Informatics, Modeling & Simulation – Page 60

REMD toolkit : A Composable Software to Generate Parallelized Simulation Programs

We developed a toolkit to generate a replica exchange method program which is suitable to solve the multiple-minima problem that prevents the accurate estimation of thermodynamical quantities. The toolkit was designed as a set of [...]

Numerical Computation of Dispersion Relations for Multi-layered Anisotropic Structures

Botkin N.D., Hoffmann K-H, Pykhteev O.A., Turova V.L., Center of Advanced European Studies and Research, DE

The paper presents an algorithm and a program for the computation of the propagation velocity of acoustic waves excited in anisotropic multi-layered structures. This investigation is motivated by the modeling of a biosensor that serves [...]

An Efficient Multiscale-Linking Algorithm for Particle Deposition

Magan R.V., Sureshkumar R., Washington University, US

A multiscale-linking computer simulation of irreversible deposition of particles is developed by integrating mesoscopic Brownian dynamics simulations with continuum level conservation laws. The algorithm accounts for the flux of the particles from the bulk suspension [...]

Computational Challenges in Nanoscale Device Modeling

Polizzi E., Sameh A., Sun H., Purdue University, US

The development of new simulation tools is critical for the exploration of quantum transport in nanoscale devices. Such simulation is commonly performed by solving self-consistently the transport problem using The Non-Equilibrium Green's Functions (NEGF) formalism [...]

Investigation of dsDNA Stretching Meso-mechanics using Finite Element Method

Yuan C.A., Chiang K.N., National Tsing Hua University, TW

A novel finite element model with equivalent meso-mechanics theory is proposed herein to simulate the dynamic structural transitions of the double strand DNA (dsDNA) under external loading. Moreover, the meso-mechanics of dsDNA molecules is then [...]

The Two-Layer ONIOM Technique in the Studies of Chemical Reactions on Carbon Nanotube Tips

Basiuk E.V., Basiuk V.A., Basiuk E.V., Basiuk V.A., Universidad Nacional Autonoma de Mexico, MX

In continuation of our combined quantum mechanics/molecular mechanics (QM/MM) studies of selective amidation (reaction 1) and esterification (reaction 2) of monocarboxy-substituted tips of zigzag and armchair single-walled carbon nanotube (SWNTs), we studied theoretically the interaction [...]

Computational Methods and Numerics

Resolved Particle Simulations of Microsphere/Cell-based Bioanalytic Systems

Pant K., Romanowicz B.F., Sundaram S., CFD Research Corporation, US

Microsphere and cell-based assays are emerging as the platform of choice for rapid quantitation of biomolecular interactions in bioagent detection, clinical diagnosis, drug therapy, etc. [1,2] Traditional assay designs have been driven by expensive trial-and-error [...]

Development of an Advanced Simulation System for the Analysis of Particle Dynamics in LASER based Protein Ion Sources

Hieke A., Ciphergen Biosystems, Inc., US

An advanced multi-physics simulation system henceforth referred to as GEMIOS (Gas and Electromagnetic Ion Optical Simulator) has been implemented which allows the computation of 3D trajectories and energy exchange of ion beams/clouds under the influence [...]

DNA and Estrogen Receptor Interaction Revealed by the Fragment Molecular Orbital Method -Implementation of SCF Convergence-

Watanabe T., Inadomi Y., Tanaka S., Nagashima U., National Institute of Advanced Industrial and Science and Technology, JP

The fragment molecular orbital (FMO) method was applied to evaluate the interaction between estrogen response element (ERE) in DNA and DNA binding domain (DBD) of estrogen receptor (ER). In order to calculate the whole electronic [...]