Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Electronic Structure Software”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
NASA NTRS2009

Spinoff 2009

Topics covered include: Image-Capture Devices Extend Medicine's Reach; Medical Devices Assess, Treat Balance Disorders; NASA Bioreactors Advance Disease Treatments; Robotics Algorithms Provide Nutritional Guidelines; "Anti-Gravity" Treadmills Speed Rehabilitation; Crew Management Processes Revitalize Patient Care; Hubble Systems Optimize Hospital Schedules; Web-based Programs Assess Cognitive Fitness; Electrolyte Concentrates Treat Dehydration; Tools Lighten Designs, Maintain Structural Integrity; Insulating Foams Save Money, Increase Safety; Polyimide Resins Resist Extreme Temperatures; Sensors Locate Radio Interference; Surface Operations Systems Improve Airport Efficiency; Nontoxic Resins Advance Aerospace Manufacturing; Sensors Provide Early Warning of Biological Threats; Robot Saves Soldier's Lives Overseas (MarcBot); Apollo-Era Life Raft Saves Hundreds of Sailors; Circuits Enhance Scientific Instruments and Safety Devices; Tough Textiles Protect Payloads and Public Safety Officers; Forecasting Tools Point to Fishing Hotspots; Air Purifiers Eliminate Pathogens, Preserve Food; Fabrics Protect Sensitive Skin from UV Rays; Phase Change Fabrics Control Temperature; Tiny Devices Project Sharp, Colorful Images; Star-Mapping Tools Enable Tracking of Endangered Animals; Nanofiber Filters Eliminate Contaminants; Modeling Innovations Advance Wind Energy Industry; Thermal Insulation Strips Conserve Energy; Satellite Respondent Buoys Identify Ocean Debris; Mobile Instruments Measure Atmospheric Pollutants; Cloud Imagers Offer New Details on Earth's Health; Antennas Lower Cost of Satellite Access; Feature Detection Systems Enhance Satellite Imagery; Chlorophyll Meters Aid Plant Nutrient Management; Telemetry Boards Interpret Rocket, Airplane Engine Data; Programs Automate Complex Operations Monitoring; Software Tools Streamline Project Management; Modeling Languages Refine Vehicle Design; Radio Relays Improve Wireless Products; Advanced Sensors Boost Optical Communication, Imaging; Tensile Fabrics Enhance Architecture Around the World; Robust Light Filters Support Powerful Imaging Devices; Thermoelectric Devices Cool, Power Electronics; Innovative Tools Advance Revolutionary Weld Technique; Methods Reduce Cost, Enhance Quality of Nanotubes; Gauging Systems Monitor Cryogenic Liquids; Voltage Sensors Monitor Harmful Static; and Compact Instruments Measure Heat Potential.

Source record↗
DOE OSTI2024

PigmentHunter: A point-and-click application for automated chlorophyll-protein simulations

Chlorophyll proteins (CPs) are the workhorses of biological photosynthesis, working together to absorb solar energy, transfer it to chemically active reaction centers, and control the charge-separation process that drives its storage as chemical energy. Yet predicting CP optical and electronic properties remains a serious challenge, driven by the computational difficulty of treating large, electronically coupled molecular pigments embedded in a dynamically structured protein environment. To address this challenge, we introduce here an analysis tool called PigmentHunter, which automates the process of preparing CP structures for molecular dynamics (MD), running short MD simulations on the nanoHUB.org science gateway, and then using electrostatic and steric analysis routines to predict optical absorption, fluorescence, and circular dichroism spectra within a Frenkel exciton model. Inter-pigment couplings are evaluated using point-dipole or transition-charge coupling models, while site energies can be estimated using both electrostatic and ring-deformation approaches. The package is built in a Jupyter Notebook environment, with a point-and-click interface that can be used either to manually prepare individual structures or to batch-process many structures at once. Here, we illustrate PigmentHunter’s capabilities with example simulations on spectral line shapes in the light harvesting 2 complex, site energies in the Fenna–Matthews–Olson protein, and ring deformation in photosystems I and II.

