction along the central molecular segment. The vertical line at α=π/4

approximately divides the plot in two regions. The first region with α < π/4 has λ/2> LC

and molecules are arranged in the supra-molecular structure of the modulated-nematic phase

illustrated in inset (1). The second region with α > π/4 has λ/2≲LC, where molecules

locally arrange with anti-ferromorphic order with adjacent layers slightly inter-penetrated, as

illustrated in inset (2). The dotted line is a guide to the eyes.

same threshold is used for all α. This value is such that ¯ρmmatches reasonably well the

density at which we observe the reentrant exponential decay of g2(r) at α≲π/13, and is

then used for all other α.

The maximization procedure illustrated in Fig. 2.12(b) for determining the order

parameter Ψmalso provides the typical distance between two layers in the modulated-

nematic phase, i.e.,λm/2 defined in Eq. (2.83). In Fig. 5.8 we show how this distance

evolves with αand compare it with the projected length of the molecule along the direction

parallel to the central molecular segment, LC=b+ 2acos(α). At small α,λm> LC,

which captures the supra-molecular structure of the modulated nematic phase. As α

increases, however, λmdecreases and becomes comparable to LCat α≈π/4. Now,

molecules locally arrange in anti-ferromorphic order [see inset (2) of Fig. 5.8] which is

favored over the supra-molecular ordering of the modulated-nematic phase. For α > π/4

the layering distance becomes smaller than LC, indicating that adjacent anti-ferromorphic

layers inter-penetrate slightly on average, as discussed in Sec. 5.4.

As discussed in Sec. 2.5, the occurrence of a three-dimensional, spontaneously formed,

modulated-nematic phase for banana-shaped mesogens and of the two-dimensional

modulated-nematic phase for bow-shaped molecules, likely results from “pathological

elasticity” [57], which has been predicted to be a consequence of the molecular curvature

radius. Our results thus indicate that there is an upper limit for the molecular curvature,

corresponding in our model to α≈π/4, beyond which the supra-molecular structure

of the modulated-nematic phase becomes unstable with respect to the anti-ferromorphic

order. The modulated-nematic phase identified here differs from the bent nematic phase

formed by V-shaped molecules [53, 250] because the latter does not present a fully

Chapter 5. Bent hard-needle model 68

a) b)

Quasi-

nematic

Smectic

Isotropic

Modulated-

nematic

Quasi-nematic

Quasi-

nematic

Smc.

Figure 5.9: Phase diagram for (a) zig-zag molecules with a= 0.25 and (b) bow-shaped

molecules with a= 0.35. Points represent the isotropic–quasi-nematic transition densities

(circles), quasi-nematic–smectic transition densities (diamonds) and the quasi-nematic– or

isotropic–modulated-nematic transition (squares) as identified from the procedures described

in Secs. 5.3, 5.4, and 5.5, respectively. For the diamond and square symbols, error bars are

estimated by propagating the standard errors of the fit parameters in Eqs. (5.2) and (5.3),

respectively. For the circular symbols, error bars are determined by propagating the standard

errors of the linear fit functions shown in Fig. 5.3. The gray area in (b) marks the transition

between modulated-nematic and quasi-nematic phases in a region where none of the identified

mesophases is found to be stabilized. Continuous lines are guides to the eyes. Where not shown,

error bars are smaller than the marker size. Dashed and dotted lines represent, respectively, the

isotropic–nematic and the nematic–smectic transition lines predicted by Onsager theory (Sec.

2.6).

developed periodicity. Most likely, this difference is geometrical in origin, and may be

due to the missing central molecular segment in the V-shaped molecules.

We already discussed in Sect. 2.4.2 that long-range order in two-dimensional smectics

is unstable. In Fig. 5.6(a) in the center a dislocation in the layering of the supramolecular

arches is visible. This might be an indication that, in analogy to two-dimensional smectics,

the layered structure is destabilized by the proliferation of dislocations in sufficiently large

systems.

5.6 Phase diagram

In Fig. 5.9 we show the simulated phase diagrams for both the zig-zag and the bow-shaped

molecules obtained using the approaches described in Secs. 5.3, 5.4, and 5.5. The dashed

red and dotted blue lines show the predictions from Onsager theory for the transition

densities ρIN and ρNS, respectively. These lines are obtained following the procedure

discussed in Sec. 2.6.

According to the phase diagram in Fig. 5.9(a), terminal segments of zig-zag particles

destabilize the quasi-nematic phase but stabilize the smectic phase. This qualitative

trend is captured by Onsager theory. Our simulation results are in rough agreement with

previous studies[51, 63] but also exhibit some significant discrepancies. In particular,

in our phase diagram both the isotropic–quasi-nematic and the quasi-nematic–smectic

transitions appear at higher ρ(Fig. 5.9(a)). In addition, for α≈π/2, the isotropic and

Chapter 5. Bent hard-needle model 69

smectic phases are well separated by the quasi-nematic phase, while the latter was not

observed at all in previous studies. Most likely, the lower transition densities reported in

Refs. [51, 63] follow from using the nematic order parameter for detecting the isotropic–

quasi-nematic transition and from considering relatively small system sizes. As already

mentioned, the nematic order parameter in a quasi-nematic phase decreases with system

size [61].

Bow-shaped molecules exhibit a remarkably rich behavior.

(1) For small α, the low-density behavior is similar to that of zig-zag molecules. The

transition density ρIN (red circles) increases with increasing αand is underestimated by

Onsager theory. Quasi-nematic order in this small-αregion is also destabilized by further

increasing the packing density. Instead of the emergence of a smectic phase, however,

a modulated-nematic phase takes precedence. We did not specifically explore the phase

behavior of bow-shaped molecules with α < π/25, but we expect the modulated-nematic

phase to appear at ever higher densities as αdecreases, as indicated by the dotted green

line. For symmetry reasons the bent-nematic phase cannot exist for α= 0.

(2) For π/13 ≲α≲π/4, both the quasi-nematic and the smectic orders are destabilized

by the modulated-nematic phase at all ρexplored. The direct isotropic–modulated-

nematic transition appears at increasing densities with α. This phase is simply not

captured by Onsager theory as formulated in Sect. 2.6.

(3) For π/4≲α≲π/3, which is indicated in the phase diagram as a gray area, we find no

clear evidence for any of the mesophases known to be formed by bow-shaped molecules. In

this region the distance between two adjacent layers approaches the projection of the total

molecular length along the molecular central segment, resulting in a strong competition

between the formation of supra-molecular layers and anti-ferromorphic domains. The

investigation of configurations at densities much higher than the ones we could reach

would be necessary to clarify what mesophase, if any, is stable in that system.

(4) For π/3≲α < π/2, the molecular curvature is too large to induce a spontaneous

bending of the nematic director and the corresponding layer formation. Quasi-nematic

order then becomes stable again, but this time the transition densities decrease with

increasing α. The isotropic–quasi-nematic transition is highly overestimated by Onsager

theory. The theory strongly relies on the excluded area, as discussed in Sec. 2.6, but the

excluded area of bow-shaped molecules is minimal in the anti-parallel configuration. In

our simulations we instead observe clusters of molecules packed in parallel. Because this

arrangement involves structural correlations between more than two molecules, it is not

surprising that Onsager theory, which only takes into account two-particle correlations

dramatically fails. Since many-particles correlation are also present in the modulated-

nematic phase, we did not include the splay-bend deformation [53, 250] in our Onsager

theory calculation.

Note that we did not study molecules with α=π/2. With this central-to-tail angle

parallel molecules cannot anymore be shifted into each other to form closely packed

clusters. A different phase is thus expected. Indeed, tetradic order has been observed in

related models [53].

5.7 Summary

Chiral zig-zag molecules assume quasi-nematic and smectic phases, depending on density

and the central-to-tail angle α. We use the orientational correlation function g2(r) in

Eq. (2.80), which decays exponentially in the isotropic phase and algebraically in the

Chapter 5. Bent hard-needle model 70

orientationally ordered phase, to identify the isotropic–quasi-nematic transition. In two-

dimensional systems with short-ranged interactions, one expects the transition to take

place via disclination unbinding [118]. Indeed, apart from packing effects, the correlation

functions described in Sec. 5.3 behave similarly to the ones already reported in other

two-dimensional anisotropic models with hard-core interactions [42, 60–62].

