We address the problem of simulating biochemical reaction networks with time-dependent rates and propose a new algorithm based on our rejection-based stochastic simulation algorithm (RSSA) [Thanh et al., J. Chem. Phys. 141(13), 134116 (2014)]. The computation for selecting next reaction firings by our time-dependent RSSA (tRSSA) is computationally efficient. Furthermore, the generated trajector...

Dynamic modelling of biochemical reaction networks has to cope with the inherent uncertainty about biological processes, concerning not only data and parameters but also kinetics and structure. These different types of uncertainty are nested within each other: uncertain network structures contain uncertain reaction kinetics, which in turn are governed by uncertain parameters. Here, the authors ...

Encyclopedic metabolic networks capture the sum of human knowledge of biochemical reactions and substrates as found across a multitude of organisms, and not one particular organism. A method for large-scale alignment of two such encyclopedic metabolic networks, KEGG and MetaCyc, has been designed to allow for a systematic comparison of their contents. A variety of methods for matching reactions...

Conformations and catalytic rates of enzymes (biological catalysts) fluctuate over a wide range of time scales. Recent experimental and theoretical investigations demonstrated case studies where the enzymatic catalysis rate follows the Michaelis-Menten (MM) rate law despite molecular fluctuations. In this paper, we investigate deviations from MM law and their effects on the dynamical behavior o...

It is commonly believed that, whenever timescale separation holds, the predictions of reduced chemical master equations obtained using the stochastic quasi-steady-state approximation are in very good agreement with the predictions of the full master equations. We use the linear noise approximation to obtain a simple formula for the relative error between the predictions of the two master equati...

Intracellular Ca2+ oscillations are often a response to external signals such as hormones. Changes in the external signal can alter the frequency, amplitude, or form of the oscillations suggesting that information is encoded in the pattern of Ca2+ oscillations. How might a cell decode this signal? We show that an excitable system whose kinetic parameters are modulated by the Ca2+ concentration ...

BACKGROUND Molecular activation pathways are inherently complex, and understanding relations across many biochemical reactions and reaction types is difficult. Visualizing and analyzing a pathway is a challenge due to the network size and the diversity of relations between proteins and molecules. RESULTS In this paper, we introduce PathwayMatrix, a visualization tool that presents the binary ...

Biochemical reaction networks grow bigger and bigger, fed by the high-throughput data provided by biologists and bred in open repositories of models allowing merging and evolution. Nevertheless, since the available data is still very far from permitting the identification of the increasing number of kinetic parameters of such models, the necessity of structural analyses for describing the dynam...

A difficulty associated with high throughput screening for enzyme inhibitors is to establish reaction conditions that maximize the sensitivity and resolution of the assay. Deduction of information from end-point assays at single concentrations requires a detailed understanding of the time progress of the enzymatic reaction, an essential but often difficult process to model. A tool to simulate t...

We develop theory for the dynamics and fluctuations in some cyclic and linear biochemical reactions. We use the approach of maximum caliber, which computes the ensemble of paths taken by the system, given a few experimental observables. This approach may be useful for interpreting single-molecule or few-particle experiments on molecular motors, enzyme reactions, ion-channels, and phosphorylatio...