14 SOLAR ENERGY↗
DOE OSTI2023

Two excited-state datasets for quantum chemical UV-vis spectra of organic molecules

Abstract We present two open-source datasets that provide time-dependent density-functional tight-binding (TD-DFTB) electronic excitation spectra of organic molecules. These datasets represent predictions of UV-vis absorption spectra performed on optimized geometries of the molecules in their electronic ground state. The GDB-9-Ex dataset contains a subset of 96,766 organic molecules from the original open-source GDB-9 dataset. The ORNL_AISD-Ex dataset consists of 10,502,904 organic molecules that contain between 5 and 71 non-hydrogen atoms. The data reveals the close correlation between the magnitude of the gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), and the excitation energy of the lowest singlet excited state energies quantitatively. The chemical variability of the large number of molecules was examined with a topological fingerprint estimation based on extended-connectivity fingerprints (ECFPs) followed by uniform manifold approximation and projection (UMAP) for dimension reduction. Both datasets were generated using the DFTB+ software on the “Andes” cluster of the Oak Ridge Leadership Computing Facility (OLCF).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2010

Controlling Precision Stepper Motors in Flight Using (Almost) No Parts

This concept allows control of high-performance stepper motors with minimal parts count and minimal flight software complexity. Although it uses a small number of common flight-qualified parts and simple control algorithms, it is capable enough to meet demanding system requirements. Its programmable nature makes it trivial to implement changes to control algorithms both during integration & test and in flight. Enhancements such as microstepping, half stepping, back-emf compensation, and jitter reduction can be tailored to the requirements of a large variety of stepper motor based applications including filter wheels, focus mechanisms, antenna tracking subsystems, pointing and mobility. The hardware design (using an H-bridge motor controller IC) was adapted from JPL's MER mission, still operating on Mars. This concept has been fully developed and incorporated into the MCS instrument on MRO, currently operating in Mars orbit. It has been incorporated into the filter wheel mechanism and linear stage (focus) mechanism for the AMT instrument. On MCS/MRO, two of these circuits control the elevation and azimuth of the MCS telescope/radiometer assembly, allowing the instrument to continuously monitor the limb of the Martian atmosphere. Implementation on MCS/MRO resulted in a 4:1 reduction in the volume and mass required for the motor driver electronics (100:25 square inches of PCB space), producing a very compact instrument. In fact, all of the electronics for the MCS instrument are packaged within the movable instrument structure. It also saved approximately 3 Watts of power. Most importantly, the design enabled MCS to meet very its stringent maximum allowable torque disturbance requirements.

Randall, David↗
DOE OSTI2021

Adoption of image-driven machine learning for microstructure characterization and materials design: A Perspective

Microstructure characterization enables the development of structure-processing-property relationships critical to several research areas within the broad field of materials science, from alloy design to the assessment of corrosion resistance, and failure analysis. Conventional approaches to material characterization have relied on either qualitative inference by the human ex-pert or software applications that can extract high-level features from images, such as boundary segmentation, average grain diameter, etc. Such approaches rely heavily on subject matter expert user intervention and knowledge of what phases or more generally, what microstructural features, are of interest. The recent surge in the adoption of machine learning techniques to address problems in materials engineering has brought with it an increased interest and application of Image Driven Machine Learning (IDML) approaches. In this work, we review the applications of IDML to the field of materials characterization. A canonical hierarchy of stages is defined, which when put sequentially together completes an IDML study: problem definition, dataset building, model selection and training, model evaluation, and integration with existing instrumentation or simulation workflow. The studies reviewed in this work are analyzed from the perspective of each of these stages. Such a review permits agranular assessment of the field, for example the impact of IDML on materials characterization at the nanoscale, the size of a typical dataset required to train a semantic segmentation model on electron microscopy images, ubiquitousness of transfer learning in the domain, etc. Finally, we discuss the importance of interpretability and explainability in the field of IDML for materials characterization, and provide an overview of two emerging techniques in the field: semantic segmentation and generative adversarial networks.

