Papers – Page 970 – TechConnect Briefs

Dimer-method Long Time Scale Simulations of Surface Growth

Henkelman G., University of Washington, US

We have carried out long time scale simulations where the dimer method [G. Henkelman and H. Joonsson, J. Chem. Phys. 111, 7010 (1999)] is used to find the mechanism and estimate the rate of transitions [...]

Temperature Accelerated Dynamics: Introduction and Application to Crystal Growth

Montalenti F., Los Alamos National Laboratory, US

Temperature accelerated dynamics (TAD) simulations allow one to reach long time scales without needing any a priori information on the system dynamics. As a consequence, TAD is a powerful method for simulating complex phenomena where [...]

Introduction to the Time Scale Problem

Voter A.F., Los Alamos National Laboratory, US

As motivation for the symposium on extended-scale atomistic methods, I briefly discuss the time scale problem that plagues molecular dynamics simulations, some promising recent developments for circumventing the problem, and some remaining challenges.

Water Conduction Through Carbon Nanotubes

Hummer G., Rassaiah J.C., Noworyta J.P., National Institutes of Health, US

In molecular dynamics simulations we found that water can form hydrogen-bonded water chains in the interior of carbon nanotubes. Water penetration is sensitive to details of thermodynamic conditions and interaction potentials, resulting in sharp, first-order [...]

DNA Translocation Across Protein Channels: How does a polymer worm through a hole?

Muthukumar M., University of Massachusetts, US

Conformational entropy of a polymer is reduced when the polymer confronts a narrow path. The reduction in entropy and the consequent free energy barriers control the polymer's translocation through narrow channels. Recent results on our [...]

Development of Thermodynamic Methods for the study of Nanopores

Paul R., Paddison S.J., University of Calgary, CA

A statistical mechanical formalism is presented for the calculation of the thermodynamic properties of the water in nanopores of polymer electrolytes, with particular emphasis on the polarization. We describe a method that exploits the variational [...]

Molecular Modeling of Proton Conduction in Polymer Electrolyte Membranes of Nafion® Type

Paddison S.J., Eikerling M., Zawodzinski_Jr. T.A., Pratt L.R., Los Alamos National Laboratory, US

Molecular mechanisms of proton conduction in polymer electrolyte membranes are addressed by ab initio molecular dynamics calculations, utilizing the VASP program, on the model system trifluoromethane sulfonic acid monohydrate solid. After establishing that the experimental [...]

Macromolecules in Microdevices: Multiscale simulation of DNA dynamics in model microfluidic geometries

Jendrejack R.M., de Pablo J.J., Graham M.D., University of Wisconsin-Madison, US

Simple arguments predict that the dynamics of a dissolved macromolecule confined to a channel comparable to its equilibrium coi size (~1 um for viral DNA) are quite different from those in free solution, because of [...]

Simulation Methodology for Dielectrophoresis in Microelectronic Lab-on-a-chip

Leonardi A., Medoro G., Manaresi N., Tartagni M., Guerrieri R., DEIS - University of Bologna, IT

Recent trends in lab-on-a-chip show a growing use of dielectrophoresis (DEP) to manipulate biological objects such as cells and organic molecules [1], [2], [3], [4]. Bringing the advances of microelectronic miniaturization into biological and clinical [...]

Biochemical Binding in Microspheres-Based-Imunoassays

Prabhakarpandian B., Shah K.B., Sundaram S., Makhijani V.B., CFD Research Corporation, US

Microspheres (referred commonly as beads) are being extensively used in biochemical assays as supports for proteins, DNA, etc. We have successfully developed |omputational models for simulating sample detection using flowing beads. The model fully integrates [...]