New Understanding of Life and Its Processes

EPIDEMIOLOGICAL MODELING

Article: Asking “What If?” About H1N1 (2010)
Computational Explorations Into The H1N1 Pandemic
Shawn Brown, Pittsburgh Supercomputing Center & University of Pittsburgh
Bruce Lee, University of Pittsburgh Graduate School of Public Health

STRUCTURE OF PROTEINS & NUCLEIC ACIDS

Article: Epic Microseconds (2012)
Four Projects in Molecular Dynamics Simulation with a Special-Purpose System
JKlaus Schulten & Martin Gruebele, University of Illinois, Urbana-Champaign; Marta Filizola, Mount Sinai School of Medicine; Alfredo Freites & Douglas Tobias, University of California, Irvine; Susan Taylor & Chris McClendon, University of California, San Diego

Article: Protein Research Leaps Forward (2011)
Four Projects in Molecular Dynamics Simulation with a Special-Purpose System
Martin Gruebele, University of Illinois, Urbana-Champaign; Emad Tajkhorshid, University of Illinois, Urbana-Champaign; David Corey, Rachelle Gaudet, Marcos Sotomayor & Wilhelm Wiehofen, Harvard University; Andrew McCammon, Cesar de Oliveira, Barry Grant & Riccardo Baron, University of California, San Diego

Article: When Cellular Bones Soften (2010)
Actin Filament Remodeling By Actin Depolymerization Factor/Cofilin
Greg Voth, University of Chicago and Jim Pfaendtner, University of Washington

How to Knockout Hepatitis C (2009)
Inhibitor Induced Structural Change in the HCV IRES Domain IIa RNA
Thomas Cheatham, Darrell Davis & colleagues, University of Utah

Opening the Glutamate Gate (2008)
Simulations of the most prevalent receptor in the brain provide new understanding of how it opens its “gate” to fire neurons
Maria Kurnikova and Tatyana Mamonova, Carnegie Mellon University


Crossroads to Cancer (2008)
Computational tools allow University of Maryland researchers to find compounds that inhibit pathways to cancer
Alexander MacKerell and Paul Shapiro, University of Maryland


Article: Bent 'Branes & Bar Domains (2007)
Simulation of BAR Domain-Induced Membrane Curvature
Gregory Voth, University of Utah; Philip Blood, Pittsburgh Supercomputing Center


Article: Strange Action at the Active Site (2007)
Quantum Mechanical Simulations of Aldehyde Dehydrogenase
Troy Wymore & D.W. Deerfield II, Pittsburgh Supercomputing Center
John Hempel, University of Pittsburgh


Article: Heavy Metal Invasion (2006)
Role of Zinc Content and the Catalytic Efficiency of B1 Metallo β-lactamases
Matteo Del Peraro and Michael Klien, University of Pennsylvania


Article: Knock, Knock, Who's There? (2006)
Binding Dynamics of Isolated Nucleoporin Repeat Regions to Importin-β
Klaus Schulten and Tim Isgro, University of Illinois, Urbana-Champaign


Article: All in Your Brain (2005)
Simulations of Anandamide and Receptor CB1 in a Phospholipid Bilayer
Diane L. Lynch, Kennesaw State University and Patricia H. Reggio, University of North Carolina, Greensboro


Article: Protein Motors Incorporated (2004)
ATP Hydrolysis in the Catalytic Sites of F1-ATPase
Klaus Schuleten, Markus Dittrich, University of Illinois, Urbana-Champaign


Article: Pretzels, Noodles & Mini-Proteins (2004)
Structure Predictions and Folding Simulations of a Stable Protein
Carlos Simmerling, The State University of New York at Stony Brook


Article: When DNA Flips Out (2003)
Protein-facilitated Base Flipping in DNA by Cytosine-5-Methyltransferase
Niu Huang, Nilesh K. Banavali & Alexander D. MacKerell, Jr., University of Maryland


Article: Precious Bodily Fluids (2002)
Selectivity of the Aquaporin Water Channel Family
Klaus Schulten, University of Illinois, Urbana-Champaign.
Emad Tajkhorshid, University of Illinois, Urbana-Champaign.
Morten Ø. Jensen, Technical University of Denmark.


New Weapons for the Germ Wars (2002)
De Novo Design of Biomimetic Antimicrobial Polymers
Michael Klein, University of Pennsylvania.


