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Molecular Science Computing FacilityPilot Projects
The MSCF supports small, short-term projects called Pilot Projects. Pilot Projects are proposals of general research (non-Grand Challenge) requiring the use of MSCF computers or Graphics & Visualization tools. They are typically directed at developing the capability to submit a Grand Challenge proposal in the future (e.g., a combination of theory/method or code development activities or doing calculations that provide the initial scientific basis of a Grand Challenge proposal). Some are for computational support of experiments performed in other EMSL facilities.
Current Projects
| Title | Project | PI | Affiliation | Members | Total MPP2 Allocation |
Reports |
|---|---|---|---|---|---|---|
| Asynchronous File System Experiments | 17999 | Margo I. Seltzer | Harvard University | 2 | 40,000 | Summary Highlights |
| Investigation of DNA Structural Perturbations Induced by the Guanine Oxidation Products Spiroiminohydantoin and Guanidinohydantoin | 17991 | Nigel D. Priestley | University of Montana | 2 | 40,000 | Summary Highlights |
| DFT Studies of Size and Structure Effects of Ir Nanoparticles on Their Catalytic Activities for Methane Dissociation | 16321 | Lichang Wang | Southern Illinois University | 1 | 75,000 | Summary Highlights |
| De Novo Structure-Based Molecular Design | 16305 | Benjamin P. Hay | Pacific Northwest National Laboratory | 2 | 30,000 | Summary Highlights |
| Proton Transport in Polymer Electrolyte Membranes | 16296 | Ram Devanathan | Pacific Northwest National Laboratory | 3 | 20,000 | Summary Highlights |
| Joint Application of Theory and Experiment to the Chemistry of Environmentally Important Organic Peroxides | 14690 | Barry K. Carpenter | Cornell University | 2 | 30,000 | Summary Highlights |
| Wet Electrons at the H2O/TiO2(110) Surface | 13894 | Hrvoje Petek | University of Pittsburg | 2 | 70,000 | Summary Highlights |
| Comparative Molecular Trajectory Analysis | 13307 | T.P. Straatsma | Pacific Northwest National Laboratory | 3 | 75,000 | Summary Highlights |
| Comparative Protein Structure Modeling: From Protein Sequence to High-Accuracy Protein Structure | 13304 | Ying Xu | University of Georgia | 3 | 75,000 | Summary Highlights |
| Real-Time Atomistic Simulation Studies of Light Harvesting and Charge Transport for Hydrogen Production in Solar Cells | 13300 | Oleg Prezhdo | University of Washington | 7 | 75,000 | Summary Highlights |
| Theoretical Treatment of the Kinetics of Uranium Reduction by Magnetite Surfaces | 12701 | Martin A.A. Schoonen | State University of New York at Stony Brook | 4 | 4,000 | Summary Highlights |
| MP2/CBS Pair Correlation Function of Liquid Water | 11994 | Robert H. Wood | University of Delaware | 1 | 15,000 | Summary Highlights |
| Sub-Grid Modeling of Diesel Particulate Filtration Using the Lattice-Boltzmann Method | 11390 | Mark Stewart | Pacific Northwest National Laboratory | 1 | 70,000 | Summary Highlights |
| Properties of Ice and Liquid Interfaces | 11106 | James P. Cowin | Pacific Northwest National Laboratory | 3 | 20,000 | Summary Highlights |
| Correlation of Structure and Function of Zinc Metalloproteins via Solid-State NMR Methods | 10910 | Andrew S. Lipton | Pacific Northwest National Laboratory | 5 | 75,000 | Summary Highlights |
| Simulation of the Conformation of Single Conjugated Polymer Molecules with Varying Conjugation Length in a Nematic Liquid Crystal | 9993 | Paul F. Barbara | University of Texas at Austin | 2 | NWVisus, 15,000 | Summary Highlights |
| Immune Response to Environmental Factors: MD Simulations of Antibody Structure | 9607 | Robert J. Woods | University of Georgia | 3 | 75,000 | Summary Highlights |
| Studies of Long Time Scale Processes of Environmental Importance | 9592 | Randall W. Hall | Louisiana State University | 6 | 75,000 | Summary Highlights |
| Accurate Ab Initio Determinations of Thermochemical Properties of Environmental and Biological Molecular Systems for Benchmarking with Experiments | 9591 | Cheuk-Yiu Ng | University of California, Davis | 4 | 75,000 | Summary Highlights |
| Molecular Orbital Studies on Peptide Secondary Structures | 9590 | Joseph J. Dannenberg | City University of New York, Hunter College and the Graduate School | 6 | 75,000 | Summary Highlights |
| PNNL Next Generation Chemistry-Meteorology-Aerosol Model | 9301 | Jerome D. Fast | Pacific Northwest National Laboratory | 3 | 75,000 | Summary Highlights |
| Oxidation and Radiation Damage in Nucleic Acid Bases | 8893 | William A. Lester | University of California, Berkeley | 3 | 200,000 | Summary Highlights |
| Investigating 3D-Coupled Geophysical Processes of the Subsurface | 8890 | Gregory A. Newman | Lawrence Berkeley National Laboratory | 2 | 75,000 | Summary Highlights |
| A Combined Approach for Protein Structure Prediction | 8491 | Silvia N. Crivelli | Lawrence Berkeley National Laboratory | 3 | 50,000 | Summary Highlights |
| Ab Initio Simulations of the Catalytic Mechanism in Protein Kinases | 7191 | John H. Weare | University of California, San Diego | 4 | 75,000 | Summary Highlights |
