Eric Bylaska | Environmental Molecular Sciences Laboratory

Developing an Automated Smart Method for Searching the Configurational Space of Micronutrients in Host Minerals, Proteins, and Soils

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Eugene Ilton

Project type

Large-Scale EMSL Research

In prior EMSL supported work we developed an ab initio molecular dynamics (AIMD) approach to interpret the EXAFS signal of impurities/micronutrients in the structure of Fe(oxyhydroxide) host minerals…

Simulating Mineral Interfaces (also related to Bylaska BES PNNL#42859:First Principles Simulation of the Supercritical Behavior)

Lead Institution

University of California, San Diego

Principal Investigator

John Weare

Project type

Exploratory Research

- Development of various ab initio molecular dynamics (AIMD) methods, including PAW-AIMD and implenting exact exchange into AIMD methods - AIMD Simulations of highly charge cations in solution. …

Experimental and Theoretical Studies of Reaction Pathways for the Breakdown of Chlorinated Hydrocarbon Molecules by Metal and Metal Oxide Nanoparticles(including PNNL Scope # 42184/44076, Baer/Amonette/Tratnyek Nano-Fe BES/EMSP project)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Amonette

Project type

Large-Scale EMSL Research

Metal and metal-oxide nanoparticles have been shown to have high reactivity towards a variety of chemical species, including chlorinated hydrocarbons and reducible oxyanions that frequently…

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…

(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…

Probing the Mesoscale Structure at Complex Electrode-Electrolyte Interfaces

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vijayakumar Murugesan

Project type

Large-Scale EMSL Research

Molecular interactions at electrode-electrolyte interface are pivotal to the modern energy storage/conversion and microelectronic devices. However, our predictive understanding about the impact 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…

Large-scale computational modeling of the chemical behavior of actinide elements at interfaces

Lead Institution

Lawrence Berkeley National Laboratory

Principal Investigator

Wibe De Jong

Project type

Capability Research

High performance parallel computational resources and scalable software has enabled computational chemistry to model actinides at various interfaces, in the presence of multiple ligands in solution,…

New Generate of Computational Tools for Exploring High Dimensional Configuration Spaces in Geosciences

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Eric Bylaska

The primary goal in this project is to develop free energy methods and techniques for the efficient exploration of phase space in the NWChem program package developed at EMSL. These techniques will…

Multiscale Design of Advanced
Materials based on Hybrid Ab-Initio
and Quasicontinuum Methods

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Eric Bylaska

Project type

Exploratory Research

A multiscale method based on hydrid ab initio and quasicontinuum methods will be developed on a rigorous mathematical, physical, and chemical foundation. Rather than being based on classical…

Complex processes in separations, catalysis, hybrid materials, and nuclear energy and waste management

Lead Institution

University of Arizona

Principal Investigator

L. Corrales

Project type

Capability Research

As computational capabilities increase, the use of first principles based methodologies allows the investigation of even more complex behavior (than has been studied before) associated with catalysis…

Simulations of Complex Chemistry at Mineral/Fluid Interfaces: Development and application of Petascale/Exaflop First Principle Simulation Technology

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Eric Bylaska

Novel first principle methods of simulations will be developed and applied to computationally intractable geochemical problems such as: i) Interpretations of structure, reactivity and electron…

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…

Ultra-high accuracy simulations for large molecular systems: Exploring the Cutting Edge Limits of NWChem

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Karol Kowalski

The main goal of the proposed proposal is to test and apply a new generation of highly scalable electronic structure methods to cutting edge problems that can be viewed as an excellent target for…

Simulations of Complex Chemistry at Mineral/Fluid Interfaces: Development and application of Petascale/Exaflop First Principle Simulation Technology

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Eric Bylaska

Novel first principle methods of simulations will be developed and applied to computationally intractable geochemical problems such as: i) Interpretations of structure, reactivity and electron…

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…

ELECTRONIC STRUCTURE CALCULATIONS OF HYDROGEN BONDING IN BIOLOGICAL MACROMOLECULES

Lead Institution

University of Washington

Principal Investigator

David Baker

Project type

Exploratory Research

Hydrogen bonding interactions play a crucial role in stabilizing native protein conformations, and in determining specifity and stability of protein-ligand docked complexes. In force field…

Can Mineral Growth by Oriented Attachment Lead to Incorporation of Uranium into the Structure of Fe(oxyhydr)oxides?

