The Center for
Computational Research

	Russ Miller, Director
	Professor, Comp Sci & Eng
	Senior Research Scientist @ Hauptman-Woodward Inst.
	Adj Prof., Electrical Engineering and Structural Biology

Overview (1)

	Leading U.S. Academic Supercomputing Center
		High-Performance Computing
		High-End Visualization
	Support ~80 Groups in ~25 Depts at UB
	Education/Outreach/Training
		H.S. Summer Program
		Work with Local Industry & Local Colleges
		Hosts Meetings/Provides Tours
		M.S. Certificate Program in Computational Science

Overview (2)

	Funding
		Initial $300K Provided by NSF (CS/Chem)
		UB Faculty/Staff have Leveraged CCR to Acquire $40M in Funding
			UB Investment: ~$2M (renovation, invest, personnel)
			CCR Vendor Donations: ~$6M
			CCR Projects: ~$2.7M
			NYS Funding: $15.3 NYSTAR; $2.7 NYSCEDII; $4M+ CCR
			Federal Funding: ~$13M
		NSF, NIH, EPA, NIMA, Sloan, Keck, Woodrow Wilson, NYS, Vendors, Industry

Overview (2)

	Corporate Partners/Relationships:
		IBM, SGI, Sun, Alias|Wavefront, Nortel, Myricom, InforMax, Celera
		Q-Chem, Praxair, Sarnoff, Occidental, M&T, Tops Markets, Performance Technologies, Believe, Kodak, Xerox,Veridian, Children’s Hospital, First Interstate Data Systems, Buffalo Medical Consortium, artN
		Peace Bridge Authority, Parsons Engineering, Bermann Associates, eMedia Inc., IBC Digital

Computational Science
and Engineering

	Third Science (Theoretical and Laboratory)
	Focuses on Scientific Problems, combining:
		Mathematics qComputer Science
		Disciplinary Science
		Biology qChemistry
		Applied and Eng. Fields qPhysics
	Impact (Simulation)
		Structural Biology qMaterials Science
		Fluid Dynamics qHigh Energy Physics
		Pharm. Drug Design qGlobal Climate Change
	NSF: “proving to be an effective way to generate new knowledge”

Sample CCR-Supported Research (1)

	Structural Biology
		Molecular Structure Determination & DNA Sequence Analysis
	Protein Folding
		Computer simulations determine the 3D structure of proteins.
	Environmentally Friendly Solvents
		Study supercritical CO2 as a solvent to reduce the need for toxic solvents.
	Groundwater Modeling
		Predict contaminant flow in groundwater & migration into streams and lakes.
	Industrial Design Optimization
		Design, modify, and perfect new products at reduced cost.
	Fluid Dynamics
		Modeling turbulent flows and combustion in order to improve design of chemical reactors, turbine engines, and airplanes.
	Volcanology
		Study of volcanoes for risk assessment. Modeling of lava flows and mudslides.

Sample CCR-Supported Research (1)

	Financial Analysis
		Datamining analaysis for prediction.
	Dental Implant Design
		Simulation and modeling of a dental implant in a jawbone to reduce failure rate.
	Physiology
		Flow & regulation in kidney.  Flow altered by aneurysm.
	Biophysics
		Measure protein conformational dynamics.
	Visualization & Multimedia
		Peace Bridge, Buffalo Medical Corridor, CCR, Events.  Networked media.  Art.
	Semiconductor Manufacturing
		New processes & chemicals to improve the manufacturing of computer chips.
	Classics
		Digital reconstruction of Assyrian Palace.

CCR Computing (0.4TFlops)

	SGI Origin2000
		128 Processors (250 MHz)
		32 GB RAM
		400 GB Fibre Channel Disk Storage
	IBM RS/6000 SP
		78 Processors
		26 GB Ram, 640 GB Disk Storage
	Sun Microsystems Cluster
		48 Sun Ultra 5 Workstations (333MHz)
		32 Sunblades (750MHz)
		Myrinet + 100BT Ethernet
	SGI Intel Linux Cluster
		150 Pentium III Processors (1 GHz)
		75 GB RAM, 2.5 TB Disk Storage
		Myrinet2000 + 100BT Ethernet

Cluster Computing at CCR

CCR Visualization

	Manufacturing
	Medical Imaging
	Computational Science
	Simulation & Modeling
	Historical Reenactments
	Multimedia Presentations

