Related papers: Side chain and backbone ordering in a polypeptide
We have investigated the potential energy surfaces for glycine 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…
Recent advances in computational power and simulation programs finally delivered the first examples of reversible folding for small proteins with an all-atom description. But having at hand the atomistic details of the process did not lead…
Two-leg spin ladders have a rich phase diagram if rung, diagonal and plaquette couplings are allowed for. Among the possible phases there are two Haldane-type spin liquid phases without local order parameter, which differ, however, in the…
We study the problem of adsorption and collapse transition of a linear polymer chain situated in a fractal container represented by a 4-simplex lattice and interacting with a surface adsorbed linear polymer chain. The adsorbed chain…
Topology is being widely adopted to understand and to categorize quantum matter in modern physics. The nexus of topology orders, which engenders distinct quantum phases with benefits to both fundamental research and practical applications…
We introduce a framework for model reduction of chain models for dissipative particle dynamics (DPD) simulations, where the characteristic size of the chain, pressure, density, and temperature are preserved. The proposed methodology reduces…
We have performed Monte Carlo simulations to investigate the temperature dependence of the ordering of the side chains of the X-shape liquid crystal molecules which are arranged in a hexagonal array. Each hexagon contains six side chains,…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
We have carried out a quantitative analysis of the chain packing in polymeric melts using molecular dynamics simulations. The analysis involves constructing Voronoi tessellations in the equilibrated configurations of the polymeric melts. In…
Focusing on a small set of proteins that i) fold in a concerted, all-or-none fashion and ii) do not contain knots or slipknots, we show that the Gauss linking integral, the torsion and the number of sequence-distant contacts provide…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
By Molecular Dynamics simulation of a coarse-grained bead-spring type model for a cylindrical molecular brush with a backbone chain of $N_b$ effective monomers to which with grafting density $\sigma$ side chains with $N$ effective monomers…
Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing…
The folding kinetics of three-dimensional lattice Go models with side chains is studied using two different Monte Carlo move sets. A flexible move set based on single, double and triple backbone moves is found to be far superior compared to…
In this work we used dissipative particle dynamics simulations to study the copolymerization process in the presence of spatial heterogeneities caused by incompatibility between polymerizing monomers. The polymer sequence details as well as…
The equilibrium thermodynamic properties of a linear polymer chain confined to a space between two impenetrable walls (lines) at a distance $D$ under various solvent conditions have been studied using series analysis and exact enumeration…
We present the exact solution of a microscopic statistical mechanical model for the transformation of a long polypeptide between an unstructured coil conformation and an $\alpha$-helix conformation. The polypeptide is assumed to be adsorbed…
The folding of a peptide chain into a three dimensional structure is a thermodynamically driven process such that the chain naturally evolves to form domains of similar amino acids. The formation of this domain occurs by curling the one…
We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…
Multiblock copolymer chains in implicit nonselective solvents are studied by Monte Carlo method which employs a parallel tempering algorithm. Chains consisting of 120 $A$ and 120 $B$ monomers, arranged in three distinct microarchitectures:…