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Eugene Ilton

Project type

Large-Scale EMSL Research

Previous laboratory work has shown that uranium can be incorporated into the structure of hematite and goethite during co-precipitation and redox transformation of ferrihydrite, respectively. However…

SGI Altix Allocation for Advanced Computing Technology Lab

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Jarek Nieplocha

This is a placeholder proposal to manage time allocation under EMSL resource tracking system.

ELECTRONIC STRUCTURE CALCULATIONS OF HYDROGEN BONDING IN BIOLOGICAL MACROMOLECULES

Lead Institution

University of Washington

Principal Investigator

David Baker

Project type

Exploratory Research

Hydrogen bonding interactions play a crucial role in stabilizing native protein conformations, and in determining specifity and stability of protein-ligand docked complexes. In force field…

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…

(gc2392)Immobilization of Radionuclides in Oxides

Lead Institution

University of Iceland

Principal Investigator

Hannes Jonsson

Project type

Capability Research

We will carry out a series of theoretical calculations related to the immobilization of radionuclides in oxides, both crystalline and amorphous. The principal questions that will be addressed are: …

The Reaction Specificity of Nanoparticles in Solution: Interactions between Iron Nanoparticles, their Coatings, and the Environment

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Donald Baer

Project type

Large-Scale EMSL Research

The objective of our research is to obtain fundamental information about the physical and chemical transformations that occur on and within mineral oxide nanoparticulates due to electron transfer…

Reactivity of Soil Organic Carbon with Minerals under Low Water Conditions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Loring

Project type

Exploratory Research

The manner in which soil organic carbon (SOC) binds to and reacts with mineral surfaces affects SOC (bio)degradation, SOC mobility, soil wettability, mineral dissolution, and the bioavailability of…

(emsl2492)Ab Initio Characterization of Unreduced And Reducted (012) Surfaces Of Hematite.

Lead Institution

University at Albany, State University of New York

Principal Investigator

Michel Dupuis

Project type

Capability Research

See attachment

(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…

The role of Fe(oxyhydr)oxides in regulating the biogeochemical cycling of Zinc; an essential micro-nutrient

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Eugene Ilton

Project type

Large-Scale EMSL Research

We propose to study the influence of Fe(III) (oxyhydr)oxides on the biogeochemical cycling of Zn, an essential micronutrient. The work is specifically focused on incorporation of Zn into the…

Ab initio calculations of oxide deposition on 3,5 semiconductors

Lead Institution

University of California, San Diego

Principal Investigator

Jonathan Sexton

Project type

Exploratory Research

We propose to use pseudopotential plane wave methods as implemented in NWChem to study the properties of oxide deposition on GaAs and InAs semiconductors. NWChem calculations will be used to optimize…

(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…

Development of advanced computational methods for molecular level characterization of complex biological, earth, and environmental systems using NWChem

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Marat Valiev

Our project is focused on development of advanced computational capabilities to support molecular level simulations of biological, biogeochemical, and physical processes. These capabilities are…

Experimental Investigation of Strontium Mass Transfer in a Dynamic Vadose Zone - Aquifer - River System

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Steven Yabusaki

Project type

Large-Scale EMSL Research

At a number of DOE sites, groundwater flowing through contaminated sediments before discharging to a river is being relied on to meet regulatory standards. This natural flushing (i.e., monitored…

Computational support to the program 'Ab Initio Molecular Dynamics Simulations of Solution species, Nanoparticles, and Geochemical Interfaces Under Extreme Conditions'.

Lead Institution

University of California, San Diego

Principal Investigator

John Weare

Project type

Exploratory Research

A grand challenge research need in geosciences is the predictions of the interaction of geochemical fluids containing solutes with minerals, nanoparticles, and colloids under extreme near surface…

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…

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 …

Fully In Silico Calibration Of Empirical Predictive Models For Environmental Fate Properties Of Novel Munitions Compounds

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Kurt Glaesemann

Project type

Large-Scale EMSL Research

Predicting chemical properties is a long-standing challenge that has received extensive study for many applications (chemical engineering, green chemistry, environmental chemistry, toxicology,…

Development of Novel First Principles Simulations for Reactions at Complex Geochemical Interfaces

