Neeraj Kumar

Development of chemical probes for live cell Raman imaging

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Sankarganesh Krishnamoorthy

Biological molecular phenotyping requires characterization tools that can record multiple biological processes and molecular transformations simultaneously in real time. Currently, fluorescence…

Predicting adverse biological effects for chemicals of concern through integration of functional profiling with artificial intelligence/machine learning (AI/ML)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Vivian Lin

We will use thermal proteome profiling (TPP) to identify protein targets and pathways affected by exposure to a chemical of concern (COC). As a next step, we will use an artificial intelligence…

Developing KBase-NWChem workflow for integrating molecular properties with Genome-Scale Metabolic Modeling

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Neeraj Kumar

One of the challenges to investigate natural and engineered biological systems at molecular-level is to accurately predict chemical properties of thousands of metabolites involved in cell metabolism…

Multiscale Modeling of Complex Metabolic and Regulatory Networks of Yarrowia lipolytica

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Neeraj Kumar

Modifying genetic and metabolic pathways in microbes/plants to design systems with desired function remains challenging. Our inability to anticipate how the host organism will respond is due to the…

COVID-19: Molecular design and analysis to inform small molecule therapeutics related to COVID-19

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Neeraj Kumar

The multi-laboratory project will apply DOE capabilities to complement resources available in the public and private sector and thereby accelerate discovery of medical therapeutics targeting SARS-COV…

Bioinspired Homogeneous and Surface-confined Catalysts for Energy Storage and Production Reactions

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Molly O'Hagan

Project type

Large-Scale EMSL Research

Three related research programs at PNNL focus on developing bioinspired electrocatalysts for energy storage, energy production, or carbon fixation reactions such as the production and oxidation of…

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…

Atomistic simulations of the nitrogen fixation by Mo-dependent nitrogenase

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Simone Raugei

Project type

Large-Scale EMSL Research

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

Bio-Inspired Homogeneous Catalysts for Energy Storage and Production

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Molly O'Hagan

Project type

Large-Scale EMSL Research

This proposal is in response to the Energy Materials and Processes Science Theme proposal call requesting resources to support three research programs at PNNL: the DOE Basic Energy Sciences &quot…

In silico Chemical Library Engine (ISICLE) for Expo/Metabo-lomics and Modeling

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Ryan Renslow

Currently, there are no nuclear magnetic resonance or IMS databases specifically built for identifying and quantifying metabolites of relevance to environmental samples in general, or to microbial…

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 and testing of efficient off-loading strategies for many-body electronic structure methods: implementations of efficient decomposition techniques for two-electron integrals

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…

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…

Yarrowia lipolytica for biotechnology and synthetic biology

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Erin Bredeweg

The team at PNNL is using a combination of flow cytometry, microscopy and lipidomics/metabolomics to establish baseline cell biological and metabolite data on DNA agility in eukaryotic organisms, and…

Development of KBase-NWChem Interface for integration of molecular properties with Genome-Scale Metabolic Modeling

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Marat Valiev

One of the challenges to investigate natural and engineered biological systems at molecular-level is to accurately predict chemical properties of thousands of metabolites involved in cell metabolism…

EMSL Science Overview

Neeraj Kumar

Projects

Development of chemical probes for live cell Raman imaging

Predicting adverse biological effects for chemicals of concern through integration of functional profiling with artificial intelligence/machine learning (AI/ML)

Developing KBase-NWChem workflow for integrating molecular properties with Genome-Scale Metabolic Modeling

Multiscale Modeling of Complex Metabolic and Regulatory Networks of Yarrowia lipolytica

COVID-19: Molecular design and analysis to inform small molecule therapeutics related to COVID-19

Bioinspired Homogeneous and Surface-confined Catalysts for Energy Storage and Production Reactions

Biology in Space and Time (BioSaT) Research Campaign

Atomistic simulations of the nitrogen fixation by Mo-dependent nitrogenase

Bio-Inspired Homogeneous Catalysts for Energy Storage and Production

In silico Chemical Library Engine (ISICLE) for Expo/Metabo-lomics and Modeling

Biology in Space and Time (BioSaT) Research Campaign

Development and testing of efficient off-loading strategies for many-body electronic structure methods: implementations of efficient decomposition techniques for two-electron integrals

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

Yarrowia lipolytica for biotechnology and synthetic biology

Development of KBase-NWChem Interface for integration of molecular properties with Genome-Scale Metabolic Modeling