Marat Valiev

Enhancing biopreparedness through a model system to understand the molecular mechanisms that lead to pathogenesis and disease transmission

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Margaret Cheung-Wyker

The science of biopreparedness to counter biological threats hinges on understanding the fundamental principles and molecular mechanisms that lead to pathogenesis and disease transmission. Our vision…

Computational Chemical Dynamics of Complex Systems

Lead Institution

University of Minnesota

Principal Investigator

Donald Truhlar

Project type

Capability Research

The goal of this project is to apply powerful new simulation techniques to tackle computationally challenging problems in chemical dynamics, with special emphasis on electrochemistry, 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…

Study of Depolymerization and Valorization of Lignin

Lead Institution

Joint BioEnergy Institute

Principal Investigator

Seema Singh

Project type

Large-Scale EMSL Research

The primary goal of the proposed work is to study and understand using both experimental and computational approaches, the depolymerization of lignin generated during the ionic liquid (IL)…

Development of Computational Chemistry Tools for Aerosol Chemistry and Molecular-Level Characterization of Secondary Organic Aerosol particles

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Edoardo Apra

Our project is focused on the development of advanced quantum chemistry capabilities to enable molecular level characterization of secondary organic aerosol (SOA) particles and aerosol chemistry. The…

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

Capability Research

The critical nature of zinc in biology requires a detailed understanding of the chemistry, structure, and bondings of these zinc complexes and how, in turn, these manifestations alter the chemistry…

(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…

Cluster Model Studies of Condensed Phase Chemical Physics

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Xuebin Wang

This program is focused on obtaining a microscopic understanding of solution chemistry and solvation of negatively charged ions using cluster models in the gas phase via combined low temperature…

Gas Phase Study of Solution Phase Species and Chemistry Using Variable Temperature Photoelectron Spectrometer

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Xuebin Wang

We propose to investigate solution phase species and chemistry in the gas phase using a recently developed low-temperature photoelectron spectrometer. The subjects include but not limited to,…

Molecular Computational Studies In Geochemistry and Environmental Chemistry

Lead Institution

Corning, Inc.

Principal Investigator

James Rustad

Project type

Capability Research

This project is focused on prediction of reaction rates, mechanisms, and associated isotopic fractionation factors of key processes in low-temperature geochemistry. Such processes can play a key role…

(gc3564)Nanostructure Formation, Aggregation, and Reactivity

Lead Institution

Argonne National Laboratory

Principal Investigator

Larry Curtiss

Project type

Capability Research

This project is the outgrowth of several projects currently funded by DOE-BES at PNNL and ANL or new proposals co-authored by the participants and submitted to DOE?s Computational Nanoscience…

Hybrid Quantum Mechanics Molecular Mechanics Simulations of Biological Systems

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Marat Valiev

Biological processes are comprised of complex interconnected chains of chemical reactions. These reactions occur in the presence of extended macromolecular structures that regulate local electronic…

Gas Phase Study of Solution Phase Species and Chemistry Using Variable Temperature Photoelectron Spectrometer and Quantum Chemical Calculations

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Xuebin Wang

We propose to investigate solution phase species and chemistry in the gas phase using the home-made cryogenic and temperature-dependent photoelectron spectrometer in combination with ab initio…

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…

Cluster Model Studies of Condensed Phase Phenomena Using Temperature-Controlled Photoelectron Spectroscopy

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Xuebin Wang

Project type

Exploratory Research

This program is aimed at obtaining a microscopic understanding of solution chemistry and solvation of negatively charged ions using cluster models in the gas phase. Our primary experimental technique…

Biology in Space and Time (BioSaT) Research Campaign

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Scott Baker

Significant research effort is currently aimed at developing cost effective plant biomass deconstruction for biofuel production. Moreover, the recalcitrance of plant cell walls to rapid degradation…

Development classical density functional methods for coarse grained simulations of biochemical processes

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Marat Valiev

The proposed research is focused on development classical density functional methods for coarse grained simulations of biochemical processes. The computational time is requested on Cascade/Tahoma…

Simulation of Aqueous Mineral Interfaces, and Development of Ab Initio Plane-Wave Methods

Lead Institution

University of California, San Diego

Principal Investigator

John Weare

Project type

Exploratory Research

We will use ab initio plane-wave methods to perform simulations on surface complexes, rearrangements, and micro-solvations of metal-oxide surfaces. These simulations will allow us to study changes…

Cluster Model Studies of Condensed Phase Phenomena at Well-Defined Conditions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Xuebin Wang

