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...

Traditional deterministic approaches for simulation of chemically reacting systems fail to capture the randomness inherent in such systems at scales common in intracellular biochemical processes. In this manuscript, we briefly review the state of the art in discrete stochastic and multiscale algorithms for simulation of biochemical systems and we present the StochKit software toolkit.

Much attention has been paid recently to bistability and switch-like behavior that might be resident in important biochemical reaction networks. There is, in fact, a great deal of subtlety in the relationship between the structure of a reaction network and its capacity to engender bistability. In common physicochemical settings, large classes of extremely complex networks, taken with mass actio...

INTRODUCTION Proteins are the most versatile molecules in biological world meant for several function including structural organization and catalytic capabilities [1]. Enzymes are the biocatalyst with higher precession and accuracy while performing biochemical reactions. The entire biological world has been evolved with diverse enzymes and microbial population shown tremendous potential in ABST...

The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performanc...

The polymerization of vinyl monomers with cleavable enzymatic substrates has been shown to lead to water-soluble double-hydrophilic block copolymers which, upon enzymatic activation of the diblock copolymers, become amphiphilic and undergo self-assembly into colloidal nanostructures. The ability to change the chemical and physical characteristics of polymeric materials by an enzymatic reaction ...

Solvent additives (cosolvents, osmolytes) modulate biochemical reactions if, during the course of the reaction, there is a change in preferential interactions of solvent components with the reacting system. Preferential interactions can be expressed in terms of preferential binding of the cosolvent or its preferential exclusion (preferential hydration). The driving force is the perturbation by ...

The dynamical solution of a well-mixed, nonlinear stochastic chemical kinetic system, described by the Master equation, may be exactly computed using the stochastic simulation algorithm. However, because the computational cost scales with the number of reaction occurrences, systems with one or more "fast" reactions become costly to simulate. This paper describes a hybrid stochastic method that ...

Many biochemical processes at the sub-cellular level involve a small number of molecules. The local numbers of these molecules vary in space and time, and exhibit random fluctuations that can only be captured with stochastic simulations. We present a novel stochastic operator-splitting algorithm to model such reaction-diffusion phenomena. The reaction and diffusion steps employ stochastic simul...