Stochastic simulation of chemical kinetics

DT Gillespie - Annu. Rev. Phys. Chem., 2007 - annualreviews.org
Stochastic chemical kinetics describes the time evolution of a well-stirred chemically
reacting system in a way that takes into account the fact that molecules come in whole …

When polymer reaction engineers play dice: applications of Monte Carlo models in PRE

ALT Brandao, JBP Soares, JC Pinto… - Macromolecular …, 2015 - Wiley Online Library
Monte Carlo methods are heuristic algorithms that use probabilities to select an outcome
among several possible events in a given process. Monte Carlo methods are useful in …

DNA damage during S-phase mediates the proliferation-quiescence decision in the subsequent G1 via p21 expression

AR Barr, S Cooper, FS Heldt, F Butera, H Stoy… - Nature …, 2017 - nature.com
Following DNA damage caused by exogenous sources, such as ionizing radiation, the
tumour suppressor p53 mediates cell cycle arrest via expression of the CDK inhibitor, p21 …

[หนังสือ][B] Monte Carlo simulation in statistical physics

K Binder, DW Heermann, K Binder - 1992 - Springer
Roughly at the time (1987) when the manuscript for the first three chapters of the present
book was completed, several breakthroughs occurred. They had a profound influence on the …

Transcriptional burst frequency and burst size are equally modulated across the human genome

RD Dar, BS Razooky, A Singh, TV Trimeloni… - Proceedings of the …, 2012 - pnas.org
Gene expression occurs either as an episodic process, characterized by pulsatile bursts, or
as a constitutive process, characterized by a Poisson-like accumulation of gene products. It …

Perspective: Stochastic algorithms for chemical kinetics

DT Gillespie, A Hellander, LR Petzold - The Journal of chemical …, 2013 - pubs.aip.org
We outline our perspective on stochastic chemical kinetics, paying particular attention to
numerical simulation algorithms. We first focus on dilute, well-mixed systems, whose …

Single-cell analysis and stochastic modelling unveil large cell-to-cell variability in influenza A virus infection

FS Heldt, SY Kupke, S Dorl, U Reichl… - Nature …, 2015 - nature.com
Biochemical reactions are subject to stochastic fluctuations that can give rise to cell-to-cell
variability. Yet, how this variability affects viral infections, which themselves involve noisy …

Gillespie-driven kinetic Monte Carlo algorithms to model events for bulk or solution (bio) chemical systems containing elemental and distributed species

AD Trigilio, YW Marien… - Industrial & …, 2020 - ACS Publications
Stochastic modeling techniques have emerged as a powerful tool to study the time evolution
of processes in many research fields including (bio) chemical engineering and biology. One …

[หนังสือ][B] Modeling in systems biology: the Petri net approach

I Koch, W Reisig, F Schreiber - 2010 - books.google.com
The emerging, multi-disciplinary field of systems biology is devoted to the study of the
relationships between various parts of a biological system, and computer modeling plays a …

Biochemical simulations: stochastic, approximate stochastic and hybrid approaches

J Pahle - Briefings in bioinformatics, 2009 - academic.oup.com
Computer simulations have become an invaluable tool to study the sometimes
counterintuitive temporal dynamics of (bio-) chemical systems. In particular, stochastic …