Project type

Large-Scale EMSL Research

This program is aimed at obtaining a microscopic understanding of solution chemistry and condensed phase phenomena using gas phase clusters as model systems.Our current focus is on the microsolvation…

Identifying the mechanism of bacterial extracellular electron transfer via conductive pili proteins

Lead Institution

Yale University

Principal Investigator

Nikhil Malvankar

Project type

Exploratory Research

Microbial metabolism plays an important role in the global cycling of carbon, nutrients, and metals. Recent discovery of microorganisms sharing energy using direct electrical connections might…

Accurately predict the spatial arrangement of protein complexes from subtomogram images through physics-informed machine learning

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Margaret Cheung-Wyker

Deducing three-dimensional (3D) structures of molecular assemblies from cryo-electron tomography (cryoET) data provides an unprecedented level of detail about biological systems in their native…

Low Temperature (10K) 25Mg Solid-State NMR of DNA Repair Proteins and Their
Complexes

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Paul Ellis

Project type

Large-Scale EMSL Research

The chemistry central to the function of the DNA repair proteins apurinic/apyrimidic endonuclease 1 (APE1) and polymerase &#946; (Pol &#946;) is the chemistry of water activated by Mg2+…

Computational and FTIR Spectroscopic Studies of Vibrational and Electronic Properties of Transition Metal Mixed-Valence Complexes in Solution

Lead Institution

University of Washington

Principal Investigator

Munira Khalil

Project type

Exploratory Research

Developing a detailed molecular picture of ultrafast photoinduced electron transfer processes in solution will aid the development of new light harvesting technologies. The goal of this project is to…

Biology in Space and Time (BioSaT) Research Campaign

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Scott Baker

Significant research effort is currently aimed at developing cost effective plant biomass deconstruction for biofuel production. Moreover, the recalcitrance of plant cell walls to rapid degradation…

Ab-initio simulations of the catalytic mechanism in protein kinases

Lead Institution

University of California, San Diego

Principal Investigator

John Weare

Project type

Capability Research

Protein kinase enzymes play an important role in controlling cellular signaling events by catalyzing a phosphorylation reaction in which the gamma-phosphate from an adsorbed ATP in the catalytic…

Studies on 1,2,3-trichloropropane (TCP) and its derivatives

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Eric Bylaska

Project type

Large-Scale EMSL Research

The widespread use of 1,2,3-trichloropropane (1,2,3-TCP) as solvents in paint and varnish removal, cleaning and degreasing, etc. has resulted in it becoming an emerging pollutant in the environment …

Linear-response, real-time electron dynamics & high-level excited-state properties of molecules and materials

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Niranjan Govind

This is a three-pronged proposal aimed to address excited state properties in molecules and materials using linear-response TDDFT, real-time electronic dynamics and high-level coupled cluster…

Gas Phase Study of Solution Phase Species and Chemistry Using Variable Temperature Photoelectron Spectrometer

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Xuebin Wang

We propose to investigate solution phase species and chemistry in the gas phase using a recently developed low-temperature photoelectron spectrometer. The subjects include but not limited to,…

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…

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

Molecular modeling and simulation studies in combination with electron transfer theory calculations will be carried out to characterize the cytochrome mediated electron transfer process across the…

Development of 1st principles dynamics with exact exchange and spin-orbit ZORA

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Eric Bylaska

Project type

Large-Scale EMSL Research

1st principles methods of dynamical simulation will be developed that can treat the complex chemistry of actinide elements. In developing new solvers, emphasis will be placed on methods that will…

Resonant X-ray spectroscopy of molecules and molecular assemblies using STEX and TDDFT

Lead Institution

University of California, Irvine

Principal Investigator

Shaul Mukamel

Project type

Exploratory Research

This is a three-pronged proposal aimed to address excited state properties in molecules and materials using linear-response TDDFT, real-time electronic dynamics and high-level coupled cluster…

Development of computational pipeline to integrate protein structure/function discovery with genome scale model

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Marat Valiev

The project is focused on developing a computational pipeline that connects genome scale model to protein structure/function at the molecular level. It addresses an immediate need of the Subcellular…

(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…

High Accuracy Modeling of Frequency Dependent Polarizabilities: Exploring the Cutting Edge Limits of NWChem

Lead Institution

Lawrence Berkeley National Laboratory

Principal Investigator

Wibe De Jong

To demonstrate the value of this new NWChem capability we propose to calculate the frequency dependent and static dipole polarizability for a selected series of very large molecular systems using…

