A5079804379- Biofuel production and bioconversion
- Lignin and Wood Chemistry
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Advanced Cellulose Research Studies
- Polysaccharides and Plant Cell Walls
- Catalysis for Biomass Conversion
- Plant Gene Expression Analysis
- Fermentation and Sensory Analysis
- Advanced NMR Techniques and Applications
- Nuclear Physics and Applications
- Parathyroid Disorders and Treatments
- Enzyme-mediated dye degradation
- Fibroblast Growth Factor Research
- Bone health and treatments
- Spectroscopy and Quantum Chemical Studies
- Photosynthetic Processes and Mechanisms
- Mass Spectrometry Techniques and Applications
- Microbial Metabolic Engineering and Bioproduction
- Computational Drug Discovery Methods
- Machine Learning in Bioinformatics
- Clay minerals and soil interactions
- Power Transformer Diagnostics and Insulation
- NMR spectroscopy and applications
- Material Dynamics and Properties
Oak Ridge National Laboratory
2015-2024
University of Tennessee at Knoxville
2015-2024
University of Tennessee Health Science Center
2022
Tennessee Technological University
2022
Oak Ridge Associated Universities
2014-2020
Knoxville College
2020
University of Maryland, College Park
2018
National Renewable Energy Laboratory
2010
University of Cambridge
2006
Lignocellulosic biomass, a potentially important renewable organic source of energy and chemical feedstock, resists degradation to glucose in industrial hydrolysis processes thus requires expensive thermochemical pretreatments. Understanding the mechanism biomass breakdown during these pretreatments will lead more efficient use biomass. By combining multiple probes structure, sensitive different length scales, with molecular dynamics simulations, we reveal two fundamental responsible for...
The conversion of plant biomass to ethanol via enzymatic cellulose hydrolysis offers a potentially sustainable route biofuel production. However, the inhibition activity in pretreated by lignin severely limits efficiency this process.By performing atomic-detail molecular dynamics simulation model containing cellulose, lignin, and cellulases (TrCel7A), we elucidate detailed mechanisms. We find that binds preferentially both elements which also bind (the hydrophobic faces) specific residues on...
We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by compound databases into representative protein binding-site conformations, thus taking account the dynamic properties binding sites. also describe preliminary obtained 24 systems involving eight proteins proteome SARS-CoV-2. The involves temperature replica exchange sampling, making massively parallel...
Lignins are hydrophobic, branched polymers that regulate water conduction and provide protection against chemical biological degradation in plant cell walls. also form a residual barrier to effective hydrolysis of biomass pretreated at elevated temperatures cellulosic ethanol production. Here, the temperature-dependent structure dynamics individual softwood lignin aqueous solution examined using extensive (17 μs) molecular simulations. With decreasing temperature lignins found transition...
Lignin transitions from a collapsed globular state to random-coil when in exposed tetrahydrofuran and water cosolvent system at CELF pretreatment temperatures.
Interactions of water with cellulose are both fundamental and technological importance. Here, we characterize the properties associated using deuterium labeling, neutron scattering molecular dynamics simulation. Quasi-elastic provided quantitative details about dynamical relaxation processes that occur was supported by structural characterization small-angle X-ray diffraction. We can unambiguously detect two populations cellulose. The first is "non-freezing bound" gradually becomes mobile...
A cellulose synthesis complex with a "rosette" shape is responsible for of chains and their assembly into microfibrils within the cell walls land plants charophyte algal progenitors. The number synthase proteins in this large multisubunit transmembrane protein microfibril have been debated many years. This work reports low resolution structure catalytic domain CESA1 from Arabidopsis (Arabidopsis thaliana; AtCESA1CatD) determined by small-angle scattering techniques provides first...
Significance A major challenge in biology is characterizing the structural flexibility of intrinsically disordered proteins (IDPs). Ensemble-averaged experimental data do not provide underlying protein structures. Here, we performed independently small-angle neutron and X-ray scattering experiments unbiased molecular dynamics simulations to probe solution structure an IDP. We report that enhancing sampling can generate ensemble IDP structures quantitative agreement with NMR, without need for...
Pretreatment facilitates more complete deconstruction of plant biomass to enable economic production lignocellulosic biofuels and byproducts. Various co-solvent pretreatments have demonstrated advantages relative aqueous-only methods by enhancing lignin removal allow unfettered access cellulose. However, there is a limited mechanistic understanding the interactions between co-solvents cellulose that impedes further improvement such pretreatment methods. Recently, tetrahydrofuran (THF) has...
