Papers by Kurt Glaesemann
A Generic Advanced Computing Framework for Executing Windows-based Dynamic Contingency Analysis Tool in Parallel on Cluster Machines
2020 IEEE Power & Energy Society General Meeting (PESGM), 2020
Dynamic contingency analysis tool (DCAT) has been developed to assess the impact and likelihood o... more Dynamic contingency analysis tool (DCAT) has been developed to assess the impact and likelihood of extreme contingencies and potential cascading events across their systems and interconnections. By including more customized protection models and corrective actions into the Windows-based commercial tools, DCAT can help operators understand the cascading behavior and find mitigation approaches to reduce the risk of cascading outages in a more realistic manner. In order to further enhance the capability of DCAT, this paper presents a design of an advanced computing framework that enables DCAT to run on a cluster machine to improve its computational performance. This framework is generic and can be applied to other Windows-based simulation tools to fill the technical gap of applying advanced computing technology to vendors’ Windows-based tools. The preliminary tests using medium to large power systems have shown the effectiveness of this framework and its potential for accelerating the ...
Fully in Silico Calibration of Empirical Predictive Models for Environmental Fate Properties of Novel Munitions Compounds
: Predicting the environmental fate of novel munitions compounds requires data for the key proper... more : Predicting the environmental fate of novel munitions compounds requires data for the key properties that control contaminant fate, and the most common way to predict these properties is with empirical quantitative structure-activity relationships (QSARs). However, the traditional approach to QSAR development (calibration with experimental data) is challenging for new explosives compounds because of limitations to the availability of these materials. Some of the necessary environmental fate properties can be calculated directly from molecular structure theory, but reliable calculations of this type require considerable theoretical expertise and computational effort. To overcome this combination of challenges, we used a hybrid, partially in silico approach to QSAR development, where some of the calibration data (both the target variable and the descriptor variables) were calculated from molecular structure theory.
MerCat (“ Mer - Cat enate”) is a parallel, highly scalable and modular property software package ... more 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 and raw sequence reads from any platform as input, MerCat performs k-mer counting of any length k, resulting in feature abundance counts tables. MerCat allows for direct analysis of data properties without reference sequence database dependency commonly used by search tools such as BLAST for compositional analysis of whole community shotgun sequencing (e.g., metagenomes and metatranscriptomes).
ISiCLE: A quantum chemistry pipeline for establishing in silico collision cross section libraries
Analytical Chemistry
ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multi-omics data analysis... more ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multi-omics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein-coding open reading frames (ORFs) rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.
Aiding Cascading Analysis Modelling with High-performance-computing Technology
IFAC-PapersOnLine
Contingency Analysis Post-Processing With Advanced Computing and Visualization
IFAC-PapersOnLine
Nature Physics, 2007
Despite decades of research, the microscopic details and extreme states of matter found within a ... more Despite decades of research, the microscopic details and extreme states of matter found within a detonating high explosive have yet to be elucidated. Here we present the first quantum molecular-dynamics simulation of a shocked explosive near detonation conditions. We discover that the wide-bandgap insulator nitromethane (CH 3 NO 2) undergoes chemical decomposition and a transformation into a semimetallic state for a limited distance behind the detonation front. We find that this transformation is associated with the production of charged decomposition species and provides a mechanism to explain recent experimental observations.
Improved heat capacity estimator for path integral simulations
The Journal of Chemical Physics, Aug 14, 2002
mSystems, 2016
Soil metagenomics has been touted as the “grand challenge” for metagenomics, as the high microbia... more Soil metagenomics has been touted as the “grand challenge” for metagenomics, as the high microbial diversity and spatial heterogeneity of soils make them unamenable to current assembly platforms. Here, we aimed to improve soil metagenomic sequence assembly by applying the Moleculo synthetic long-read sequencing technology. In total, we obtained 267 Gbp of raw sequence data from a native prairie soil; these data included 109.7 Gbp of short-read data (~100 bp) from the Joint Genome Institute (JGI), an additional 87.7 Gbp of rapid-mode read data (~250 bp), plus 69.6 Gbp (>1.5 kbp) from Moleculo sequencing. The Moleculo data alone yielded over 5,600 reads of >10 kbp in length, and over 95% of the unassembled reads mapped to contigs of >1.5 kbp. Hybrid assembly of all data resulted in more than 10,000 contigs over 10 kbp in length. We mapped three replicate metatranscriptomes derived from the same parent soil to the Moleculo subassembly and found that 95% of the predicted genes,...
