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At least 793 records · Page 44

Theoretical study of intrinsic defects in cubic silicon carbide 3C-SiC

Using the local moment counter charge (LMCC) method to accurately represent the asymptotic electrostatic boundary conditions within density functional theory supercell calculations, we present a comprehensive analysis of the atomic structure and energy levels of point defects in cubic silicon carbide (3C-SiC). Finding that the classical long-range dielectric screening outside the supercell induced by a charged defect is a significant contributor to the total energy. we describe and validate a modified Jost screening model to evaluate this polarization energy. This leads to bulk-converged defect levels in finite size supercells. With the LMCC boundary conditions and a standard Perdew-Burke-Ernzerhof (PBE) exchange correlation functional, the computed defect level spectrum exhibits no band gap problem: the range of defect levels spans ~2.4 eV, an effective defect band gap that agrees with the experimental band gap. Comparing with previous literature, our LMCC-PBE defect results are in consistent agreement with the hybrid-exchange functional results of Oda et al. [J. Chem. Phys. 139, 124707 (2013)] rather than their PBE results. The difference with their PBE results is attributed to their use of a conventional jellium approximation rather than the more rigorous LMCC approach for handling charged supercell boundary conditions. The difference between standard dft and hybrid functional results for defect levels lies not in a band gap problem but rather in solving a boundary condition problem. The LMCC-PBE entirely mitigates the effect of the band gap problem on defect levels. The more computationally economical PBE enables a systematic exploration of 3C-SiC defects, where, most notably, we find that the silicon vacancy undergoes Jahn-Teller-induced distortions from the previously assumed T d symmetry, and that the divacancy, like the silicon vacancy, exhibits a site-shift bistability in p -type conditions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Navier-Stokes computations of lee-side flows over delta wings

Solutions to the Navier-Stokes equations for the flow over delta wings are computed with emphasis on the separated vortical flows developing on the lee side at high angles of attack. A recently developed implicit algorithm is used which employs upwind differencing for the pressure and convection terms and central differencing for the shear stress and heat transfer terms. Solutions to both the three-dimensional equations and the approximate conical flow equations are compared parametrically with an extensive experimental data base at supersonic speeds. The computations indicate that the conical flow approximation provides results in close agreement with the three-dimensional equations, even to angles of attack as high as 20 degrees. Good agreement with experimentally measured pressures and vapor screen photographs is obtained for the conditions investigated. The method predicts the classical pattern of vortical flow over a delta wing and transition to other flow patterns as the leading edge sweep angle and leading edge normal Mach number are varied.

Thomas, J. L.↗

Development and experimentation of an eye/brain/task testbed

The principal objective is to develop a laboratory testbed that will provide a unique capability to elicit, control, record, and analyze the relationship of operator task loading, operator eye movement, and operator brain wave data in a computer system environment. The ramifications of an integrated eye/brain monitor to the man machine interface are staggering. The success of such a system would benefit users of space and defense, paraplegics, and the monitoring of boring screens (nuclear power plants, air defense, etc.)

Harrington, Nora↗

Advanced Technology Development for Stirling Convertors

A high-efficiency Stirling Radioisotope Generator (SRG) for use on potential NASA Space Science missions is being developed by the Department of Energy, Lockheed Martin, Stirling Technology Company, and NASA Glenn Research Center (GRC). These missions may include providing spacecraft onboard electric power for deep space missions or power for unmanned Mars rovers. GRC is also developing advanced technology for Stirling convertors, aimed at substantially improving the specific power and efficiency of the convertor and the overall power system. Performance and mass improvement goals have been established for second- and thirdgeneration Stirling radioisotope power systems. Multiple efforts are underway to achieve these goals, both in-house at GRC and under various grants and contracts. The status and results to date for these efforts will be discussed in this paper. Cleveland State University (CSU) is developing a multi-dimensional Stirling computational fluid dynamics code, capable of modeling complete convertors. A 2-D version of the code is now operational, and validation efforts at both CSU and the University of Minnesota are complementing the code development. A screening of advanced superalloy, refractory metal alloy, and ceramic materials has been completed, and materials have been selected for creep and joining characterization as part of developing a high-temperature heater head. A breadboard characterization is underway for an advanced controller using power electronics for active power factor control with a goal of eliminating the heavy tuning capacitors that are typically needed to achieve near unity power factors. Key Stirling developments just initiated under recent NRA (NASA Research Announcement) awards will also be discussed. These include a lightweight convertor to be developed by Sunpower Inc. and an advanced microfabricated regenerator to be done by CSU.

