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

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

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

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

Large-scale thalamocortical network model for simulating physiological and paroxysmal brain rhythms: version 1

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

Bottom-up dynamical modeling of biological systems using ordinary, partial, and stochastic differential equations.

Simulation of an FtsZ filament in C++