Bioinformatics

	The use of HPC to analyze data generated by the Human Genome Project to improve medical treatment.
	Precise sequence of ~30K human genes have been mapped
		Critical to elucidate the function of each gene.
		Leads to greater understanding of human development.
		Potential to treat many diseases, including AIDS cancer, MS, and Alzheimer’s and provide personalized treatment.
	From Human Genome
		locate genes
		determine what protein a gene regulates
		determine protein function
		determine structure
		devise drugs to block or enhance protein function

Molecular Structure Determination

	SnB Software by UB/HWI
		“Top Algorithms of the Century”
	Critical to Rational Drug Design
	Important Link in Structural Biology
	Vancomycin - Antibiotic of Last Resort
	Collaboratory – Incorporated in Backend of System
	HWI, CSE, CCR

Protein Folding

	Ability of proteins to perform biological function is attributed to their 3-D structure.
	Protein folding problem refers to the challenge of predicting 3-D structure from amino-acid sequence.
	Solving the protein folding problem will impact drug design.

Protein Folding

	Diffusion-Collision Model
	Both Simulations: 5 CPU Hours
	Collapse-Reorganization Model
	Biophysics

Protein Dynamics

	Dynamics of Hemoglobin (Example)
	50 Days of Processing on 16 Processors (800 CPU Days)
	Key
		White – Heme Groups
		Red – Phe97
		Red – Oxygen (in the subunit at bottom)
		Green – His 69 and 101
		Blue – Tyr 72
		Cyan (Ball) – Water Molecules
		Yellow – Helix E/F
	Interest
		Flip of the Phe97 ring at top
		Water movement around Phe97
		Heme-heme relative movement

Children’s Hospital CT

	3D Reconstruction of CT Dataset
	Created with the Visualization Toolkit (VTK) on a Linux Workstation
	3D Isosurface Shows Structure that is Nearly Impossible to Determine from 2D Slices
	Children’s & CCR

Confocal Microscopy

	3D Reconstruction of an Oral Epithelial Cell
	Translucent White Surface Represents the Cell Membrane
	Reddish Surface Represents Groups of Bacteria
	Photonics & CCR

Pan Am Exposition

	1901 Celebration
		Hightlighted Americas
		Featured all Aspects of Life
			Arts to Technology
	Buffalo
		1st American City to Light Streets with Electricity
		Most Paved Streets in World
	Walk Through
	PSCHologram
		Pan Am Temple of Music
		3D & LightBox
		Burchfield Art Gallery
	Media & CCR

UB Virtual Site Museum
(Northwest Palace of King Ashur-nasir-pal II,
883-859 B.C., ancient Assyria)

	Document and Publish Unique Historical Perspective of Best-Preserved Assyrian Palace
	Create a Multimedia Interactive Educational and Scholarly Research Tool
	Combine Traditional Research with Modern Computer Graphics
		Completely Immersive
		Animated Characters
		Interactive Storyboard
	Classics, VR Lab, CCR

The Thing Growing

	VR Interactive Fiction
	User as Protagonist
	Emotional Relationship between User & Virtual Character
	CAVE library, Performer, XP
	Media Study

Peace Bridge
(IBC Digital / UB VR Lab / CCR)

	International Crossing (USA/Canada)
	Existing Bridge: Old (75yrs) & Small (3 lanes)
	Existing USA Plaza: Small & Poor Design
	IBC, VR Lab, CCR
	Proposed Options
		Relocate USA Plaza
		Build a 3 Lane Companion & Rehab Original
		Build a 6 Lane Signature Span
	CCR Provides Immersive 3D Viz
		All Bridge & Plaza Options

Buffalo Medical Corridor

	Realtime Visualization of the Downtown Medical Complex
	Photorealistic Representation
	Alias|Wavefront and Multigen
	3D Tool for Future Development
	IBC & CCR

Sarnoff Project
Enhanced Visualization Modalities

	Commodity Cluster-Based Viz
	$2.3M/yr Subcontract
	Parallel File Database Servers
	High-Redundancy/Low-Failure
	IBM Intel Linux Cluster
		28 Pentium III Processors (1 GHz)
		28 GB RAM, 2.2 TB Disk storage
		Emulex + 100BT Ethernet
	CCR

Future Acquisitions

	Hardware
		2-6TFlops of Cluster Computing
		ACCESS Grid
		Commodity Viz Clusters
		Portable Viz Systems
		Additional Viz Workbench
		Commodity Projection Systems
	Software
		Bioinformatics
		Modeling and Simulation Packages
		Database & Data Mining
		Storage Management

"CCR Grand Opening"

	CCR Grand Opening

Contact Information
(www.ccr.buffalo.edu  miller@ccr.buffalo.edu)