For zig-zag molecules the isotropic–nematic transition density ρIN increases with

increasing central-to-tail angle α, while the nematic–smectic transition, ρNS, exhibits

the opposite trend. Such behavior is qualitatively captured by Onsager theory although

both ρIN and ρNS are underestimated by the theory, as discussed in Sec. 2.6. Furthermore,

we observe a smectic C phase, where the central segment of the zig-zag molecule is tilted

against the layer normal. The clear formation of smectic layers, however, indicates that

our systems are too small to observe the dislocation unbinding scenario predicted in Ref.

[149].

Achiral bow-shaped molecules have a much richer phase behavior. It can be divided

into three regions, depending on the value of α. For small αmolecules form isotropic,

quasi-nematic, and modulated-nematic phases, as density increases. The isotropic–quasi-

nematic transition is defect driven, which makes the orientational correlation function

switch from an exponential to power-law decay with increasing density. No polar order is

found in the quasi-nematic phase. Further increasing density destabilizes the orientational

order of the quasi-nematic phase.

A modulated-nematic phase then takes over, wherein bow-shaped molecules form

layers of supramolecular arches. The orientational correlation function g2(r) shows a

reentrant exponential decay that corresponds to the development of the supramolecular

arches. At intermediate α, a direct transition from the isotropic to the modulated-

nematic phase takes place. The modulated-nematic structure becomes less pronounced

with increasing α,i.e., the layer thickness decreases towards the molecule length, up

to the point where the formation of supramolecular arches becomes unfavored and anti-

ferromorphic domains develop instead. For α≳π/3, the curvature radius of the molecules

becomes too small to induce spontaneous bending of the nematic director and quasi-

nematic order reenters. Anti-ferromorphic smectic order is then found at even higher

density.

Chapter 6

Birefringence Relaxation of

Photo-Switchable Molecules on a

Surface

In this Chapter we discuss a molecular model, which we developed to capture the

essential physics behind a series of experiments involving photo-switchable molecules.

The experiments are described in Ref. [1] and have been discussed extensively in Sec.

3.4. They can be summarized as follows. Photo-switchable molecules are tethered to

a monolayer at high in-plane density. Orientational order is induced in the monolayer

via illumination with linearly polarized light (writing process). Linearly polarized light

generates trans-to-cis and cis-to-trans isomerizations, therefore both isomers are found

at the end of the writing process, when the anisotropic trans molecules are aligned

perpendicularly to the light polarization and the monolayer shows some birefringence.

Subsequently, orientational order is erased either by leaving the monolayer in the dark

(thermal erasure) or by illuminating it with circularly polarized light (CP erasure), which

induces trans-cis isomerization cycles. During these processes, the birefringence decays

toward zero following a power law (typical for glasslike systems), but during CP erasure

the relaxation is remarkably faster than during thermal erasure. A schematic illustration

of the essential experimental results is given in Fig. 3.5.

The Chapter is structured as follows. In Sec. 6.1 we introduce the molecular model.

In Sec. 6.2 we discuss how the model dynamics is generated using a kinetic Monte Carlo

algorithm. In Sec. 6.3 we explain how the monolayer birefringence is obtained during the

numerical simulation and how we discriminate between different functional forms for its

relaxation dynamics. In Sec. 6.4 we discuss a simplified version of the model, in which

only trans molecules are present. In this way we can demonstrate that the power-law

relaxation of the birefringence can be traced to the formation of dynamic heterogeneity.

In Sec. 6.5 we introduce trans and cis isomers and we model the thermal and CP erasure

processes, inspired by the formalism presented in Sec. 3.4.1. The presence of both the

isomeric species allows us to study the influence of the isomerization process on the

development of dynamic heterogeneity and, thus, on the dynamics of the relaxation.

This Chapter is essentially based on the material in Ref. [B].

Chapter 6. Birefringence relaxation 72

a) b)

Figure 6.1: (a) The step-potential U(O) gives the energy of a molecular configuration as a

function of the number of overlaps Othat a molecule forms with its neighbors. All the steps

have a fixed height Ustep. (b) A small fraction of a typical initial configuration of the kinetic

Monte Carlo simulation showing cis (black) and trans (red) model molecules attached to a

two-dimensional surface.

6.1 Molecular model

As explained in Sec. 3.4, when the monolayer of tethered molecules studied in Ref. [1] is

illuminated by light, molecules cycle between an anisotropic, rod-like trans configuration

and a nearly isotropic, bent-like cis configuration [see Fig. 1.1(a)]. We model the trans

isomer as an infinitely thin, straight needle of unit length L= 1 and the cis isomer as a

bent, infinitely thin needle also of total length L[see Fig. 1.1(b)]. In the cis configuration

we fix the angle between the central and the tail segments to α=π/3, while each tail

segment has a length of a= 0.35L(both αand aare defined as for the bow-shaped

needle in Fig. 1.1(c)). The total number of trans (Nt) and cis (Nc) molecules is fixed,

i.e., Nt+Nc=N. Since the transition moment of the dMR molecules, to which the light

polarization couples, is nearly parallel to the monolayer surface, we consider the system

to be purely two-dimensional. To mimic the effect of the covalent tethering, molecules

are allowed to rotate within the plane but cannot translate.

In our model, the complicated isomerization process of the azobenzene (described in

Sec. 3.2) is drastically simplified: it consists of a simple switch from the straight to the

bent needle and vice-versa. Also, we assume that the conformational change happens

instantaneously, a reasonable assumption given the relative time scales involved. The

relaxation of the birefringence happens at least on the second scale (see Fig. 3.5), while

the isomerization occurs on the picosecond scale even in relatively dense organic solvents

[191].

In order to incorporate isomerization as described in Sec. 3.4 in the kinetic Monte

Carlo simulation, we define the following set of rules:

1) thermal erasure: only the cis →trans spontaneous transition is allowed and

isomerization occurs with probability Pth(c→t).

2) CP erasure: illumination with circularly polarized light induces trans-cis

isomerization cycles. As explained in Sec. 3.3, the isomerization rate is proportional to

the light intensity, the quantum yield of the transition process, and the absorption cross

sections of the isomers [197, 252]. To limit the number of free parameters, we incorporate

all these factors in the two isomerization probabilities PCP(t→c) and PCP(c→t) for

Chapter 6. Birefringence relaxation 73

trans-to-cis and cis-to-trans isomerization, respectively. When birefrigence has relaxed

towards zero, a steady state is reached, where the numbers of cis and trans isomers fulfill

NcPCP(c→t) = NtPCP(t→c). Hence, the ratio

R=PCP(t→c)

PCP(c→t)=Nc

.(6.1)

is an essential parameter of our model. Previous measurements show that the absorbance

of the two isomers is very similar at 514 nm, therefore Rshould be in the order of unity

[204]. Because light-induced isomerization cycles occur at a much faster rate than the

spontaneous cis-trans relaxation, the latter is neglected during CP erasure. Importantly,

we assume that after an isomerization event, the orientation of the molecule is chosen at

random [202, 253].

As anticipated in Sec. 3.4, because of the high in-plane packing density of the SAM,

molecules must overlap during the relaxation process in order to become randomly

oriented. Following again a minimal approach, and because we restricted molecular

motion to a plane, we allow the molecules to overlap by introducing a simple interaction

potential U(O) = UstepO, which is proportional to the number of overlaps Oand the

energetic cost Ustep of each overlap, which sets the unit of energy. We clarify below how

U(O) affects the rotational dynamics of our model molecules.

