Existing Software

Stochastic simulation of chemical reaction networks with evolutionary dynamics. Models autocatalytic sets and chemical selection in prebiotic environments.

Lee Cronin's automated chemistry platform for exploring assembly theory and the algorithmic origins of complex molecules from simple precursors.

Graded Autocatalysis Replication Domain model — simulates compositional genomes in lipid assemblies, exploring the "lipid world" hypothesis for abiogenesis.

Photochemical kinetics model for planetary atmospheres — simulates atmospheric photochemistry and climate on early Earth and other rocky planets relevant to prebiotic chemistry.

Digital evolution platform where self-replicating computer programs mutate, compete for resources, and evolve complex features. Used extensively in evolutionary biology research.

Tom Ray's pioneering artificial life system — self-replicating programs evolve parasites, immunity, and ecological dynamics in a virtual computer. Foundational ALife work from the 1990s.

Continuous cellular automaton framework that produces diverse lifelike organisms from simple mathematical rules. Explores the boundary between chemistry and biology.

Open-source project to build the first digital organism — a complete computational model of C. elegans from molecular to behavioral level. Demonstrates bottom-up biological modeling.

High-performance molecular dynamics engine widely used to simulate lipid bilayer self-assembly, membrane fusion, and vesicle formation at atomic resolution.

Scalable molecular dynamics for large biomolecular systems. Used to model prebiotic membrane assembly, peptide-lipid interactions, and protocell energetics.

Coarse-grained molecular dynamics framework enabling simulation of lipid self-assembly and vesicle formation at timescales relevant to prebiotic chemistry.

Python Suite for Advanced General Ensemble Simulations — enhanced sampling methods for studying rare events like spontaneous vesicle formation and membrane encapsulation.

Comprehensive toolkit for RNA secondary structure prediction, folding kinetics, and the evolution of RNA sequences — central to testing RNA World hypotheses computationally.

Toolkit for designing and simulating 3D RNA structures. Relevant to understanding how early ribozymes could fold into functional catalysts in the RNA World.

Nucleic Acid Package — thermodynamic analysis and design of nucleic acid structures, sequences, and devices. Essential for modelling RNA folding and hybridisation in prebiotic contexts.

In silico experimental evolution platform — simulates the evolution of digital organisms with realistic genotype-to-phenotype mapping, exploring how genetic systems emerge and evolve.

USGS aqueous geochemistry modelling program. Simulates reactions, mineral dissolution, and ion speciation in hydrothermal vent and ocean chemistry conditions relevant to abiogenesis.

Calculates standard thermodynamic properties of minerals, gases, and aqueous species at high T/P — essential for modelling deep-sea vent and early Earth geochemistry.

Framework for coupled atmosphere-interior evolution of rocky planets. Models early Earth conditions including magma ocean cooling and atmospheric composition where prebiotic chemistry began.

Virtual Planet Simulator — models the evolution of planetary habitability including tidal heating, atmospheric escape, and surface conditions over billions of years.