AIP Conference Proceedings, 2006
We describe improvements to the Cheetah thermochemical-kinetics code's equilibrium solver to enab... more We describe improvements to the Cheetah thermochemical-kinetics code's equilibrium solver to enable it to find a wider range of thermodynamic states. Cheetah supports a wide range of elements, condensed detonation products, and gas phase reactions. Therefore, Cheetah can be applied to a wide range of shock problems involving both energetic and non-energetic materials. An improve equation of state is also introduced. New experimental validations of Cheetah's equation of state methodology have been performed, including both reacted and unreacted Hugoniots
Ab Initio Calculations of Reactive Pathways for r-Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine ( r-HMX)
J Phys Chem a, 2000
Integrated State Estimation and Contingency Analysis Software Implementation using High Performance Computing Techniques
IFAC-PapersOnLine, 2015
Purpose With the trend towards needing information about chemistry at conditions significantly di... more Purpose With the trend towards needing information about chemistry at conditions significantly different from 298K and 1 atm., methods need to be developed to generate and interpret this data. This demand for information about chemistry at extreme conditions comes from many fields. The study of atmospheric chemistry requires knowledge of unusual species that are formed when molecules are exposed to ultraviolet radiation. Studying of energetic materials requires knowledge of the thermochemical and structural properties of a myriad of chemical species under a wide range of temperatures. Basic scientific understanding of the very nature of a chemical bond requires detailed information. Studying these problems computationally requires multiple capabilities. The methodology used must provide both high accuracy and computational efficiency. Studying extreme chemistry also suffers from all the challenges of studying chemistry under non-extreme conditions. Therefore, either a new method must be developed or an old method must be applied in an innovative way. The approach The method we have chosen to use is path integral Monte Carlo (PIMC) for the nuclear degrees of freedom and ab initio electronic structure methods for the electronic degrees of freedom. PIMC and ab initio electronic structure are methods of treating the quantum nature of particles. These methods have been chosen, because an accurate treatment requires treating both the electrons and the nuclei as quantum particles. We developed new "projected" methods that reduce the computational demands. These methods along with PIMC in general are described in two Journal of Chemical Physics articles (UCRL-JC-144960 and UCRL-JC-147423). This methodology was implemented into a PIMC code developed as part of this LDRD. The code was parallelized in order to utilize the computational resources of LLNL. Technical accomplishments By coupling quantum treatment of the electrons via ab initio method to the quantum motion of the nuclei with PIMC, a method that is able to produce accurate results is obtained. This level of accuracy is necessary under extreme conditions, because traditional "empirical" corrections are not applicable under such conditions. Because the electronic structure is tightly coupled to the motion of the nuclei, ab initio methods must be used to treat the electrons. These methods have explicit molecular orbital dependence are not parameterized to simply reproduce an equilibrium geometry. This method can calculate structural information, energetics, and heat capacities. The thermochemical results are described in detail in a Journal of Chemical Physics article (UCRL-JC-149046). Conclusion A theoretical method must provide the level of accuracy needed to answer the question of interest; otherwise, the results could be potentially misleading. This methodology used in this LDRD provided both structural and energetic information. The method used provides a fully quantum approach to calculation properties of molecules under extreme conditions. The software to perform these calculations is written and is integrated with a variety of electronic structure codes (GAMESS and Fireball). The code incorporates new computer time saving methodologies. This method calculates the properties needed, such as energy and heat capacity. The code continues to be used after the completion of the LDRD.
On the Ordering of Orbital Energies in High-Spin ROHF
The Journal of Physical Chemistry a, May 1, 2010
The restricted open-shell Hartree-Fock (ROHF) method is a standard tool used by quantum chemists ... more 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 a problem with some implementations of the ROHF method is presented along with an elegant solution. The ground state (2)A(2) potential energy surface of the 5,5'-(4H, 4H')-spirobi[cyclopenta[c]pyrrole]-2,2'6,6'-tetrahydro cation is the molecular test case, which elucidates the underlying problem. For this molecule, four distinct ROHF perturbation theories yield smooth (and parallel) potential energy curves. The arbitrariness of the ROHF orbital energies is illustrated with diatomic CN. The method proposed will also fix Aufbau principle violations reported by Plakhutin and Davidson [Plakhutin, B. N.; Davidson, E. R. J. Phys. Chem. A 2009, 113, 12386-12395].
Sub-second state estimation implementation and its evaluation with real data
2015 IEEE Power & Energy Society General Meeting, 2015
We introduce a new thermodynamic theory for detonation products that includes polar and ionic spe... more We introduce a new thermodynamic theory for detonation products that includes polar and ionic species. The new formalism extends the domain of validity of the previously developed EXP6 equation of state library and opens the possibility of new applications. We illustrate the scope of the new approach on PETN detonation properties and water ionization models.
Long timescale dynamics of shocked nitromethane
ABSTRACT
A semi-metallic layer in detonating nitromethane
ABSTRACT
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Papers by Kurt Glaesemann