The Resource for Concurrent Biological Computing pursues research projects in Molecular Biology, Neurobiology, Magnetic Resonance Imaging (MRI) and other areas which are extremely demanding computationally or not even possible on today's computers. For this purpose the Resource explores the use of massively parallel computers, developing expertise and programs for the computational biologist. The Resource seeks access to the highest performance machines at National Centers. It will operate a Gflop machine for program development, testing and limited production runs as well as operate a scalable parallel computer linked to a virtual molecular environment. The Resource will also pioneer the use of networked workstations as single machines for large scale biological computing. The Resource will develop numerical algorithms for parallel machines, e.g., for efficient description of electrostatic forces. It will provide molecular dynamics programs running across networks and translate physical concepts into computer programs, e.g., for long-time simulation and protein folding. It will also develop a neural simulator for parallel computers. Resource staff carries out projects in modelling large biomolecular systems like water-membrane-protein systems, redox proteins, and protein-DNA interactions, and studies biopolymer electrostatics. They also simulate the development of brain maps in the striate cortex and the development of motor control, model cognitive processing through coherent neural firing such as image segmentation, and study MRI microscopy. Collaborative projects include new approaches to structure determination from protein sequences, DNA-protein interaction, photosynthesis, membrane systems, molecular recognition by the immune system, sequence data bases, computational MRI, and adaptive filtering in vertebrate sensory systems. The Resource will closely cooperate with the National Center for Supercomputing Applications sharing the major hardware and utilizing Center staff for machine operation and user services. The visitor and workshop program of the Resource will be administered by the Beckman Institute at the University of Illinois.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
2P41RR005969-03
Application #
3104311
Study Section
Special Emphasis Panel (SSS (F))
Project Start
1990-08-01
Project End
1997-07-31
Budget Start
1992-08-01
Budget End
1993-07-31
Support Year
3
Fiscal Year
1992
Total Cost
Indirect Cost
Name
University of Illinois Urbana-Champaign
Department
Type
Schools of Engineering
DUNS #
041544081
City
Champaign
State
IL
Country
United States
Zip Code
61820
Shim, Jiwook; Banerjee, Shouvik; Qiu, Hu et al. (2017) Detection of methylation on dsDNA using nanopores in a MoS2 membrane. Nanoscale 9:14836-14845
Wolfe, Aaron J; Si, Wei; Zhang, Zhengqi et al. (2017) Quantification of Membrane Protein-Detergent Complex Interactions. J Phys Chem B 121:10228-10241
Decker, Karl; Page, Martin; Aksimentiev, Aleksei (2017) Nanoscale Ion Pump Derived from a Biological Water Channel. J Phys Chem B 121:7899-7906
Radak, Brian K; Chipot, Christophe; Suh, Donghyuk et al. (2017) Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. J Chem Theory Comput 13:5933-5944
Sun, Chang; Taguchi, Alexander T; Vermaas, Josh V et al. (2016) Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli. Biochemistry 55:5714-5725
Belkin, Maxim; Aksimentiev, Aleksei (2016) Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores. ACS Appl Mater Interfaces 8:12599-608
Poudel, Kumud R; Dong, Yongming; Yu, Hang et al. (2016) A time course of orchestrated endophilin action in sensing, bending, and stabilizing curved membranes. Mol Biol Cell 27:2119-32
Vermaas, Josh V; Taguchi, Alexander T; Dikanov, Sergei A et al. (2015) Redox potential tuning through differential quinone binding in the photosynthetic reaction center of Rhodobacter sphaeroides. Biochemistry 54:2104-16
Belkin, Maxim; Chao, Shu-Han; Jonsson, Magnus P et al. (2015) Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA. ACS Nano 9:10598-611
Shen, Rong; Han, Wei; Fiorin, Giacomo et al. (2015) Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments. PLoS Comput Biol 11:e1004368

Showing the most recent 10 out of 371 publications