| Computational Study of Protein-Protein Interaction Dynamics | 5690 | Jin Wang | State University of New York at Stony Brook | 3 | 50,000 | Summary Highlights |
| Ab Initio Calculations on a Proposed Gating Mechanism for the KcsA Channel | 4796 | Michael E. Green | City College of New York | 3 | 75,000 | Summary Highlights |
| Computer Simulation of Radiation Effects in Zircon | 3534 | Ram Devanathan | Pacific Northwest National Laboratory | 2 | 60,000 | Summary Highlights |
| A Grid-Based Exact or High-Accuracy Solution of the Electronic Schroedinger Equation | 3484 | So Hirata | University of Florida | 6 | 50,000 | Summary Highlights |
| Local Motions in Protein Structures | 3436 | Edward W. Schlag | Technical University Munich | 2 | 25,000 | Summary Highlights |
| Computational Chemistry Modeling of Main-Group and Transition-Metal Cluster Systems | 3227 | Lai-sheng Wang | Washington State University Tri-Cities | 7 | 30,000 | Summary Highlights |
| Investigation of Aromatic and Other Novel Gas Phase Atomic Clusters and Molecules | 3226 | Alexander I. Boldyrev | Washington State University Tri-Cities | 5 | 10,000 | Summary Highlights |
Completed Projects
- [ Summary ] Defects, Defect Processes, and Ion-Solid Interactions in Ceramics
- [ Highlights ] [ Summary ] Ab initio Study of Catalytic GTP Hydrolysis
- [ Highlights ] [ Summary ] Molecular Energetics of Clustered Damage Sites in DNA
- [ Summary ] Computational Characterization of Two Lesions in DNA: 8-oxo-adenine and Abasic Site
- [ Summary ] NAMD Benchmarking Simulations
- [ Highlights ] [ Summary ] Fundamental Assessment of the Accuracy of Time-Dependent Density Functional Theory
- [ Summary ] Quantification of the Ligand Effects in Transition Metal Coordination Compounds Using Electronic Structure Calculation Methods
- [ Highlights ] [ Summary ] Calculated Rates of Water-Exchange on Large Aqueous Aluminum Nanoclusters
- [ Summary ] NMR Chemical Shift Calculations for Novel Bioactive Metabolites from an Acid Mine Waste Organism
- [ Highlights ] [ Summary ] Geometry Optimizations of Aqueous Aluminum Clusters
- [ Summary ] Computational Molecular Dynamics Simulation of Protein-Protein Interaction and Binding Dynamics
- [ Summary ] Physical Chemistry of Heterogeneous Atmospheric Processes
- [ Summary ] Computed Frequencies to Support Experimental Quests for Novel Molecules:
- [ Summary ] Advanced Process Control for Glass Manufacture:
- [ Summary ] Computer simulation of single-cell irradiation studies using the PNNL electron microbeam.:
- [ Summary ] Data structures for dynamic lists in computational science applications:
- [ Summary ] Development of Modeling Tools for Joining of Hydroformed Multi-Component Lightweight Structures:
- [ Summary ] Electroactive Materials for Anion Separation:
- [ Summary ] Electronic Structure Calculations of the Hemes of Flavocytochrome Ifc3:
- [ Summary ] Elucidation of Mechanisms for Selective Alkane Oxidation:
- [ Summary ] Large Scale Code Development Applied to Building A Geometry Based Computational Framework for Biology and Ecology Applications:
- [ Summary ] Lattice Boltzmann Methods:
- [ Summary ] Materials and Nuclear Physics Design of a Readily Deployable Space Reactor
- [ Summary ] Parameter Development and Initial MD Simulation of Flavocytochrome Ifc3
- [ Summary ] Subsurface Multifluid Flow and Multicomponent Reactive Transport: Characterization of Processes and Properties:
- [ Highlights ] [ Summary ] A study of massively parallel implementations of quantum statistical mechanics algorithms.:
- [ Highlights ] Ab Initio Calculations of the Methanol Dimer Potential Energy Surface:
- [ Highlights ] Alkali Binding Modes in Calixarenes:
- [ Highlights ] [ Summary ] Computational Methods for Atmospheric Chemistry:
- [ Highlights ] [ Summary ] Development of a Parallel Computational Environment for Imaging Science:
- [ Highlights (.pdf) ] [ Summary ] Dynamic processes in metastable materials:
- [ Highlights ] [ Summary ] Graphic presentation of conformational motions of dye-labeled enzyme:
- [ Highlights ] [ Summary ] Hanford Site-wide Flow and Transport Modeling:
- [ Highlights ] [ Summary ] He Scattering on Cubic Ice and Amorphous Solid Water:
- [ Highlights ] [ Summary ] Investigation of Electronic Structure of Fe-S Clusters:
- [ Highlights ] [ Summary ] Investigation of electrostatic interactions and solvation effects in multiply charged anions:
- [ Highlights ] [ Summary ] MCNP Radiation Dosimety and Shielding:
- [ Highlights ] [ Summary ] MD calculation of gramicidin conformational dynamics:
- [ Highlights ] [ Summary ] NWGrid and NWPhys Development, Implementation, and Application:
- [ Highlights ] Oxygen Sensor Coating Analysis:
- [ Highlights ] Parallelization of a Regional Climate Model:
- [ Highlights ] [ Summary ] Simulation of Solid Oxide Fuel Cell Operation:
- [ Highlights ] [ Summary ] Structural and Electrochemical Analysis of Solid Oxide Fuel Cells:
- [ Highlights ] [ Summary ] Structure of Borate Glasses:
- [ Highlights ] [ Summary ] The Molecular Basis for Polymerase-beta Fidelity During DNA Repair:
- [ Highlights ] Theoretical Characterization of Organic Reaction Intermediates in High Level Wastes:
- [ Highlights ] [ Summary ] Visualization and Active Guidance of Scientific Computations: