Multiparticle collision dynamics: Simulation of complex systems on mesoscales

R Kapral - Advances in Chemical Physics, 2008 - Wiley Online Library
V. Hydrodynamic Equations A. Simulation of Hydrodynamic Flows VI. Reactive MPC
Dynamics VII. Hybrid MPC–MD Dynamics VIII. Simulating Real Systems with MPC Dynamics …

Detailed simulations of cell biology with Smoldyn 2.1

SS Andrews, NJ Addy, R Brent… - PLoS computational …, 2010 - journals.plos.org
Most cellular processes depend on intracellular locations and random collisions of
individual protein molecules. To model these processes, we developed algorithms to …

Spatial simulations in systems biology: from molecules to cells

M Klann, H Koeppl - International journal of molecular sciences, 2012 - mdpi.com
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 …

Fast global registration of 3D sampled surfaces using a multi-z-buffer technique

R Benjemaa, F Schmitt - Image and Vision Computing, 1999 - Elsevier
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 …

Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm

D Ridgway, G Broderick, A Lopez-Campistrous… - Biophysical journal, 2008 - cell.com
We present a general-purpose model for biomolecular simulations at the molecular level
that incorporates stochasticity, spatial dependence, and volume exclusion, using diffusing …

ReaDDy-a software for particle-based reaction-diffusion dynamics in crowded cellular environments

J Schöneberg, F Noé - PloS one, 2013 - journals.plos.org
We introduce the software package ReaDDy for simulation of detailed spatiotemporal
mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with …

Lattice microbes: High‐performance stochastic simulation method for the reaction‐diffusion master equation

E Roberts, JE Stone… - Journal of computational …, 2013 - Wiley Online Library
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: sugar phosphotransferase system (PTS): an interface between energy and signal transduction

B Erni - Journal of the Iranian Chemical Society, 2013 - Springer
The bacterial phosphoenolpyruvate (PEP): sugar phosphotransferase system (PTS)
mediates the uptake and phosphorylation of carbohydrates, and is involved in signal …

MEDYAN: mechanochemical simulations of contraction and polarity alignment in actomyosin networks

K Popov, J Komianos, GA Papoian - PLoS computational biology, 2016 - journals.plos.org
Active matter systems, and in particular the cell cytoskeleton, exhibit complex
mechanochemical dynamics that are still not well understood. While prior computational …

Simulation of stochastic reaction-diffusion processes on unstructured meshes

S Engblom, L Ferm, A Hellander, P Lötstedt - SIAM Journal on Scientific …, 2009 - SIAM
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 …