What Happens at the Active Site (2002)
Computational Chemistry of Aldehyde Dehydrogenases
Troy Wymore, David Deerfield & Hugh Nicholas, Pittsburgh Supercomputing Center
John Hempel, University of Pittsburgh
Martin Field, Institut de Biologie Structurale, Grenoble, France


Article: Fishy Proteins (2001)
Hydrogen-Bond Analysis of a Type I Antifreeze Protein
Jeffry Madura, Duquesne University.


Article: Touchy Proteins (2001)
Molecular Dynamics Simulations of a Mechanosensitive Ion Channel
Klaus Schulten, University of Illinois.


Article: The Road to La-La Land (2001)
Simulations of Halothane in a Fully-Hydrated Membrane with Ion-Channel
Pei Tang, University of Pittsburgh.


Article: Getting a Grip on AIDS (2000)
Molecular Dynamics of HIV-1 RT Indicates Increased Flexibility
Marcela Madrid, Pittsburgh Supercomputing Center.
Jonathan Lukin, Carnegie Mellon University.


Article: The Rude Mechanicals (2000)
Mechanical Unfolding Intermediates in Titin Modules
Klaus Schulten, University of Illinois.


Article: A Thumb-Lock on AIDS (1999)
Subdomain Rearrangement in HIV-1 Reverse Transcriptase
Marcela Madrid, Pittsburgh Supercomputing Center.


Article: The Bridge From Genes To Proteins (1998)
Exploring Protein Folding Free Energy Landscapes
Charles L. Brooks III, Scripps Research Institute.


Article: Long Distance Charges (1996)
Unrestrained Molecular Dynamics for Biomolecular Systems
Peter Kollman, University of Calfornia, San Francisco.
Thomas Cheatham, University of Calfornia, San Francisco.


Article: New Twists in Globs and Zippers (1996)
Protein Folding: Simulations of a Three-Helix Protein and Leucine Zipper Dimer
Charles L. Brooks III, Scripps Research Institute.
Erik Boczko, Georgia Institute of Technology.
William Young, Pittsburgh Supercomputing Center.


Article: Melting Proteins (1995)
Long-Range Forces in Molecular Dynamics Simulations
Tom Darden, National Institute of Environmental Health Science.
Lee Pedersen, University of North Carolina.


Article: Shifty Biomolecules (1995)
Macromolecular Structures in Solution via Analysis of 2D NMR Experiments
Thomas James, University of California, San Francisco


Article: New Blood (1994)
Design of Compensatory Substitutions in Mutants of Hemoglobin
Chien Ho, Carnegie Mellon University
Marcela Madrid, Pittsburgh Supercomputing Center


Article: Kinky DNA (1991)
Structure and Dynamical Simulations of the DNA-Eco RI Endonuclease Complex
John M. Rosenberg, University of Pittsburgh


Article: How Proteins Get In Shape (1993)
Molecular Dynamics Simulations of Protein Folding
Charles L. Brooks III, Carnegie Mellon University


Article: Shake and Bake (1993)
Parallel Solutions to the Phase Problem in X-Ray Crystallography
Herbert A. Hauptman and Charles Weeks, Medical Foundation of Buffalo, Inc.
Russ Miller, State University of New York at Buffalo


Article: Protein Zippers (1994)
Molecular Modeling of Structure-Function Relationships in Biomolecules
Bruce Tidor, Whitehead Institute for Biomedical Research


Article: Shaking Hands with DNA (1993)
The Refinement of trp -Repressor Structure by Simulated Annealing and Restrained Molecular Dynamics
Oleg Jardetzky and Daqing Zhao, Stanford University


PROTEIN & NUCLEIC ACID SEQUENCE ANALYSIS

Article: Shared Memory Gene Assembly (2012)
Two Projects in Sequence-Data Assembly from Next-Generation Sequencers
Matthew MacManes & Eileen Lacey, University of California, Berkeley, Mostafa Elshahed, Rolf Prade & Brian Couger, Oklahoma State University

Article: Putting Genes Together Really Fast (2011)
Two Projects in Sequence-Data Assembly from Next-Generation Sequencers
James Vincent, University of Vermont; Cecilia Lo, University of Pittsburgh


Article: The Story of a Phage (2004)
Complete Genomic Sequence of Bacteriophage SP6
Aleisha T. Dobbins, Howard University
Graham Hatfull & Roger Hendrix, University of Pittsburgh


Article: All in the Family (1999)
Relationships within the Aldehyde Dehydrogenase Family
John Hempel, Univesity of Pittsburgh.
Hugh Nicholas, Pittsburgh Supercomputing Center.


