Related papers: Exploring the Protein G Helix Free Energy Surface …
Free-energy landscape theory is often used to describe complex molecular systems. Here, a microscopic description of water structure and dynamics based on configuration-space-networks and molecular dynamics simulations of the TIP4P/2005…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
We study the free energy and dynamics of a closed elastic filament (a one-dimensional curve in two dimensions) whose local internal state is specified by curvature, stretch, and a scalar density field representing, for example, the…
We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are…
In this work, we study the dynamics of complex systems with time-dependent transition rates, focusing on $p$-adic analysis in modeling such systems. Starting from the master equation that governs the stochastic dynamics of a system with a…
The concept of a protein diffusing in its free energy folding landscape has been fruitful for both theory and experiment. Yet the choice of the reaction coordinate (RC) introduces an undesirable degree of arbitrariness into the problem. We…
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…
The results of minimal model calculations suggest that the stability and the kinetic accessibility of the native state of small globular proteins are controlled by few "hot" sites. By mean of molecular dynamics simulations around the native…
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…
The self-assembly of proteins into $\beta$-sheet-rich amyloid fibrils has been observed to occur with sigmoidal kinetics, indicating that the system initially is trapped in a metastable state. Here, we use a minimal lattice-based model to…
Simple classical thermodynamic approach to the general description of metastable states is presented. It makes possible to calculate the explicit dependence of the Gibbs free energy on temperature, to calculate the heat capacity, the…
We introduce a simple and predictive model for determining the phase stability of ternary phospholipid-cholesterol mixtures. Assuming that competition between the liquid and gel order of the phospholipids is the main driving force behind…
A coarse grained model of a random polypeptide chain, with only discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues is shown to display stretched exponential relaxation under Metropolis…
A fundamental challenge in protein design is the trade-off between generating structural diversity while preserving motif biological function. Current state-of-the-art methods, such as partial diffusion in RFdiffusion, often fail to resolve…
Due to the development of efficient algorithms and the improvement of computer power it is now possible to map out potential energy surfaces (PES) of reactions at surfaces in great detail. This achievement has been accompanied by an…
Recent analysis of well-tempered metadynamics (WTmetaD) showed that it converges without mollification artifacts in the bias potential. Here we explore how metadynamics heals mollification artifacts, how healing impacts convergence time,…
Atomistic simulations are employed to demonstrate the existence of a well-defined thermodynamic phase transformation between grain boundary (GB) phases with different atomic structures. The free energy of different interface structures for…
The study of free piston Stirling engine (FPSE) requires both accurate thermodynamic and dynamic modelling to predict its performances. The steady state behaviour of the engine partly relies on non linear dissipative phenomena such as…
The high-temperature properties of the Al(111) surface are studied by molecular-dynamics simulation. This surface does not melt below the bulk melting point, but can be superheated. Superheating of metal surfaces has been recently observed…