Projects

Manipulating Monocot (Grass) Lignin-forming Dirigent Protein Complexes for Optimal Bioenergy/Bioproducts

Lead Institution

Washington State University

Principal Investigator

Norman Lewis

Project type

Large-Scale EMSL Research

The overall objective of this proposal is to establish the (bio)chemical basis as to why monocot (grass) lignocellulosic tissues are significantly less recalcitrant to (bio)degradation than their …

Dinitrogen Activation and Electron and Proton Delivery in the Nitrogenase Complex

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Simone Raugei

Project type

Large-Scale EMSL Research

We are requesting EMSL supercomputing resources to tackle the mechanism of electron and proton delivery to dinitrogen (N2) to yield ammonia (NH3) in the Mo-dependent nitrogenase -- biological…

CO2 activation and conversion by the CODH/ACS enzymatic complex

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Simone Raugei

Project type

Large-Scale EMSL Research

The purpose of the proposal is to computationally characterize the key biochemical and biophysical features of carbon monoxide dehydrogenase (CODH) and acetyl-coenzyme A synthase (ACS) enzymatic…

Contaminant immobilization through heterogeneous carbonate growth at mineral/water and mineral/microbe interfaces

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Sebastien Kerisit

Project type

Large-Scale EMSL Research

The presence of mineral surfaces and microorganisms significantly impacts the nature and composition of mineral phases formed in biogeochemical systems. Despite the importance of these heterogeneous…

A cross-scale modeling framework of organic matter biochemistry in river corridor system: Scaling biogeochemical reaction kinetics from molecular to reach scales

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Peiyuan Gao

Project type

Large-Scale EMSL Research

Predicting the decomposition of organic matter in biochemical processes driven by microbes at reach scale remains challenging. These challenges are deeply rooted in the scarcity of rate measurements…

Micro to Macro - Molecular and Spatial Controls on Microbial Function

Lead Institution

Kula Bio, Inc.

Principal Investigator

Darian Smercina

Project type

Large-Scale EMSL Research

Establishing a clear and predictable link between the structure and function of soil microbial communities and ecosystem processes remains one of the greatest challenges in soil ecology. Soil…

Investigating Oiliness: Systems Comparison of Photoautotrophic and Heterotrophic Lipid Production in Auxenochlorella protothecoides.

Lead Institution

University of California, Berkeley

Principal Investigator

Jeffrey Moseley

Project type

Large-Scale EMSL Research

Auxenochlorella protothecoides is a photosynthetic, Trebouxiophyte alga, with a small, highly compact nuclear genome. Auxenochlorella strains are highly oleaginous, accumulating up to 60% of dry…

Understanding Mechanisms Coupling the Fates of Iron Oxides, Organic Matter, and Micronutrient Metals at Redox Hot Spots

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kevin Rosso

Project type

Large-Scale EMSL Research

Iron (oxyhydr)oxide minerals are ubiquitous in soils and sediments and play an commanding role in nutrient cycling, microbial metabolism, carbon protection, and contaminant immobilization. Among them…

Role of Ca in Organic Matter Preservation

Lead Institution

Stanford Linear Accelerator Center

Principal Investigator

Sharon Bone

Project type

Large-Scale EMSL Research

Calcium can play a major role in the preservation of carbon in the subsurface due to its ability to participate in cation bridging. Ca2+ can link together two negatively charged moieties, such as two…

A Colloid is Born: Understanding iron-rich colloid genesis and transformation for improved watershed biogeochemical models

Lead Institution

Stanford Linear Accelerator Center

Principal Investigator

Kristin Boye

Project type

Large-Scale EMSL Research

Interfaces between subsurface layers of floodplains are ‘hot spots’ for thriving biogeochemical activity and exchange, owing to distinct compositional and permeability/porosity differences between…

High-resolution spatio-temporal modeling of root-associated microbial communities

Lead Institution

Boston University

Principal Investigator

Daniel Segre

Project type

Large-Scale EMSL Research

The goals of the proposed project is to implement high-resolution simulations of synthetic microbial ecosystems around the roots of plants. Towards this goal, we will use our platform for Computation…

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…

Waterborne Plastics Environmental Weathering Leachates

Lead Institution

National Renewable Energy Laboratory

Principal Investigator

Benjamin Maurer

Project type

Large-Scale EMSL Research

Aquatic plastics pollution is anticipated to triple globally by 2040, and many of the effects of aquatic plastics and associated degradation products and contaminants are hitherto unknown. This…

Connecting the Physicochemical Properties with Ice Nucleation Properties of Secondary Organic Aerosols (SOAs) Formed from Multiphase Chemical Processes

Lead Institution

Texas A&M University

Principal Investigator

Yue Zhang

Project type

Large-Scale EMSL Research

Organic aerosols (OA), especially secondary organic aerosols (SOA), make up a large fraction of tropospheric fine particulate matter (PM) and up to 80% of the total fine PM in the upper troposphere…

Probing the Martian atmosphere and hydrosphere using micro- and nano-scale analyses

Lead Institution

Royal Ontario Museum

Principal Investigator

Kimberly Tait-Sena

Project type

Large-Scale EMSL Research

Mars has long been the primary target in the search for possible life beyond our planet, mainly due to widespread evidence that water once flowed on its surface. Water is an essential ingredient for…

A new approach to protein folding by reducing dimensionality of protein conformational space

Lead Institution

Oak Ridge National Laboratory

Principal Investigator

Al Geist

Project type

Exploratory Research

The objectives of this proposal are to develop and implement an efficient method to address the problem of protein folding. Our approach is based on reducing the multi-scale and multi-dimensional…

Identification of the SecB residue that is labeled by methanethiosulfonate

Lead Institution

University of Missouri - Columbia

Principal Investigator

Linda Randall

Project type

Exploratory Research

Aim: To identify the residue of SecB that is labeled by methanethiosulfonate (MTSL), a stable nitroxide spin label. SecB, a small tetrameric cytosolic chaperone in E.coli, facilitates the export…

Characterizing Key Factors That Influence Recalcitrance of Lignocellulosic Biomass Deconstruction via in-situ liquid IR SNOM Approach

Lead Institution

Washington State University Tri-Cities

Principal Investigator

Bin Yang

Project type

Exploratory Research

Call Topic: This proposal is in response to Functional and Systems Biology on EMSL’s suite of surface science capabilities are ideal for chemical imaging organic matter mineral interactions…

Model systems for understanding potassium transformations in fungal biomass

Lead Institution

Stanford Linear Accelerator Center

Principal Investigator

Ritimukta Sarangi

Project type

Exploratory Research

Soil biota plays an important role in nutrient cycling processes through breakdown of nutrients from soil minerals or organic matter and rebuilding new nutrient structures for storage within their…

Diel dynamics and physical interactions of phototrophic isolates from a hot spring microbial mat

Lead Institution

Carnegie Institution for Science

Principal Investigator

Devaki Bhaya

Project type

Exploratory Research

The microbial mats in the hot springs of Yellowstone National Park (YNP) are composed of diverse thermophilic microbial communities that have evolved to optimize sharing and utilization of scarce…