A5057783289- Advanced Chemical Physics Studies
- Energetic Materials and Combustion
- Combustion and Detonation Processes
- Genomics and Phylogenetic Studies
- Spectroscopy and Quantum Chemical Studies
- Metabolomics and Mass Spectrometry Studies
- High-pressure geophysics and materials
- Mass Spectrometry Techniques and Applications
- Photochemistry and Electron Transfer Studies
- Optimal Power Flow Distribution
- Microbial Community Ecology and Physiology
- Quantum, superfluid, helium dynamics
- Power System Optimization and Stability
- Bioinformatics and Genomic Networks
- Crystallography and molecular interactions
- Distributed and Parallel Computing Systems
- X-ray Diffraction in Crystallography
- Advanced NMR Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Analytical Chemistry and Chromatography
- Electric Power System Optimization
- Atomic and Subatomic Physics Research
- Chemical Thermodynamics and Molecular Structure
- Research Data Management Practices
- Hemoglobin structure and function
Environmental Molecular Sciences Laboratory
2010-2023
Pacific Northwest National Laboratory
2010-2020
Battelle
2010
John Wiley & Sons (United States)
2010
Lawrence Livermore National Laboratory
2002-2007
Massachusetts Institute of Technology
2007
University of Utah
2000-2001
Iowa State University
1998-2000
Ames National Laboratory
1998-2000
United States Department of Energy
1998-2000
Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support guide experimental efforts for prediction atomistic electronic properties. In this regard, structure played a special role using first-principle-driven methodologies model complex processes. Over past few decades, rapid development computing technologies tremendous increase in power offered unique chance study transformations sophisticated...
Improvements to the Sankey-Niklewaki method [O. F. Sankey and D. J. Niklewski, Phys. Rev. B 40, 3979 (1989)] for computing total energies forces, within an ab initio tight-binding formalism, are presented here. In particular, improved (called FIREBALL) uses separable pseudopotential (Hamann or Troullier) goes beyond minimal ${\mathrm{sp}}^{2}$ basis set of Sankey-Niklewski method, allowing double numerical sets with addition polarization orbitals d set. A major improvement includes use more...
High-throughput, comprehensive, and confident identifications of metabolites other chemicals in biological environmental samples will revolutionize our understanding the role these chemically diverse molecules play systems. Despite recent technological advances, metabolomics studies still result detection a disproportionate number features that cannot be confidently assigned to chemical structure. This inadequacy is driven by single most significant limitation metabolomics, reliance on...
Soil microorganisms carry out key processes for life on our planet, including cycling of carbon and other nutrients supporting growth plants. However, there is poor molecular-level understanding their functional roles in ecosystem stability responses to environmental perturbations. This knowledge gap largely due the difficulty culturing majority soil microbes. Thus, use culture-independent approaches, such as metagenomics, promises direct assessment potential microbiomes. is, however, a...
The natural orbitals and their corresponding occupation numbers are constructed for several interesting problems to demonstrate that the existence of negative orbital single reference correlation methods provides a simple diagnostic need multiconfigurational description wave function.
Using the BLYP and B3LYP level of density functional theory, four possible decomposition reaction pathways HMX in gas phase were investigated: N−NO2 bond dissociation, HONO elimination, C−N scission ring, concerted ring fission. The energetics each these mechanisms are reported. Dissociation is putatively initial mechanism nitramine phase. Our results find dissociation energy this to be 41.8 kcal/mol at 40.5 level, which comparable experimental results. Three other calculated found...
The restricted open-shell Hartree-Fock (ROHF) method is a standard tool used by quantum chemists for studying molecules with unpaired electrons. In this work problem some implementations of the ROHF presented along an elegant solution. ground state (2)A(2) potential energy surface 5,5'-(4H, 4H')-spirobi[cyclopenta[c]pyrrole]-2,2'6,6'-tetrahydro cation molecular test case, which elucidates underlying problem. For molecule, four distinct perturbation theories yield smooth (and parallel)...
New path integral Monte Carlo constant volume specific heat (CV) estimators are presented that improve upon the thermodynamic, virial, and centroid virial CV via a free particle projection. These projected significantly reduce numerical noise of traditional estimators. The new thermodynamic estimator has particular advantages when derivatives potential expensive to evaluate. A double is derived for real space integrals comparisons made it. found be better than noncentroid
ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multi-omics data analysis pipeline that massively parallel and scalable. contains modular assembly, annotation, quantification genome binning of metagenomics metatranscriptomics framework reference metaproteomic database construction. transforms raw sequence into functional taxonomic at the microbial population level provides genome-centric resolution through binning. robust taxonomy based on majority voting...
A new path integral energy estimator is presented that improves upon the thermodynamic via a free particle projection. This centroid significantly reduces numerical noise of estimator. The debate as to which better (virial, virial, or thermodynamic) partially resolved. estimators are found be than their noncentroid analogues. has accuracy close virial estimator, and may have particular advantages when derivatives potential expensive evaluate.