The complex structure of plant cell walls resists chemical or biological degradation, challenging the breakdown lignocellulosic biomass into renewable precursors that could form basis future production green chemicals and transportation fuels. Here, experimental computational results reveal effect tetrahydrofuran (THF)–water cosolvents on lignin its interactions with cellulose in wall drives multiple synergistic mechanisms leading to efficient fractionation valuable precursors. Molecular...
Abstract Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange (HREMD) led unbiased and accurate ensembles, reproducing small-angle scattering NMR chemical shift experiments, for three IDPs varying sequence properties two recently optimized force fields, indicating general...
A strategy is described for a fast all-atom molecular dynamics simulation of multimillion-atom biological systems on massively parallel supercomputers. The developed using benchmark particular interest to bioenergy research, comprising models cellulose and lignocellulosic biomass in an aqueous solution. approach involves the reaction field (RF) method computation long-range electrostatic interactions, which permits efficient scaling many thousands cores. Although range applicability RF...
The precipitation of lignin onto cellulose after pretreatment lignocellulosic biomass is an obstacle to economically viable cellulosic ethanol production. Here, 750 ns nonequilibrium molecular dynamics simulations are reported a system and in aqueous solution. Lignin found strongly associate with itself the cellulose. However, noncrystalline regions observed have lower tendency than crystalline regions, this arise from stronger hydration chains. results suggest that recalcitrance hydrolysis...
We develop a comprehensive molecular mechanics force field for lignin and evaluate its performance in terms of thermodynamics structure with respect to experimental observables. The developed can be used model polymers, including their covalent linkages carbohydrates, interaction other biomolecules.
The scattering of neutrons can be used to provide information on the structure and dynamics biological systems multiple length time scales. Pursuant a National Science Foundation-funded workshop in February 2018, recent developments this field are reviewed here, as well future prospects that expected given advances sources, instrumentation computational power methods. Crystallography, solution scattering, dynamics, membranes, labeling imaging examined. For extraction maximum information,...
Abstract A CHARMM molecular mechanics force field for lignin is derived. Parameterization based on reproducing quantum mechanical data of model compounds. Partial atomic charges are derived using the RESP electrostatic potential fitting method supplemented by examination methoxybenzene:water interactions. Dihedral parameters optimized to critical rotational potentials and bonded obtained optimizing vibrational frequencies normal modes. Finally, validated performing a dynamics simulation...
Lignin, a major polymeric component of plant cell walls, forms aggregates in vivo and poses barrier to cellulosic ethanol production. Here, neutron scattering experiments molecular dynamics simulations reveal that lignin are characterized by surface fractal dimension is invariant under change scale from $~$1--1000 \AA{}. The also extensive water penetration the heterogeneous chain corresponding rigid core with fluid surface.
Abstract Lignocellulosic biomass provides a sustainable source of sugars for biofuel and biomaterial production. However, resistance to degradation imposes difficulties economical conversion plant carbohydrates fermentable sugars. One the key contributors recalcitrance is lignin. Understanding properties lignin macromolecules in cell wall matrix useful manipulating structure generate more easily degradable biomass. Along with experimental techniques such as 2D‐NMR mass spectrometry,...
Hemicellulose–cellulose strong associations at elevated temperatures slows cellulose conversion significantly.
The ionic liquid (IL) 1-ethyl-3-methylimidazolium acetate ([EMIM]Acetate) has been widely used for biomass processing, i.e., to pretreat, activate, or fractionate lignocellulosic produce soluble sugars and lignin. However, this IL does not achieve high solubility, therefore minimizing the efficiency of processing. In study, [EMIM]Acetate three other ILs composed different 3-methylimidazolium cations carboxylate anions ([EMIM]Formate, 1-allyl-3-methylimidazolium ([AMIM]) formate,...
Abstract Low‐molecular‐weight lignin binds to cellulose during the thermochemical pretreatment of biomass for biofuel production, which prevents efficient hydrolysis sugars. The binding properties are influenced strongly by conformations it adopts. Here, we use molecular dynamics simulations in aqueous solution investigate dependence shape polymers on chain length and temperature. Lignin is found adopt collapsed water at 300 500 K. However, K, a discontinuous transition polymer as function...
The doublet C4 peaks at ~ 85 and 89 ppm in solid-state 13C NMR spectra of native cellulose have been attributed to signals atoms on the surface (solvent-exposed) interior microfibrils, designated as sC4 iC4, respectively. relative intensity ratios iC4 observed used estimate degree crystallinity number glucan chains microfibrils. However, molecular structures responsible for specific not positively confirmed. Using density functional theory (DFT) methods produced from classical dynamics...
Selective solvation of xylan by water in the THF–Water miscibility gap allows tunable solubilization.