Bulletin of the American Physical Society
2006 Four Corners Section of the APS Fall Meeting
Friday–Saturday, October 6–7, 2006; Logan, Utah
Session B1: Computational Physics Symposium |
Hide Abstracts |
Chair: Eric Held, Utah State University Room: Eccles Conference Center Room 216 |
Friday, October 6, 2006 10:30AM - 11:06AM |
B1.00001: Computational Approaches to Viral Evolution and Rational Vaccine Design Invited Speaker: Viral pandemics, including HIV, are a major health concern across the world. Experimental techniques available today have uncovered a great wealth of information about how these viruses infect, grow, and cause disease; as well as how our body attempts to defend itself against them. Nevertheless, due to the high variability and fast evolution of many of these viruses, the traditional method of developing vaccines by presenting a heuristically chosen strain to the body fails and an effective intervention strategy still eludes us. A large amount of carefully curated genomic data on a number of these viruses are now available, often annotated with disease and immunological context. The availability of parallel computers has now made it possible to carry out a systematic analysis of this data within an evolutionary framework. I will describe, as an example, how computations on such data has allowed us to understand the origins and diversification of HIV, the causative agent of AIDS. On the practical side, computations on the same data is now being used to inform choice or defign of optimal vaccine strains. [Preview Abstract] |
Friday, October 6, 2006 11:06AM - 11:42AM |
B1.00002: Recent discoveries from massive computation in beam physics Invited Speaker: In the last decade, computational beam physics, the study of the generation, propagation, and dynamics of charged particle beams, has moved from workstation computing to the use of massive parallelism, in which the power of hundreds to thousands of cpus are simultaneously harnessed to solve problems at the forefront of beam and accelerator science. The result has been multiple discoveries, including the prediction of the generation of GeV beams from lasers interacting with only a few centimeters of plasma. The field has gained in importance and prediction capability to where no accelerator will be built without extensive prior analysis of designs by computation in order to predict performance. This is especially important in the design of large accelerators, like the proposed International Linear Collider, which will have two 17 km long beams and has a cost estimated to be of the order of \$10B. This talk will summarize the recent advances in capability, the underlying computational technology, and some of the recent discoveries in this area. [Preview Abstract] |
Friday, October 6, 2006 11:42AM - 12:18PM |
B1.00003: Simulating Biological Cells Invited Speaker: Cells interact with their environment via a cascade of biochemical reactions that invoke a signaling, metabolic, or regulatory response. The properties of these reaction networks can be modeled at various levels of detail from continuum to stochastic, and steady-state to kinetic. Our group (and others) have been developing tools that attempt to simulate these networks in cellular geometries with spatio-temporal detail. In our model a single particle represents a protein, complex, or other biomolecule. Membranes and cellular compartments are represented as idealized or triangulated surfaces. Particles diffuse via 3d Brownian motion within the cytoplasm, or in 2d on membrane surfaces. When particles are near each other, they interact in accord with Monte Carlo rules to perform biochemical reactions which represent complex formation, dissociation events, ligand binding, etc. In this talk, I'll describe the reaction algorithms we use and the underlying physics they attempt to capture. I'll illustrate the effects stochasticity and spatial organization have on biochemical networks at the cellular scale and show some simple examples of how such models can address biological questions. This is an emerging field of simulation, so there are many issues still to be addressed, but the eventual goal is to enable whole-cell models of protein networks with realistic numbers of biomolecules. [Preview Abstract] |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700