Dayle Smith | Environmental Molecular Sciences Laboratory

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…

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…

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…

(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…

(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…

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…

Understanding structure-function relationships for developing catalysts for energy storage and production reactions.

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Wendy Shaw

Project type

Large-Scale EMSL Research

The DOE Basic Energy Sciences Energy Frontier Research Center entitled “Center for Molecular Electrocatalysis” (Bullock), the DOE Basic Energy Sciences “Modular Energy-Based Approach to Molecular…

Dynamic Imaging of Structurally Heterogeneous Protein Complexes

Lead Institution

Western University of Health Sciences

Principal Investigator

Thomas Squier

Project type

Large-Scale EMSL Research

Our long-term goal is to identify biological design principles that will enable synthetic biology approaches for bioenergy applications. We hypothesize that the targeted engineering of selected…

Multi-scale investigation of the nitrogen fixation mechanism of Mo-dependent nitrogenase

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Simone Raugei

Project type

Large-Scale EMSL Research

We propose to use EMSL NMR and supercomputing resources to gain a molecular level understanding of how substrate binding, electron, and proton delivery is controlled by the nitrogenase metalloenzyme…

Development of efficient implementations of many-body electronic structure methods for the Intel MIC

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Karol Kowalski

We propose to modernize the NWChem suite of computational chemistry codes towards effective utilization of the emergent hybrid parallel computer systems based on the Intel Many Integrated Core…

Thrust Area #2: Molecular modeling of electron transfer in Fe(III) oxides

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kevin Rosso

Project type

Grand Challenge

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…

Projects