Related papers: Hydrogen Bonds in Polymer Folding
A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative…
We consider a lattice model of a semiflexible homopolymer chain in a bad solvent. Beside the temperature $T$, this model is described by (i) a curvature energy $\varepsilon_h$, representing the stiffness of the chain (ii) a…
In order to identify potential hydrogen storage materials, worldwide attention has been focused on hydrides with high gravimetric and volumetric capacity. Hydrogen is a unique element that possess positive, negative or neutral oxidation…
Sequence heterogeneity broadens the binding transition of a polymer onto a linear or planar substrate. This effect is analyzed in a real-space renormalization group scheme designed to capture the statistics of rare events. In the strongly…
We analyze the interaction of two conducting, charged polymer chains in solution using a minimal model for their electronic degrees of freedom. We show that a crossing of the two chains in which the polymers pass within Angstroms of each…
We investigate theoretically the effect of polymer tension on the collective behavior of reversibly binding cross-links. For this purpose, we employ a model of two weakly bending wormlike chains aligned in parallel by a tensile force, with…
Conjugated polymers are soft, one-dimensional conductors that admit complex interactions between their polymeric, conformational degrees of freedom and their electronic ones. The presence of extended electronic states along their backbone…
The density of states contains all informations on energetic quantities of a statistical system, such as the mean energy, free energy, entropy, and specific heat. As a specific application, we consider in this work a simple lattice model…
Relevant information about the nature of the dynamics of ions in electrolytes can be obtained by studying the nonlinear dependence on an applied electric field. Here we use molecular dynamics (MD) simulations to study the field effects for…
Self-mated hydrogel contacts show extremely small friction coefficients at low loads but a distinct velocity dependence. Here we combine mesoscopic simulations and experiments to test the polymer-relaxation hypothesis for this velocity…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
Hydrogel consists of a crosslinked polymer matrix imbibed with a solvent such as water at volume fractions that can exceed 90\%. They are important in many scientific and engineering applications due to their tunable physiochemical…
The kinetic behavior of a three-dimensional off-lattice heteropolymer model is studied in terms of the time dependence of the average mean-square displacement between configurations. It is found that at short time-scales similar behavior is…
Hydrogen exhibits quantum phenomena, such as tunneling in materials. According to theory, the quantum properties of hydrogen change significantly in superconductors due to the emergence of an energy gap on the Fermi surface, which reduces…
A lattice model of a hetero-polymer with random hydrophilic-hydrophobic charges interacting with the solvent is introduced, whose continnuum counterpart has been proposed by T. Garel, L. Leibler and H. Orland {J. Phys. II France 4, 2139…
The shear-jamming of dense suspensions can be strongly affected by molecular-scale interactions between particles, e.g. by chemically controlling their propensity for hydrogen bonding. However, hydrogen bonding not only enhances…
Equations of state for hydrogen bonding fluids are typically described by two energy scales. A short range highly directional hydrogen bond energy scale, as well as a reference energy scale which accounts for dispersion and orientationally…
We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the…
The resistance of hydrogen-bond networks to ambient flow in water produces viscoelectric stresses and contributes to electrostrictive pressure. Within Onsager's nonequilibrium thermodynamic framework, a lattice-gas description of aqueous…
Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free…