Related papers: Folding kinetics of a polymer [corrigendum]
We investigate by Monte Carlo simulations the zipping and unzipping dynamics of two polymers connected by one end and subject to an attractive interaction between complementary monomers. In zipping, the polymers are quenched from a high…
We apply density functional theory to study the freezing of superfluid {$^{4}\rm{He}$}, charged bosons and charged fermions at zero temperature. We employ accurate Quantum Monte Carlo data for the linear response function in the uniform…
We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…
The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…
By taking advantage of the molecular weight dependence of the glass transition of polymers and their ability to form perfectly miscible blends, we propose a way to modify the fragility of a system, from fragile to strong, keeping the same…
Using the AdS/CFT correspondence, we probe the scale-dependence of thermalization in strongly coupled field theories following a quench, via calculations of two-point functions, Wilson loops and entanglement entropy in d=2,3,4. In the…
Dynamics of a polymer chain in solution gets significantly affected by the temperature and the frictional forces arising due to solvent viscosity. Here, using an explicit solvent framework for polymer simulation with the liberty to tune the…
We study the Renyi entropy in the finite temperature crossover regime of a Hubbard chain using quantum Monte Carlo. The ground state entropy has characteristic features such as a logarithmic divergence with block size and $2\kF$…
Purpose - This paper presents a first step toward developing a comprehensive methodology for fully resolved numerical simulations of fusion deposition modeling. Design/methodology/approach - A front-tracking/finite volume method previously…
We use Monte Carlo simulations to study polymer melts consisting of fully flexible and moderately stiff chains in the bond fluctuation model at a volume fraction $0.5$. In order to reduce the local density fluctuations, we test a…
Using density functional theory in a time dependent approach we determine the frequencies of the compressional modes of the normal phase of a Fermi gas at unitarity as a function of its polarization. Our energy functional accounts for the…
The potential of mean force (PMF) between two nano crystals (NCs) represents an effective interaction potential that can be used to study the assembly of NCs to various superstructures. For a given temperature, the effective interaction is…
The widely used double-bridging hybrid (DBH) method for equilibrating simulated entangled polymer melts [R. Auhl et al., J. Chem. Phys. v. 119, p. 12718, 2003] loses its effectiveness as chain stiffness increases into the semiflexible…
We propose a new mathematical tool for the study of transport properties of models for lattice vibrations in crystalline solids. By replication of dynamical degrees of freedom, we aim at a new dynamical system where the "local" dynamics can…
We analyze structural and conformational properties in a simulated bead-spring model of a non-entangled, supercooled polymer melt. We explore the statics of the model via various structure factors, involving not only the monomers, but also…
We theoretically investigate the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decrease with an increase in the number of monomers in a collapsed domain, suggesting that the…
We study numerically a lattice model of semiflexible homopolymers with nearest neighbor attraction and energetic preference for straight joints between bonded monomers. For this we use a new algorithm, the "Pruned-Enriched Rosenbluth…
Entanglement entropy under a particle bipartition provides complementary information to mode entanglement as it is sensitive to interactions and particle statistics at leading order and does not depend on any externally imposed length…
We have developed a new multiscale simulation technique to investigate history-dependent flow behavior of entangled polymer melt, using a smoothed particle hydrodynamics simulation with microscopic simulators that account for the dynamics…
It has been revealed by mean-field theories and computer simulations that the nature of the collapse transition of a polymer is influenced by its bending stiffness $\epsilon_{\rm b}$. In two dimensions, a recent analytical work demonstrated…