Biochemical simulations on GPU

My second project is a CUDA implementation of Smoldyn simulator. Smoldyn is cell-scale biochemical simulator which simulates each molecule of interest individually to capture natural stochasticity and for nanometer-scale spatial resolution. This is a particle-based method that allows simulation of chemical molecules with Brownian motion and different reaction types.

GPU-based Direct Simulation Monte Carlo

It's been a while since my last post. Lots of things have changed. Now I'm a PhD student at UW-Milwaukee and a research assistant at the Complex Systems Simulation Lab. In this post I will describe my first project which is a GPU (CUDA) implementation of DSMC method for particle simulations.

DSMC is a computational method for fluid mechanics simulation. Simply put, it can be used for simulation of interaction between gas molecules and a solid body. For example, the case, when a space ship enters the atmosphere can be simulated. The method is relatively simple, but it requires simulation of huge number of molecules for an accurate result, so it is a good candidate for parallelization.