evolutionary-dynamics

Toolbox for Evolutionary Game Theory.

Simulate evolutionary biology models with Gillespie algorithm.

Julia package to easily build and simulate evolutionary models

Digital evolution model dedicated to bacterial in silico experimental evolution.

A two-player dynamic game where deep Q-learning agents collaborate to find optimal solutions to a stochastic version of the graph coloring problem, featuring α-Rank for joint policy ranking and evaluation.

Framework for testing strategic reasoning in LLMs using evolutionary Iterated Prisoner’s Dilemma tournaments. Features 28 agents, variable horizons, memory conditions, high-concurrency execution, and detailed analysis of cooperation rates, strategic fingerprints, and LLM decision rationales across providers and temperatures.

Open-ended evolving multi-agent ecosystem

System to simulate individual interactions and capture ecological and evolutionary dynamics

Blind governance, simulated: can an arbiter keep evolving agents healthy without reading their internals? The only working control is consequence-gated anti-concentration — one coupled mechanism, not two independent levers (~89k seeded runs). A tribute to Machines of Loving Grace.

Résolution du Paradoxe de Levinthal et de l'Abiogenèse par la Frustration Géométrique. La vie comme état métastable de la matière, pilotée par la minimisation de l'énergie libre sur des paysages rugueux.

4th Year Project - Optimal Control of Directed Evolution

Stochastic Python models of mutation accumulation and clonal evolution with applications to cancer evolutionary dynamics.

C++ codes describing an agent-based model of tumour growth, with implementation of subclone labelling and lineage tracing.

Evolutionary dynamics in tree networks

Repository exploring how network structure shapes evolutionary-game outcomes through ER and BA network simulations, structural analyses, and R-based replicator, BNN, Smith, and Logit dynamics.

A command line program to generate phylogenies and SNP configurations using simulation of coalescent models with structured populations.

C++ codes describing an agent-based model of tumour growth, with implementation of random mutations and therapy resistance.

Additional analysis at SSP at Albion College: Investigating Erythromycin resistance in V. natriegens (2025). Beyond identifying atpD and XRE regulator mutations, we utilized PCA of k-mer frequency vectors and 3D base composition modeling to map fitness landscapes. Findings reveal how environmental stress reshapes adaptive evolutionary trajectories.

This repository contains Python and NetLogo simulations based on the paper "The conditional defector strategies can violate the most crucial supporting mechanisms of cooperation" (Scientific Reports, 2022). The models explore evolution of cooperation, conditional defection, and mechanisms like kin selection, spatial structure, and punishment.

Bacterial quorum sensing as a Bayesian game: static equilibria vs. evolutionary stability.