T. Straatsma

(EMSL34)Parameter Development and Initial MD Simulation of Flavocytochrome Ifc3

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Erich Vorpagel

Project type

Capability Research

As part of the DOE Office of Science Program Notice 01-21 for Advanced Modeling and Simulation of Biological Systems, we have received funding for development of new modeling capabilities for the…

(gc11-2002)Biomolecular Simulation of Base Excision Repair and Protein Signaling

Lead Institution

Oak Ridge National Laboratory

Principal Investigator

T. Straatsma

Project type

Capability Research

Environmental factors including ionizing radiation contribute to continuous damage of cellular DNA, in addition to endogenous sources. The damage resulting from oxidative stress and ionizing…

Comparative Protein Structure Modeling:
From Protein Sequence to High-accuracy Protein Structure

Lead Institution

eMAT Technology LLC

Principal Investigator

Xingling Xu

Project type

Capability Research

We propose to implement a computational pipeline for high-accuracy protein structure prediction from protein sequence, and carry out testing and evaluation of this computational pipeline on proteins…

(GC5-2002)Chemical Fate of Contaminants in the Environment: Chlorinated Hydrocarbons in the Groundwater

Lead Institution

University of Minnesota

Principal Investigator

Donald Truhlar

Project type

Capability Research

Chlorinated hydrocarbons (CHCs) are the most common contaminant found at hazardous waste sites and are the most prevalent contaminants on Department of Energy (DOE) weapons production sites. Many of…

Comparative Molecular Trajectory Analysis

Lead Institution

Oak Ridge National Laboratory

Principal Investigator

T. Straatsma

Project type

Capability Research

The large-scale simulation of biological systems as an integral component of a systems approach to biological research can only be accomplished if the emphasis in this field shifts to greater depth…

(GC5-2002)Chemical Fate of Contaminants in the Environment: Chlorinated Hydrocarbons in the Groundwater

Lead Institution

University of Minnesota

Principal Investigator

Donald Truhlar

Project type

Capability Research

Chlorinated hydrocarbons (CHCs) are the most common contaminant found at hazardous waste sites and are the most prevalent contaminants on Department of Energy (DOE) weapons production sites. Many of…

(GC8)Computational Studies in Molecular Geochemistry and Biogeochemistry

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Herman Cho

Project type

Capability Research

The ability to predict the transport and transformations of contaminants within the subsurface is critical for decisions on virtually every waste disposal option, from remediation technologies such…

Electronic Transfer Calculations for the Hemes of Flavocytochrome c3

Lead Institution

Intel Corporation

Principal Investigator

Dayle Smith

Project type

Exploratory Research

As part of the DOE Office of Science Program Notice 01-21 for Advanced Modeling and Simulation of Biological Systems, we have received funding for development of new large-scale electron transfer…

(GC8)Computational Studies in Molecular Geochemistry and Biogeochemistry

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Herman Cho

Project type

Capability Research

The ability to predict the transport and transformations of contaminants within the subsurface is critical for decisions on virtually every waste disposal option, from remediation technologies such…

Advanced Biomolecular Simulations - Development and Applications

Lead Institution

Oak Ridge National Laboratory

Principal Investigator

T. Straatsma

Project type

Capability Research

This project focuses on two important components of biomolecular modeling and simulation: i) the development of novel molecular modeling capabilities and their efficient parallel implementations, and…

Free radical Reactions in the Catalytic Cycle of Cytochrome bc Complexes

Lead Institution

University of Alabama

Principal Investigator

Michael Bowman

Project type

Large-Scale EMSL Research

The cytochrome bc complex is a large ~750 kiloDalton molecular weight protein complex that is embedded in the mitochondrial or cellular membrane and is a central component of the electron transport…

Structural Characterization and Interactions of Conformationally Heterogeneous States of Biomolecules

Lead Institution

Universidade Federal de Pernambuco

Principal Investigator

Thereza Soares Da Silva

Project type

Large-Scale EMSL Research

This proposal seeks computational resources for the application of long-scale and enhanced sampling techniques to characterize the inherently flexible and conformationally highly heterogeneous…

Correlation of Structure and Function of Zinc Metalloproteins Via a Combined NMR/Molecular Theory Approach

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Andrew Lipton

Project type

Large-Scale EMSL Research

One of the most significant challenges in the metallobiochemistry of Zn2+ is the a priori determination of how the metal center will facilitate a particular chemical reaction. Two examples…

