Related papers: Statistical Mechanics of Integral Membrane Protein…
In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes…
We study the stress distribution profiles and the height and thickness fluctuations of lipid membranes in the tilted gel state by Monte Carlo simulations of a generic coarse-grained model for lipid membranes, which reproduces many known…
We present a theoretical investigation of thermal fluctuation statistics in a molecular motor. Energy transfer in the motor is described using a multidimensional discrete master equation with nearest-neighbor hopping. In this theory, energy…
Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio…
Half-space directed polymers in random environments are models of interface growth in the presence of an attractive hard wall. They arise naturally in the study of wetting and entropic repulsion phenomena. In 1985, Kardar predicted a…
The theory of mesoscopic fluctuations is applied to inhomogeneous solids consisting of chaotically distributed regions with different crystalline structure. This approach makes it possible to describe statistical properties of such mixture…
Path integrals similar to those describing stiff polymers arise in the Helfrich model for membranes. We show how these types of path integrals can be evaluated and apply our results to study the thermodynamics of a minority stripe phase in…
A theoretical model of a two-component fluid membrane containing lipids and two-state active inclusions is presented. Under strong inclusion activities the membrane can be unstable due to pump-driven undulation or aggregation of high…
Jamming is a geometric phase transition occurring in dense particle systems in the absence of temperature. We use computer simulations to analyse the effect of thermal fluctuations on several signatures of the transition. We show that…
The folding of a peptide chain into a three dimensional structure is a thermodynamically driven process such that the chain naturally evolves to form domains of similar amino acids. The formation of this domain occurs by curling the one…
In these lectures I discuss long-scale properties of fluctuating polymerized membranes in the presence of network anisotropy and random heterogeneities. Amazingly, even infinitesimal amount of these seemingly innocuous but physically…
We examine the question of whether the formal expressions of equilibrium statistical mechanics can be applied to time independent non-dissipative systems that are not in true thermodynamic equilibrium and are nonergodic. By assuming the…
We present that a statistical method known as the Complexity-Entropy analysis is useful to characterize a state of plasma turbulence and flux in the resonant magnetic perturbation (RMP) edge localized mode (ELM) control experiment. The RMP…
In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [1] and perform detail analysis of alpha helix-random coil transition in alanine polypeptides of…
The space-time dynamics of rigid inhomogeneities (inclusions) free to move in a randomly fluctuating fluid bio-membrane is derived and numerically simulated as a function of the membrane shape changes. Both vertically placed (embedded)…
By means of lattice-based Monte Carlo simulations, we address properties of two-component lipid membranes on the experimentally relevant spatial scales of order of a micrometer and time intervals of order of a second, using DMPC/DSPC lipid…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the…
All-atom molecular dynamics (MD) computer simulations are a valuable tool for characterizing the conformational ensembles of intrinsically disordered proteins (IDPs). IDP conformational ensembles are highly heterogeneous and contain…