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Eric Bylaska

The proposed development work in this theoretical cross-cutting staff proposal include: (1) Development of new algorithms supporting high-level electron structure calculation of reaction mechanisms…

Development of Time-Dependent Quantum Reaction Dynamics for Surface Reactions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Eric Bylaska

Project type

Large-Scale EMSL Research

We propose to develop multi-dimensional, state-of-the-art time-dependent quantum dynamics (TDQD) computational methods for catalytic surface reactions. Our aim is to obtain accurate initial-state…

Catalysis Research Campaign: An Integrated Multi-Capability Approach for Analysis of Catalytic Systems

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Charles Peden

Project type

Research Campaign

In this research campaign, advanced capabilities within the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory will be integrated for in-depth, molecular…

Development of Novel First Principles Simulations for Reactions at Complex Geochemical Interfaces

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Eric Bylaska

The proposed development work in this theoretical cross-cutting staff proposal include: (1) Development of new algorithms supporting high-level electron structure calculation of reaction mechanisms…

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…

Carbon Tetrachloride Degradation Reaction Mechanisms (Amonette/Bylaska EMSP-CCl4, PNNL Scope #44012)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Amonette

Project type

Exploratory Research

Characterize the mechanisms and kinetics of competing degradation reactions of carbon tetrachloride (CCl4) through laboratory experiments in simple model systems closely coordinated with theoretical…

Development of Novel First Principles Simulations for Reactions at Complex Geochemical Interfaces

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Eric Bylaska

The proposed development work in this theoretical cross-cutting staff proposal include: (1) Development of new algorithms supporting high-level electron structure calculation of reaction mechanisms…

Real-Time Atomistic Simulation Studies of Light Harvesting and Charge Transport for Hydrogen Production in Solar Cells

Lead Institution

University of Washington

Principal Investigator

Oleg Prezhdo

Project type

Capability Research

Fundamental mechanisms of the excitation energy ow in novel materials for hydrogen production in solar cells will be investigated in a series of theoretical studies with emphasis on the simulation…

Reaction Specificity of Nanoparticles in Solution (PNNL Scope # 42184/44076)

Lead Institution

University of Minnesota

Principal Investigator

R. Penn

Project type

Exploratory Research

This User Proposal is being submitted as part of an approved NSET proposal under PIs Don Baer and Paul Tratnyek to perform fundamental basic science studies that will benefit a whole range of…

Large-scale computational modeling of the chemical transformation of actinide elements at interfaces

Lead Institution

Lawrence Berkeley National Laboratory

Principal Investigator

Wibe De Jong

Project type

Large-Scale EMSL Research

Subsurface migration of radioactive waste resulting from nuclear energy and weapons production is a critical issue to the U.S. Department of Energy (DOE), and the safe and cost-effective disposal of…

The role of Fe(oxyhydr)oxides in regulating the biogeochemical cycling of the essential micronutrients zinc and copper

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Eugene Ilton

Project type

Large-Scale EMSL Research

Elements essential for plant growth and nutritious crops (e.g., Fe, Cu, and Zn) are often strongly associated with Fe (oxyhydr)oxides, particularly in more weathered terrains. For example, Zn…

Simulating Mineral Interfaces (also related to Bylaska BES PNNL#42859:First Principles Simulation of the Supercritical Behavior)

Lead Institution

University of California, San Diego

Principal Investigator

John Weare

Project type

Exploratory Research

- Development of various ab initio molecular dynamics (AIMD) methods, including PAW-AIMD and implenting exact exchange into AIMD methods - AIMD Simulations of highly charge cations in solution. …

Reaction Specificity of Nanoparticles in Solution (PNNL Scope # 42184/44076, Baer/Amonette Nano-Fe BES/EMSP project)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Donald Baer

Project type

Exploratory Research

This User Proposal is being submitted as part of an approved NSET proposal under PIs Don Baer and Paul Tratnyek to perform fundamental basic science studies that will benefit a whole range of…

Sorption of aqueous organic molecules and amino acids on mineral surfaces: determination of binding geometry, local water structure and topological interactions

Lead Institution

Lawrence Berkeley National Laboratory

Principal Investigator

Glenn Waychunas

Project type

Large-Scale EMSL Research

A large frontier in geochemistry is the interaction of organic species with mineral surfaces. Compared to inorganic sorbates which form covalent and hydrogen bonds, organic structures may have…

Projects