6.2 Details of kinetic Monte Carlo simulations

In Sec. 3.4.1 we showed how the rotational dynamics of the dMR molecules tethered to

the monolayer can be explained in terms of the temporal evolution of the orientational

distribution functions for cis and trans isomers through Eqs. (3.7) and (3.8), a set of

Fokker-Plank equations with source terms. We discussed how this approach gives an

exponential relaxation of the monolayer birefringence unless the results from several

sets of equations are averaged together, a procedure that suggests a multi-domain

structure of the monolayer. Our approach is radically different because we generate the

rotational dynamics for each single molecule in the system (taking into account molecular

interactions and the molecular conformational change upon isomerization) using a kinetic

Monte Carlo algorithm [64].

The kinetic Monte Carlo simulation method has been introduced in Sec. 4.3, were we

discussed how the random walk in the space of configurations, performed in a standard

Monte Carlo simulation, can give rise to a reliable dynamics when only local moves are

considered and upon introducing an unique Monte Carlo time scale. In the following, we

detail the kinetic Monte Carlo simulation for the model introduced in Sec. 6.1. Rotational

dynamics is implemented by picking a molecule at random and rotating it by an angle δθ

chosen with equal probability from the interval [−Θ,Θ]. The maximum rotational step

size Θ is connected to the molecular self-diffusion constant Dθvia a Monte Carlo time

step dt [237]

Θ = 2Dθdt .(6.2)

The Monte Carlo time step dt is set such that a single Monte Carlo trial move is accepted

with a rate close to one, which avoids non-local moves and guarantees a reliable dynamics

[64, 237, 254]. In Sec. 6.4 we fix dt = 10−4while in Sec. 6.5 we fix dt = 10−5to increase

the time resolution. Both values ensure an acceptance probability close to one. For the

self-diffusion constant of our simple molecular model, we rely on the result for a very long

Chapter 6. Birefringence relaxation 74

cylinder [48, 255]

Dθ=3D0

πL2ln σ−0.622 + 0.917/σ −0.050/σ2),(6.3)

where Lis the cylinder length, σthe cylinder aspect ratio and D0=kBT/(ηSL) with

kBthe Boltzmann constant, Tthe temperature, and ηSthe shear viscosity of the fluid.

Since our needles are infinitely thin, we choose σ= 1000 and for simplicity, the rotational

diffusion constants of trans and cis molecule is assumed to be the same.

Both rotational motion and isomerization take place under the influence of the

interaction potential U(O). At each Monte Carlo step a molecule is picked at random and

rotated and isomerized using the set of rules defined in the previous section. For example,

during thermal erasure the cis-to-trans isomerization rate is fixed by the probability

Pth(c→t). Thus, when the randomly selected molecule is in the cis isomeric state, a

random number rand ∈(0,1) is extracted from an uniform distribution and the molecule

is isomerized if rand ≤Pth(c→t). After a trial move of a single molecule, the number of

overlaps and the energy U(Onew) of the new configuration are evaluated and compared to

the old configuration with U(Oold). Following the standard Metropolis scheme, the move

is accepted with probability

p= min 1,exp(−1/(kBT)[U(Onew)−U(Oold)]) .(6.4)

In the following we express kBTin units of Ustep.

A complete sweep consists of Ntrial moves and the running Monte Carlo time is

measured in units of dt. Thus, tMC =Ns, where Nsis the number of Monte Carlo

sweeps. The number density of the model molecules is defined as ρ=N/l2, where l, in

units of L, is the side length of the square simulation box. For all the results presented in

this Chapter, we use a total of N= 10000 molecules under periodic boundary conditions.

As initial condition, we use a configuration, in which both isomers are equally present.

The trans molecules exhibit orientational order while cis molecules are randomly oriented.

Starting from this configuration, we then follow the relaxation of the birefringence towards

equilibrium.

6.3 Birefringence relaxation

The degree of alignment within the system is evaluated by the nematic order parameter

S(t). Since trans isomers have much higher shape anisotropy than cis isomers [32, 200],

we evaluate the nematic order parameter only for the trans isomers. We calculate the

nematic order parameter as the positive eigenvalue of the tensor order parameter

Tαβ(t) = ⟨N−1

t(t)

Nt(t)



i=1

i∈{trans}

(2ui

α(t)ui

β(t)−δαβ)⟩,(6.5)

where ui

α(t) is the α-th Cartesian coordinate of the unit vector pointing along the central

segment of the i-th molecule in the trans configuration at time tand ⟨. . .⟩denotes non-

equilibrium averaging, for which we used at least 10 different runs. As demonstrated in

Sec. 2.2.3, the monolayer birefringence ∆n(t) is proportional to the degree of molecular

alignment in a single-component system. In a mixture of isotropic and anisotropic

Chapter 6. Birefringence relaxation 75

Figure 6.2: Time evolution of Q(t) as defined in Eq. (6.6). Blue points are the kinetic Monte

Carlo data. Fitting functions are shown as continuous lines. The horizontal blue line gives

the equilibrium value Qeq of Q(t). The inset zooms in on the squared area with log scale on

the horizontal axis and linear scale on the vertical axis. The simulation data correspond to a

thermal erasure process with kBT= 4.5, ρ= 20, S(0) = 0.633, Nt(0) = Nand dt = 10−4.

molecules, the birefringence is also proportional to the number of rod-like molecules [104].

Therefore, to monitor birefringence relaxation, we keep track of

Q(t) = ∆n(t)

∆n(0) =S(t)Nt(t)

S(0)Nt(0) .(6.6)

The data points in Fig. 6.2 give a typical temporal relaxation of Q(t) from our kinetic

Monte Carlo scheme.

We now illustrate how we discriminate between three possible functional forms of the

relaxation dynamics of Q(t). Recall that simple relaxation processes are expected to show

an exponential form ϕ(t) = e−t/τ (a Maxwell-Debye relaxation), which is characterized

by a well-defined time τthat fully determines the kinetics of the system. In some

systems, however [205], the relaxation significantly deviates from an exponential form

and is described either by a stretched exponential decay ϕ(t) = e−(t/τ)βwith 0 < β < 1

or by an asymptotic power law as in Eq. (3.5).

The following procedure is used to discriminate between an exponential, a stretched-

exponential, and an asymptotic power-law relaxation of Q(t). For each choice of model

parameters, we run kinetic Monte Carlo simulations until Q(t) has reached a clear steady-

state value Qeq (illustrated as an horizontal line in Fig. 6.2). The equilibration time teq

is the first time for which Q(teq) = Qeq.Q(t) is then fitted by least-square minimization

over the range t∈[0, teq] with the three functional forms given in Fig. 6.2.

For each fit curve a goodness-of-fit test is performed [256]. We evaluate the reduced

chi-squared statistics using

χ2

red =χ2

ν=1



i=1

(Ei−Oi)2

σ2

,(6.7)

where nis the number of Monte Carlo points in the fitting interval (blue points before

equilibration in Fig. 6.2), Oiis the observed value of the i-th point, Eiis the corresponding

Chapter 6. Birefringence relaxation 76

a) b)

Figure 6.3: Equilibrium value of the nematic order parameter Seq in a system of trans

molecules with finite size. (a) Seq versus ρfor hard needles that are not allowed to overlap. (b)

Seq versus kBTfor fixed ρ= 20. Lines are guides for the eye.

value as obtained from the least-square minimization, σiis the standard deviation of the

i-th observed value (error bars in Fig. 6.2), and ν=n−k−1 is the number of degrees of

freedom with knumber of fitting parameters. In general, χ2

red ≫1 indicates that the data

are poorly fitted by the model. Instead, when χ2

red ≪1 the data are over-fitted by the

model (for example there are too many fitting parameters). Thus, the most reliable fit

function is chosen as the one with the value of the reduced χ2

red closest to 1 [256]. In the

example given in Fig. 6.2, we obtain χ2

red = 9.65 for the exponential function, χ2

red = 2.32

for the stretched-exponential, and χ2

red = 0.54 for the asymptotic power law. The power

law thus clearly provides the best fit of the simulation data. The results of the fitting

procedure in different regions of parameter space and under different initial conditions

will be discussed in the following two sections.

6.4 Relaxation dynamics in a pure trans system

In this section we present the results of the kinetic Monte Carlo simulations for a system

that only contains trans molecules.

