Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface
SS Andrews - Bioinformatics, 2017 - academic.oup.com
Motivation Smoldyn is a spatial and stochastic biochemical simulator. It treats each molecule
of interest as an individual particle in continuous space, simulating molecular diffusion …
of interest as an individual particle in continuous space, simulating molecular diffusion …
Particle-based stochastic simulators
SS Andrews - Encyclopedia of computational neuroscience, 2022 - Springer
How to answer this question? We first assume that the oscillation is a limit cycle–a trajectory
through state space that is repeated reliably every cycle. The phase of a limit cycle, defined …
through state space that is repeated reliably every cycle. The phase of a limit cycle, defined …
Effects of surfaces and macromolecular crowding on bimolecular reaction rates
SS Andrews - Physical Biology, 2020 - iopscience.iop.org
Biological cells are complex environments that are densely packed with macromolecules
and subdivided by membranes, both of which affect the rates of chemical reactions. It is well …
and subdivided by membranes, both of which affect the rates of chemical reactions. It is well …
Reaction-diffusion kinetics on lattice at the microscopic scale
WX Chew, K Kaizu, M Watabe, SV Muniandy… - Physical Review E, 2018 - APS
Lattice-based stochastic simulators are commonly used to study biological reaction-diffusion
processes. Some of these schemes that are based on the reaction-diffusion master equation …
processes. Some of these schemes that are based on the reaction-diffusion master equation …
Biophysical attributes that affect CaMKII activation deduced with a novel spatial stochastic simulation approach
X Li, WR Holmes - PLOS Computational Biology, 2018 - journals.plos.org
Calcium/calmodulin-dependent protein kinase II (CaMKII) holoenzymes play a critical role in
decoding Ca2+ signals in neurons. Understanding how this occurs has been the focus of …
decoding Ca2+ signals in neurons. Understanding how this occurs has been the focus of …