Baskaran, Arun↗
NASA NTRS2013

Development of the Code RITRACKS

A document discusses the code RITRACKS (Relativistic Ion Tracks), which was developed to simulate heavy ion track structure at the microscopic and nanoscopic scales. It is a Monte-Carlo code that simulates the production of radiolytic species in water, event-by-event, and which may be used to simulate tracks and also to calculate dose in targets and voxels of different sizes. The dose deposited by the radiation can be calculated in nanovolumes (voxels). RITRACKS allows simulation of radiation tracks without the need of extensive knowledge of computer programming or Monte-Carlo simulations. It is installed as a regular application on Windows systems. The main input parameters entered by the user are the type and energy of the ion, the length and size of the irradiated volume, the number of ions impacting the volume, and the number of histories. The simulation can be started after the input parameters are entered in the GUI. The number of each kind of interactions for each track is shown in the result details window. The tracks can be visualized in 3D after the simulation is complete. It is also possible to see the time evolution of the tracks and zoom on specific parts of the tracks. The software RITRACKS can be very useful for radiation scientists to investigate various problems in the fields of radiation physics, radiation chemistry, and radiation biology. For example, it can be used to simulate electron ejection experiments (radiation physics).

Plante, Ianik↗
NASA NTRS2011

Wireless Sensor Networks for Developmental and Flight Instrumentation

Wireless sensor networks (WSN) based on the IEEE 802.15.4 Personal Area Network and ZigBee Pro 2007 standards are finding increasing use in home automation and smart energy markets providing a framework for interoperable software. The Wireless Connections in Space Project, funded by the NASA Engineering and Safety Center, is developing technology, metrics and requirements for next-generation spacecraft avionics incorporating wireless data transport. The team from Stennis Space Center and Mobitrum Corporation, working under a NASA SBIR grant, has developed techniques for embedding plug-and-play software into ZigBee WSN prototypes implementing the IEEE 1451 Transducer Electronic Datasheet (TEDS) standard. The TEDS provides meta-information regarding sensors such as serial number, calibration curve and operational status. Incorporation of TEDS into wireless sensors leads directly to building application level software that can recognize sensors at run-time, dynamically instantiating sensors as they are added or removed. The Ames Research Center team has been experimenting with this technology building demonstration prototypes for on-board health monitoring. Innovations in technology, software and process can lead to dramatic improvements for managing sensor systems applied to Developmental and Flight Instrumentation (DFI) aboard aerospace vehicles. A brief overview of the plug-and-play ZigBee WSN technology is presented along with specific targets for application within the aerospace DFI market. The software architecture for the sensor nodes incorporating the TEDS information is described along with the functions of the Network Capable Gateway processor which bridges 802.15.4 PAN to the TCP/IP network. Client application software connects to the Gateway and is used to display TEDS information and real-time sensor data values updated every few seconds, incorporating error detection and logging to help measure performance and reliability in relevant target environments. Test results from our prototype WSN running the Mobitrum software system are summarized and the implications to the scalability and reliability for DFI applications are discussed. Our demonstration system, incorporating sensors for life support system and structural health monitoring is described along with test results obtained by running the demonstration prototype in relevant environments such as the Wireless Habitat Testbed at Johnson Space Center in Houston. An operations concept for improved sensor process flow from design to flight test is outlined specific to the areas of Environmental Control and Life Support System performance characterization and structural health monitoring of human-rated spacecraft. This operations concept will be used to highlight the areas where WSN technology, particularly plug-and-play software based on IEEE 1451, can improve the current process, resulting in significant reductions in the technical effort, overall cost and schedule for providing DFI capability for future spacecraft. RELEASED -

Alena, Richard↗
DOE OSTI2023

Assessment of ITER radiation environment during the remote-handling operation of In-Vessel components with D1SUNED

During ITER operational life, a remote-handled cask will be used to transfer In-Vessel components to the Hot Cell for maintenance, storage and decommissioning purposes. Due to the distribution of penetrations for system allocation in the facility, the radiation field of each transfer operation presents a high spatial variability; all operations must be studied independently for workers and electronics protection. In this paper, we present a fully representative approach to describe the radiation environment during the complete remote-handling scenario of In-Vessel components in the ITER facility. The impact of all relevant radiation sources during different stages of the operation is addressed. As-built structures and 2020 baseline designs are considered to produce the most detailed neutronics model of the Tokamak Complex, the 400,000-tonne civil structure hosting the tokamak, up to date. Novel capabilities of the D1SUNED code have allowed to compute the integral dose, the dose rate and the photon-induced neutron flux of both moving and static radiation sources. Time bins are included in the simulations to compute the dose rate caused by In-Vessel components at all positions along the transfer. The time evolution of the dose rate is built in video format with a 1-m resolution, especially valuable for hot-spots identification.

