[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 …
obstacle to be overcome, depending on the situation. Traditionally, when constructing …
Asynchrony between virus diversity and antibody selection limits influenza virus evolution
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 …
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 …
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
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 …
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 …
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 …
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 …
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 …
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 …
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 …
diffusion models arising in biochemical signaling pathways. We study moderately stiff …