Projects in Scientific Computing

New Understanding of Life and Its Processes




STRUCTURE OF PROTEINS & DNA

Article: Heavy Metal Invasion
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?
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
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
ATP Hydrolysis in the Catalytic Sites of F1-ATPase
Klaus Schuleten, Markus Dittrich, University of Illinois, Urbana-Champaign


Article: Proteins, Noodles & Mini-Proteins
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
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
Selectivity of the Aquaporin Water Channel Family
Klaus Schulten, University of Illinois, Urbana-Champaign.
Emad Tajkhorshid, University of Illinois, Urbana-Champaign.
Morten . Jensen, Technical University of Denmark.


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


What Happens at the Active Site
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
Hydrogen-Bond Analysis of a Type I Antifreeze Protein
Jeffry Madura, Duquesne University.


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


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


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


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


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


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


Article: Long Distance Charges
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
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
Long-Range Forces in Molecular Dynamics Simulations
Tom Darden, National Institute of Environmental Health Science.
Lee Pedersen, University of North Carolina.


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


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


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


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


Article: Shake and Bake
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
Molecular Modeling of Structure-Function Relationships in Biomolecules
Bruce Tidor, Whitehead Institute for Biomedical Research


Article: Shaking Hands with DNA
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: The Story of a Phage
Complete Genomic Sequence of Bacteriophage SP6
Aleisha T. Dobbins, Howard University
Graham Hatfull & Roger Hendrix, University of Pittsburgh


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


Article: Proteins in Profile
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
Distribution of Founding Lineage Haplotypes in Native Americans
D. Andrew Merriwether & Robert E. Ferrell , University of Pittsburgh


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


NEUROSCIENCE

Article: Fire in the Brain
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
Microphysiological Modeling of Slow-Channel Myasthenic Syndrome
Joel Stiles, Pittsburgh Supercomputing Center.


PATHOLOGY

Article: An Objective View of Cancer
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

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


Stroke Busters in Turbulent Blood
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
Cardiac Cell Excitation with Monophasic and Biphasic Field Stimuli
Matthew Fishler & Nitish Thakor, John Hopkins University.


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


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


UNDERSTANDING THE BRAIN

Article: Watching the Brain in Action
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
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
Computational Analysis of Small Airway Fluid Dynamics
Jeffery R. Hammersley, Medical College of Ohio


Articles by topic:
New Understanding of Life and Its Processes

Earth, the Environment and Society We Live In

Evolution and Structure of the Universe

New Technology and Manufacturing Processes

At the Frontier of Physics and Chemistry

 

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