The proper description of electron transfer (ET) processes in mixed-valence compounds poses a significant challenge for commonly used theoretical approaches. In this paper we analyze the 1(2)A(2) and 2(2)A(2) potential energy surfaces Spiro cation (5,5'(4H,4H')-spirobi[cyclopenta[c]pyrrole]2,2',6,6'-tetrahydro cation) which is frequently model to study ET processes. We compare contrast results obtained with three different methods: multireference perturbation theory, equation-of-motion...
A study of FeCO+ and Fe+ using both the second-order multi-configurational quasi-degenerate perturbation theory (MC-QDPT2) method coupled cluster with single double replacements (augmented by perturbative triples) [CCSD(T)] are presented. An all-electron triple-ζ valence plus polarization basis set was used in all calculations. The equilibrium CCSD(T) geometry is found to be linear (4Σ-) a CO distance 1.905 Å bond 1.133 Å. dissociation energy D0 4Σ- 6D 1Σ+ predicted 28.8 kcal mol-1, which...
Electronic structure methods were used to calculate the gas and aqueous phase reaction energies for reductive dechlorination (i.e., hydrogenolysis), β-elimination, dehydrochlorination, nucleophilic substitution by OH− of 1,2,3-trichloropropane. The thermochemical properties ΔHf°(298.15 K), S°(298.15 K, 1 bar), ΔGS(298.15 bar) calculated using ab initio electronic calculations, isodesmic reactions schemes, gas-phase entropy estimates, continuum solvation models 1,2,3-trichloropropane several...
The calculation of thermochemical data requires accurate molecular energies. When such high accuracy is needed, often a method as G1, G2, or G3 used to calculate the energy. These methods rely upon standard harmonic normal mode analysis vibrational and rotational contributions We present for going beyond analysis, which uses path integral Monte Carlo contributions. Anharmonic effects are found be large 2.5 kcal/mol molecules studied. Analytical determining an optimal discretization...
This paper describes the performance of a parallel state estimation (PSE) software implemented using advanced computing techniques. The developed code is able to solve large-size, practical power systems within one second. Benchmarking tests against commercial Energy Management System tool shows that computational speed more than 10 times faster with same level accuracy. Benefits brought by sub-second are also discussed in aspects improving robustness estimation, maintaining system...
Density functional theory (DFT) has gained popularity, because it can frequently give accurate energies and geometries. Because evaluating DFT integrals fully analytically is usually impossible, most implementations use numerical quadrature over grid points, which lead to instabilities. To avoid these instabilities, the Almlöf-Zheng (AZ) grid-free approach was developed. This involves application of resolution identity (RI) evaluate integrals. The focus current work on implementation AZ into...
ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multi-omics data analysis pipeline that massively parallel and scalable. contains modular assembly, annotation, quantification genome binning of metagenomics metatranscriptomics framework reference metaproteomic database construction. transforms raw sequence into functional taxonomic at the microbial population level provides genome-centric resolution through binning. robust taxonomy based on majority voting...
Power system simulation tools are traditionally developed in sequential mode and codes optimized for single core computing only. However, the increasing complexity power grid models requires more intensive computation. The traditional will soon not be able to meet operation requirements. Therefore, need evolve accordingly provide faster better results operations. This paper presents an integrated state estimation contingency analysis software implementation using high performance techniques....
The calculation of thermochemical data requires accurate molecular energies and heat capacities. Traditional methods rely upon the standard harmonic normal-mode analysis to calculate vibrational rotational contributions. We utilize path-integral Monte Carlo for going beyond contributions ab initio energies. This is an application extension a method previously developed in our group [J. Chem. Phys. 118, 1596 (2003)].
We describe improvements to the Cheetah thermochemical‐kinetics code’s equilibrium solver enable it find a wider range of thermodynamic states. supports wide elements, condensed detonation products, and gas phase reactions. Therefore, can be applied shock problems involving both energetic non‐energetic materials. An improve equation state is also introduced. New experimental validations Cheetah’s methodology have been performed, including reacted unreacted Hugoniots.
Dynamic contingency analysis tool (DCAT) has been developed to assess the impact and likelihood of extreme contingencies potential cascading events across their systems interconnections. By including more customized protection models corrective actions into Windows-based commercial tools, DCAT can help operators understand behavior find mitigation approaches reduce risk outages in a realistic manner. In order further enhance capability DCAT, this paper presents design an advanced computing...
Density functional theory (DFT) has gained popularity because it can frequently give accurate energies and geometries. The evaluation of DFT integrals in a fully analytical manner is generally impossible; thus, most implementations use numerical quadrature over grid points. grid-free approaches were developed as viable alternative based upon the resolution identity (RI). Of particular concern convergence RI with respect to basis set approach. Conventional atomic sets are inadequate for...
MerCat (“ Mer - Cat enate”) is a parallel, highly scalable and modular property software package for robust analysis of features in next-generation sequencing data. Using assembled contigs raw sequence reads from any platform as input, performs k-mer counting length k, resulting feature abundance counts tables. allows direct data properties without reference database dependency commonly used by search tools such BLAST compositional whole community shotgun (e.g., metagenomes metatranscriptomes).