Thieme, Lanny G.↗

Aerothermal Testing for Project Orion Crew Exploration Vehicle

The Project Orion Crew Exploration Vehicle aerothermodynamic experimentation strategy, as it relates to flight database development, is reviewed. Experimental data has been obtained to both validate the computational predictions utilized as part of the database and support the development of engineering models for issues not adequately addressed with computations. An outline is provided of the working groups formed to address the key deficiencies in data and knowledge for blunt reentry vehicles. The facilities utilized to address these deficiencies are reviewed, along with some of the important results obtained thus far. For smooth wall comparisons of computational convective heating predictions against experimental data from several facilities, confidence was gained with the use of algebraic turbulence model solutions as part of the database. For cavities and protuberances, experimental data is being used for screening various designs, plus providing support to the development of engineering models. With the reaction-control system testing, experimental data were acquired on the surface in combination with off-body flow visualization of the jet plumes and interactions. These results are being compared against predictions for improved understanding of aftbody thermal environments and uncertainties.

Berry, Scott A.↗

Machine Learning Reduced Order Model for Cost and Emission Assessment of a Pyrolysis System

Biomass pyrolysis is a promising approach for producing economic and environmentally-friendly fuels and bioproducts. Biomass pyrolysis experiments show that feedstock properties have a significant impact on product yields and composition. Scientists are developing detailed chemical reaction mechanisms to capture the relationships between biomass composition and pyrolysis yields. These mechanisms can be computationally intensive. In this study, we investigate the use of a machine learning reduced order model (ROM) for assessing the costs and emissions of a pyrolysis biorefinery. Here, we developed a Kriging-based ROM to predict pyrolysis yields of 314 feedstock samples based on the results of a detailed chemical kinetic pyrolysis mechanism. The ROM is integrated into a chemical process model for calculating mass and energy yields in a commercial-scale (2000 tonne/day) biorefinery. The ROM estimated biofuel yields of 65 to 130 gallons per ton of dry biomass. This results in biofuel minimum fuel-selling prices of $2.62 to $5.43 per gallon and emissions of -13.62 to 145 kg of CO 2 per MJ. The ROM achieved an average mean square error of 1.8e-20 and a mean absolute error of 0.53%. These results suggest that ROMs can facilitate rapid feedstock screening for biorefinery systems.

09 BIOMASS FUELS↗

Supercomputing Pipelines Search for Therapeutics Against COVID-19

The urgent search for drugs to combat SARS-CoV-2 has included the use of supercomputers. The use of general-purpose graphical processing units (GPUs), massive parallelism, and new software for high-performance computing (HPC) has allowed researchers to search the vast chemical space of potential drugs faster than ever before. We developed a new drug discovery pipeline using the Summit supercomputer at Oak Ridge National Laboratory to help pioneer this effort, with new platforms that incorporate GPU-accelerated simulation and allow for the virtual screening of billions of potential drug compounds in days compared to weeks or months for their ability to inhibit SARS-COV-2 proteins. Here, this effort will accelerate the process of developing drugs to combat the current COVID-19 pandemic and other diseases.

60 APPLIED LIFE SCIENCES↗

Synthetic accessibility and stability rules of NASICONs

In this paper we develop the stability rules for NASICON-structured materials, as an example of compounds with complex bond topology and composition. By first-principles high-throughput computation of 3881 potential NASICON phases, we have developed guiding stability rules of NASICON and validated the ab initio predictive capability through the synthesis of six attempted materials, five of which were successful. A simple two-dimensional descriptor for predicting NASICON stability was extracted with sure independence screening and machine learned ranking, which classifies NASICON phases in terms of their synthetic accessibility. This machine-learned tolerance factor is based on the Na content, elemental radii and electronegativities, and the Madelung energy and can offer reasonable accuracy for separating stable and unstable NASICONs. This work will not only provide tools to understand the synthetic accessibility of NASICON-type materials, but also demonstrates an efficient paradigm for discovering new materials with complicated composition and atomic structure.

25 ENERGY STORAGE↗

Programmed Multiphasic Health Testing

Multiphase health screening procedures are advocated for detection and prevention of disease at an early stage through risk factor analysis. The use of an automated medical history questionnaire together with scheduled physical examination data provides a scanning input for computer printout. This system makes it possible to process laboratory results from 1,000 to 2,000 patients for biochemical determinations on an economically feasible base.

Hershberg, P. I.↗

SPACEBAR: Kinematic design by computer graphics

The interactive graphics computer program SPACEBAR, conceived to reduce the time and complexity associated with the development of kinematic mechanisms on the design board, was described. This program allows the direct design and analysis of mechanisms right at the terminal screen. All input variables, including linkage geometry, stiffness, and applied loading conditions, can be fed into or changed at the terminal and may be displayed in three dimensions. All mechanism configurations can be cycled through their range of travel and viewed in their various geometric positions. Output data includes geometric positioning in orthogonal coordinates of each node point in the mechanism, velocity and acceleration of the node points, and internal loads and displacements of the node points and linkages. All analysis calculations take at most a few seconds to complete. Output data can be viewed at the scope and also printed at the discretion of the user.

