[HTML][HTML] Stochastic simulation in systems biology

T Székely Jr, K Burrage - Computational and structural biotechnology …, 2014 - Elsevier
Natural systems are, almost by definition, heterogeneous: this can be either a boon or an
obstacle to be overcome, depending on the situation. Traditionally, when constructing …

Asynchrony between virus diversity and antibody selection limits influenza virus evolution

DH Morris, VN Petrova, FW Rossine, E Parker… - Elife, 2020 - elifesciences.org
Seasonal influenza viruses create a persistent global disease burden by evolving to escape
immunity induced by prior infections and vaccinations. New antigenic variants have a …

[图书][B] Stochasticity in processes

P Schuster - 2016 - Springer
The theory of probability and stochastic processes is often neglected in the education of
chemists and biologists, although modern experimental techniques allow for investigations …

A review of stochastic and delay simulation approaches in both time and space in computational cell biology

K Burrage, P Burrage, A Leier… - … , multiscale modeling, and …, 2017 - Springer
Heterogeneity and variability is ubiquitous in biology and physiology and one of the great
modelling challenges is how we cope with and quantify this variability. There are a wide …

[HTML][HTML] An adaptive tau-leaping method for stochastic simulations of reaction-diffusion systems

J Padgett, S Ilie - AIP Advances, 2016 - pubs.aip.org
Stochastic modelling is critical for studying many biochemical processes in a cell, in
particular when some reacting species have low population numbers. For many such …

[HTML][HTML] Efficient Finite-Difference Estimation of Second-Order Parametric Sensitivities for Stochastic Discrete Biochemical Systems

F Jabeen, S Ilie - Mathematical and Computational Applications, 2024 - mdpi.com
Biochemical reaction systems in a cell exhibit stochastic behaviour, owing to the
unpredictable nature of the molecular interactions. The fluctuations at the molecular level …

A weak second order tau-leaping method for chemical kinetic systems

Y Hu, T Li, B Min - The Journal of chemical physics, 2011 - pubs.aip.org
Recently Anderson and Mattingly [Comm. Math. Sci. 9, 301 (2011)] proposed a method
which can solve chemical Langevin equations with weak second order accuracy. We extend …

An efficient finite-difference strategy for sensitivity analysis of stochastic models of biochemical systems

M Morshed, B Ingalls, S Ilie - Biosystems, 2017 - Elsevier
Sensitivity analysis characterizes the dependence of a model's behaviour on system
parameters. It is a critical tool in the formulation, characterization, and verification of models …

Variable time-stepping in the pathwise numerical solution of the chemical Langevin equation

S Ilie - The Journal of Chemical Physics, 2012 - pubs.aip.org
Stochastic modeling is essential for an accurate description of the biochemical network
dynamics at the level of a single cell. Biochemically reacting systems often evolve on …

Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics

R Strehl, S Ilie - The Journal of Chemical Physics, 2015 - pubs.aip.org
In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-
diffusion models arising in biochemical signaling pathways. We study moderately stiff …