42 ENGINEERING↗
DOE OSTI2024

FY24 Progress Report: SRNL Analysis of ICCWR LCM and WAMS data for Corrosion and Cracking

Algorithms for Machine Learning (ML) and data analysis for the 3013 Surveillance Program have been developed in an ongoing collaborative effort by the Savannah River National Laboratory (SRNL) and the University of South Carolina (USC). The objective of the algorithms is to automate the identification of corrosion and crack formation in the Inner Container Closure Weld Region (ICCWR) of the canister system used to store Pu-bearing material. Data for corrosion and cracking is collected from large binary files generated by a Laser Confocal Microscope (LCM), the Wide Area 3D Measurement System (WAMS), or,in a recent proposal, by a Scanning Electron Microscope (SEM). The ML software uses the physical attributes in the data files (e.g., one or more of: height, color, and 16-bit grayscale values as functions of position in a plane projection) to detect signs of surface corrosion and cracking after being trained on similar data, with the features to be detected. Although the initial scope included screening for broader indicators of corrosion, e.g., pitting, identification of potential cracks was prioritized for the past several years at the request of program leadership. Labeled training data is essential to developing the ML algorithm, and enhancements to data labeling capability have been developed to address this essential precursor to application of ML routines. Efficient labeling is particularly important in view of the large volume of data required to train ML algorithms and the relative rarity of cracks in the ICCWR data set. The updated program will read binary data from either LCM, WAMS or SEM files, interrogate data attributes, facilitate user labeling of data for training ML algorithms, execute ML algorithms, output parameters from trained ML algorithms, report ML model accuracy with respect to labeled data, and generate graphical representations for various analyses. In FY24, hourglass neural networks (HNNs) that were initiated in FY22 were further developed and tested using available LCM data, and their performance was tested against that of the alternative U-Net Neural Network algorithm structure. HNNs along with previously developed Convolutional Neural Networks (CNNs) and Deep Neural Networks (DNNs) comprise a suite of ML tools for identification of cracks in the ICCWR

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
NASA NTRS1990

Thermomechanical deformation testing and modeling in the presence of metallurgical instabilities

A number of viscoplastic constitutive models were developed to describe deformation behavior under complex combinations of thermal and mechanical loading. Questions remain, however, regarding the validity of procedures used to characterize these models for specific structural alloys. One area of concern is that the majority of experimental data available for this purpose are determined under isothermal conditions. This experimental study is aimed at determining whether viscoplastic constitutive theories characterized using an isothermal data base can adequately model material response under the complex thermomechanical loading conditions typical of power generation service. The approach adopted was to conduct a series of carefully controlled thermomechanical experiments on a nickel-based superalloy, Hastelloy Alloy X. Previous investigations had shown that this material experiences metallurgical instabilities leading to complex hardening behavior, termed dynamic strain aging. Investigating this phenomenon under full thermomechanical conditions leads to a number of challenging experimental difficulties which up to the present work were unresolved. To correct this situation, a number of advances were made in thermomechanical testing techniques. Advanced methods for dynamic temperature gradient control, phasing control and thermal strain compensation were developed and incorporated into real time test control software. These advances allowed the thermomechanical data to be analyzed with minimal experimental uncertainty. The thermomechanical results were evaluated on both a phenomenological and microstructural basis. Phenomenological results revealed that the thermomechanical hardening trends were not bounded by those displayed under isothermal conditions. For the case of Hastelloy Alloy X (and similar dynamic strain aging materials), this strongly suggests that some form of thermomechanical testing is necessary when characterizing a thermoviscoplastic deformation model. Transmission electron microscopy was used to study the microstructural physics, and analyze the unique phenomenological behavior.