Ricci, R. J.↗

Non-Electricity Based Renewable Fuels: Theory and Computation for Solar Thermochemical Hydrogen

Dominated by photovoltaics and wind, current renewable energy sources generate mostly electricity, but 80% of the global final energy consumption occurs in form of fuels. Therefore, direct solar fuel generation would be a major breakthrough for the energy transition. Solar thermochemical hydrogen (STCH) is one of the very few potential routes towards scalable renewable fuels, but currently suffers from lack of an oxide working material that could optimally perform energy conversion within the thermodynamic boundary conditions. Theory and computation can contribute in two distinct ways, through materials search and discovery, but also by providing detailed mechanistic models for specific systems so to advance our understanding of possible design strategies. To enable high-throughput materials screening, we developed a defect graph neural network (dGNN) machine learning approach,[1] which accelerates the prediction of defect formation energies by replacing the tedious density functional theory (DFT) supercell calculations for all possible defect sites. This approach enables high-throughput database screening of oxides, which was integrated with thermodynamic modeling to extract the reduction entropies as additional selection criterion for STCH. Once potential candidate materials are identified, detailed models can guide materials design by predicting performance characteristics. One challenge is to quantitatively predict thermochemical equilibria at high concentrations when the redox active defects start to interact with each other, thereby impeding the formation of additional defects. Introducing a model for the free energy of defect interaction, parametrized on the basis of DFT data, we simulated the complete STCH redox cycle for (Sr,Ce)MnO3 alloys, achieving near-quantitative agreement with experimental data.[2] The analysis of these simulations reveals how defect interactions diminish the reduction entropy and H2 yield, suggesting to include these interactions in design considerations. Finally, we revisit the popular van't Hoff method for analyzing reduction enthalpies and entropies. This method is not ideal, as it involves a temperature-dependent convolution of gas-phase and solid-state entropies, causing uncertainties in the same order of magnitude as the physical quantities of interest. To avoid this problem, we suggest a simple alternative approach which can be applied to experimental and simulated data alike.

first-principles calculations↗

Fast estimation of ion-pairing for screening electrolytes: A cluster can approximate a bulk liquid

The propensity for ion-pairing can often dictate the thermodynamic and kinetic properties of electrolyte solutions. Fast and accurate estimates of ion-pairing can thus be extremely valuable for supplementing design and screening efforts for novel electrolytes. We introduce an efficient cluster model to estimate the local ion-pair potential-of-mean-force between ionic solutes in electrolytes. The model incorporates an ion-pair and a few layers of explicit solvent in a gas-phase cluster and leverages an enhanced sampling approach to achieve high efficiency and accuracy. We employ harmonic restraints to prevent solvent escape from the cluster and restrict sampling of large inter-ion distances. We develop a cluster ion-pair sampling tool that implements our cluster model and demonstrate its potential utility for screening simple and poly-electrolyte systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Investigation of the Effect of Framework Flexibility on CO 2 Adsorption in SIFSIX-3-Cu Using a Machine-Learned Force Field

Metal–organic frameworks (MOFs) offer promise as selective CO 2 sorbents, but successful MOF sorbent materials need high CO 2 binding affinity and selectivity for CO 2 over water. This work focuses on the use of machine-learned force fields (MLFFs) to model CO 2 adsorption in flexible MOFs, with a focus on SIFSIX-3-Cu, an anion-pillared MOF known for its high CO 2 affinity. A preliminary high-throughput screening of over 900 anion-pillared MOFs was performed using rigid UFF+DDEC6 force fields to predict zero-loading heats of adsorption for CO 2 and H 2 O. SIFSIX-3-Cu was selected for further computational study due to its predicted CO 2 heat of adsorption and experimental relevance. A DeePMD-based MLFF was trained to reproduce DFT (PBE+D3) energies and forces, with an iterative sampling scheme combining molecular dynamics, geometry optimization, random geometric insertion, and NVT Monte Carlo-based configuration generation to capture both attractive and repulsive regions of the potential energy surface. Flexibility of the MOF was explicitly included, contrasting with previous models that approximated the MOF as rigid. Hybrid Monte Carlo/molecular dynamics (MC/MD) simulations with the MLFF produced CO 2 adsorption isotherms in good agreement with experimental data at direct air capture (DAC) pressures (e.g., 40 Pa), in contrast to previous overestimations of CO 2 sorption by models with rigid structures. Bond and angle histogram analysis showed that MOF flexibility increased the variance of fluorine–fluorine diagonal distances at adsorption sites, resulting in a lower predicted sorption for flexible, asymmetric SIFSIX-3-Cu pore geometries compared to the rigid, symmetric DFT-optimized SIFSIX-3-Cu pore geometry. A detailed description of flexibility afforded by the MLFF resulted in an accurately predicted CO 2 uptake (0.88 mmol/g) at low pressure (40 Pa) compared to the experimentally measured value (1.24 mmol/g). In conclusion, these results underscore the importance of including framework flexibility when modeling adsorption phenomena in MOFs, particularly for low-pressure applications.

