John Weare

(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…

Insights into the RNase A mechanism

Lead Institution

University of California, San Diego

Principal Investigator

John Weare

Project type

Limited Scope

mRNA-polymers copied from DNA are degraded after transcription by cleavage of diphosphate bonds in the RNA backbone by Ribonuclease enzymes (RNase) as part of cell metabolism. In our study we employ…

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…

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 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…

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…

Simulating Mineral Interfaces

Lead Institution

University of California, San Diego

Principal Investigator

John Weare

Project type

Exploratory Research

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…

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. …

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…

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. …

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…

(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…

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…

(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…

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…

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…

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…

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…

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…

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…

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,…

Projects