Computational Chemical Dynamics of Complex Systems

Lead Institution

University of Minnesota

Principal Investigator

Donald Truhlar

Project type

Large-Scale EMSL Research

The ultimate goal of this project is to develop and apply innovative user-friendly high-performance computing techniques and simulation methods for computational chemical dynamics of complex systems…

Molecular modeling of nanoscale and sub-nanoscale processes relevant to subcellular, intercellular and extracellular strategic science areas electronic structure methods in NWChem

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Karol Kowalski

We propose to use the array of quantum mechanical methods and integrated modeling framework in NWChem to elucidate the molecular scale (nanoscale and sub-nanoscale) processes like structure, bonding…

Developing a Parallel Blochl Code

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Marat Valiev

Project type

Exploratory Research

This project will develop a massively parallel version of Bloch's PAW method. PAW is an all-electron method that combines the adaptability of linear augmented plane wave methods with the…

Development of accurate force fields for aqueous biological environments using a massively parallel multiscale approach

Lead Institution

Intel Corporation

Principal Investigator

Jeffrey Hammond

Project type

Capability Research

The ability to calculate accurate energies and properties of large molecules with massively-parallel computers presents an extraordinary opportunity to develop new models for bonded and non-bonded…

The free energy of the HHZn enzyme reaction path from NWChem QM/MM Simulations

Lead Institution

University of California, San Diego

Principal Investigator

John Weare

Project type

Limited Scope

In this program we will collaborate with Marat Valiev (PNNL) to utilize the NWChem QM/MM package to simulate the free energy of the HHZn reaction path. There are a number of tasks that must be…

Using High-Resolution Mass Spectrometry, NMR and Computation to Elucidate Biomolecular Structural Features that Enable Efficient Oxygen Reduction Reaction Catalysis in Fuel Cells

Lead Institution

University of Texas at Austin

Principal Investigator

Yi Lu

Project type

Large-Scale EMSL Research

This proposal addresses a major under-explored area of research in our understanding of foundational principles for predictive biology central to energy production, i.e., the role of post…

Developing a Parallel Blochl Code

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Marat Valiev

Project type

Exploratory Research

This project will develop a massively parallel version of Bloch's PAW method. PAW is an all-electron method that combines the adaptability of linear augmented plane wave methods with the…

Fine-Tuning Ambipolar Charge-Transport Properties of Organic Materials By Computational Design

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Asanga Padmaperuma

Project type

Exploratory Research

We propose to use EMSL computational facilities for developing predictive models which will guide the design of new ambipolar organic charge transporting materials. Designing new materials for flat…

The Mechanism of the Hammerhead Ribozyme RNA Cleavage Reaction: Determining Optimized Free Energy Reaction Paths from QM/MM Simulations

Lead Institution

University of California, San Diego

Principal Investigator

John Weare

Project type

Exploratory Research

Ribonucleic acids (RNA) play a central role in the transmission of genetic information. However, the identification of additional non-coding roles of RNA polymers continues to grow. An important…

Collaborative Access Team: Pacific Northwest Cryo-EM Center (PNCC)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

James Evans

PNNL will create and operate the Pacific Northwest Center for Cryo-EM (PNCC), a state-of-the-art national center for cryo-electron microscopy (Cryo-EM) that will rapidly and efficiently collect and…

Design Criteria for Organic Charge Transporting Materials through Computational Modeling

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Linda Sapochak

Project type

Large-Scale EMSL Research

ABSTRACT We propose to use EMSL computational facilities for developing predictive models which will guide the design of new organic charge transporting materials for thin film energy conversion…

Theoretical Modeling of Fluorescence Properties in Biological Systems

Lead Institution

Temple University

Principal Investigator

Spiridoula Matsika

Project type

Capability Research

In this project high level ab initio methods will be used to study photophysical properties of nucleic acid bases and their fluorescent analogs. The natural nucleobases have ultrashort excited state…

Cluster Model Studies of Condensed Phase Phenomena

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Xuebin Wang

This is a request for continuing a previous program (proposal ID 44676) which was closed on September 30, 2012. This program is focused on obtaining a microscopic understanding of solution chemistry…

Agile BioFoundry

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Scott Baker

This proposed EMSL Resource Owner project, is a sub-project supporting two DOE-EERE-BETO supported PNNL projects: FY16-17 four-national laboratory “Agile BioFoundry” (ABF) seed project and a larger…

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…

Projects