Related papers: Lipid thermodynamics : melting is molecular
Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently in [Plattner et al, J. Chem. Phys. 135, 134111 (2011)] a method was proposed to implement infinite…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
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…
We study the indentation of a free-standing lipid membrane suspended over a nanopore on a hydrophobic substrate by means of molecular dynamics simulations. We find that in the course of indentation, the membrane bends at the point of…
We introduce a simple model, a binary mixture of patchy particles, which has been designed to form a gel upon heating. Due to the specific nature of the particle interactions, notably the number and geometry of the patches as well as their…
The nucleation of crystals in liquids is one of nature's most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and…
The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant…
We discuss the possibility of existence of entanglement in biological systems. Our arguments centre on the fact that biological systems are thermodynamic open driven systems far from equilibrium. In such systems error correction can occur…
We consider a model of bilayer lipid membrane with bola-lipids. The bola-lipid is modeled by linking tails of the hydrophobic chains in the opposite monolayers within bilayer as a first approximation. A number of thermodynamical…
Under an external field a double-stranded peptide chain can separate in a fragile or ductile transition. It is usually believed that these two regimes are driven either by chemical and thermal fields, or through non-local mechanical…
The powerful molecular dynamics (MD) simulation is basically based on a picture that the atoms experience classical-like trajectories under the exertion of classical force field determined by the quantum mechanically solved electronic…
Classical and path integral molecular dynamics (PIMD) simulations are used to study alpha-quartz and beta-quartz in a large range of temperatures at zero external stress. PIMD account for quantum fluctuations of atomic vibrations, which can…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the…
A multiphysics modeling approach for heat conduction in metal hydride powders is presented, including particle shape distribution, size distribution, granular packing structure, and effective thermal conductivity. A statistical geometric…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
The melting of a binary system of charged particles confined in a {\it quasi}-one-dimensional parabolic channel is studied through Monte Carlo simulations. At zero temperature the particles are ordered in parallel chains. The melting is…
A two-dimensional (2D) model is developed to describe the growth of spotty patterns (domains) in the lipid membranes which result from the coagulation of ion channels. It is assumed that the ion channels can coagulate when activated, e.g.…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…