相关论文: Hydrogen Bonds in Polymer Folding

The phase structure of a homopolymer chain is investigated in terms of a universal theoretical model, designed to describe the infrared limit of slow spatial variations. The effects of chirality are studied and compared with the influence…

We introduce an exactly solvable statistical-mechanical model of the hydration of non-polar compounds, based on grouping water molecules in clusters where hydrogen bonds and isotropic interactions occur; interactions between clusters are…

By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…

Protein-protein binding enables orderly and lawful biological self-organization, and is therefore considered a miracle of nature. Protein-protein binding is steered by electrostatic forces, hydrogen bonding, van der Waals force, and…

We investigated the impact of hydrodynamic interactions (HI) on protein folding using a coarse-grained model. The extent of the impact of hydrodynamic interactions, whether it accelerates, retards, or has no effect on protein folding, has…

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,…

We have performed parallel tempering Monte Carlo simulations using a simple continuum heteropolymer model for proteins. All ten heteropolymer sequences which we have studied have shown first-order transitions at low temperature to ordered…

Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…

The first principles approaches, density functional theory (DFT) and quantum Monte Carlo, have been used to examine the balance between van der Waals (vdW) forces and hydrogen (H) bonding in ambient and high pressure phases of ice. At…

We investigate the dynamics of the collapse of a single copolymer chain, when the solvent quality is suddenly quenched from good to poor. We employ Brownian dynamics simulations of a bead-spring chain model and incorporate fluctuating…

We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal…

Using modified Arrhenius approximations, the activation energies of water, alcohols, and hexane structure rearrangement reactions responsible for temperature dependences of their dynamic and dielectric characteristics were determined. The…

To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…

We investigate numerically the dynamical behaviour of a polymer chain collapsing in a dilute solution. The rate of collapse is measured with and without the presence of hydrodynamic interactions. We find that hydrodynamic interactions both…

Supercooled water exhibits remarkably slow dynamics similar to the behavior observed for various glass-forming liquids. The local order of tetrahedral structures due to hydrogen-bonds (H-bonds) increases with decreasing temperature. Thus,…

We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling (TPS). The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are…

Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…

We propose and solve a simple model describing secondary structure formation in random hetero-polymers. It describes monomers with a combination of one-dimensional short-range interactions (representing steric forces and hydrogen bonds) and…

We explore the consequences of very high dimensionality in the dynamical landscape of protein folding. Consideration of both typical range of stabilising interactions, and folding rates themselves, leads to a model of the energy…

Water is an associated liquid in which the main intermolecular interaction is the hydrogen bond (HB) which is limited to four per atom, independently of the number of neighbours. We have considered a hydrogen bond net superposed on Bernal's…