molecular dynamics – Page 8 – TechConnect Briefs

Molecular Simulation of DNA Microarrays – an Application of 2D particle mesh Ewald algorithm

Watanabe T., Kawata M., Nagashima U., National Institute of Advanced Industrial and Science and Technology, JP

We have developed the two-dimensional particle mesh Ewald (2D-PME) algorithm for molecular dynamics (MD) simulation, and applied it to have knowledge of the behavior of DNA and its interaction on microarrays, which crucial in the [...]

Water-Carbon Interactions: Potential Energy Calibration Using Experimental Data

Werder T., Walther J.H., Jaffe R.l., Koumoutsakos P., NASA Ames Research Center, US

Functionalized carbon nanotubes (CNT) are being studied for use as nanoscale biosensors and water or proton channels. Several molecular dynamics (MD) studies of water in carbon nanotubes have recently been performed to gain further insight [...]

A Comparison of Straight- and Branch-Chained Lipid Bilayers for the Static and Dynamic Properties: A molecular dynamics study

Shinoda W., Mikami M., Baba T., Hato M., National Institute of Advanced Industrial Science & Technology, JP

A bilayer composed of branched chain lipid molecules is generally believed to have high bilayer stability and low ion leakage. To understand how the chain branching affects the bilayer properties on the molecular level, two [...]

Coarse-Grained Molecular Dynamics for Nano-Design

Rudd R.E., Lawrence Livermore National Laboratory, US

The design of nanoscale mechanical systems poses a novel set of challenges for modeling and simulation. The need for an accurate model of the nanoscale components is clear. This can be of the form of [...]

Single-molecule Fluorescence and Force Microscopy Employing Carbon Nanotubes

Wade L.A., Shapiro I., Ma Z., Quake S.R., Collier C.P., California Institute of Technology, US

The observation of spectroscopic signals, in response to mechanically induced changes in biological macromolecules can be enabled at an unprecedented level of resolution by coupling single-molecule manipulation/sensing using carbon nanotubes with single-molecule fluorescence imaging. Proteins, [...]

Ab Initio Simulation on Deposit Process of Al on Si Surface

Umeno Y., Kitamura T., Kyoto University, JP

It is important to clarify structure of contact between different materials for evaluation of properties of interfaces, which are substantial in electronic devices. Since interaction between different materials has to be evaluated based on the [...]

Molecular Dynamics Simulation of Timescale Effect and Lattice Transformation of Copper Nanorod Under Bending

Wu H.A., Wang X.X., Liu G.R., National University of Singapore, SG

Mechanical behaviors of materials and structures at nanoscale are essentially different from those at macroscale, resulting from surface effect, size effect and time scale effect. In some experimental research at nanoscale, the bending displacement of [...]

Melting of Ultrathin Copper Nanobridges

Kang J-W, Hwang H-J., Chung-Ang University, KR

The previous studies on nanoclusters and infinite nanowires have shown the physical phenomena related to only the melting of nanoclusters and nanowires. This study showed the various physical phenomena of ultrathin nanobridges, such as the [...]

Fast, Accurate Molecular Dynamics Simulations for Surfaces and Membranes

Kawata M., Nagashima U., National Institute of Advanced Industrial Science and Technology, JP

We have developed new fast method for calculating the accurate Coulomb interactions for quasi-2D systems and implemented in the MD calculations. We present the details of the computational steps to implement the 2D-PME method, focusing [...]

Calculation of Shock Waves and Temperatures of FCC Single Crystals (Nickel) using Large-Scale Molecular Dynamics

Kum O., Clemson University, US

Multimillion-atom molecular dynamics simulations using double-SPMD (SPSPMD) have been applied to calculate fcc single crystal, Nickel, shock wave and temperature profiles on a CrayT3E. Three well known model potentials, analytical EAM, Morse type simple pair, [...]