The second entropy theory for nonequilibrium thermodynamics is extended to the nonlinear regime and to systems of mixed parity (even and odd functions of molecular velocities). The steady state phase space probability density is given for systems of mixed parity. The nonlinear transport matrix is obtained and it is shown to yield the analog of the linear Onsager-Casimir reciprocal relations. It...

The Fano factor, an observable quantifying fluctuations of product generation by a single enzyme, can reveal information about the underlying reaction scheme. A lower bound on this Fano factor that depends on the thermodynamic affinity driving the transformation from substrate to product constrains the number of intermediate states of an enzymatic cycle. So far, this bound has been proven only ...

We consider random nondirected networks subject to dynamics conserving vertex degrees and study, analytically and numerically, equilibrium three-vertex motif distributions in the presence of an external field h coupled to one of the motifs. For small h, the numerics is well described by the "chemical kinetics" for the concentrations of motifs based on the law of mass action. For larger h, a tra...

Conventional equations for enzyme kinetics are based on mass-action laws, that may fail in low-dimensional and disordered media such as biological membranes. We present Monte Carlo simulations of an isolated Michaelis-Menten enzyme reaction on two-dimensional lattices with varying obstacle densities, as models of biological membranes. The model predicts that, as a result of anomalous diffusion ...

Proton transfer reactions play an important role in many areas of biology. We reimplemented a method introduced by Taraphder et al. to characterize putative proton transfer pathways in proteins along hydrogen bonded networks and could retrace their results on cytochrome P450cam. By combining this method with our established Q-HOP approach to compute proton transfer probabilities we present here...

A model of barrier crossing dynamics governed by fractional Gaussian noise and the generalized Langevin equation is used to study the reaction kinetics of single enzymes subject to conformational fluctuations. The direct application of Kramers's flux-over-population method to this model yields analytic expressions for the time-dependent transmission coefficient and the distribution of waiting t...

This report documents a Fortran computer code package that is used for the evaluation of gas-phase multicomponent viscosities, thermal conductivities, diiusion coeecients, and thermal diiusion coeecients. The package is in two parts. The rst is a preprocessor that computes polynomial ts to the temperature dependent parts of the pure species viscosities and binary diiusion coeecients. The coeeci...

Abstract. This article is concerned with the asymptotic accuracy of the Computational Singular Perturbation (CSP) method developed by Lam and Goussis to reduce the dimensionality of a system of chemical kinetics equations. The method exploits the presence of disparate time scales to model the dynamics by an evolution equation on a lower-dimensional slow manifold. In this article it is shown tha...

background: the presence of even a very small quantity of dye in water bodies is undesirable and affects the water bodies. dye removal from industrial waste water is significant; hence in this study, a material that is an economical waste product was employed to test its acid dye removing capacity from aqueous solution. methods: in this study, batch mode experiments were performed in the sorpti...

in this work, based on experimental observations and exact theoretical predictions, the kinetic scheme of raft polymerization is extended to a wider range of reactions such as irreversible intermediate radical terminations and reversible transfer reactions. the reactions which have been labeled as kinetic scheme are the more probable existing reactions as the theoretical point of view. the deta...