Related papers: Temperature- and Force-Induced beta-Sheet Unfoldin…
We present the exact solution of a microscopic statistical mechanical model for the transformation of a long polypeptide between an unstructured coil conformation and an $\alpha$-helix conformation. The polypeptide is assumed to be adsorbed…
We investigate freely cooling systems of rough spheres in two and three dimensions. Simulations using an event driven algorithm are compared with results of an approximate kinetic theory, based on the assumption of a generalized homogeneous…
The plastic deformation of Polybutylene terephthalate (PBT) is investigated at three temperatures (120$^\circ$C, 150$^\circ$C, 180$^\circ$C) representative of the span between glass transition, $T_g \approx 55^\circ$C and melting $T_m…
We consider the adsorption of a random heteropolymer onto an interface within the model by Garel et al. [1] by taking into account self-interactions between the monomers. Within the replica trick and by using a self-consistent preaveraging…
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…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Using large scale quantum Monte Carlo simulations of lattice bosonic models, we precisely investigate the effect of weak Josephson tunneling between 2D superfluid or superconducting layers. In the clean case, the Kosterlitz-Thouless…
Contact inhibition is the process by which cells switch from a motile growing state to a passive and stabilized state upon touching their neighbors. When two cells touch, an adhesion link is created between them by means of transmembrane…
A quasi 2-dimensional recursive lattice formed by planar elements have been designed to investigate the surface thermodynamics of Ising spin glass system with the aim to study the metastability of supercooled liquids and the ideal glass…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…
By means of Metropolis Monte Carlo simulations of a coarse-grained model for flexible polymers, we investigate how the integrated autocorrelation times of different energetic and structural quantities depend on the temperature. We show…
We calculate the location of the quantum phase transitions of a bose gas trapped in an optical lattice as a function of effective scattering length $a_{\eff}$ and temperature $T$. Knowledge of recent high-loop results on the shift of the…
The buckling of thin elastic sheets is a classic mechanical instability that occurs over a wide range of scales. In the extreme limit of atomically thin membranes like graphene, thermal fluctuations can dramatically modify such mechanical…
We consider polymers made of magnetic monomers (Ising or Heisenberg-like) in a good solvent. These polymers are modeled as self-avoiding walks on a cubic lattice, and the ferromagnetic interaction between the spins carried by the monomers…
We present simulation results for a model polymer melt, consisting of short, nonentangled chains, in the supercooled state. The analysis focuses on the monomer dynamics, which is monitored by the incoherent intermediate scattering function.…
A discrete model for the sintering of polydisperse, inhomogeneous arrays of cylinders is presented with empirical contact force-laws, taking into account plastic deformations, cohesion, temperature dependence (melting), and long-time…
First-principles calculations are performed for electronic structures of two high pressure phases of solid selenium, $\beta$-Po and bcc. Our calculation reproduces well the pressure-induced phase transition from $\beta$-Po to bcc observed…
Wetting and drying phenomena are studied for flexible and semiflexible polymer solutions via coarse-grained molecular dynamics simulations and density functional theory calculations. The study is based on the use of Young's equation for the…