In biochemical systems some of the chemical species are present with only small numbers of molecules. In this situation discrete and stochastic simulation approaches are more relevant than continuous and deterministic ones. The fundamental Gillespie’s stochastic simulation algorithm (SSA) accounts for every reaction event, which occurs with a probability determined by the configuration of the s...

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Hybrid molecular dynamics/Monte Carlo simulations are used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in separating the effects of thermodynamics and chemical kinetics on the dynamics and mechanics of these systems, and is extensible to arbitrarily nonequilibrium sit...

The aim of this short note is to show that the class of problem involving kinetic or thermo–kinetic constraints in addition to the usual stoechiometric one is non convex.

Gene expression, signal transduction and many other cellular processes are subject to stochastic fluctuations. The analysis of these stochastic chemical kinetics is important for understanding cell-to-cell variability and its functional implications, but it is also challenging. A multitude of exact and approximate descriptions of stochastic chemical kinetics have been developed, however, tools ...

The model developed previously for evaluating the impact of direct ethanol injection on the avoidance of knock in spark ignition engines is used to evaluate the trends of changes in compression ratio and variation in the inlet pressure. The ethanol fraction requirements through the engine map is calculated using detailed chemical kinetics model, and a vehicle simulation is used to determine the...

Three different heparin-catalyzed inhibitor/protease reactions were studied: antithrombin III/thrombin, heparin cofactor II/thrombin, antithrombin III/factor Xa. The three reactions were saturable with respect to both inhibitor and protease. The initial reaction velocity, for each reaction, could be described by the general rate equation for a random-order bireactant enzyme-catalyzed reaction. ...