adsorption↗

Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting

Abstract Drug response prediction (DRP) methods tackle the complex task of associating the effectiveness of small molecules with the specific genetic makeup of the patient. Anti-cancer DRP is a particularly challenging task requiring costly experiments as underlying pathogenic mechanisms are broad and associated with multiple genomic pathways. The scientific community has exerted significant efforts to generate public drug screening datasets, giving a path to various machine learning models that attempt to reason over complex data space of small compounds and biological characteristics of tumors. However, the data depth is still lacking compared to application domains like computer vision or natural language processing domains, limiting current learning capabilities. To combat this issue and improves the generalizability of the DRP models, we are exploring strategies that explicitly address the imbalance in the DRP datasets. We reframe the problem as a multi-objective optimization across multiple drugs to maximize deep learning model performance. We implement this approach by constructing Multi-Objective Optimization Regularized by Loss Entropy loss function and plugging it into a Deep Learning model. We demonstrate the utility of proposed drug discovery methods and make suggestions for further potential application of the work to achieve desirable outcomes in the healthcare field.

Biochemistry & Molecular Biology↗

Curvilinear projection developments

Gradient projection is a powerful algorithm for minimization of a function subject to constraints. Constraint nonlinearities hamper projection computations. The constraints must then be restored before another projection cycle. The restoration steps taken in the process of following nonlinear constraint surfaces can be used as a guide to the construction of a curve which more nearly follows the constraints than does the straight line in the projected gradient direction. This scheme, termed 'curvilinear projection', was explored in earlier research. The study presently reported carries out some computational experiments using a related version of the technique. Some other details of projection computations which turn out to be practically important are taken up: rules for updating the variable metric in projection when early termination of the one-dimensional search on constraint violation occurs, and active-constraint logic for screening inequalities that makes use of the Kuhn-Tucker necessary conditions.

Kelley, H. J.↗

Investigations of rhesus monkey video-task performance: evidence for enrichment

We have developed the Language Research Center's Computerized Test System (LRC-CTS) for psychological research. Basically, the LRC-CTS is a battery of software tasks--computerized versions of many of the classic testing paradigms of cognitive and comparative psychology--and the hardware required to administer them. An XT- or 386-compatible computer is connected to a color monitor, onto which computer-generated stimuli are presented. Sound feedback is delivered through an external speaker/amplifier, and a joystick is used as an input device. The animals reach through the mesh of their home cages to manipulate the joystick, which causes isomorphic movements of a cursor on the screen thereby allowing animals to respond according to the varied demands of the tasks. Correct responses are rewarded with a fruit-flavored chow pellet. Using this technology, we have trained and tested rhesus monkeys, a variety of apes, human adults, and normally developing or mentally retarded human children. Other labs using the LRC-CTS are beginning to report encouraging results with other monkey species as well. From this research, a number of interesting and important psychological findings have resulted. In the present paper, however, evidence will be reviewed which suggests that the LRC-CTS is an effective means of providing environmental enrichment to singly housed rhesus monkeys.

Non-NASA Center↗

Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences

Abstract RNA-guided nucleases from CRISPR-Cas systems expand opportunities for precise, targeted genome modification. Endogenous CRISPR-Cas systems in many prokaryotes are attractive to circumvent expression, functionality, and unintended activity hurdles posed by heterologous CRISPR-Cas effectors. However, each CRISPR-Cas system recognizes a unique set of protospacer adjacent motifs (PAMs), which requires identification by extensive screening of randomized DNA libraries. This challenge hinders development of endogenous CRISPR-Cas systems, especially those based on multi-protein effectors and in organisms that are slow-growing or have transformation idiosyncrasies. To address this challenge, we present Spacer2PAM, an easy-to-use, easy-to-interpret R package built to predict and guide experimental determination of functional PAM sequences for any CRISPR-Cas system given its corresponding CRISPR array as input. Spacer2PAM can be used in a ‘Quick’ method to generate a single PAM prediction or in a ‘Comprehensive’ method to inform targeted PAM libraries small enough to screen in difficult to transform organisms. We demonstrate Spacer2PAM by predicting PAM sequences for industrially relevant organisms and experimentally identifying seven PAM sequences that mediate interference from the Spacer2PAM-informed PAM library for the type I-B CRISPR-Cas system from Clostridium autoethanogenum. We anticipate that Spacer2PAM will facilitate the use of endogenous CRISPR-Cas systems for industrial biotechnology and synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