Nucleosome sliding can influence the spreading of histone modifications.

Nucleosomes are the fundamental building blocks of chromatin that not only help in the folding of chromatin, but also in carrying epigenetic information. It is known that nucleosome sliding is responsible for dynamically organizing chromatin structure and the resulting gene regulation. Since sliding can move two neighboring nucleosomes physically close or away, can it play a role in the spreading of histone modifications? We investigate this by simulating a stochastic model that couples nucleosome dynamics with the kinetics of histone modifications.

Continuous variable responses and signal gating form kinetic bases for pulsatile insulin signaling and emergence of resistance.

Understanding kinetic control of biological processes is as important as identifying components that constitute pathways. Insulin signaling is central for almost all metazoans, and its perturbations are associated with various developmental disorders, metabolic diseases, and aging. While temporal phosphorylation changes and kinetic constants have provided some insights, constant or variable parameters that establish and maintain signal topology are poorly understood.

Solving the problem of negative populations in approximate accelerated stochastic simulations using the representative reaction approach.

Methods based on the stochastic formulation of chemical kinetics have the potential to accurately reproduce the dynamical behavior of various biochemical systems of interest. However, the computational expense makes them impractical for the study of real systems. Attempts to render these methods practical have led to the development of accelerated methods, where the reaction numbers are modeled by Poisson random numbers.

A theoretical study of metal-metal cooperativity in the homogeneous water gas shift reaction.

The possibility of metal-metal cooperativity in improving the yield of the homogeneous water gas shift reaction (WGSR) has been investigated through full quantum mechanical density functional theory calculations. The calculations indicate that bimetallic catalysts would be likely to be more highly active than mononuclear metal-based catalysts for the WGSR. The results have implications for the design of improved WGSR catalysts in the future.

A new approximate method for the stochastic simulation of chemical systems: the representative reaction approach.

We have developed two new approximate methods for stochastically simulating chemical systems. The methods are based on the idea of representing all the reactions in the chemical system by a single reaction, i.e.