First, we characterize the equilibrium properties of the system with temperature T

and density ρ. Figure 6.3 shows the equilibrium value of the nematic order parameter, Seq,

determined after equilibration. Fig. 6.3(a) refers to molecules with hard-core interactions

that cannot overlap at all. The steady-state value of the nematic order parameter shows

a steep increase with ρ. Fig. 6.3(b) instead plots Seq versus kBTat ρ= 20. If the

temperature is sufficiently high, molecules can pass over their neighbors by creating

overlaps and thereby drastically reduce Seq. So, allowing the molecules to overlap,

results in an isotropic state at sufficiently high temperatures even at high in-plane packing

density.

We now characterize the relaxation dynamics of the birefringence at different

temperatures. We fix the initial degree of the nematic order to S(0) = 0.6 (the same

qualitative results are obtained using values from S(0) ≈0.5 to S(0) ≈1.0) and follow

the temporal evolution of S(t) while it relaxes back to its equilibrium value Seq. First,

we analyze the rotational diffusion of the molecules, which results in the decay of Q(t),

Chapter 6. Birefringence relaxation 77

a) b)

Figure 6.4: Rotational dynamics in a system of trans molecules for different kBT, at density

ρ= 20, and with initial nematic order S(0) = 0.6. The legend in (a) applies to both graphs.

(a) Rotational mean square displacement ⟨∆θ2(t)⟩versus time. (b) The logarithmic derivative

of ⟨∆θ2(t)⟩to extract the local exponent νin ⟨∆θ2(t)⟩ ∝ tν. The extent of the subdiffusive

regime (ν < 1) increases with decreasing temperature. The inset shows the short- (blue circles)

and long-time (red squares) diffusion constants as a function of kBT.

by looking at the rotational mean square displacement

⟨∆θ2(t)⟩=1



i=1

(θi(t)−θi(0))2,(6.8)

where θi(t) is the orientation angle of the i-th molecule at time t. In Fig. 6.4(a), we plot

⟨∆θ2(t)⟩versus tMC for different temperatures in a system with fixed density ρ= 20.

In addition, Fig. 6.4(b) shows the logarithmic derivative of the rotational mean square

displacement, which gives the local exponent νin ⟨∆θ2(t)⟩ ∝ tν. Anomalous diffusion

has ν= 1. Initially, the molecules diffuse with a diffusion constant Dsthat increases

linearly with temperature, as expected from the Einstein relation [see inset of Fig. 6.4(b)].

When the needles start to overlap, a subdiffusive regime emerges and its extent increases

with decreasing temperature [see Fig. 6.4(b)]. Ultimately, normal diffusion is recovered

even in systems where nematic order is well developed (for instance at kBT= 2.5 one

finds Seq ≈0.6 in Fig. 6.3). In order to diffuse, molecules have to pass each other

by creating overlaps. At low temperatures, crossing energy barriers makes rotational

diffusion an activated process. Hence, the long-time diffusion constant Dlis no longer

linear in temperature [see inset of Fig. 6.4(b)]. We remind the reader that both a transient

subdiffusive regime and a breakdown of the Einstein relation are common signatures of

glasslike dynamics, as pointed out in Sec. 3.4.2.

Rotational diffusion causes initial nematic order to fully decay for kBT≥4.

Figure 6.5(a) shows the relaxation of Q(t) = S(t)/S(0) at fixed ρ= 20 and different

kBT, while in Figure 6.5(b) we keep temperature at kBT= 4.5 and vary density ρ. In a

high-temperature or low-density regime the relaxation is very well fitted by an exponential

function [kBT≥7.0 in Fig. 6.5(a) and ρ≤14.0 in Fig. 6.5(b)], while in a high-density,

low-temperature regime [kBT≤5.0 in Fig. 6.5(a) and ρ≥18.0 in Fig. 6.5(b)] the power-

law decay defined in Eq. (3.5) provides an excellent fit of the simulation data. In this

Chapter 6. Birefringence relaxation 78

Figure 6.5: Relaxation of the birefringence Q(t) in a system of trans molecules with initial

nematic order S(0) = 0.6: (a) for different kBTat density ρ= 20, and (b) at different ρfor

kBT= 4.5. Circles show the numerical results and the continuous lines the best-fitting functions

with blue for exponential, green for stretched-exponential, and red for power-law decay. The

characteristic times of the relaxation curves are indicated as diamonds. Horizontal dashed lines

show the equilibrium value of Q(t) with matching colors.

regime both the exponential and stretched-exponential functions give significant residual

errors. Our Monte Carlo results are best fitted by a stretched exponential function with

β≈0.8 in an intermediate regime [kBT= 5.5,6 in Fig. 6.5(a) and ρ= 16.0 in Fig. 6.5(b)].

To summarize, the interaction with neighboring molecules, which is more relevant at low

temperatures and high densities, causes a transition from an exponential decay of Q(t)

to a power-law relaxation.

As anticipated in Sec. 3.4.2, non-exponential relaxation originates from the presence

of a wide distribution of relaxation times in the system. In the concept of dynamic

heterogeneity [65, 66], this distribution is traced back to spatial and temporal variations

in the local structure of the system, which then determines its dynamic evolution.

Molecules diffusing slower or faster than the average become spatially correlated, giving

rise to regions with slow and fast dynamics. Hence, averaging the dynamics over this

heterogeneous environment leads to an overall non-exponential relaxation. A typical

quantity to monitor this dynamic heterogeneity is a four-point correlation function, which

we introduce here for the angular displacement following Ref. [65]. We define the mobility

ci(t), in order to quantify how mobile the molecule iis,

ci(t) = exp[−∆θi(t)2]−1



j=1

exp[−∆θj(t)2],(6.9)

where ∆θi(t)2is defined as in Eq. (6.8). The variable ci(t) has zero mean and is positive

(negative) if the i-th molecule moves less (more) than the average. The four-point

correlation function is then

G4(r, t) = i,j ci(t)cj(t)δ(r−|rij|)

i,j δ(r−|rij|),(6.10)

Chapter 6. Birefringence relaxation 79

a) b)

Figure 6.6: (a) Temporal evolution of the dynamical susceptibility χ4(t) for different kBT

at ρ= 20 and with S(0) = 0.6. (b) Four-point correlation function G4(r, t) plotted versus r

at different times for kBT= 4.0 and ρ= 20.0. The peak in χ4(t) indicates extended domains

of correlated rotational motion. (c) The mobility ci(t) defined in Eq. (6.9) color-coded in the

whole simulation box for kBT= 4.0, ρ= 20.0, and at time tMC = 3.0×104, right at the

maximum of χ4(t).

where |rij|is the distance between molecule iand jand δis the Dirac delta function. The

correlation function G4(r, t) measures the spatiotemporal correlations in the dynamics of

the molecules over a distance rat time t. We remark the difference between Eq. (6.10)

and Eq. (3.13): a four-point correlation function as in Eq. (3.13) is typically used to

characterize systems at equilibrium (for instance a supercooled liquid). Since we are

interested in a relaxation process, the correlation function in Eq. (6.10) does not imply

any ensemble average. The presence of correlated domains in space and the degree of

dynamic heterogeneity is monitored by the dynamical four-point susceptibility for the

angular displacement [66, 257],

χ4(t) = dr G4(r, t).(6.11)

Chapter 6. Birefringence relaxation 80

a) b)

Figure 6.7: (a) Square displacement of selected individual molecules plotted versus time for

kBT= 4.0 and ρ= 20.0. The thick black line is the mean value over all molecules. (b)

Temporal evolution of the non-Gaussian parameter α2of the probability distribution P(∆θ(t))

for different kBTat ρ= 20 and with S(0) = 0.6. Values of α2= 0 indicate non-Gaussian

tails in the distribution P(∆θ(t)) of rotational steps, i.e., an excessive number of molecules

significantly faster or slower than the average. Inset: Example of P(∆θ(t)) at tMC = 7.0×103

and for kBT= 4.0. The red line shows a Gaussian distribution.

