Related papers: Nanosecond chain dynamics of single-stranded nucle…
Large-scale molecular dynamics simulations are used to simulate a layer of nanoparticles diffusing on the surface of a liquid. Both a low viscosity liquid, represented by Lennard-Jones monomers, and a high viscosity liquid, represented by…
Neural network-based molecular dynamics (NNMD) simulations incorporating long-range electrostatic interactions have significantly extended the applicability to heterogeneous and ionic systems, enabling effective modeling critical physical…
Exact numerical methods and stochastic simulation methods are developed to study the force stretching single RNA issue on the secondary structure level in equilibrium. By computing the force-extension curves on the constant force and the…
Experiments measuring contact formation between a probe and quencher in disordered chains provide information on the fundamental dynamical timescales relevant to protein folding, but their interpretation usually relies on simplified…
Using Langevin dynamics complemented by Wang-Landau Monte Carlo simulations, we study the phase behavior of single and multiple semiflexible polymer chains in solution under poor-solvent conditions. In the case of a single chain, we obtain…
Solutions of polymer chains are modelled using non-equilibrium Brownian dynamics simulations, with physically associative beads which form reversible crosslinks to establish a system-spanning physical gel network. Rheological properties…
We present modeling approaches to explain mechanisms of control of uniformity (narrow distribution) of sizes and shapes in synthesis of nanosize crystals and micron-size colloids. We consider those situations when the nanocrystals are…
Structure and reaction studies with a method of antisymmetrized molecular dynamics (AMD) were reviewed. Applications of time-independent and time-dependent versions of the AMD were described. In applications of time-independent AMD to…
We build on the simplified spectral deferred corrections (SDC) coupling of hydrodynamics and reactions to handle the case of nuclear statistical equilibrium (NSE) and electron/positron captures/decays in the cores of massive stars. Our…
We construct and analyze monomeric and multimeric models of the stochastic disassembly of a single nucleosome. Our monomeric model predicts the time needed for a number of histone-DNA contacts to spontaneously break, leading to dissociation…
We modify and extend the recently developed statistical mechanical model for predicting the thermodynamic properties of chain molecules having noncovalent double-stranded conformations, as in RNA or ssDNA, and $\beta-$sheets in protein, by…
In order to predict the long-term effects of irradiation on the material properties of tungsten, a continuum approach to simulating the interactions of dislocation loops, which arise from radiation damage, is proposed. Continuum models of…
We present a thermodynamically robust coarse-grained model to simulate folding of RNA in monovalent salt solutions. The model includes stacking, hydrogen bond and electrostatic interactions as fundamental components in describing the…
Self-positioned nanomembranes such as rolled-up tubes and wrinkled thin films have been potential systems for a variety of applications and basic studies on elastic properties of nanometer-thick systems. Although there is a clear driving…
Molecular Nanomagnets have attracted the attention of the scientific community since the rich physics behind their magnetic behaviour make them ideal test-beds for fundamental concepts in quantum mechanics. Sophisticated experiments and…
We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in {\it Phys. Rev. Lett.} {\bf 94} (2005) 168103). The model consists of a chain of one-flavor base…
Achieving dynamic manipulation and control of single molecules at high spatio-temporal resolution is pivotal for advancing atomic-scale computing and nanorobotics. However, this endeavour is critically challenged by complex nature of atomic…
Asymmetric behaviors of capacitance and charging dynamics in the cathode and anode are general for nanoporous supercapacitors. Understanding this behavior is essential for the optimal design of supercapacitors. Herein, we perform…
A new approach for characterizing the dislocation microstructure obtained from atomistic simulations is introduced, which relies on converting properties of discrete lines to continuous data. This data is represented by a number of density…
The self-assembly of nanocrystals enables new classes of materials whose properties are controlled by the periodicities of the assembly, as well as by the size, shape and composition of the nanocrystals. While self-assembly of spherical…