The atomic stick-slip behavior of a Pt tip sliding on a Au(111) surface is studied with atomic force microscopy (AFM) experiments and accelerated (i.e., reduced sliding speed) molecular dynamics (MD) simulations. The MD and AFM conditions are controlled to match, as closely as possible, the geometry and orientation, load, temperature, and compliance. We observe clear stick-slip without any dama...

Over the past 20 years, molecular simulation methods have been applied to the modeling of reversed-phase liquid chromatography (RPLC). The purpose of these simulations was to provide a molecular-level understanding of: (i) the structure and dynamics of the bonded phase and its interface with the mobile phase, (ii) the interactions of analytes with the bonded phase, and (iii) the retention mecha...

We study the impact of wall corrugations in microchannels on the process of capillary filling by means of three broadly used methods: computational fluid dynamics (CFD), lattice Boltzmann equations (LBE), and molecular dynamics (MD). The numerical results of these approaches are compared and tested against the Concus-Finn (CF) criterion, which predicts pinning of the contact line at rectangular...

Carbonate anion exchange reactions with water in the uranyl-carbonate and calcium-uranyl-carbonate aqueous systems have been investigated using computational methods. Classical molecular dynamics (MD) simulations with the umbrella sampling technique were employed to determine potentials of mean force for the exchange reactions of water and carbonate. The presence of calcium counter-ions is pred...

The cationic amphiphilic lipid type compound 1,1’-{[3,5-bis(dodecyloxycarbonyl)-4-phenyl-1,4dihydropyridin-2,6-diyl]dimethylene} bispyridinium dibromide (1,4-DHP lipid) (charge +2), is a gene transfection agent. The electronic structure of 1,4-DHP lipid molecule was investigated by ab initio quantum mechanics, the charges were derived, and the supramolecular structure formed by 1,4-DHP lipid mo...

The charge-induced unfolding and refolding of unsolvated cytochrome c have been studied by molecular dynamics (MD) simulations. Simulations were performed for protonated charge states between +3 and +19. The charge-induced unfolding of cytochrome c in the gas phase has previously been examined by ion mobility measurements. The main features of the experimental results are reproduced by the MD s...

The isotope effect and excitation-energy dependence have been measured in the oxygen K-edge x-ray emission spectrum (XES). The use of XES to monitor core decay processes provides information about molecular dynamics (MD) on an ultrafast time scale through the O1s lifetime of a few femtoseconds. Different nuclear masses give rise to differences in the dynamics and the observed isotope effect in ...

Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic level of detail, but they have been limited to time scales shorter than those of many biologically critical conformational changes. We examined two fundamental processes in protein dynamics--protein folding and conformational change within the folded state--by means of extremely long all-atom MD simulation...

FPGA-centric clusters use FPGAs for both computation and communication and thereby address three fundamental problems of future High Performance Clusters: efficient use of silicon, power, and removing communication bottlenecks. In this study we report on the plausibility of using such clusters for Molecular Dynamics simulations, in particular by determining the communication requirements for su...

We study the tagged-particle dynamics by solving equations of the mode-coupling theory (MCT). The numerical solutions are compared with results obtained by the molecular dynamics (MD) simulations from a unified point of view proposed by Tokuyama [Phys. Rev. E 80, 031503 (2009)]. We propose a way of comparison in which the reduced long-time self-diffusion coefficient is used to characterize stat...