Related papers: Predicting Non-Equilibrium Folding Behavior of Pol…
Molecular dynamics computer simulations are used to study the aging dynamics of SiO2 (modeled by the BKS model). Starting from fully equilibrated configurations at high temperatures T_i =5000K/3760K the system is quenched to lower…
An algorithm to calculate the density of states, based on the well-known Wang-Landau method, is introduced. Independent random walks are performed in different restricted ranges of energy, and the resultant density of states is modified by…
Cells use genetic switches to shift between alternate stable gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Conceptually, these stable phenotypes can be considered as attractive states on an…
We study flexible polymer macromolecules in a crowded (porous) environment, modelling them as self-attracting self-avoiding walks (SASAW) on site-diluted percolative lattices in space dimensions d=2, 3. The influence of stretching force on…
We present a new approach to treat correlations in nonequilibrium quantum many-particle system. The method is based on ideas of configuration interaction theory of exact nonperturbative ground state electronic structure calculations. We use…
In this paper, explicit method of constructing approximations (the Triangle Entropy Method) is developed for nonequilibrium problems. This method enables one to treat any complicated nonlinear functionals that fit best the physics of a…
Many-body quantum-mechanical stationary states that have real valued wavefunctions are shown to satisfy a classical conservation of energy equation with a kinetic energy function. The terms in the equation depend on the probability…
We build a predictive theory for the evolution of mixture of helium and supercooled helium at low temperature. The absolute temperature and the volume fraction of helium, which is dominant at temperature larger than the phase change…
We study the unfolding of a single polymer chain due to an external force. We use a simplified model which allows to perform all calculations in closed form without assuming a Boltzmann-Gibbs form for the equilibrium distribution.…
We present a new approach for predicting stable equilibrium shapes of crystalline islands on flat substrates, as commonly occur through solid-state dewetting of thin films. The new theory is a generalization of the widely used Winterbottom…
The three-dimensional bimodal random-field Ising model is studied via a new finite temperature numerical approach. The methods of Wang-Landau sampling and broad histogram are implemented in a unified algorithm by using the N-fold version of…
Self-consistent field theory (SCFT) is one of the most widely-used framework in studying the equilibrium phase behaviors of inhomogenous polymers. For liquid crystalline polymeric systems, the main numerical challenges of solving SCFT…
Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…
Accurate phase diagram calculation from molecular dynamics requires systematic treatment and convergence of statistical averages. In this work we propose a Gaussian process regression based framework for reconstructing the free energy…
A mesoscopic, mixed particle- and field-based Brownian dynamics methodology for the simulation of entangled polymer melts has been developed. Polymeric beads consist of several Kuhn segments, and their motion is dictated by the Helmholtz…
An alternative approach - nonequilibrium evolution thermodynamics, is compared with classical Landau approach. A statistical justification of the approach is carried out with help of probability distribution function on an example of a…
We study the energy distribution during the emergence of a quasi-equilibrium (QE) state in the course of relaxation to equipartition in slow-fast Hamiltonian systems. A bead-spring model where beads (masses) are connected by springs is…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
Entanglement entropy (EE) of a state is a measure of correlation or entanglement between two parts of a composite system and it may show appreciable change when the ground state (GS) undergoes a qualitative change in a quantum phase…
Molecular dynamics simulations are used to generate an ensemble of saddles of the potential energy of a Lennard-Jones liquid. Classifying all extrema by their potential energy u and number of unstable directions k, a well defined relation…