Simulation tools for particle-based reaction-diffusion dynamics in continuous space
نویسندگان
چکیده
منابع مشابه
Simulation tools for particle-based reaction-diffusion dynamics in continuous space
Particle-based reaction-diffusion algorithms facilitate the modeling of the diffusional motion of individual molecules and the reactions between them in cellular environments. A physically realistic model, depending on the system at hand and the questions asked, would require different levels of modeling detail such as particle diffusion, geometrical confinement, particle volume exclusion or pa...
متن کاملCoarse-Grained Stochastic Particle-based Reaction-Diffusion Simulation Algorithm
In recent years, several particle-based stochastic simulation algorithms (PSSA) have been developed to study the spatially resolved dynamics of biochemical networks at a molecular scale. A challenge all these approaches have to address is to allow for simulations at cell-biologically relevant timescales without neither neglecting important spatial and biochemical properties of the simulated sys...
متن کاملAdaptive space and time numerical simulation of reaction-diffusion models for intracellular calcium dynamics
Adaptivity in space and time for the numerical simulation of stochastic and deterministic equations for intracellular calcium dynamics is presented. The modeling of diffusion, reaction and membrane transport of calcium ions in cells leads to a system of reaction-diffusion equations. We describe the modulation of cytosolic and ER calcium concentrations close to the membrane of the cell organelle...
متن کاملReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments
We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be mode...
متن کاملAnomalous diffusion with linear reaction dynamics: from continuous time random walks to fractional reaction-diffusion equations.
We have revisited the problem of anomalously diffusing species, modeled at the mesoscopic level using continuous time random walks, to include linear reaction dynamics. If a constant proportion of walkers are added or removed instantaneously at the start of each step then the long time asymptotic limit yields a fractional reaction-diffusion equation with a fractional order temporal derivative o...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: BMC Biophysics
سال: 2014
ISSN: 2046-1682
DOI: 10.1186/s13628-014-0011-5