US – Page 447 – TechConnect Briefs

Ionic Channels as Biodevices

Eisenberg R.S., Rush Medical Center, US

Ion channels are proteins with a hole down their middle of great biological and medical importance studied in thousand of laboratories. Ions move through channels of known structure obeying the relatively simple laws of electrodiffusion. [...]

Statistical Theory for Protein Combinatorial Libraries

Kono H., Zou J., Saven J.G., University of Pennsylvania, US

Combinatorial experiments provide new ways to probe the determinants of protein folding and to identify novel folding amino acid sequences. These types of experiments, however, are complicated by both enormous conformational complexity and by large [...]

Detecting Secondary Peptide Structures by Scaling a Genetic Algorithm

Michaud S.R., Zydallis J.B., Lamont G.B., Pachter R., Air Force Institute of Technology, US

The ability to accurately predict a polypeptide's molecular structure given its amino acid sequence is important to numerous scientific, medical, and engineering applications. Studies have been conducted in the application of Genetic Algorithms (GAs) to [...]

Structure Based Design of Protein Ligands: A Study of Antibody-like Scaffolds Targeted Against the Anthrax Toxin

Shiflett P., Hong-Geller E., Allen D., Lauer S., Lehnert B., Lehnert N., Nolan J., Lehnert B., Lehnert N., Gupta G., Los Alamos National Laboratories, US

We have adopted structure-based approaches to enhance the affinities of two single chain antibodies, scFv1 and scFv4, that bind to two different epitopes on the Protective Antigen (PA), a toxin from Bacillus anthracis. In one [...]

The Photocycle Movie of Photoactive Yellow Protein from Nanoseconds to Seconds

Ren Z., Perman B., Srajer V., Teng T.-Y., Pradervand C., Bourgeois D., Schotte F., Ursby T., Kort R., Wulff M., Moffat K., University of Chicago, US

Photoactive yellow protein (PYP; Meyer, 1985; Meyer et al., 1987) from the photoautotrophic purple eubacterium Ectothiorhodospira halophila is a 14-kD, water-soluble, cytoplasmic blue-light receptor, in which a 4-hydroxycinnamic acid chromophore is covalently linked by a [...]

Molecular Dynamics Studies on Folic Acid and Fluorescein-Derivatized PAMAM Dendrimers

Lee I., Athey B.D., Wetzel A.W., Baker Jr. J.R., University of Michigan, US

Molecular dynamics simulations on PAMAM dendrimers were performed to design and optimize the condition for cancer cell targeting and imaging. Folic acid and fluorescein-conjugated dendrimers with a primary amine surface group (without capping) and with [...]

Stochastic Simulations of Cell-Cell Signalling in Hepatocytes

Gracheva M.E., Toral R., Gunton J.D., Lehigh University, US

We present results of a Monte Carlo simulation of stochastic effects for two models of intercellular calcium wave propagation in rat hepatocytes. Both models involve gap junction diffusion by a second messenger. In general taking [...]

Applications of the Structural Comparison Algorithm for Simulated Annealing Optimizations and Stochastic Simulations

Curotto E., Beaver College, US

The use of a structural comparison algorithm as a potential energy surface attractor map is introduced. The numerical procedure determines if two structures of a Xn and Xn-YZ species are identical from the respective Cartesian [...]

A 2D Visualization Tool for SUMMiT V Designs

Yarberry V.R., Jorgensen C.R., Sandia National Laboratories, US

This paper describes the 2D Process Visualizer, a CAD tool that enables a SUMMiT (Sandia Ultra-Planar Multilevel MEMS Technology) MEMS designer to visualize the results of applying the process sequence to a mask set by [...]

Modeling of Electromagnetic Fields in High Speed Electronic Interconnects Using a Least Squares FD-TD Algorithm

Tramel R.W., Turowski M., Przekwas A.J., Schultz J., Frey R.G., CFD Research Corporation, US

A new Finite-Surface Time-Domain (FS-TD) numerical method is presented which is a generalization of the classical Finite-Difference Time-Domain (FD-TD) method of Yee. The method is divergence/charge preserving on arbitrary grids. It reverts to the standard [...]