2007 SBU/BNL Seed Grant Winners

Monica Fernandez-Bugallo, Department of Electrical and Computer Engineering, SBU
& Helio Takai, Physics Department, BNL
"Development of Radar-based Methods for Cosmic Ray Detection."

The scientific goal of this project is the detection of ultra-high-energy cosmic rays (UHECRs) using radar-based methods. An UHECR is a cosmic ray (subatomic particle) which appears to have extreme kinetic energy, far beyond energies typical of other cosmic rays. The source of UHECRs is a deep mystery. There are no known astrophysical sources within our galaxy or those close to us that could accelerate particles to such enormous energies. Yet, interactions of such particles with the cosmic microwave background would not allow their propagation from greater distances. So, where do they come from? Therefore the question of what these particles come from is a one that has bewildered astrophysicists and cosmologists since the discovery of UHECRs. Professor Fernandez-Bugallo and colleagues hope to identify the location of their source, obtaining a highly valuable insight about the origins and evolution of the universe.

Gary Halada, Department of Materials Science and Engineering, SBU
& Aaron Neiman, Department of Biochemistry and Cell Biology, SBU
Oleg Gang, Center for Functional Nanomaterials, BNL
Elaine DiMasi, National Synchrotron Light Source, BNL
"Design of Biomimetic Materials: Cross-linked and Functionalized Chitosan as Bio-inspired Coatings and Engineering Materials."

The goal of this proposal is to (a) characterize the chemistry and structure of cross-linked chitosan in yeast spore walls using a suite of spectroscopic and microscopy techniques; (b) create a biomimetic chitosan layer using electrochemical deposition; and (c) use this deposited layer to analyze the nature of cross-linking and its effects on chemistry, structure and properties. Chitosan, a glucosamine polymer, is the second most abundant polysaccharide on the planet. It is the predominant component of crustacean shells and is also found in insect cuticle and in the walls of microorganisms such as yeast. In these natural structures chitosan is found in complexes with additional components to confer important physical properties. This chitosan/dityrosine macromolecule confers upon the spore resistance to a wide variety of environmental insults including UV irradiation, heat, desiccation, exposure to organic compounds as well as extremes of pH. These remarkable properties make modified chitosan a promising avenue for biologically inspired materials.

Erwin London, Department of Biochemistry and Cell Biology, SBU
& Subramanyam Swaminathan, Biology Department, BNL
"Determination of the Structure of the T Domain of Membrane-Inserted Botulinum Neurotoxin A."

This team aims to use methods developed in our lab to define the structure of diphtheria toxin (DT) in membranes in order to define the structure of botulinum neurotoxin A (BoT). Bacterial infections often involve the penetration of bacterial toxin proteins into cell membranes. This is followed by toxin translocation across membranes and into the cell cytoplasm, where the toxin disrupts critical cellular processes. During the period of the seed grant they will demonstrate that the methodology developed by lab to aid studies of DT can be successfully adapted to BoT, and define the position of a few key segments of BoT in relation to membranes. Many aspects of protein movement across membranes remain mysterious, and self-translocating toxins are one of the best systems for studying this process. In addition, bacterial toxins are virulence factors in disease, and insights into the mechanism their entry into cells aid in design of medically useful inhibitors that either prevent membrane insertion, or alter the structure of a membrane-inserted toxin in a fashion preventing translocation of its catalytic domain into the cell cytoplasm. Such methods would also be useful in treating the sporadic cases of botulinum toxin poisoning (botulism) from food contaminated with C. botulinum, and they are more urgent because BoT a class A bioterrorism agent.

K. Daniel O'Leary, Department of Psychology, SBU
& Patricia Woicik, Medical Department, BNL
Nelly Alia-Klein, Medical Department, BNL
"Chronic Violent Behavior and its Underlying Neurobiology."

In the past decade empirical studies have identified multiple factors that contribute to repeated violent behavior directed at intimate others (domestic violence). This behavior affects up to 30% of couples in the US and the research evidence for this phenomena points to a complex and dynamic relationship between personality styles, psychiatric disorders, and serious relationship problems. The lack of behavioral control observed in domestic abusers (as with any other individual) is likely a result of brain function, which is evaluated through neuropsychological testing and functional neuroimaging. The main objective of this collaborative effort is to evaluate personality and neurobiological factors as potential predictors of violence in alcoholic domestic abusers. Despite the growing understanding that domestic abuse is multi-faceted, no studies to date have collectively investigated the relationship between personality, alcohol abuse, and the underlying neurobiological brain structure and function associated with this harmful behavior.

Carlos Simmerling , Department of Chemistry, SBU
& James Davenport, Computational Science Center, BNL
"Simulations of Biomolecular Systems on Massively Parallel Supercomputers."

Atomic-detail simulations have begun to make significant contributions to a wide variety of research areas, in the case of biomolecular systems, a major obstacle to further progress is the long timescales associated with important events such as protein folding, drug binding, and conformational changes associated with biological function. Direct simulation of such events remains largely inaccessible using current computers. The new purchase of a massively parallel supercomputer for the New York Computational Science Center, will provide unprecedented computer power to both SBU and BNL. The Amber simulation package is a leading program for biomolecular simulation; however, it is currently unable to take advantage of more than ~200 CPUs for a single simulation, far below the >20 thousand available in the planned NYCCS Blue Gene. This team proposes to combine their detailed knowledge of Amber and the requirements of biomolecular simulation with their computational physics/algorithms expertise in order to pursue performance enhancements for Amber on the Blue Gene architecture. The ability to use Amber on the NYCCS computer will dramatically extend the range of biologically relevant events that can be simulated, improving the research capabilities in multiple fields including Chemistry, Pharmacology, Biology and Applied Mathematics and Statistics.

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