Electron and Proton Transfer Reactions in Photobiological H2 Production

Lead Institution

Universidade Federal de Pernambuco

Principal Investigator

Thereza Soares Da Silva

Project type

Capability Research

The biological photoproduction of hydrogen by microbial photosynthetic organism requires light as the energy source, an electron-donating substrate, and a catalyst that combines electrons and protons…

Structural Engineering of the de novo Designed Protein Top7 as
a Scaffold for Antigen-binding

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Cheryl Baird

Project type

Large-Scale EMSL Research

Deployable biosensors for detecting environmental contaminants at the source require molecular sensing elements or affinity reagents that can survive the fluctuations in temperature and complex…

(gc3551)Complex Enzymatic Reactions Studied by Molecular Modeling and Electronic Structure Calculations.

Lead Institution

Oak Ridge National Laboratory

Principal Investigator

T. Straatsma

Project type

Capability Research

This proposal concerns the continued development and application of modeling capabilities for the study of complex enzymatic reactions, in particular those that involve electron transfer and/or…

Capture and Reduction of Metal Ions out of the
Environment by Biomolecular Systems

Lead Institution

Universidade Federal de Pernambuco

Principal Investigator

Roberto Lins Neto

Project type

Grand Challenge

The use of microbes and/or microbial components has been proven to be an efficient strategy for in situ environmental remediation technologies. The requested allocation of computer time is for…

(gc3563)Molecular Computational Studies In Environmental Chemistry, Geochemistry, and Biogeochemistry

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Eric Bylaska

Project type

Capability Research

Addressing the overwhelming environmental cleanup problems facing the Department of Energy?s nuclear production sites as well as other polluted sites in the nation is hampered by a lack of knowledge…

Advanced Peta-Scale Molecular Dynamics Simulations

Lead Institution

Oak Ridge National Laboratory

Principal Investigator

T. Straatsma

Project type

Capability Research

Next generation supercomputers are expected to have tens of thousands of processors to achieve multiple teraflops, and likely up to hundreds of thousands of processors to achieve multiple petaflops…

Molecular simulation of microbial membrane proteins and protein-DNA complexes

Lead Institution

Oak Ridge National Laboratory

Principal Investigator

T. Straatsma

Project type

Large-Scale EMSL Research

Two biochemical systems that are crucial for the integrity of microbial cells in complex environments are studied using molecular dynamics simulations. The first system is the homologous…

Complex Enzymatic Reactions

Lead Institution

Universitat des Saarlandes

Principal Investigator

Volkhard Helms

Project type

Capability Research

This proposal seeks computational resources for the continued development and application of modeling capabilities for the study of complex enzymatic reactions, in particular those that involve…

Structure and Recognition in Microbial Membranes Proteins, and DNA

Lead Institution

Oak Ridge National Laboratory

Principal Investigator

T. Straatsma

Project type

Capability Research

Developments in simulation methodologies as well as computer hardware have enabled the molecular simulation of biological systems of increasing size and with increasing accuracy, providing molecular…

First Principles Multiscale Analysis of Biochemical Processes: Signal Transduction and Spectroscopic Analysis of Local Structure-Folding Relations in Membrane Proteins

Lead Institution

University of California, San Diego

Principal Investigator

John Weare

Project type

Capability Research

We propose computational work in two application areas: first principles simulation of posttranslation modification in signal transduction in eukaryote cells and the use of spectroscopic methods to…

Scaling up for large metagenomic computations with ScalaBLAST

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Christopher Oehmen

Project type

Capability Research

The recent emphasis on understanding genomes at the level of whole organisms from the U.S. Department of Energy, National Institutes of Health, and other major agencies has driven a worldwide effort…

The Molecular Basis for Polymerase-beta Fidelity During DNA Repair

Lead Institution

Oak Ridge National Laboratory

Principal Investigator

T. Straatsma

Project type

Capability Research

Computational modeling studies of polymerase beta (pol b) will be carried out to provide novel insight into the role that protein dynamics plays in Pol b fidelity. If molecular dynamics were found to…

(EMSL33)Electronic Structure Calculations of the Hemes of Flavocytochrome Ifc3

Lead Institution

Oak Ridge National Laboratory

Principal Investigator

T. Straatsma

Project type

Capability Research

See attached file

Projects