Biomedical subjects
Publications and source records attributed to V Popkov.
The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered. Referring to the case of the T7 RNA-polymerase, we show that the protein should follow a noise-influenced sequence-dependent motion which deviate from the standard random walk usually assumed. The general validity and the implications of the results are discussed.
A class of models, generalizing asymmetric exclusion process for many parallel interacting channels, is proposed. We couple the models with boundary reservoirs, study boundary-driven phase transitions, and show that usually taken hydrodynamic description fails. The adequate hydrodynamic limit is then derived. We support our findings with Monte Carlo simulations of the original stochastic system.
We study the formation of localized shocks in one-dimensional driven diffusive systems with spatially homogeneous creation and annihilation of particles (Langmuir kinetics). We show how to obtain hydrodynamic equations that describe the density profile in systems with uncorrelated steady state as well as in those exhibiting correlations. As a special example of the latter case, the Katz-Lebowitz-Spohn model is considered. The existence of a localized double density shock is demonstrated in one-dimensional driven diffusive systems. This corresponds to phase separation into regimes of three distinct densities, separated by localized domain walls. Our analytical approach is supported by Monte Carlo simulations.
We consider classical hard-core particles moving on two parallel chains in the same direction. An interaction between the channels is included via the hopping rates. For a ring, the stationary state has a product form. For the case of coupling to two reservoirs, it is investigated analytically and numerically. In addition to the known one-channel phases, two new regions are found, in particular one, where the total density is fixed, but the filling of the individual chains changes back and forth, with a preference for strongly different densities. The corresponding probability distribution is determined and shown to have a universal form. The phase diagram and general aspects of the problem are discussed.
We investigate boundary-driven phase transitions in open driven diffusive systems. The generic phase diagram for systems with short-ranged interactions is governed by a simple extremal principle for the macroscopic current, which results from an interplay of density fluctuations with the motion of shocks. In systems with more than one extremum in the current-density relation, one finds a minimal current phase even though the boundaries support a higher current. The boundary layers of the critical minimal current and maximal current phases are argued to be of a universal form. The predictions of the theory are confirmed by Monte Carlo simulations of the two-parameter family of stochastic particle hopping models of Katz, Lebowitz, and Spohn and by analytical results for a related cellular automaton with deterministic bulk dynamics. The effect of disorder in the particle jump rates on the boundary layer profile is also discussed.