It increases with increasing size of correlated domains.

Figure 6.6(c) illustrates the heterogeneity in the rotational mobility of the molecules

by plotting the color-coded ci(t) in the whole simulation box for kBT= 4.0, ρ= 20,

and at tMC = 3.0×104. Extended domains of correlated molecular rotations are clearly

visible. Figure 6.6(b) shows the corresponding four-point correlation function G4(r, t) for

kBT= 4.0 in blue, where the correlations in time and space are largest compared to other

times (green and red circles). In order to monitor the complete temporal evolution of the

dynamical heterogeneities, we present the susceptibility χ4(t) in Fig. 6.6(a) for different

temperatures and at density ρ= 20. The dynamical susceptibility shows a clear peak,

which coincides with the time window, during which the power-law relaxation of Q(t)

is observed in Fig. 6.5(a). The color plot of Fig. 6.6(c) is obtained at the maximum of

χ4(t) at kBT= 4. The maximum increases with decreasing temperature and therefore

demonstrates that regions of correlated motion become more relevant at low temperatures.

Spatio-temporal variations in the local environment of the pinned molecules are also

responsible for the anomalous diffusion, which we demonstrate in Fig. 6.4. In Fig. 6.7(a)

we show individual molecular trajectories for kBT= 4.0 and ρ= 20. One already senses

that some molecules rotate significantly faster than the average (shown as a thick black

line), while all trajectories indicate that rotational diffusion proceeds by sudden jumps.

This feature, together with the spatio-temporal correlations discussed before, are also

common signatures of a glass-like dynamics [227, 258–261] . As pointed out already in Sec.

3.4.2, a non-Gaussian distribution of molecular displacements is another universal feature

of finite-dimensional glass-like dynamics [220]. To investigate this point, we evaluated the

non-Gaussian parameter α2of the distribution of molecular displacement P(∆θ). In two

dimensions it is calculated using the second and fourth moment of P(∆θ),

α2(t) = ⟨∆θ4(t)⟩

⟨∆θ2(t)⟩2−3,(6.12)

where for a Gaussian distribution one has α2= 0. In Fig. 6.7(b), we show α2for different

Chapter 6. Birefringence relaxation 81

temperatures kBTand at density ρ= 20. The distribution P(∆θ) becomes highly non-

Gaussian as also demonstrated in the inset, which shows P(∆θ) for kBT= 4.0 and at the

time, when α2(t) maximal. Fast rotating molecules are responsible for the non-Gaussian

tails of the distribution. The peak in α2increases and shifts to later times upon cooling,

which again coincides with the developing non-exponential relaxation of the birefringence.

Interestingly, the characteristic times in the relaxation laws for Q(t), shown as diamond

markers in Fig. 6.7(a), agree nicely with the locations of the maxima in α2(t).

6.5 Relaxation dynamics during isomerization

In this section we explore the relaxation of birefringence Q(t) in a system, in which

both trans and cis molecules are present. In particular, we investigate how the nearly

isotropic cis molecules influence the relaxational dynamics of Q(t) under two different

isomerization scenarios: thermal erasure and CP erasure.

The model has a rather rich parameter space and its full exploration is beyond our

scope. In the following, we fix the initial conditions to be close to the experimental

values and explore the relaxational dynamics of Q(t) for different isomerization rates. We

prepare the initial state with an equal number of trans and cis molecules, Nt(0) = Nc(0),

and order parameter S(0) = 0.6; both values are close to the estimates carried out in Ref.

[1]. The cis molecules are randomly oriented at t= 0 and do not contribute to S(t). In

this section we choose the time step dt = 10−5to increase the temporal resolution, which

results in an equilibration time of up to 9 weeks on an Intel Xeon X5550 machine with a

2.66 GHz CPU. In order to compare the results of this section directly with the results

of Sec. 6.4, we still give the Monte-Carlo time tMC in units of dt = 10−4.

6.5.1 Thermal erasure

Here, we discuss the relaxation of the birefringence, when the monolayer is not

illuminated. Since the trans isomer is the ground-state of the dMR, all the molecules

in the cis configuration will isomerize back to the trans state after some characteristic

time. As discussed in detail in Sec. 6.1, the cis to trans isomerization rate of isolated

molecules is the isomerization probability Pth(c→t).

In view of the results discussed in Sec. 6.4, we expect the relaxation dynamics

to be exponential in the high-temperature and low-density regime, regardless of the

isomerization probability. Therefore, we fix both temperature and density to kBT= 4.0

and ρ= 20.0, respectively, where the pure trans system shows a clear power-law decay

of the birefringence, and monitor how this decay is influenced by the isomerization rate.

Figure 6.8(b) shows the temporal evolution of the number of trans isomers for different

Pth(c→t). We expect an exponential relaxation and, indeed, the Monte Carlo data

(circles) are well fitted with

Nt(t)

N= 1 −Nc(0)

Ne−t/τc,(6.13)

where the fit parameter, the relaxation time τc, is proportional to the inverse isomerization

probability, τc= 1.54 P−1

th (c→t) [see inset of Fig. 6.8(b)]. We find τc> P−1

th (c→t)

because in a crowded environment some of the attempted isomerization events are rejected

as they generate more overlaps between the molecules.

Chapter 6. Birefringence relaxation 82

Figure 6.8: Relaxation towards equilibrium during thermal erasure in a system with ρ= 20.0

and kBT= 4.0. The legend in (c) applies to all graphs. (a) Temporal evolution of the nematic

order parameter S(t)/S(0). The horizontal dashed line marks the equilibrium value to which

all the curves have to converge. The inset shows the equilibrium value Seq as a function of the

relative number of trans isomers, Nt/N. (b) Relative number of trans isomers, Nt/N, during

thermal erasure. Fits of the simulation data with Eq. (6.13) are shown as solid lines with

matching colors. The inset plots the isomerization time τcversus P−1

th (c→t) (red squares).

The fitted blue line is τc= 1.54 P−1

th (c→t). (c) Temporal relaxation of the birefringence Q(t).

The horizontal dashed line marks the equilibrium value of Q(t). The full lines are the best fits

to an exponential (magenta), a stretched exponential (green), or a power law (red). Diamonds

indicate the characteristic times of the power law relaxation. The inset shows the dynamical

susceptibility χ4(t) for trans molecules already present at t= 0. As a reference the black circles

give χ4(t) for the pure trans system at the same ρand kBT.

In Figs. 6.8(a) and (c) we show the respective temporal evolutions of the nematic

order parameter S(t)/S(0) and the birefringence Q(t)∝Nt(t)S(t), which originate

from the alignment of the trans isomers. We also evaluate the dynamical susceptibility

χ4(t) defined in Eq. (6.11), but only on the subset of molecules that are in the trans

configuration at the beginning of the simulation at tMC = 0. The results are plotted in

the inset of Fig. 6.8(c), where we also include the dynamical susceptibility for the pure

trans system at ρ= 20 at kBT= 4.0 (black circles) as a reference. This will allow us to

to quantify how the presence of the cis isomers influences the development of dynamic

heterogeneities. The temporal relaxation of both S(t) and Q(t) strongly depends on the

isomerization rate. Analyzing Figs. 6.9(a), (b) and (c), we identify four different regimes:

1) For sufficiently small relaxation rate [Pth(c→t) = 10−5in Fig. 6.8], the

birefringence Q(t) relaxes exponentially. On the time scale of the declining S, the number

of cis molecules stays constant [compare plots (a) and (b)]. They thus create a more

uniform environment, as indicated by the nearly vanishing dynamical susceptibility χ4,

in which S(t) and Q(t) relax exponentially and much faster than the pure trans system

for the same temperature and density in Sec. 6.4. Note that at late times Q(t) first

Chapter 6. Birefringence relaxation 83

falls below its equilibrium value (dashed horizontal line) and then increases again. The

reason is that the equilibrium value of Sdepends on the number of trans molecules [inset

of Fig. 6.8(a)] because the presence of the nearly isotropic cis molecules decreases Seq.

