Biomaterials – Page 117 – TechConnect Briefs

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 [...]

Bio Nano Computational Methods and Applications

Toward an Integrated Computational Environment for Multiscale Computational Design of Nanoscale Ion Channel Semiconductors

Natarajan S., Varma S., Tang Y., Parker S., Mashl J., Jakobsson E., NCSA, US

This paper describes the design and operation of an integrated multiscale computational environment for design of nanoscale ion channel semiconductors, the Ion Channel Workbench. The present work builds on an earlier multiscale calculation from our [...]

Hybrid MD-PNP Simulations of the Alpha-Hemolysin Open Ion Currents

Cozmuta I., O'Keeffe J.T., Stolc V., Eloret Corp, NASA Ames Research Center, US

Recent experimental studies have used the alpha hemolysin protein as a model system to decipher ionic signature patterns in the genetic code of nucleic acids. These studies show that single stranded nucleic acids polymers can [...]

BioMOCA: A Transport Monte Carlo Approach to Ion Channel Simulation

van der Straaten T.A., Kathawala G., Ravaioli U., Beckman Institute, University of Illinois, US

Ion channels are highly charged proteins found in the cell membrane, which regulate ion transport to the cell. Most channels switch between conducting and non-conducting states and many can selectively transmit or block a particular [...]