Related papers: Side chain and backbone ordering in a polypeptide
We consider the semi-infinite (q)-state Potts model. We prove, for large (q), the existence of a first order surface phase transition between the ordered phase and the the so-called "new low temperature phase" predicted in \cite{Li}, in…
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…
We propose a model describing the phase behavior of two-component membranes consisting of binary mixtures of electrically charged and neutral lipids. We take into account the structural phase transition (main-transition) of the hydrocarbon…
In this work, the nonequilibrium pathways of the collapse of the helix-forming biopolymer polyalanine are investigated. To this end, the full time evolution of the helix-coil transition is simulated using molecular dynamics simulations. At…
Surface-induced liquid crystalline phase transitions evoke fundamental interest and can provide deeper insight into the nature of low-dimensional phase transitions. Board-like conjugated polymers are particularly interesting because they…
We demonstrate that ultracold polyatomic symmetric top molecules, such as methyl fluoride, loaded into an optical lattice and subject to DC electric and microwave field dressing, can display topological order via a self-consistent analog of…
Trapped ions are a promising candidate for large scale quantum computation. Several systems have been built in both academic and industrial settings to implement modestly-sized quantum algorithms. Efficient cooling of the motional degrees…
We study the aggregation of peptides using the discrete molecular dynamics simulations. At temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multi-layer parallel beta-sheet…
Microphase separated structure consisting of the periodic alternation of the layers of stretched homopolymer chains surrounded by perpendicularly oriented oligomeric tails is studied for both, strongly bonded (ionic) systems and weakly…
Experimental observations suggest that proteins follow different pathways under different environmental conditions. We perform molecular dynamics simulations of a model of the SH3 domain over a broad range of temperatures, and identify…
The emergence of biochemical activities in a protein seem to commence with the onset of atomic mean-square displacements along the protein lattice. The ensuing protein dynamical transition has been discussed extensively in the literature,…
The interplay of nematic order and phase separation in solutions of semiflexible polymers in solvents of variable quality is investigated by density functional theory (DFT) and molecular dynamics (MD) simulations. We studied coarse-grained…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
We predict that ultracold bosonic dipolar gases, confined within a multilayer geometry, may undergo self-assembling processes, leading to the formation of chain gases and solids. These dipolar chains, with dipoles aligned across different…
It is known that steric blocking by peptide sidechains of hydrogen bonding, HB, between water and peptide groups, PGs, in beta sheets accords with an amino acid intrinsic beta sheet preference. The present observations with Quantum…
The present work continues our previous studies of pom-pom molecule [K. Haydukivska, O. Kalyuzhnyi, V. Blavatska, and J. Ilnytskyi, J. Mol. Liq. 328, 115456 (2021); Condens. Matter Phys. 25, 23302 (2022)]. The molecule consists of a linear…
In a recent work we proposed a coarse-grained methodology for studying the response of peptides when simulated at different values of pH; in this work we extend the methodology to analyze the pH-dependent behavior of coiled coils. This…
Molecular dynamics simulations have been employed to study the formation of a physical (thermoreversible) gel by amphiphilic A-B-A triblock copolymers in aqueous solution. In order to mimic the structure of hydrogel-forming polypeptides…
Phase separation of sequence-disordered liquid crystalline polymers, a promising class of technological and biological relevance, is studied by field theory, and thermodynamic mechanisms responsible for orientational ordering observed in…
The effect of topology on the collapse transition and instantaneous shape of an energy polydisperse polymer (a model heteropolymer) is studied by means of computer simulations. In particular, we consider three different chain topology,…