Since Ntincreases for tMC >104,Q(t) also increases.

2) For Pth(c→t) = 10−4and 2.5·10−4the best fitting function for the temporal

evolution of Q(t) is provided by a stretched exponential with β≈0.8 indicating the

transition to the power-law decay.

3) At intermediate isomerization rates Pth(c→t)=3.5·10−4and 5.0·10−4the

power-law relaxation provides the best fit of the simulation data. Here, the isomerization

of the randomly oriented cis molecules into the trans state happens on the same time

scale as the relaxation of the nematic order parameter. Thus, Q(t) does not decay in

the static disordered distribution of cis molecules but in a dynamic and heterogeneous

environment, as demonstrated by the clear peak in χ4(t). As a result, the relaxation of

Q(t) follows a power law. Its characteristic time τtdoes not change significantly, but the

isomerization probability seems to control the power-law exponent. We find η= 0.281 at

Pth(c→t)=3.5·10−4and η= 0.225 at Pth(c→t) = 5.0·10−4.

4) The situation changes again if the isomerization rate is very large [Pth(c→t) =

10−2in Fig. 6.8]. All the cis isomers rapidly isomerize into trans molecules with random

orientation and S(t) drops to S(0)/2. This is compensated by the resulting increase in

Nt(t), which ultimately generates a bump in Q(t) at tMC ≈102. Once isomerization is

completed at tMC ≈103, the system is composed of only trans molecules the aligment of

which relaxes via rotational motion. This is the same situation as discussed in Sec.

6.4. The environment is heterogeneous as indicated by the peak in the dynamical

susceptibility, which is nearly as large as in the pure trans system of Sec. 6.4. Without

the initial bump, Q(t) is fitted well by a power-law with a larger characteristic time and

a larger power-law exponent η≈0.5 as compared to case 3) but similar to the pure trans

system.

Summarizing the results in Fig. 6.8, we find that cis isomers pinned at random

positions not only accelerate the birefringence relaxation compared to the pure trans

system but also prevent the development of the dynamical heterogeneity that is

responsible for a non-exponential decay. We attribute this behavior to the nearly isotropic

shape of cis isomers, which, regardless of their orientations, create a similar environment

for the exisiting trans isomers. In contrast, newly formed trans isomers can adjust

their orientations to their neighbors and thereby allow for the formation of dynamical

heterogeneities. In the experiments of Ref. [204] the lifetime of cis isomers during

thermal erasure is estimated as 0.7s, while the characteristic time of the power-law decay

is measured as τth ≈2s. These values are achievable by isomerization rates between our

cases 3) and 4).

6.5.2 CP erasure

Illumination of the SAM with CP light induces trans-cis isomerization cycles at a rate

much faster than the spontaneous relaxation due to thermal erasure. Therefore, we

neglect the thermally induced cis-to-trans transition when modeling the CP erasure

process. As discussed in Sec. 6.1, in order to take into account the different light

absorption of the two isomers, we introduce the two respective probabilities, PCP(t→c)

and PCP(c→t), for trans-to-cis and cis-to-trans isomerization. Since light is circularly

polarized, the isomerization probabilities do not depend on the molecular orientation.

Chapter 6. Birefringence relaxation 84

a) b)

Figure 6.9: Relaxation of the birefringence Q(t) and of the relative number of trans isomers,

Nt(t)/N, during CP erasure for different ratio Rat fixed ρ= 20 and kBT= 4. The trans-to-cis

isomerization rate is PCP(t→c) = 5.0·10−1in (a) and PCP(t→c) = 10−1in (b). The

cis-to-trans isomerization rates are PCP(c→t) = PCP(t→c)/R. The best-fitting function for

the relaxation of Q(t) are shown as solid lines, blue for the exponential, green for the stretched-

exponential, and red for the power-law relaxation of Eq. (3.5). The diamond markers with

matching colors indicate the characteristic times τt. The fitted exponents are given in Table

6.1. The horizontal dashed lines mark the the steady-state value of Q(t) for different Rwith

matching colors. The numerical results for Nt(t)/N are fitted with Eq. 6.15 (solid lines).

In order to limit the computational cost, we do not explore the full range of

isomerization probabilities. Instead, we choose their values such that the characteristic

times of birefringence relaxation for thermal and CP erasure matches the experimental

observations, where they differ by approximately two decades in time (see the diamond

markers in Fig. 3.5). Because illumination of the monolayer produces a very negligible

amount of heat [1], we fix both density and temperature at ρ= 20 and kBT= 4, exactly

as during thermal erasure discussed in Sec. 6.5.1.

In Fig. 6.9 we show the relaxation of Q(t) and Nt(t) towards their steady-state values

starting with Nt= 0.5 at t= 0. In Fig. 6.9(a) we set PCP(t→c)=5.0·10−1while

in Fig. 6.9(b) PCP(t→c) = 10−1. The backward isomerization rates, PCP(c→t), are

chosen by the ratio R=PCP(t→c)/PCP(c→t), which also determines the number of

isomers in steady state: R=Nc(t→ ∞)/Nt(t→ ∞), as discussed in Sec. 6.1.

The implementation of our kinetic Monte-Carlo simulations suggests that the number

of trans isomers evolves according to the following kinetic equation,

d Nt(t)

d t =−1

τtc

Nt(t) + 1

τct

Nc(t),(6.14)

Chapter 6. Birefringence relaxation 85

a) b)

Figure 6.10: (a) The fit parameter ain Eq. (6.15), which gives the relative number of trans

isomers in steady state, plotted versus 1/(1 + R). (b) The cis-to-trans relaxation time τct

plotted versus the inverse isomerization probability P−1

CP(c→t). In both figures red squares

are from simulations with PCP(t→c) = 10−1and blue circles for PCP(t→c)=5.0·10−1. The

straight black lines have zero y-intercept and unit slope.

PCP(t→c)R β PCP(t→c)R η

5.0·10−10.7 0.78 5.0·10−10.3 1.37

5.0·10−10.5 0.77 5.0·10−10.2 0.95

10−10.7 0.84 5.0·10−10.15 0.82

10−10.5 0.81 10−10.3 1.31

10−10.2 1.10

10−10.15 0.71

Table 6.1: Fit parameters for the solid lines in Fig. 6.9. Table on the left gives the exponent

for the stretched-exponential fit (green lines) and table on the right gives the exponent for the

power-law fit (red lines).

where τct and τtc are characteristic relaxation times and Nc(t) = N−Nt(t). It is solved

Nt(t)/N =a+bexp(−t/τ),(6.15)

with

a=1

1 + τct/τtc

, a +b=Nt(0)

N,and 1

τ=1

τtc

τct

(6.16)

Since ais the steady-state value at t→ ∞, we also have a= 1/(1+R), which is confirmed

in Fig. 6.10(a). Thus, the ratio of isomerization probabilities also determines the ratio of

the two relaxation times, R=τct/τtc. The fits of the simulated Nt(t)/N in Figs. 6.9(a)

and (b) excellently confirm the kinetic model. However, as in the case of thermal erasure,

we find τct > P−1

CP(c→t) [see Fig. 6.10(b)], because in a crowded environment some of

the attempted isomerization events are rejected.

In Fig. 6.9 we show the best fitting functions for Q(t) as continuous lines. In both Figs.

6.9(a) and (b) the relaxation of the birefringence is exponential for R < 0.7, stretched-

exponential for 0.7≤R < 0.3, and follows a power-law for R≤0.3. The characteristic

times of the relaxation are shown as diamond markers and the exponents are given in

Chapter 6. Birefringence relaxation 86

Thermal Erasure

CP Erasure

Figure 6.11: Comparison of the birefringence relaxation during both CP and thermal erasure

as obtained by kinetic Monte Carlo simulations. Solid red lines are fits to the power-law decay of

Eq. (3.5). The characteristic times of the power-law relaxation are shown as diamond markers.

For both curves kBT= 4 and ρ= 20. The isomerization probabilities are given in the legend.

Compare with Fig. 3.5.

Table 6.1.

