Related papers: Cooperative melting in double-stranded peptide cha…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
The melting of a binary system of charged particles confined in a {\it quasi}-one-dimensional parabolic channel is studied through Monte Carlo simulations. At zero temperature the particles are ordered in parallel chains. The melting is…
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…
A double-stranded system, modeled by a Frenkel-Kontorova lattice, is studied through nonequilibrium molecular dynamics simulations. We have investigated the thermal conductance influenced by the intra-chain interaction as well as by the…
Biological adhesion is a critical mechanical function of complex organisms operating at multiple scales. At the cellular scale, cell-cell adhesion is remarkably tunable to enable both cohesion and malleability during development,…
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered…
We uncover the dynamics of particles with Gaussian core interactions across melting in pure and disordered two-dimensional (2D) systems. Intriguing signatures of cooperative motion of particles in string-like paths are found at low…
We present a solvable model that predicts the folding kinetics of two-state proteins from their native structures. The model is based on conditional chain entropies. It assumes that folding processes are dominated by small-loop closure…
Single particle states in a chain with quasiperiodic potential show a metal-insulator transition upon the change of the potential strength. We consider two particles with local interaction in the single particle insulating regime. The two…
We study the influence of quenched disorder on the two-dimensional melting behavior by using both video-microscopy of superparamagnetic colloidal particles and computer simulations of repulsive parallel dipoles. Quenched disorder is…
Recently, a simple non-interacting-electron model, combining local quantum tunneling via quantum point contacts and global classical percolation, has been introduced in order to describe the observed ``metal-insulator transition'' in two…
A new phenomenon, called cooperative internal conversion process, in which the coupling of bound-free electron and neutron transitions due to the dipole term of their Coulomb interaction permits cooperation of two nuclei leading to neutron…
Atomistic (atom-scale) and coarse-grained (meso-scale) simulations of structure and dynamics of poly-isoprene melts are compared. The local structure and chain packing is mainly determined by the atomistic details of the polymer…
The mechanical behaviors of polycrystalline solids are determined by the interplay between phenomena governed by two different thermodynamic temperatures: the configurational effective temperature that controls the density of dislocations,…
We study the statistical mechanics of double-stranded semi-flexible polymers using both analytical techniques and simulation. We find a transition at some finite temperature, from a type of short range order to a fundamentally different…
Melting kinetics of polycrystalline materials is analyzed on the basis of a new model which explicitly couples homogeneous and heterogeneous melting mechanisms. The distinct feature of this approach lies in its ability to evaluate not only…
Collapse of the polypeptide backbone is an integral part of protein folding. Using polyglycine as a probe, we explore the nonequilibrium pathways of protein collapse in water. We find that the collapse depends on the competition between…
We elucidate the physics of the dynamical transition via 10-100ns molecular dynamics simulations at temperatures spanning 160-300K. By tracking the energy fluctuations, we show that the protein dynamical transition is marked by a cross-over…
When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates roughly twice its initial contour length at a pulling force about 70 pN. The transition to this highly overstretched form of DNA is very…
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…