biophysical-modeling

🧬 Python code that implements the active finite Voronoi (AFV) model.

Toolbox for parameter estimation of the Standard Model of diffusion in white matter

CHARM, a model that estimates the GHG impacts and land-use requirements of forestry

This toolbox allows to simulate interactions between neural mass potentials (resonating at 40Hz) in the structural connectome. Here, a single brain region is seen as an oscillator whose dynamics is explained by a Stuart Landau Equation (Hopf Bifurcation including time delay).

Python toolbox for creating and validating single-cell neuronal models with active dendrites.

A comprehensive computational biophysics simulation suite consisting of various ecological interactions between microorganisms of different characteristics in varying environments. We plan to expand this into a complete biophysics education interface for anyone interested in an interdisciplinary approach to simulations in ecological sciences.

Feed-forward neural network that predicts cytokine dynamics of T-cells in response to antigens

Nitrogen balance model components and test procedures

Materials for the PANGEOS Uncertainty Quantification workshop

GPyTool, a Bayesian framework developed to estimate the diffusive properties of a stochastic time trajectory

Biophysical modeling of ribosome motion during mRNA translation using TASEP and ballistic models, including analytical derivations and validation with simulation and Ribo-seq data.

These are python version of codes that I wrote to analyze images and videos of a macromolecule, that I took via fluorescence microscopy, in my research in grad school.

Processing agro-environmental data

Model of BG components to learn more about mechanisms of DBS

A modular molecular dynamics engine with the aim of being part of a user-friendly project to turn MD simulation into agentic-based workflows.

Large-scale thalamocortical network model for simulating physiological and paroxysmal brain rhythms: version 2

Review paper describing how a systems modelling approach can help predict how biological systems respond to extreme heat

💾 Code & data to reproduce the results presented in "Divergence of detachment forces in the finite Voronoi model".

Solar grazing agrivoltaic system design for the LASSO Agrivoltaics Competition at UW–MARS (UW–Madison), integrating PV layout, livestock movement, forage recovery, and animal welfare constraints for field deployment in Wisconsin.