Ishaan Madan
This guide is only mean as a p ac ical checklis . Fo heo y, backg ound, and de ailed
me hodology, consul he manusc ip and SI.
Wo k low Ins uc ions: The modynamic Modeling o Amino
Acid Syn hesis on Ti an
This a chi e con ains all da a and code used in he s udy “P ebio ic Chemis y Insigh s o
D agon ly: The modynamics o amino acid syn hesis in Selk-sized c a e s on Ti an” (Madan e
al.). The goal o his documen is o p o ide s ep-by-s ep guidance o ep oducing o lea ning
om he wo k low, especially o e iewe s and ea ly-s age s uden s.
O e iew o Wo k low
1. Collec /es ima e Gibbs ee ene gy da a.
2. Polynomial i ing o gene a e coe icien s.
3. YAML inpu ile se up.
4. Can e a Equilib ium Models.
5. Da a collec ion/analysis.
File In en o y
● Gibbs ene gy da a: Gibbs_Ene gies_All.cs
● Gibbs ene gy es ima o : Gibbs_Ene gy_Es ima o _298K.ipynb
● Polynomial Fi ing: Polynomial_Fi ing.ipynb
● YAML da a: yaml_en y_all.yaml
○ No e: This is a culmina ion o species en ies, no a di ec ly unnable inpu ile.
Indi idual YAML inpu iles mus be c ea ed pe simula ion.
● YAML example inpu ile: Alanine_Example_Inpu .yaml
○ This is an example o how o s uc u e he inpu iles.
● Can e a Model Example: Can e a_Equilibi um_Skele on.ipynb
S ep-by-S ep Wo k low
1. Collec /es ima e Gibbs ee ene gies.
a. Re e ence Gibbs_Ene gies_All.cs o all he Gibbs da a we collec ed o
es ima ed.
b. Fo es ima ion o a molecule o you choice, you can un
Gibbs_Ene gy_Es ima o _298K.ipynb as pe he ins uc ions in he no ebook. The
ca ea is ha o any molecule lacking published da a, you will need o un a
quan um chemical simula ion (OPT, hen FREQ a 298 K) using he le el o
heo y, basis se , and sol a ion model de ined in he manusc ip .
2. Fi NASA9 polynomials.
a. Open Polynomial_Fi ing.ipynb and i Gibbs ene gy s. T cu es.
b. You will ob ain he wo 9- e m coe icien se s ha will go in o he species en y
in he yaml inpu iles.
3. Build YAML inpu iles.
a. Use Alanine_Example_Inpu .yaml as a empla e.
b. Copy species en ies om yaml_en y_all.yaml as needed o each model.
4. Run equilib ium models
a. Open Can e a_Equilib ium_Skele on.ipynb and un as pe he ins uc ions.
5. Collec and analyze esul s.
a. You can p in ou he esul s o expo o a cs o ma o easie p ocessing la e
on.
