Papers – Page 35 – TechConnect Briefs

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 [...]

A Monte Carlo Study of a Model of Globular Protein Nanoparticles

Pagan D.L., Gracheva M.E., Gunton J.D., Lehigh University, US

We explore the metastable fluid-fluid coexistence curve of the modified Lennard-Jones model of globular proteins of ten Wolde and Frenkel [4]. Using grand canonical Monte Carlo simulations along with mixed-field finitesize scaling and histogram rewighting, [...]

Self Assembly of Globular Protein Nanoparticles

Shiryayev A., Gunton J.D., Lehigh University, US

A continuum model of the self-assembly of globular protein nanoparticles proposed by Talanquer and Oxtoby (J. Chem. Phys. 109, 223 (1998)) is investigated numerically, with particular emphasis on the region near the metastable fluid-fluid coexistence [...]

Biomolecule Electrostatic Optimization with an Implicit Hessian

Bardhan J.P., Lee J-H., Altman M.D., Leyffer S., Benson S., Tidor B., White J.K., Massachusetts Institute of Technology, US

Computational rational drug design is the application of computer simulation techniques to improve screening processes for new drugs or to design them de novo. The goal is to identify molecules that have high affinity and [...]

Monte Carlo Study of Models of Membrane Proteins

Connor T.P., Pagan D.L., Shiryayev A., Gunton J.D., Lehigh University, US

The crystallization of membrane proteins from solution is sensitive to the role of initial conditions. In order to understand this dependence, we report preliminary results for two models for membrane proteins, each with short range [...]

Crystallization of Membrane Protein Nanoparticles

Shiryayev A., Holby E.F., Gunton J.D., Lehigh University, US

The self-assembly of membrane proteins from solution into two-dimensional crystals is studied numerically using a continuum model proposed by Talanquer and Oxtoby (J. Chem. Phys. 109, 223 (1998)). Although the mean ¯eld theory presented here [...]

Mathematical Modeling for Immunocolloid Labeling

Raymond C., Milewksi P., New Jersey Institute of Technology, US

For many biological applications, it is becoming increasingly important to extend imaging capabilities to simultaneously identify multiple molecular species in order to gain insight into the structural and functional elements of cells. A key part [...]

Numerical Modeling of Diffusion in Extracellular Space of Biological Cell Clusters and Tumors

Berthier J., Rivera F., Caillat P., CEA-LETI, FR

Biological cluster of cells may be seen as porous media, where the cells are the “solid grains” and the extracellular space (ECS) the “pores”. It is often the case in dense clusters of cells that [...]