US – Page 474 – TechConnect Briefs

Mesoscopic Breathing Sphere Model for Computer Simulation of Laser Ablation and Damage

Zhigilei L.V., Garrison B.J., Penn State University, US

A breathing sphere model has been developed for molecular dynamics simulations of laser ablation of organic solids. The novel feature of this model is an approximate representation of the internal molecular motion, which permits a [...]

Multiscale Modeling of Polycrystalline Diamond

Shenderova O.A., Brenner D.W., Omeltchenko A., Su X., Yang L.H., Nazarov A., North Carolina State University, US

Two modeling techniques used to characterize fracture behavior of polycrystalline diamond films are discussed. The first technique is a multiscale modeling method in which atomic level calculations on selected structures are combined with an analytic [...]

New Materials Design.Free-Base Porphyrin and Its Meso-Tetrahalogenated Derivatives

Nguyen K.A., Pachter R., Air Force Research Laboratory, US

Ab initio electronic structure theory has been applied to predict the structures and electronic spectra of free-base porphyrin (PH2) and its meso-tetrahalogenated derivatives (m-PX8H2, X = F, Cl, Br). Structures, singlet-triplet energy gaps, and electronic [...]

Template Recognition of Organosiloxane Stereoregular Macrocycles. Computational and Experimental Modeling of Sol-Gel Systems Formation

Timofeeva T.V., Clark R.D., Shchegolikhina O.I., Allinger N.L., New Mexico Highlands University, US

Recently a series of cage-like organometalla-siloxanes (OMS) were synthesized, isolated, and chara terized by single crystal X-ray analysis. Synthesis of these compounds resemble processes which occur during sol gel structure formation. The main attractive feature [...]

Towards the Reconstruction of Gene Regulatory Networks

Tobin F.L., Damian-Iordache V., Greller L.D., SmithKline Beecham, US

Gene expression data in biology is becoming important as the amount and quality of the data rapidly increases. However, the amount generated can be daunting and its direct interpretation is often difficult. The interaction of [...]

3D Protein Databases Integrated with Genomic and Chemical Data

Edwards D., Yan L., Olszewski K., Donlan M., MSI, US

The function of a protein is determined more directly by its three-dimensional structure than its sequence, it is therefore particularly useful to know the structure of a protein. This has been demonstrated by the many [...]

Structural Genomics and Automated X-ray Crystal Structure Solution

Terwilliger T.C., Berendzen J., LANL, US

Rapid advances in genomic sequencing are changing the focus and pace of structural biology, shifting from a reductionist approach to a broad view of all the pieces that come into play in a cell or [...]

Global Description of Amino Acid & Nucleotide Sequences: Application to Predicting Protein Folds, Intron-Exon Discrimination, & RNA Gene Identification

Dubchak I., Holbrook S.R., Muchnik I., Lawrence Berkeley National Laboratory, US

General global sequence descriptors have been developed which proved to be widely applicable to the prediction of properties of biological genes and gene products. These descriptors include composition, transition, and distribution of defined attributes in [...]

Exploring the Universe of Organic Molecules for Potent New Drugs

Bohacek R., McMartin C., Glunz P., Ripka A., Rich D.H., Ariad Pharmaceuticals, US

It has been estimated that the number of molecules with 30 atoms that can be constructed from carbon, oxygen, nitrogen, and sulfur is in excess of 10e60 [1]. The daunting challenge of the medicinal chemist [...]

Biotechnology, Drug Discovery, and Biomedical Research In Silico: The State of the Art

Bussiere D.E., Abbott Laboratories, US

During the last two decades, new techniques and advancements have added layers of complexity to the research done in biotechnology, drug discovery, and biomedical research. Many of the techniques developed have been computational in nature: [...]