Parse molecule catalog formulas and SMILES where available.
Computational Validation
Open-Source Modeling Stack
A reproducible software stack for checking molecule descriptors, thermodynamics, reaction assumptions, process flowsheets, and validation readiness.
Scientific position
Programmatic verification reduces uncertainty; it does not replace experiments
The stack is designed to verify as much as software can reasonably verify: molecule parsing, formula checks, thermodynamic inputs, reaction-screening assumptions, and process flows. It cannot perfectly prove plant performance without measured sludge composition, HTL runs, hydrotreating data, aqueous phase treatment tests, PFAS/metals screening, TEA, LCA, and permits.
Installed or reproducible services
Tool roles
Open source
RDKit
Open-source cheminformatics for SMILES parsing, molecular descriptors, formula checks, and molecule catalog validation.
Open sourceCantera
Open-source thermodynamics, transport, and chemical kinetics for reaction and gas-phase screening where mechanisms are available.
Open sourceOpenMM
Open-source molecular simulation toolkit for molecular dynamics where a suitable model and force-field assumptions exist.
Open sourceDWSIM
Open-source process simulation environment for flowsheet-level mass, energy, separation, and TEA review.
Open sourceCoolProp
Open-source thermophysical property database for fluids, useful for water, gas, and heat-duty property checks.
Open sourceThermo
Open-source Python chemical-engineering thermodynamics package for pure-component and mixture property screening.
Open sourceChemicals
Open-source chemical engineering property correlations and constants used by Thermo and direct property checks.
Open sourcePyomo
Open-source optimization modeling framework for scenario optimization, constrained balances, and process decision problems.
Open sourceDocker Compose
Reproducible service orchestration for the modeling workbench without installing chemistry libraries directly on the host.
Open sourceOpenUSD
Open 3D scene description for process digital-twin artifacts that can be inspected or converted by external 3D tools.
Verification workflow
How the software checks the sewage-to-fuel model
Compute formula mass, H/C ratio, O/C ratio, and heteroatom burden.
Use RDKit in Docker to export descriptor rows for molecule entries with SMILES.
Use Cantera for thermodynamic and reaction-screening checks where mechanisms exist.
Use OpenMM only for molecular dynamics questions with clear force-field assumptions.
Use DWSIM or equivalent process simulation for flowsheet-level mass and energy review.
Use CoolProp, Thermo, and Chemicals for fluid and chemical-property checks.
Use Pyomo to formulate constrained TEA/LCA and process-balance optimization problems.
Use OpenUSD to generate portable process-scene assets for the digital twin.
Generate RDKit 3D conformers for molecule catalog entries with SMILES.
Keep every simulation result tied to an experimental validation gate.
Docker command
Run the reproducible modeling workbench
docker compose -f docker-compose.modeling.yml run --rm molecule-workbenchThe container validates RDKit molecule parsing against 33 catalog entries, loads Cantera, and initializes OpenMM. Descriptor outputs are written under the ignored `modeling/reports/` directory.