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