V. Hydrodynamic Equations A. Simulation of Hydrodynamic Flows VI. Reactive MPC
Dynamics VII. Hybrid MPC–MD Dynamics VIII. Simulating Real Systems with MPC Dynamics …

Most cellular processes depend on intracellular locations and random collisions of
individual protein molecules. To model these processes, we developed algorithms to …

Cells are highly organized objects containing millions of molecules. Each biomolecule has a
specific shape in order to interact with others in the complex machinery. Spatial dynamics …

We present a new method for the global registration of several overlapping three-
dimensional (3D) surfaces sampled on an object. The method is based on the ICP algorithm …

We present a general-purpose model for biomolecular simulations at the molecular level
that incorporates stochasticity, spatial dependence, and volume exclusion, using diffusing …

We introduce the software package ReaDDy for simulation of detailed spatiotemporal
mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with …

Spatial stochastic simulation is a valuable technique for studying reactions in biological
systems. With the availability of high‐performance computing (HPC), the method is poised to …

The bacterial phosphoenolpyruvate (PEP): sugar phosphotransferase system (PTS)
mediates the uptake and phosphorylation of carbohydrates, and is involved in signal …

Active matter systems, and in particular the cell cytoskeleton, exhibit complex
mechanochemical dynamics that are still not well understood. While prior computational …

We model stochastic chemical systems with diffusion by a reaction-diffusion master
equation. On a macroscopic level, the governing equation is a reaction-diffusion equation for …