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Ishaan Madan This guide is only meant as a practical checklist. For theory, background, and detailed methodology, consult the manuscript and SI. Workflow Instructions: Thermodynamic Modeling of Amino Acid Synthesis on Titan This archive contains all data and code used in the study “Prebiotic Chemistry Insights for Dragonfly: Thermodynamics of amino acid synthesis in Selk-sized craters on Titan” (Madan et al.). The goal of this document is to provide step-by-step guidance for reproducing or learning from the workflow, especially for reviewers and early-stage students. Overview of Workflow 1. Collect/estimate Gibbs free energy data. 2. Polynomial fitting to generate coefficients. 3. YAML input file setup. 4. Cantera Equilibrium Models. 5. Data collection/analysis. File Inventory ● Gibbs energy data: Gibbs_Energies_All.csv ● Gibbs energy estimator: Gibbs_Energy_Estimator_298K.ipynb ● Polynomial Fitting: Polynomial_Fitting.ipynb ● YAML data: yaml_entry_all.yaml ○ Note: This is a culmination of species entries, not a directly runnable input file. Individual YAML input files must be created per simulation. ● YAML example input file: Alanine_Example_Input.yaml ○ This is an example of how to structure the input files. ● Cantera Model Example: Cantera_Equilibirum_Skeleton.ipynb Step-by-Step Workflow 1. Collect/estimate Gibbs free energies. a. Reference Gibbs_Energies_All.csv for all the Gibbs data we collected or estimated. b. For estimation of a molecule of your choice, you can run Gibbs_Energy_Estimator_298K.ipynb as per the instructions in the notebook. The
caveat is that for any molecule lacking published data, you will need to run a quantum chemical simulation (OPT, then FREQ at 298 K) using the level of theory, basis set, and solvation model defined in the manuscript. 2. Fit NASA9 polynomials. a. Open Polynomial_Fitting.ipynb and fit Gibbs energy vs. T curves. b. You will obtain the two 9-term coefficient sets that will go into the species entry in the yaml input files. 3. Build YAML input files. a. Use Alanine_Example_Input.yaml as a template. b. Copy species entries from yaml_entry_all.yaml as needed for each model. 4. Run equilibrium models a. Open Cantera_Equilibrium_Skeleton.ipynb and run as per the instructions. 5. Collect and analyze results. a. You can print out the results or export to a csv format for easier processing later on.