As expected, a larger isomerization rate PCP(t→c) shifts the birefringence relaxation

to smaller times [compare Figs. 6.9 (a) and (b)] because aligned trans molecules are faster

transformed to the cis state. Unlike the case of thermal erasure, the steady value of

Nt(t)/N is reached well before stretched-exponential or power-law relaxation sets in. The

relevant characteristic times τtare indicated by diamond markers in Fig. 6.9. Interestingly,

for constant PCP(t→c) the ratio of isomerization rates Rcontrols the functional form

of the relaxation. In the power-law regime, the characteristic times τtdo not change

significantly, while the power-law exponent ηheavily depends on R(see Table 6.1).

At a first glance, the behavior in Fig. 6.9 seems surprising. For increasing Rthe

isomerization rate PCP(c→t) = PCP(t→c)/R decreases and consequently the molecular

orientations after isomerization become randomized less frequently. So, we expect the

birefringence relaxation to become slower in contrast to the results presented in Fig. 6.9.

However, we know already from thermal erasure that cis isomers create a uniform

environment, where the orientation of trans molecules relaxes faster and exponentially.

This is the case for R > 1, where the cis isomers are in the majority in steady state.

Decreasing Rincreases the number of rod-like trans molecules, Nt. As discussed already

for thermal erasure, they hinder the orientational relaxation of their neighbors more

efficiently than cis molecules. But they also create a more heterogeneous environment,

where the birefringence relaxation first follows a stretched exponential and then for further

decreasing Rbecomes a power law. However, we were not able to quantify the dynamic

heterogeneity using the dynamical susceptibility of Eq. (6.11) for a subset of molecules

as in Sec. 6.5.1 since they continuously cycle between their two configurations.

6.5.3 Comparison between thermal and CP erasure

In Fig. 6.11 we show the power-law relaxation of Q(t) for both thermal and CP erasure

using typical parameters. Comparing it with Fig. 3.5 gives an idea of the degree of

agreement between our model and the experimental results. Birefringence relaxation

Chapter 6. Birefringence relaxation 87

is efficiently accelerated by the isomerization cycles induced by illumination with CP

light. A similar speedup was demonstrated in Refs. [261–263], where isomerization of an

azo-dye embedded in a molecular matrix significantly increased translational diffusion

of surrounding molecules. By tuning the isomerization probabilities for CP erasure,

we achieved a difference between the characteristic times τtin the power-law decay of

approximately two orders of magnitude, in good agreement with the experimental results.

The larger isomerization rates during CP erasure and the presence of cis isomers

in steady state give a faster power-law relaxation with a larger exponent η, again in

qualitative agreement with the experimental results. Our model also accounts for the

smaller steady-state value of Q(t) after illumination with CP light as reported in Ref.

[1]. This is due to the presence of the nearly isotropic cis molecules that destabilize

orientational order.

6.6 Summary

First, we studied a system of pure trans molecules. Here, the non-exponential, glass-

like relaxation of the orientational order inscribed in the monolayer emerges naturally

at high densities and low temperatures due to the presence of dynamic heterogeneity.

Rotational motion develops a transient sub-diffusive regime upon cooling. At the same

time, molecules with dynamics faster and slower than the average become spatially

correlated. The spatial average over these regions with different orientational mobilities

results in the power-law decay of birefringence.

In a second step we included the possibility that the molecules can assume two different

isomeric forms. During thermal erasure, the nearly isotropic cis isomers create a uniform

environment because they do not align locally with their neighboring molecules. Hence,

the orientation of trans molecules relaxes exponentially. The experimental power-law

relaxation of birefringence is only recovered if a sufficient number of trans isomers is

present. They slow down orientational relaxation but also initiate the formation of

dynamic heterogeneities as in the pure trans system.

During CP erasure, light adsorption induces a fast isomerization cycle between cis and

trans isomers and thereby the overall orientational relaxation becomes faster in agreement

with experimental results. The functional form of the birefringence relaxation is controlled

by the ratio of the two isomerization probabilities, which determine the number of trans

and cis molecules in steady state. As in thermal erasure, a larger number of cis isomers

speeds up the exponential birefringence relaxation, whereas trans isomers in the majority

hinder relaxation and ultimately give rise to a power-law decay. Finally, the presence

of the nearly isotropic cis isomers also explains the smaller steady-state value, which

birefringence reaches during CP erasure.

Chapter 7

Conclusion

In this Thesis we investigated how liquid-crystal order in two dimensions can be controlled

both by molecular geometry and by the interaction of photo-switchable mesogens with

light. We used two approaches: first, we studied how molecular geometry influences

the formation of self-organized liquid-crystal structures at equilibrium. This study

resulted in the complete phase diagram of the bent hard-needle model. Second, we

considered an out-of-equilibrium process during which molecules can assume different

isomeric configurations. This enabled us to trace the effect of the isomerization process

on the system dynamics. In both cases we employed model molecules, whose shape is

inspired by that of the azobenzene, an important photo-switchable compound.

We started the Thesis by reviewing some fundamental concepts for the liquid-crystal

state of matter in Chapter 2. We discussed several theories of liquid-crystal ordering

using free-energy, symmetry and topology arguments. We focused on the mesophases

identified in the bent hard-needle model, for which we defined proper order parameters

and correlation functions.

In Chapter 3 we discussed photo-switchable molecules and some of their interesting

applications. We explained the photo-chemical properties of the azobenzene compound,

which is widely used in applications where photo-switchable molecules control liquid-

crystal order in thin films. We discussed how illumination with light can influence the

molecular ordering in a nematic liquid crystals, in particular when photo-switchable

molecules act as mesogens. We explained in detail a series of experiments performed

by Fang et al. [1], where light is used to significantly speed up the glasslike relaxation

of orientational order in a self-assembled monolayer. These experiments motivated the

molecular model presented in Chapter 6.

In Chapter 4 we described the numerical methods used in this work. These include

Monte Carlo simulations in the canonical and in the isothermal-isobaric ensemble and

kinetic Monte Carlo simulations. We also discussed some specialized optimization

techniques used to save computational time.

The results for the equilibrium phase behavior of the bent hard-needle model are

presented in Chapter 5. We demonstrated that, despite its semplicity, the bent hard-

needle model shows a variety of liquid-crystal phases. The stability of these phases

is strongly dependent on the molecular shape. For both molecular configurations, we

demonstrated the isotropic–quasi-nematic transition to be consistent with a Kosterlitz-

Thouless theory of a disclination unbinding scenario. Here, the transition from a

isotropic to a quasi-nematic phase makes the orientational correlation function switch

from exponential to power-law decay with increasing density. Even if smectic order is

expected to be destabilized by thermal fluctuations in two dimensions, we find evidence for

Chapter 7. Conclusion 90

fully stabilized smectic phases in the bent hard-needle model. Further studies, using larger

system sizes, are needed to clarify the long-range stability of these layered phases. In

particular, the scenario described in Sec. 2.4.2, with the appearance of quasi-nematic order

in the layer orientations due to the presence of dislocations, remains to be demonstrated.

In this regard, understanding the role of topological defects in the formation of two-

dimensional structures is crucial for significant technological advancements [264].

A very appealing result of our investigation is the identification of the modulated-

nematic phase made from supramolecular layers. Our simulations are the first to clearly

demonstrate such a layered structure in two dimensions and to relate it to molecular

geometry. We find the optimal value of the curvature radius to be around α≈π/10,

when the modulated-nematic phase occurs at the lowest packing density. This finding

might particularly be useful in developing novel functional optical materials based on

organic bent-core liquid crystals [265, 266], where the formation of polar domains can be

used to tune the nonlinear optical properties of the material.

In analogy with the smectic phase, the long-range stability of the modulated-nematic

phase also needs to be further investigated. Some dislocations in the supra-molecular

layered structure of the modulated-nematic phase already appear in our simulations. It

would be interesting to study how to increase the stability of this phase, for example

by placing the molecules on a properly textured substrate [267]. This question can be

addressed in future numerical studies.

