The present paper aims at evaluating non-classical continuum parameters for each class of armchair and zigzag single-walled CNTs focusing on the scale effect in their flexural behavior observed molecular dynamics (MD) simulations. Through a non-linear optimization approach, bending rigidities obtained from atomistic simulations are compared to those derived continua. For MD simulations, novel m...

Three-dimensional long-range ordered structures in smaller and near-spherically symmetric Coulomb crystals of (40)Ca(+) ions confined in a linear rf Paul trap have been observed when the number of ions exceeds approximately 1,000 ions. This result is unexpected from ground state molecular dynamics (MD) simulations, but found to be in agreement with MD simulations of metastable ion configuration...

Molecular dynamics (MD) simulation and Density functional theory (DFT) methods were applied to the two thiocarbohydrazides derivatives (T1 and T2) as corrosion inhibitors for carbon steel in aqueous phase. Experimental results have shown that the corrosion rate follows the below order: T1>T2. Quantum chemical parameters such as hardness (η), electrophilicity (ω),polarizability (α), dipole momen...

Accurate simulation and control of nanoparticle aggregation in chemical reactors requires that population balance equations be solved by using realistic expressions for aggregation and breakage rate kernels. Obtaining such expressions requires that atomistic simulation approaches that can account for microscopic details of particle collisions be used. In principle, molecular dynamics simulation...

The hydration free energies, structures, and dynamics of open- and closed-shell trivalent lanthanide and actinide metal cations are studied using molecular dynamics simulations (MD) based on a polarizable force field. Parameters for the metal cations are derived from an ab initio bottom-up strategy. MD simulations of six cations solvated in bulk water are subsequently performed with the AMOEBA ...

Molecular dynamics (MD) solves a system of ordinary differential equations governing the motion of the particles (atoms) in a system [2]. MD is very useful in many applications. In a biomolecular system such as solvated proteins, for example, one can use MD to study the coordinated motion of the side chains, the closing and opening of certain binding domains, the diffusion of small molecules in...

We describe methods to perform replica exchange molecular dynamics (REMD) simulations asynchronously (ASyncRE). The methods are designed to facilitate large scale REMD simulations on grid computing networks consisting of heterogeneous and distributed computing environments as well as on homogeneous high-performance clusters. We have implemented these methods on NSF (National Science Foundation)...

We are developing the MDGRAPE-4, a special-purpose computer system for molecular dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations through the integration of general-purpose cores, dedicated pipelines, memory banks and network interfaces (NIFs) to create a system on chip (SoC). Each SoC has 64 dedicated pipelines that are used for non-bond...

Lactose permease of Escherichia coli (LacY) catalyzes symport of a galactopyranoside and an H⁺ via an alternating access mechanism. The transition from an inward- to an outward-facing conformation of LacY involves sugar-release followed by deprotonation. Because the transition depends intimately upon the dynamics of LacY in a bilayer environment, molecular dynamics (MD) simulations may be the o...

The evaluation of molecular dynamics models incorporating temperature control methods is of great importance for molecular dynamics practitioners. In this paper, we study the way in which biomolecular systems achieve thermal equilibrium. In unthermostatted (constant energy) and Nosé-Hoover dynamics simulations, correct partition of energy is not observed on a typical MD simulation timescale. We...