Article: Proteins in Profile (1998)
Novel Application of Profile Analysis : Evidence for a Two-Helix Bundle in Human CCK-58
Grace Rosenquist, Univesity of California, Davis.
Hugh Nicholas, Pittsburgh Supercomputing Center.


Article: Getting to the New World (1996)
Distribution of Founding Lineage Haplotypes in Native Americans
D. Andrew Merriwether & Robert E. Ferrell , University of Pittsburgh


Article: Fighting the Flu (1993)
Computer-Predicted RNA Secondary Structure for Influenza Virus Genes
M. Louise Herlocher, University of Michigan & St. Jude Children's Research Hospital


NEUROSCIENCE

Nanomappers of the Mind (2011)
Network Anatomy and In Vivo Physiology of Visual Cortical Nuerons
Davi Bock, Wei-Chung Lee & Clay Reid, Harvard University,
Arthur W. Wetzel & Greg Hood, Pittsburgh Supercomputing Center


Wiring Diagram of the Brain (2009)
Assembling Image Sets from High-Throughput Electron Microscopy of Calcium-Imaged Neurons in the Mouse Visual Cortex
Davi Bock, Wei-Chung Lee & Clay Reid, Harvard University,
Greg Hood & Arthur W. Wetzel, Pittsburgh Supercomputing Center


Article: Fire in the Brain (2005)
Neurotransmitter Exocytosis Predictions from Spatially Realistic Monte Carlo Simulations
Joel Stiles, Pittsburgh Supercomputing Center, University of Pittsburgh, Carnegie Mellon University


CELLULAR BIOLOGY

Article: Where Nerve and Muscle Meet (2001)
Microphysiological Modeling of Slow-Channel Myasthenic Syndrome
Joel Stiles, Pittsburgh Supercomputing Center.


PATHOLOGY

Article: An Objective View of Cancer (2000)
Pathology Image Classification and Evaluation by Content-Based Retrieval
Art Wetzel, Pittsburgh Supercomputing Center
Michael Becich, University of Pittsburgh Medical Center


BLOOD CIRCULATION AND THE HEART

Article: OffBeat Hearts (2010)
Termination of Atrial Fibrilation UsingPulsed Low-Energy Far-Field Stimulation
Elizabeth Cherry, Rochester Institute o f Technology and Flavio Fenton, Cornell University

Hearts Gone Wild (2003)
Suppression of Alternans Despite Steep Restitution
Flavio Fenton & Elizabeth Cherry. Beth Israel Medical Center, New York City


Stroke Busters in Turbulent Blood (2002)
Transition to Turbulence in a Stenosed Carotid Artery
Francis Loth, University of Illinois, Chicago
Paul Fischer & Henry M. Tufo, Argonne National Laboratory
Hisham Bassiouny, University of Chicago Hospital


Article: Shocking Research (1996)
Cardiac Cell Excitation with Monophasic and Biphasic Field Stimuli
Matthew Fishler & Nitish Thakor, John Hopkins University.


Article: Heart Throb (1993)
Cardiac Fluid Dynamics and the Immersed Boundary Method
Charles S. Peskin and David M. McQueen, New York University


Article: Your Cheatin' Heart (1997)
Modeling Cardiac Arrythmias by Bifurcation Analysis
Teresa Chay, University of Pittsburgh


UNDERSTANDING THE BRAIN

Article: It Knows What You’re Thinking (2010)
Integrating Multiple FMRI Datasets Using Canonical Correlation Analysis
Tom Mitchell & Indrayana Rustandi, Carnegie Mellon University

Article: Watching the Brain in Action (1997)
Functional Topographic Mapping of the Cortex with Conventional MRI Scanners
Jonathan Cohen, University of Pittsburgh and Carnegie Mellon University.
Nigel Goddard, Pittsburgh Supercomputing Center.


Article: A New Look at Seeing (1995)
A Unified Self-Organizing Model of the Primary Visual Cortex
Risto Miikkulainen & Joseph Sirosh, University of Texas at Austin


RESPIRATION AND THE LUNGS

Article: Breathing Lessons (1995)
Computational Analysis of Small Airway Fluid Dynamics
Jeffery R. Hammersley, Medical College of Ohio


© Pittsburgh Supercomputing Center, Carnegie Mellon University, University of Pittsburgh
300 S. Craig Street, Pittsburgh, PA 15213 Phone: 412.268.4960 Fax: 412.268.5832

This page last updated: December 12, 2012