theoretical-biology

A spatially distributed stochastic simulation of competition for space (a lattice population of replicating particles)

Code repository for the publication. Contains MATLAB codes and sequence data used for evolutionary analysis.

My personal homepage

A constraint-based systems biology framework interpreting DNA as structural congruity memory, with applications to aging, disease, resilience, and AI proportionality.

A rerun of the simulations of a Goldbeter paper

Repository with a programming algorithm that creates and analyzes signaling networks using knockouts and the RME index.

Code for Bishop et al 2024, separated by simulation and manuscript figures (Main Code) in addition to supplementary analyses (Sup Code). Contact corresponding author megan.bishop@emory.edu with any questions.

Theoretical frameworks modeling Pycnogonida (sea spider) parasitism as an ancient biomimetic analog for neoplastic cellular progression and nitrogen-limited tumor growth kinetics.

Unified metabolic collapse framework describing diabetes and Alzheimer’s disease as branched outcomes of the same APOE-TREM2-PSEN1 structural process.

Biomimetic Schlieren vision as a sensory modality, theoretical exploration.

A New Metaphysical Framework on the Relationship between Contingency and Necessity

Python implementation of a minimal resilience-based model of dopaminergic neuron degeneration, including deterministic stability analysis, stochastic simulations, first-passage dynamics, and Monte Carlo survival analysis.

Universe Master Framework: From First Cause to Equilibrium Civilization

AI-collaboration stress test and research-control-room prototype with telemetry, campaign reports, and reproducible method notes.

A theoretical biology framework exploring potential evolutionary or biomimetic links between Pycnogonid (sea spider) palp mutations and structural mechanisms in HIV pathogenesis.