Journal ArticleDOI
The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior
TLDR
This work examines the performance of different versions of Gillespie's stochastic simulation algorithm when applied to several biochemical models and proposes a new algorithm called the sorting direct method that maintains a loosely sorted order of the reactions as the simulation executes.About:
This article is published in Computational Biology and Chemistry.The article was published on 2006-02-01. It has received 211 citations till now. The article focuses on the topics: Tau-leaping & Gillespie algorithm.read more
Citations
More filters
Journal ArticleDOI
Stochastic Simulation of Chemical Kinetics
TL;DR: Some recent advances in methods for using that theory to make numerical simulations include improvements to the exact stochastic simulation algorithm (SSA) and the approximate explicit tau-leaping procedure, as well as the development of two approximate strategies for simulating systems that are dynamically stiff.
Journal ArticleDOI
Transcriptional burst frequency and burst size are equally modulated across the human genome
Roy D. Dar,Brandon S. Razooky,Brandon S. Razooky,Brandon S. Razooky,Abhyudai Singh,Thomas V. Trimeloni,James M. McCollum,Christopher Cox,Michael L. Simpson,Michael L. Simpson,Leor S. Weinberger,Leor S. Weinberger,Leor S. Weinberger +12 more
TL;DR: Time-lapse fluorescence microscopy is used to analyze 8,000 individual human genomic loci and finds that at virtually all loci, episodic bursting—as opposed to constitutive expression—is the predominant mode of expression.
Journal ArticleDOI
Gas-phase spectroscopy of biomolecular building blocks.
TL;DR: Recent results help elucidate structure and hydrogen-bonded interactions, as well as showcase a successful interplay between theory and experiment in gas-phase spectroscopy.
Journal ArticleDOI
Perspective: Stochastic algorithms for chemical kinetics
TL;DR: The perspective on stochastic chemical kinetics is outlined, paying particular attention to numerical simulation algorithms, and some of the more promising strategies for dealing stochastically with stiff systems, rare events, and sensitivity analysis are taken.
Journal ArticleDOI
DNA damage during S-phase mediates the proliferation-quiescence decision in the subsequent G1 via p21 expression
Alexis R. Barr,Sam Cooper,Sam Cooper,Frank S. Heldt,Francesca Butera,Henriette Stoy,Jörg Mansfeld,Bela Novak,Chris Bakal +8 more
TL;DR: It is shown that naturally occurring DNA damage incurred over S-phase causes p53-dependent accumulation of p21 during mother G2- and daughter G1-phases, and mathematical modelling reveals that a bistable switch, created by CRL4Cdt2, promotes irreversible S- Phase entry by keeping p21 levels low, preventing premature S- phase exit upon DNA damage.
References
More filters
Journal ArticleDOI
Exact Stochastic Simulation of Coupled Chemical Reactions
TL;DR: In this article, a simulation algorithm for the stochastic formulation of chemical kinetics is proposed, which uses a rigorously derived Monte Carlo procedure to numerically simulate the time evolution of a given chemical system.
Journal ArticleDOI
A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions
TL;DR: In this paper, an exact method is presented for numerically calculating, within the framework of the stochastic formulation of chemical kinetics, the time evolution of any spatially homogeneous mixture of molecular species which interreact through a specified set of coupled chemical reaction channels.
Journal ArticleDOI
The MATLAB ODE Suite
TL;DR: This paper describes mathematical and software developments for a suite of programs for solving ordinary differential equations in MATLAB.
Journal ArticleDOI
Stochasticity in gene expression: from theories to phenotypes
TL;DR: Stochasticity in gene expression can provide the flexibility needed by cells to adapt to fluctuating environments or respond to sudden stresses, and a mechanism by which population heterogeneity can be established during cellular differentiation and development.
Journal ArticleDOI
Approximate accelerated stochastic simulation of chemically reacting systems
TL;DR: With further refinement, the τ-leap method should provide a viable way of segueing from the exact SSA to the approximate chemical Langevin equation, and thence to the conventional deterministic reaction rate equation, as the system size becomes larger.
Related Papers (5)
Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels
Michael A. Gibson,Jehoshua Bruck +1 more