Laboratory and clinical studies of cells maintaining the body's health and battling disease are increasingly complemented by computational modeling of cellular processes and diagnostic tools. Modeling involving nanoscale structures and processes has been particularly successful in structural cell biology, cellular mechanics, and in nanosensor development. The PI's laboratory develops a software package, NAMD/VMD, that is used by thousands of NIH-funded researchers as well as by pharmacological and biotechnological companies studying viral infection, developing new antibiotics, and providing faster gene sequencing methods. The impact of the computational tools, which provide profound microscopic views not available otherwise, is often limited by computing speed, hardware costs, and modeling ac- curacy. Recent dramatic advances in computer technology, namely multi-core processors and graphics processing units (GPUs), promise now a means of accelerating biomedical computing, while decreasing hardware cost and permitting more accurate simulations. The main investment needed is programmer ingenuity and time, as effective programming of multi-core processors requires different strategies and algorithms than used for conventional processing units. The PI and two co-PIs, long time collaborators with complementary backgrounds in biophysics, computer science, and electrical engineering, seek funds to hire two programmers and a graduate student research assistant, to program multi-core processors and serve three missions in biomedicine: the determination of very large cellular structures as they arise in cellular processes, the investigation of mechanical mechanisms underlying cellular dynamics, and the improvement of nanodevice simulation accuracy to better guide the development of sensors in medical diagnostics. Five computational bottlenecks will be addressed through revolutionary solutions involving multi-core capable software. In structural biology the merging of crystallographic and electron microscopy data through so-called grid forces and cross-correlation optimization will be greatly enhanced;in micro-mechanics of the body's cells interactive simulation and better analysis will permit investigators to feel and see simulated cellular mechanical responses on-the-fly, rather than only after hours or days;in nanomedicine an atomic resolution computational microscope will offer design engineers more accurate views of device behavior than ever achieved before. The approach taken combines biomedicine with physics, chemistry, parallel programming, and computer processing unit know-how in a unique way. Software improvements achieved will not only serve the stated applications, but many further applications of modern computational biomedicine.

Public Health Relevance

This project seeks to increase the speed and reduce the cost of biomedical computing through new software that can run on a new generation of computer chips. The software, presently already in use by thousands of investigators, aids in understanding how cells maintain health and battle disease, in developing drugs like new antibiotics, and in designing sensors for genetic diseases. The planned advances require new mathematical algorithms and programming strategies.

National Institute of Health (NIH)
Research Project (R01)
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Biodata Management and Analysis Study Section (BDMA)
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Brazhnik, Paul
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University of Illinois Urbana-Champaign
Biomed Engr/Col Engr/Engr Sta
United States
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Stone, John E; McGreevy, Ryan; Isralewitz, Barry et al. (2014) GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting. Faraday Discuss 169:265-83
Li, Qufei; Wanderling, Sherry; Paduch, Marcin et al. (2014) Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Nat Struct Mol Biol 21:244-52
McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei et al. (2014) xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures. Acta Crystallogr D Biol Crystallogr 70:2344-55