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Funding Sources

DOE Office of Science, Office of Biological and Environmental Research

Multi-Scale Modeling Framework for Mercury Biogeochemistry
This project establishes a multiscale modeling toolkit to track mercury speciation inn environmental systems. Log K values are computed form quantum chemistry and input into thermodynamic speciation models for environmental systems.
Funding periond 2016-2019
Current Researchers: Jeremy Smith (PI), Jerry Parks

Oak Ridge National Laboratory, Scientific Focus Area “Biofuels”
The combined capabilities of the Spallation Neutron Source, the High Flux Isotope Reactor, and the National Center for Computational Sciences at Oak Ridge National Laboratory provide new information on lignocellulosic degradation for cellulosic ethanol production.
Funding Period: 2015-2017
Current CMB Researchers: Jeremy Smith, Loukas Petridis

Bioenergy Science Center
Our task in this center is to perform computer simulations of enzymes involved in cellulose deconstruction, including cellulosome component modeling and quantum mechanical/molecular mechanical investigations of cellulase action.
Funding Period: 2007-2017
Current CMB Researchers: Jeremy Smith, Loukas Petridis, Micholas Smith, Barmak Mostofian

Biogeochemical Transformations at Critical Interfaces
Since its inception in 2008, the Oak Ridge National Laboratory (ORNL) Science Focus Area (SFA) program has made substantial progress in fulfilling the overarching objective of elucidating the mechanisms by which inorganic mercury (Hg) is transformed into methylmercury (MeHg) at the sediment–water interface and the processes that determine net MeHg production at contaminated sites. Unique attributes of the ORNL SFA include the range of spatiotemporal scales studied—spanning from watershed to molecular scale and from picoseconds to seasonal variations—and the effective integration of technical expertise from widely varying science disciplines, including hydrology, geochemistry, microbiology, biomolecular sciences, high-performance computer simulations and neutron science.
Funding Period: 2013-2018
Current CMB Researchers: Jeremy Smith, Jerry Parks, Ryne Johnston, Jing Zhou

Active Biosystems Imaging
Understanding how observable biological processes, carried out over wide ranging temporal and spatial scales, arise from molecular scale events represents a grand challenge facing biological and environmental research. Underpinning this challenge is the need to monitor the flow of materials and information in response to environmental perturbations. Therefore, we propose to develop and apply an adaptive approach to imaging, wherein computational modeling and simulation guide interactive, molecular imaging measurements to couple systems models to observable phenomena. We will apply the unique resources of ORNL and our academic collaborators to advance and integrate new instrumentation, stable-isotope probes and supercomputer-driven simulation tools to trace the production, transport and fate of selected metabolites in bacterial systems. Our pilot efforts will focus on understanding the structure and organization of cellular membranes and the movement of chemicals within and between cells and within their environment. The resulting capability will serve as a framework for designing and implementing bioimaging experiments that reach across the hierarchies and dimensions of biological systems to provide understanding to a diverse array of biological and environmental processes.
Funding Period: 2014-2016
Current CMB Researchers: Xiaolin Cheng, Jeremy Smith

DOE Office of Science, Basic Energy Sciences

Center for Lignocellulose Structure and Formation- Energy Frontier Research Centers
CLSF (Center for Lignocellulose Structure and Formation) is a DOE Energy Frontiers Research Center focused on developing a detailed understanding of lignocellulose, the main structural material in plants, from cellulose synthesis and fibril formation to a mature plant cell wall, forming a foundation for significant advancement in sustainable energy and materials. (Description taken from CLSF website)
Funding Period: 2014-2018
Current CMB Researchers: Loukas Petridis

Oak Ridge National Laboroatroy projects

Integrating Small-Angle Neutron Scattering with Molecular Simulation to Determine Structural Ensembles of Complex Biological Systems
Source: ORNL- Laboratory Directed Reasearch and Developement project
The goal of this project is to understand neutron scattering from kinase systems in terms of ensembles of structures. High-performance computational simulation is married with small-angle neutron scattering experiments and deuterium labeling.
Funding Period: 2016-2018
Current CMB Researchers: Loukas Petridis (PI), Jeremy Smith, Xiaolin Cheng

Overcoming Antibiotic Resistance: Neutron Crystallographic and Quantum Chemical Studies of a Beta-Lactamase Enzyme
Source: ORNL – Laboratory Directed R&D Seed Fund
Description: Combine neutron crystallography and computational chemistry to determine key steps in the inactivation of the antibiotic cefotaxime by a class A beta-lactamase.
Funding Period: 2015-2017
Current CMB Researchers: Jerry Parks

Functional domains in model membranes and protocells probed with high-performance simulation and neutron scattering
Source: ORNL LDRD funds
Description: We aim to combine high performance computing (HPC) simulation, neutron scattering and bottom-up assembly of asymmetric membrane systems to investigate the interplay between membrane organization and membrane asymmetry.
Funding Period: 2014-2017
Current CMB Researchers: Xiaolin Cheng, Barmak Mostofian

National Science Foundation

NIMBioS- Center for Synthesis of Mathematics and Biology
A major goal of mathematical models and analysis in biology is to provide insight into the complexities arising from the non-linearity and hierarchical nature of biological systems. The Center fosters the maturation of cross-disciplinary approaches in mathematical biology and fosters the development of a cadre of researchers who are capable of conceiving and engaging in creative and collaborative connections across disciplines to address fundamental and applied biological questions. The Center : 1) addresses key biological questions by facilitating the assembly and productive collaboration of interdisciplinary teams; and 2) fosters development of the critical and essential human capacity to deal with the complexities of the multi-scale systems that characterize modern biology.
Funding Period: 2008-2018
Current CMB Researchers: Jeremy Smith, Quentin Johnson, Tongye Shen

INTEL Corporation

Porting and Optimization of the General-Purpose Molecular Dynamics Code GROMACA on the Next-Generation Intel-Based Computers
This grant is for the Porting and Optimization of the General-Purpose Molecular Dynamics Code GROMACS on Next-Generation Intel-Based Computers.
Funding Period: 2014-2017
Current CMB Researchers: John Eblen

National Institutes of Health-National Institute of Allergy and Infectious Diseases

Transport Across Two Membranes by AcrAB-TolC
Our long-term goal is to understand the molecular mechanism of drug efflux in Gram-negative bacteria and to develop approaches to inhibit multidrug efflux transporters. Our findings exposed a previously unknown vulnerability of multidrug pumps that could be targeted in the development of new inhibitors. Our specific aims are: (i) to investigate the activation of multidrug efflux pumps; (ii) to investigate the mechanisms of drug efflux inhibition; (iii) to identify new allosteric inhibitors of drug efflux transporters.
Funding Period: 2014-2019
Current CMB Researchers: Jerry Parks, Jerome Baudry, Jeremy Smith, Adam Green

Design of Accelerated Acetylcholin-esterase Reactivators through Mechanistic Neutron Diffraction Studies
Funding Period: 2014-2019
Current CMB Researchers: Xiaolin Cheng, Mikolai Fajer

Other projects

Mechanism of Drug Permeation Across Gram-Negative Outer Membranes
SOURCE: Defense Threat Reduction Agency
Description: Measure rates of drug uptake and efflux by Gram-negative bacteria for a diverse range of compounds and develop predictive models of drug permeation across Gram-negative outer membranes.
Funding Period: 2016-2017
Current CMB Researchers: Jerry Parks, Sarah Cooper

Zinkicide A Nanotherapeutic for HLB
Source: U.S. Department of Agriculture
Description: need
Funding Period: 2015-present
Current CMB Researchers: Loukas Petridis

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