Related papers: Conformational changes in glycine tri- and hexapep…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
Molecular dynamics simulations are carried out to explore the dynamical crossover phenomenon in strongly confined and mildly supercooled water in graphene oxide nanopores. In contrast to studies where confinement is used to study the…
The force laws governing the extension behavior of homopolypeptides are obtained from a phenomenological free energy capable of describing the helix-coil transition. Just above the melting temperature of the free chains, T*, the plot of…
In this paper, we have studied the energy spectra and B(E2) transition probabilities of 124-130Ba isotopes in the shape phase transition region between the spherical and gamma unstable deformed shapes. We have used a transitional…
The free-energy landscape of two peptides is evaluated at various temperatures and an estimate for its fractal dimension at these temperatures calculated. We show that monitoring this quantity as a function of temperature allows to…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
We show that a protein can be trained to recognise multiple conformations, analogous to an associative memory, and provide capacity calculations based on energy fluctuations and information theory. Unlike the linear capacity of a Hopfield…
One of the major challenges towards understanding and further utilizing the properties and functional behaviors of grain boundaries (GB) is the complexity of general GBs with mixed tilt and twist characters. Here, we report the correlations…
Twisted graphene layers exhibit extremely low friction for relative sliding. Nevertheless, previous studies suggest that the area contribution to friction for commensurate moir\'e systems is finite and might restrict macroscopic…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
We study several models of staircase polygons on the $45^\circ$ rotated square lattice, which interact with an impenetrable surface while also being pushed towards or pulled away from the surface by a force. The surface interaction is…
In the present work, we discuss how the functional form of thermodynamic observables can be deduced from the geometric properties of subsets of phase space. The geometric quantities taken into account are mainly extrinsic curvatures of the…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
Monte Carlo simulations are used to study the conformational properties of a folded semiflexible polymer confined to a long channel. We measure the variation in the conformational free energy with respect to the end-to-end distance of the…
We investigate the formation of polycrystalline structures in a class of particle systems. The atomistic energy is modeled as a sum of particle energies that favor atoms being locally isometric to a reference lattice. The discrete frame…
Using molecular dynamic simulations we study three families of continuous core-softened potentials consisting of two length scales: a shoulder scale and an attractive scale. All the families have the same slope between the two length scales…
Semiflexible polymers in poor solvents exhibit a rich variety of collapsed morphologies, including globules, toroids, and rodlike bundles, arising from the competition between attractive interactions and chain stiffness. Computer…
The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with the ability for hydrogen bonding with solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide…
A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate…