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).

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

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

Nitrogen balance model components and test procedures

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

Materials for the PANGEOS Uncertainty Quantification workshop

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

DFOC Group Project Repository

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++

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

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.

Data and figures (R-notebooks) for the in-silico biodiversity experiment using DART biophysical model