The results for our out-of-equilibrium study are given in Chapter 6. We discussed in

detail a molecular model for experiments performed with a self-assembled monolayer of

tethered light-switchable dye molecules [1], which can be found in a stable trans and a

light-induced cis state. The monolayer shows power-law relaxation of initial birefringence

during thermal erasure and CP erasure. In the latter case, the relaxation is considerably

faster. Despite its simplicity, the molecular model discussed in Chapter 6 is able to

reproduce the experimental results.

We provided a direct measure for the extension of spatio-temporal correlated

domains by defining a out-of-equilibrium dynamical susceptibility, the spatial integral

of a four-point correlation function. At high density and low temperature, the

spontaneous formation of extended domains of fast- and slowly-rotating molecules

(dynamic heterogeneity), is responsible for the power-law decay of the initial birefringence.

We found that the presence of the cis isomers, which do not align with their neighboring

molecules, prevents the formation of dynamic heterogeneity, and causes the relaxation to

be exponential. Nevertheless, the experimental power-law relaxation can be reproduced

by properly tuning isomerization probabilities.

We attribute the different effect of the two isomers on the system dynamics mainly

to their different geometric shapes. The anisotropic trans isomers create locally aligned

domains, while the nearly isotropic cis isomers create a uniform environment. This result

suggests the possibility to engineer photo-switchable molecules, and control the difference

in the shape anisotropy of the two isomers, in order to ease or obstruct both the formation

and the relaxation of orientational order under illumination.

To reproduce the power-law decay of birefringence in our model, we had to fine-tune

the parameters within a range of values that are experimentally reasonable. It remains

to be demonstrated if the need for this fine tuning is due to our simplified model or a

general feature of light-switchable molecules. Future work should address this question by

exploring the effect of more complex molecular geometries with more realistic molecular

Chapter 7. Conclusion 91

interactions. These additional improvements could be implemented in our model within

the kinetic Monte Carlo simulation scheme.

Another interesting direction for future research would be the investigation of how a

transition from different liquid-crystal phases, identified in the bent-needle model, takes

place under a conformational switch of the mesogens. For example, one can imagine a

quasi-nematic to modulate-nematic transition induced by a sudden increase in the central-

to-tail angle of the molecules at fixed temperature and density. This could be achieved

experimentally by employing light-switchable mesogens. Indeed, recent experiments

demonstrated the possibility to control liquid-crystal order with light [27], but the kinetics

of the underlying process is still far from being understood. Computer simulation can

clarify the dynamics of the light-induced transition at the molecular level, and our results

indicate that kinetic Monte Carlo simulations are a reliable and powerful tool for these

investigations.

Our study further illustrates the richness of structures, including supra-molecular

organization, formed by self-assembling particles of different shapes in two dimensions.

Additionally, as azobenzene-based material are attracting growing interest as light-

tunable systems, our findings strongly suggest the possibility to change the monolayer

dynamics by controlling the light-absorption properties of the molecules and their

geometrical shapes. Being able to control molecular geometry thus offers the possibility of

designing novel materials, in particular in two dimensions, and of tuning their properties

accordingly.

Appendix A

Power-law birefringence relaxation

In this appendix we detail the calculation of the relaxation of the birefringence discussed

in Sec. 3.4.2. In Ref. [1] the relaxation is interpreted as a process which happens against

a distribution f(U) of energy barriers. The birefringence Q(t) is defined as

Q(t) = dU exp[−t/τ(U)]f(U).(A.1)

In the following we evaluate Eq. (A.1) under the assumption that the energetic barriers

are distributed accordingly to a generalized Gumbel distribution

f(U) = γ

UmΓ(1/γ)exp −U/Um−exp(−γ(U/Um)),(A.2)

where Umand γare distribution parameters and Γ is the Euler gamma function. The

characteristic time of a single τenvironment is governed by the Arrhenius law

τ(U) = τtexp(U/kBT),(A.3)

and τtis a characteristic time scale for molecular fluctuations.

The evaluation of Eq. (A.1) proceeds by changing variable in the time domain

Q(t) = dU exp[−t/τ(U)]f(U) = ∞

exp[−t/τ]H(τ) dτ , (A.4)

where H(τ) = f(U(τ))|dU/dτ|. Using Eq. (A.3) one gets

f(U(τ)) = γ

UmΓ(1/γ)τ

τt−ηexp[−τ

τt−ηγ],(A.5)

where we defined Um=kBTmand η=T/Tm. Again from Eq. (A.3) we have

dU/dτ=kBT/τ, thus

H(τ) = γη

Γ(1/γ)

τtτt

tη+1 exp[−τt/τηγ].(A.6)

Appendix A 94

Substituting Eq. (A.6) in Eq. (A.4) results in

Q(t) = ∞

exp[−t/τ]H(τ) dτ=γη

Γ(1/γ)

τt∞

exp[−t/τ]τt

tη+1 exp[−τt/τηγ]

 

(A.7)

It is convenient to expand the exponential exp[−t/τ] in the integral Aas a power series

A=∞

exp[−t/τ]τt

tη+1 exp[−τt/τηγ] =

∞



n=0

n!∞

(−t/τ)nτt

tη+1 exp[−τt/τηγ].(A.8)

Eq. (A.8) can be rewritten as

∞



n=0

n!(−t

τt

)n∞

(−τt

τ)n+η+1 exp[−τt/τηγ]

 

.(A.9)

where we multiplied everything by (τt/τt)n= 1. We can now evaluate the integral B:

B=∞

(−τt

τ)n+η+1 exp[−τt/τηγ].(A.10)

By introducing y= (τt/τ)ηγ and changing variable, Eq. (A.10) becomes

B=τt

ηγ ∞

ηβ (n+η)−1e−ydy=τt

ηγ Γ1

ηγ (n+η).(A.11)

Substituting Eq. (A.11) in Eq. (A.9), integral Abecomes

∞



n=0

n!(−t

τt

)nτt

ηγ Γ1

ηγ (n+η).(A.12)

We can now go back to Eq. A.7 and substitute Eq. A.12, which gives

Q(t) =

∞



n=0

n!(−t

τt

Γ1

ηγ (n+η)

Γ(1/γ).(A.13)

Under the assumption η= 1/γ and using the properties of the gamma functions, Eq.

(A.13) can be rewritten as

Q(t) =

∞



n=0

n!(−t

τt

)nΓ(n+η)

Γ(η)=

∞



n=0

n!(−t

τt

n−1



j=0 η+j(A.14)

and it is easy to verify that Eq. (A.14) is the Taylor expansion of:

Q(t) = 1

(1 + ( t

τt))η(A.15)

Appendix A 95

which is exactly the expression for the birefringence relaxation used in Eq. (3.5) and in

Ref. [1].

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B. Tavarone, R., Charbonneau, P. & Stark, H. Kinetic Monte Carlo simulations for

birefringence relaxation of photo-switchable molecules on a surface. J. Chem. Phys.

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Acknowledgements

The work presented in this Thesis would not have been possible without the help of

many colleagues and friends.

First, I would like to show my gratitude to my advisor Prof. Holger Stark for

his constant and meticulous support. Under his intellectual guidance, I have learned

that proper scientific work must be rigorously formulated and clearly explained. His

meaningful questions and suggestions have been essential in making this work more solid

and relevant.

I am also grateful to Dr. Patrick Charbonneau for the many discussions we had, the

important suggestions he gave me, and also for hosting me in his laboratory in Duke

University for several months.

I sincerely thank my colleagues from the research group ”Statistische Physik weicher

Materie und biologischer Systeme” in TU Berlin. In particular, I am grateful to Oliver

Pohl, Dr. Tapan Chandra Adhyapak, Dr. Andreas Z¨ottl and Maria Zeitz for the

stimulating conversations and for the nice time we spent together in our offices.

My thanks also go to the international research training group IRTG 1524, who

supported this work, with special regard to Prof. Martin Schoen, Dr. Daniela Fliegner,

Petra Erdmann, and Beatrix Thiele.

Last but not the least, I would like to thank my family and friends, who gave me

unlimited support during the last years.

115