Related papers: Ab initio study of alanine polypeptide chains twis…
Suspensions of Active Brownian Particles (ABP) undergo motility induced phase separation (MIPS) over a wide range of mean density and activity strength [1], even in the absence of an explicit attraction. Negative values of the mechanical…
A polarizable force-field (FF) model for short- and long-alkane chains and amide derivatives was constructed based solely on accurate quantum chemical (QC) calculations. First, the FF model accuracy was accessed by performing molecular…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
We analyze a model statistical description of the polypeptide chain helix-coil transition, where we take into account the specificity of its primary sequence, as quantified by the phase space volume ratio of the number of all accessible…
Monte Carlo computer simulations are used to study the conformational free energy of a folded polymer confined to a long cylindrical tube. The polymer is modeled as a hard-sphere chain. Its conformational free energy $F$ is measured as a…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
In order to better understand the occurrence of phase transitions, we adopt an approach based on the study of energy landscapes: The relation between stationary points of the potential energy landscape of a classical many-particle system…
Within self-consistent field theory we study the phase behavior of a symmetrical binary AB polymer blend confined into a thin film. The film surfaces interact with the monomers via short range potentials. One surface attracts the A…
We present a study of the potential energy surface (PES) of anthracene, tetracene and pentacene clusters with up to 30 molecules. We have applied the basin-hopping Monte Carlo (BHMC) algorithm to clusters of acene molecules in order to find…
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…
Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased Molecular…
Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and…
We present efficient angle-dependent low-energy Hamiltonians to describe the properties of the twisted bilayer graphene (tBLG) heterostructure, based on {\it ab initio} calculations of mechanical relxation and electronic structure. The…
We study the relaxations, surface energies, and work functions of low index metallic surfaces using pseudopotential plane-wave density-functional calculations within the generalized gradient approximation. We study here the (100), (110),…
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…
We present a theoretical study of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not…
We present a scaled particle density functional study of two-dimensional binary mixtures of hard convex particles with one or both species being ellipses. In particular, we divide our study into two parts. The first part is devoted to the…
We study the binding pattern of the amino acid alanine on the naturally chiral Pt surfaces Pt(531), Pt(321) and Pt(643). These surfaces are all vicinal to the {111} direction but have different local environments of their kink sites and are…
We have carried out a detailed study of the chemical bonding for two room-temperature stable platinum silicide phases, tetragonal alpha-Pt_2Si and orthorhombic PtSi. An analysis of the valence electronic charge density reveals surprising…
Characterization of protein energy landscape and conformational ensembles is important for understanding mechanisms of protein folding and function. We studied ensembles of bound and unbound conformations of six proteins to explore their…