Related papers: Exploring the Protein G Helix Free Energy Surface …
An equilibrated model glass-forming liquid is studied by mapping successive configurations produced by molecular dynamics simulation onto a time series of inherent structures (local minima in the potential energy). Using this ``inherent…
Rapid advances in additive manufacturing over the past decade have kindled widespread interest in the rational design of metamaterials with unique properties. However, many applications require multi-physics metamaterials, where multiple…
The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
In contrast to the well-known destabilization of globular proteins by high pressure, re- cent work has shown that pressure stabilizes the formation of isolated {\alpha}-helices. However all simulations to date have obtained a qualitatively…
Simulations of protein folding and protein association happen on timescales that are orders of magnitude larger than what can typically be covered in all-atom molecular dynamics simulations. Use of low-resolution models alleviates this…
Two proteins, one belonging to the mainly alpha class and the other belonging to the alpha/beta class, are selected to test a kinetic mechanism for protein folding. Targeted molecular dynamics is applied to generate folding pathways for…
Under dehydration conditions, amphipathic Late Embryogenesis Abundant (LEA) proteins fold spontaneously from a random conformation into alpha-helical structures and this transition is promoted by the presence of membranes. To gain insight…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure.…
While recent advances in AI have transformed protein structure prediction, protein function is also strongly influenced by the thermodynamic and kinetic features encoded in its underlying free-energy surface. Here, we propose a…
We calculate thermodynamic quantities of HP lattice proteins by means of a multicanonical chain growth algorithm that connects the new variants of the Pruned-Enriched Rosenbluth Method (nPERM) and flat histogram sampling of the entire…
Relations between the thermodynamics and dynamics of supercooled liquids approaching a glass transition have been proposed over many years. The potential energy surface of model liquids has been increasingly studied since it provides a…
FeTi-based hydrides have recently re-attracted attention as stationary hydrogen storage materials due to favorable reversibility, good sorption kinetics and relatively low costs compared to alternative intermetallic hydrides. Employing the…
We refine a protein model that reproduces fundamental aspects of protein thermodynamics. The model exhibits two transitions, hot and cold unfolding. The number of relevant parameters is reduced to three: 1) binding energy of folding…
Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling…
We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a non-equilibrium umbrella sampling method, in this case the recently developed…
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…
We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…