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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 …
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
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 …
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
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 …
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 …
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
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 …
as a constitutive process, characterized by a Poisson-like accumulation of gene products. It …
Perspective: Stochastic algorithms for chemical kinetics
We outline our perspective on stochastic chemical kinetics, paying particular attention to
numerical simulation algorithms. We first focus on dilute, well-mixed systems, whose …
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
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 …
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
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 …
of processes in many research fields including (bio) chemical engineering and biology. One …
[หนังสือ][B] Modeling in systems biology: the Petri net approach
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 …
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 …
counterintuitive temporal dynamics of (bio-) chemical systems. In particular, stochastic …