Marat Valiev

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…

EMSL Science Overview

Marat Valiev

Projects

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

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

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

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

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

Biology in Space and Time (BioSaT) Research Campaign

Ab-initio simulations of the catalytic mechanism in protein kinases

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

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

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

Structure and Recognition in Microbial Membranes Proteins, and DNA

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

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

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

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