Castelli, Michael G.↗
NASA NTRS2000

HTMT-class Latency Tolerant Parallel Architecture for Petaflops Scale Computation

Computational Aero Sciences and other numeric intensive computation disciplines demand computing throughputs substantially greater than the Teraflops scale systems only now becoming available. The related fields of fluids, structures, thermal, combustion, and dynamic controls are among the interdisciplinary areas that in combination with sufficient resolution and advanced adaptive techniques may force performance requirements towards Petaflops. This will be especially true for compute intensive models such as Navier-Stokes are or when such system models are only part of a larger design optimization computation involving many design points. Yet recent experience with conventional MPP configurations comprising commodity processing and memory components has shown that larger scale frequently results in higher programming difficulty and lower system efficiency. While important advances in system software and algorithms techniques have had some impact on efficiency and programmability for certain classes of problems, in general it is unlikely that software alone will resolve the challenges to higher scalability. As in the past, future generations of high-end computers may require a combination of hardware architecture and system software advances to enable efficient operation at a Petaflops level. The NASA led HTMT project has engaged the talents of a broad interdisciplinary team to develop a new strategy in high-end system architecture to deliver petaflops scale computing in the 2004/5 timeframe. The Hybrid-Technology, MultiThreaded parallel computer architecture incorporates several advanced technologies in combination with an innovative dynamic adaptive scheduling mechanism to provide unprecedented performance and efficiency within practical constraints of cost, complexity, and power consumption. The emerging superconductor Rapid Single Flux Quantum electronics can operate at 100 GHz (the record is 770 GHz) and one percent of the power required by convention semiconductor logic. Wave Division Multiplexing optical communications can approach a peak per fiber bandwidth of 1 Tbps and the new Data Vortex network topology employing this technology can connect tens of thousands of ports providing a bi-section bandwidth on the order of a Petabyte per second with latencies well below 100 nanoseconds, even under heavy loads. Processor-in-Memory (PIM) technology combines logic and memory on the same chip exposing the internal bandwidth of the memory row buffers at low latency. And holographic storage photorefractive storage technologies provide high-density memory with access a thousand times faster than conventional disk technologies. Together these technologies enable a new class of shared memory system architecture with a peak performance in the range of a Petaflops but size and power requirements comparable to today's largest Teraflops scale systems. To achieve high-sustained performance, HTMT combines an advanced multithreading processor architecture with a memory-driven coarse-grained latency management strategy called "percolation", yielding high efficiency while reducing the much of the parallel programming burden. This paper will present the basic system architecture characteristics made possible through this series of advanced technologies and then give a detailed description of the new percolation approach to runtime latency management.

Sterling, Thomas↗
DOE OSTI2022

Strength of tantalum to 276 GPa determined by two x-ray diffraction techniques using diamond anvil cells

Tantalum (Ta) is a metal that has useful properties that make it useful in extreme environments. It is therefore important to understand how Ta performs in such extreme conditions by accurately measuring its properties. In this work, the yield strength of tantalum has been measured at pressures up to 276 GPa using axial and radial x-ray diffraction (XRD) methods in diamond anvil cells (DAC). We measured strength using XRD in a radial DAC to 50 GPa, in an axial DAC to 60 GPa using diamonds with standard flat culets, and in a final experiment to 276 GPa using toroidal diamond anvils. The radial XRD data were refined using the Material Analysis Using Diffraction (MAUD) Rietveld software package to extract lattice strain and the yield strength. The axial data were refined using the General Structure Analysis System (GSAS) II and a linewidth method was used to calculate the yield strength. The yield strength measured near ambient pressure was found to be 0.5 GPa and increased with pressure up to 50 GPa, where the yield strength plateaued at a value of 2.4 GPa. At pressures above 60 GPa, the strength increased again to a maximum value of 9 GPa at the highest pressure of 276 GPa. Here, the data from the three experiments show good agreement between the methods and previously reported experimental data. This agreement illustrates the value of axial diffraction data for material strength determination and allows for measurements at multihundreds of GPa using toroidal DACs.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Modern quantum chemistry with [Open]Molcas

MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree–Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Elucidating the Determinants of Alkali Ionic Conductivity in Oxide and Sulfide Frameworks

