Water autoionization plays a critical role in determining pH and properties of various chemical and biological processes occurring in the water mediated environment. The strikingly unsymmetrical potential energy surface of the dissociation process poses a great challenge to the mechanistic study. He…
In a previous paper (math-ph/0202002) an Euler angle parameterization for SU(4) was given. Here we present the derivation of a generalized Euler angle parameterization for SU(N). The formula for the calculation of the Haar measure for SU(N) as well as its relation to Marinov's volume formula for SU(…
Let H be a self-adjoint operator such that exp(-aH) is of trace class for some a<1. Let V be a symmetric operator, Kato bounded relative to H. We show that log Tr[exp(-H+xV)] is a real analytic function of x in a hood of x=0. We show that the Gibbs states of H+xV form a real analytic Banach manifold…
When a chromophore interacts with titrable molecular sites, the modeling of its photophysical properties requires to take into account all their possible protonation states. We have developed a multi-scale protocol, based on constant-pH molecular dynamics simulations coupled to QM/MM excitation ener…
The mathematical model describing the stationary natural pH-gradient arising under the action of an electric field in an aqueous solution of ampholytes (amino acids) is constructed and investigated. The model is a part of a more general model of the isoelectrofocusing process. Investigation is based…
The urea-urease clock reaction is a pH switch from acid to basic that can turn into a pH oscillator if it occurs inside a suitable open reactor. We study the confinement of the reaction to lipid vesicles, which permit the exchange with an external reservoir by differential transport, enabling the re…
An association behavior of uranyl ions in aqueous solutions is explored. For this purpose a set of all-atom molecular dynamics simulations is performed. During the simulation, the fractions of uranyl ions involved in dimer and trimer formations were monitored. To accompany the fraction statistics on…
Redox processes are important in chemistry, with applications in biomedicine, chemical analysis, among others. As many redox experiments are also performed at a fixed value of pH, having an efficient computational method to support experimental measures at both constant redox potential and pH is ver…
Stochastic gene expression has been implicated in a variety of cellular processes, including cell differentiation and disease. In this issue of Cell, Weinberger et al. (2005) take an integrated computational-experimental approach to study the Tat transactivation feedback loop in HIV-1 and show that …
We present a detailed analysis, based on the Forward Flux Sampling (FFS) simulation method, of the switching dynamics and stability of two models of genetic toggle switches, consisting of two mutually-repressing genes encoding transcription factors (TFs); in one model (the exclusive switch), they mu…