Spatial stochastic intracellular kinetics: A review of modelling approaches
Abstract Models of chemical kinetics that incorporate both stochasticity and diffusion are an
increasingly common tool for studying biology. The variety of competing models is vast, but …
increasingly common tool for studying biology. The variety of competing models is vast, but …
Turing patterns in systems with high-order interactions
Turing theory of pattern formation is among the most popular theoretical means to account
for the variety of spatio-temporal structures observed in Nature and, for this reason, finds …
for the variety of spatio-temporal structures observed in Nature and, for this reason, finds …
Macromolecular crowding directs the motion of small molecules inside cells
It is now well established that cell interiors are significantly crowded by macromolecules,
which impede diffusion and enhance binding rates. However, it is not fully appreciated that …
which impede diffusion and enhance binding rates. However, it is not fully appreciated that …
Building macroscale models from microscale probabilistic models: a general probabilistic approach for nonlinear diffusion and multispecies phenomena
CJ Penington, BD Hughes, KA Landman - Physical Review E—Statistical …, 2011 - APS
A discrete agent-based model on a periodic lattice of arbitrary dimension is considered.
Agents move to nearest-neighbor sites by a motility mechanism accounting for general …
Agents move to nearest-neighbor sites by a motility mechanism accounting for general …
[图书][B] Stochastic dynamics in computational biology
S Winkelmann, C Schütte - 2020 - Springer
Computational biology is the science of developing mathematical models and numerical
simulation techniques to understand biological and biochemical systems. Since the early …
simulation techniques to understand biological and biochemical systems. Since the early …
Emergence of power-law distributions in self-segregation reaction-diffusion processes
Many natural or human-made systems encompassing local reactions and diffusion
processes exhibit spatially distributed patterns of some relevant dynamical variable. These …
processes exhibit spatially distributed patterns of some relevant dynamical variable. These …
[HTML][HTML] The Influence of Local Constraints on Solvent Motion in Polymer Materials
K Hałagan, P Duniec, M Kozanecki, A Sikorski - Materials, 2024 - pmc.ncbi.nlm.nih.gov
The influence of obstacles in the form of polymer chains on the diffusion of a low-molecular-
weight solvent was the subject of this research. Studies were performed by computer …
weight solvent was the subject of this research. Studies were performed by computer …
Hopping in the crowd to unveil network topology
We introduce a nonlinear operator to model diffusion on a complex undirected network
under crowded conditions. We show that the asymptotic distribution of diffusing agents is a …
under crowded conditions. We show that the asymptotic distribution of diffusing agents is a …
Turing instabilities in reaction-diffusion systems with cross diffusion
The Turing instability paradigm is revisited in the context of a multispecies diffusion scheme
derived from a self-consistent microscopic formulation. The analysis is developed with …
derived from a self-consistent microscopic formulation. The analysis is developed with …
[HTML][HTML] Fast simulation of Brownian dynamics in a crowded environment
Brownian dynamics simulations are an increasingly popular tool for understanding spatially
extended biochemical reaction systems. Recent improvements in our understanding of the …
extended biochemical reaction systems. Recent improvements in our understanding of the …