The aim of this project is to elucidate the structural and chemical factors determining alkali conductivity in oxide and sulfide frameworks using large scale first principles calculations and topological analysis. The facile conduction of alkali ions in oxide and sulfide host structures is of critical importance in energy storage. Today, the dominant form of energy storage in portable electronics is the rechargeable alkali-ion battery, a device that functions entirely on the basis of the reversible transport of alkali ions. The Li+/Na+ conductivity of a cathode has a direct influence on the rate capability of a Li/Na-ion battery, i.e., the speed at which it can be charged and discharged. Alkali conductivity is arguably of even greater importance in the solid electrolytes currently being investigated for high safety, high energy all-solid-state batteries. The research performed in this project has provided critical new insights into the diffusion mechanisms in state-of-the-art alkali superionic conductors such as Li 7 P 3 S 11 , Li 3 OCl 1-x Br x anti-perovskite, argyrodite Li 6 PS 5 Cl. Two potential novel lithium superionic conductors (Li 3 Y(PS 4 ) 2 and Li 5 PS 4 Cl 2 ) with improved electrochemical stabilities were predicted. We have also conducted in-depth studies into alkali conduction in several important classes of electrodes, including the layered P2 NaMO 2 oxides and the highly promising novel disordered rock salt Li 3+x V 2 O 5 anode for high-rate applications. This project has resulted in more than 10 peer-reviewed articles in highly regarded journals as well as a new open-source software framework (pymatgen-analysis-diffusion) that is widely used by the materials research community for the study of diffusion in materials.

25 ENERGY STORAGE↗
DOE OSTI2021

Numerical Investigation of Enhanced Dehumidification Processes By Using Dielectrophoresis Principles in Moist Airflows

Dispersed particle-laden flows are encountered in many building and industrial applications, such as flow in a fluidized bed, hydrocarbon transportation in pipelines, and the fouling of air-cooled heat exchangers (Kuruneru et al., 2016; Ray et al., 2019; Wang et al., 2019). Computational fluid dynamic (CFD) models have been developed in recent years to depict particle-fluid and particle-particle interactions in laminar or turbulent flows with increasing accuracy and stability. One particular particle-laden system of interest for moisture control is electrically-enhanced condensation in air and water droplet flows. Electrically-enhanced condensation consists of the use of highly charged water droplets injected in the moist air. The droplets become electric seeds that attract polar water vapor molecules to their surfaces and promote condensation. The nucleation and growth of the charged droplets deplete the vapor phase near a droplet, which is compensated for by the dielectrophoresis flow and diffusion. Dielectrophoresis flow involves surrounding vapor at a distance of about 10 to 100 nm for droplets charged by an electrospray compared to ~2 nm for a single electron charge in a droplet. As the vapor molecules collapse on the surface of the droplets, their initial electrical charge decreases with time due to the neutralization of the ions. While the physics of this phenomena is well known, engineering models for predicting the condensation rates are not available. This work computationally investigates dehumidification of moist airflow in a converging rectangular duct. The objective is to develop an engineering model that predicts water vapor condensation by employing dielectrophoresis principles. We construct a Computational Fluid Dynamics (CFD) model of the duct with electrically-enhanced condensation. The model is implemented in the open-source software OpenFOAM. We utilize the Multi-Phase Particle-In-Cell (MP-PIC) method coupled with a Population Balance Equation (PBE) approach to simulate the particle-laden system. This methodology is an Eulerian-Lagrangian approach used to simulate the droplets' behavior in the humid air. The MP-PIC approach (Andrews and O'Rourke, 1996) mitigates the computational cost by parceling several fundamental particles with similar properties (such as types, sizes, and temperature) into one computational particle. Thus, the billions of particles can be substituted by millions of computational particles without significant loss of information. The PBE was considered with the Lagrangian frame to combine the particle distribution function used in MP-PIC (Kim et al., 2020). This approach preserves mass and energy conservation between the phases in the Eulerian and Lagrangian structures. The PBE in this procedure was directly linked to the discrete parcels, making the simulation of the particle distribution computationally efficient and robust. The MP-PIC-PBE approach used in the present work was applied to the dehumidification of air. Water droplets were injected in the air stream and forced to grow according to experimentally derived correlation. The experiments were conducted on a converging duct with the same geometry and boundary conditions used to build the CFD model. This approach enabled us to approximate the effect of dielectrophoresis phenomena on the droplet and air interface. This presentation will discuss the details of the new CFD model built for the duct, the implementation of the model in OpenFOAM CFD programming language, and the experimental validation of the newly developed model. The results revealed a moderate yet measurable increase in droplet diameter due to water vapor condensation at the vapor-liquid interface of the electrically charged droplets' surface. The seed water droplet particles grew in size by capturing the water vapor in the surrounding air. The OpenFOAM model predicted reductions of humidity in the air from 5 to 10 percent.

