Related papers: Statistical Mechanics of Integral Membrane Protein…
Membrane shape fluctuations induce attractive interactions between rigid inclusions. Previous analytical studies showed that the fluctuation-induced pair interactions are rather small compared to thermal energies, but also that multi-body…
We show that the interplay between excluded volume effects, hydrophobicity, and hydrogen bonding of a tube-like representation of a polypeptide chain gives rise to free energy landscapes that exhibit a small number of metastable minima…
Self-assembly of protein monomers into distinct membrane protein oligomers provides a general mechanism for diversity in the molecular architectures, and resulting biological functions, of membrane proteins. We develop a general physical…
This paper reports all-atom computer simulations of five phospholipid membranes (DMPC, DPPC, DMPG, DMPS, and DMPSH) with focus on the thermal equilibrium fluctuations of volume, energy, area, thickness, and chain order. At constant…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…
The interpretation electrical phenomena in biomembranes is usually based on the assumption that the experimentally found discrete ion conduction events are due to a particular class of proteins called ion channels while the lipid membrane…
We use Markov state models (MSMs) to analyze the dynamics of a $\beta$-hairpin-forming peptide in Monte Carlo (MC) simulations with interacting protein crowders, for two different types of crowder proteins [bovine pancreatic trypsin…
Biological membranes and vesicles play a central role in living systems, forming dynamic interfaces that regulate cellular organization and function. Classical descriptions of membrane mechanics that are rooted in equilibrium statistical…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…
Biomembranes wrapping cells and organelles are not only the partitions that separate the insides but also dynamic fields for biological functions accompanied by membrane shape changes. In this review, we discuss the spatiotemporal patterns…
We study the size properties of the largest intermediate mass fragments in each partition mode, produced in the prompt statistical breakup of a thermally equilibrated nuclear source, at different temperatures. We find that an appreciable…
We apply the Lifshitz theory of dispersion forces to find a contribution to the free energy of peptide films which is caused by the zero-point and thermal fluctuations of the electromagnetic field. For this purpose, using available…
Current theories of heteropolymers are inherently macrpscopic, but are applied to folding proteins which are only mesoscopic. In these theories, one computes the averaged free energy over sequences, always assuming that it is self-averaging…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
Random lateral translocation of lipids and proteins is a universal process on membrane surfaces. Local aggregation or organization of lipids and proteins can be induced when this lateral random diffusion is mediated by the electrostatic…
This dissertation develops, for several families of statistical mechanical and random growth models, techniques for analyzing infinite-volume asymptotics. In the statistical mechanical setting, we focus on the low-temperature phases of spin…
An important indicator of membrane performance are free volume elements (FVEs): microporous void spaces created by the inefficient packing of bulky groups along the polymer chain. FVEs tend to degrade over time as polymer chains reorganize…
Free-energy landscapes for short peptides -- specifically for variants of the pH Low Insertion Peptide (pHLIP) -- in the heterogeneous environment of a lipid bilayer or cell membrane are constructed, taking into account a set of dominant…