Yel Mahi, Maliha↗
DOE OSTI2020

Experimental demonstration of externally driven millimeter-wave particle accelerator structure

We report the experimental demonstration of a mm-wave electron accelerating structure powered by a high-power rf source. We demonstrate reliable coupling of an unprecedented rf power—up to 575kW into the mm-wave accelerator structure using a quasi-optical setup. This standing wave accelerating structure consists of a single-cell copper cavity and a Gaussian to TM 01 mode converter. The accelerator structure is powered by 110 GHz, 10-ns long rf pulses. These pulses are chopped from 3 microsecond pulses from a gyrotron oscillator using a laser-driven silicon switch. We show an unprecedented high gradient up to 230MV/m that corresponds to a peak surface electric field of more than 520 MV/m. We have achieved these results after conditioning the cavity with more than 100,000 pulses. We also report preliminary measurements of rf breakdown rates, which are important for understanding rf breakdown physics in the millimeter-wave regime. Furthermore, these results open up many frontiers for applications not only limited to the next generation particle accelerators but also x-ray generation, probing material dynamics, and nonlinear light-matter interactions at mm-wave frequency.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

EI_MS_ML

The unambiguous identification of compounds from their electron ionization mass (EI-MS) spectra remains a significant unsolved problem in the field of metabolomics and analytical chemistry as a whole. Typically EI-MS spectra are compared using various mathematical operations that convert the spectral similarity or differences into a distance-like metric that roughly approximates the similarity of any two spectra. A commonly used metric for this is the cosine similarity metric which has values close to one for very similar spectra and a value of zero for very dissimilar spectra; however, no metric is perfect. Due to the prevalence of structurally-similar compounds such as isomers and the prevalence of certain fragmentation patterns across structurally-dissimilar compounds, the unambiguous assignment of EI-MS spectra compounds remains difficult. Frequently, querying an observed EI-MS spectrum against a large database such as the NIST17 library yields multiple possible assignments requiring the end user to distinguish between multiple high scoring hits, or multiple low scoring hits while keeping in mind that the correct hit may not be in the database at all. Although techniques such as orthogonal information from techniques such as chromatography can greatly aid in unambiguous assignment, this also requires more complicated experimental designs and access to more complicated analytical instrumentation. Substructures can be trivially detected and represented as strings using a previously published technique called node coloring from a known chemical structure. However, for experimentally-derived EI-MS spectra this information must be derived from the spectra itself (i.e., because we do not know what compound it represents). To achieve this, the software uses techniques from the field of machine learning and a large training dataset of EI-MS spectra corresponding to known structures annotated with substructure strings, to build models that can predict the presence of a given chemical substructure from an EI-MS spectrum directly.If these predictions are of high-quality (i.e., are unlikely to be false positives), the presence of one or more predicted substructures can be used to constrain the number of possible hits for a query spectrum. Mathematically, this restriction could be expressed in many forms, but the most straight-forward implementation is to weight the cosine similarity of a query spectrum and a plausible database match with a Tanimoto-like coefficient based on the ratio of the number of substructures predicted to the number of substructures present in the potential database hit. Determining which combination of models best reduces assignment ambiguity will be achieved using a combination of manual curation and optimization techniques such as genetic algorithms. This software will perform all the steps necessary to construct said models from a training dataset and evaluate them using a holdout dataset. Various statistical analyses can be performed to determine if this approach does decrease assignment ambiguity. For example, if this approach works, on average, the rank-order of the correct assignment for the holdout set of EI-MS spectra should decrease and the weighted cosine similarities for most of the possible matches in the database should be better than the unweighted cosine similarities. Furthermore, this same pipeline can be used on real experimental data to generate less ambiguous assignments.

Mitchell, Joshua↗
DOE OSTI2023

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary- structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. Here, we introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehydrogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 Å, map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