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At least 1,513 records · Page 84

Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach

The unprecedented scientific achievements in combating the COVID-19 pandemic reflect a global response informed by unprecedented access to data. We now have the ability to rapidly generate a diversity of information on an emerging pathogen and, by using high-performance computing and a systems biology approach, we can mine this wealth of information to understand the complexities of viral pathogenesis and contagion like never before. These efforts will aid in the development of vaccines, antiviral medications, and inform policymakers and clinicians. Here we detail computational protocols developed as SARS-CoV-2 began to spread across the globe. They include pathogen detection, comparative structural proteomics, evolutionary adaptation analysis via network and artificial intelligence methodologies, and multiomic integration. These protocols constitute a core framework on which to build a systems-level infrastructure that can be quickly brought to bear on future pathogens before they evolve into pandemic proportions.

Teixeira Prates, Erica↗

Numerical Evaluation of an Ejector-Enhanced Resonant Pulse Combustor with a Poppet Inlet Valve and a Converging Exhaust Nozzle

A computational investigation of a pressure-gain combustor system for gas turbine applications is presented. The system consists of a valved pulse combustor and an ejector, housed within a shroud. The study focuses on two enhancements to previous models, related to the valve and ejector components. First, a new poppet inlet valve system is investigated, replacing the previously used reed valve configuration. Secondly, a new computational approach to approximating the effects of choked turbine inlet guide vanes present immediately downstream of the Ejector-Enhanced Resonant Pulse Combustor (EERPC) is investigated. Instead of specifying a back pressure at the EERPC exit boundary (as was done in previous studies) the new model adds a converging-diverging (CD) nozzle at the exit of the EERPC. The throat area of the CD nozzle can be adjusted to obtain the desired back pressure level and total mass flow rate. The results presented indicate that the new poppet valve configuration performs nearly as well as the original reed valve system, and that the addition of the CD nozzle is an effective method to approximate the exit boundary effects of a turbine present downstream of the EERPC. Furthermore, it is shown that the more acoustically reflective boundary imposed by a nozzle as compared to a constant pressure surface does not significantly affect operation or performance.

Computational Fluid Dynamics (CFD↗

Reflectance of vegetation, soil, and water

The author has identified the following significant results. Iron deficient and normal grain sorghum plants were sufficiently different spectrally in ERTS-1 band 5 CCT data to detect chlorotic sorghum areas 2.8 acres (1.1 hectares) or larger in size in computer printouts of the MSS data. The ratio of band 5 to band 7 or band 7 minus band 5 relates to vegetation ground cover conditions and helps to select training samples representative of differing vegetation maturity or vigor classes and to estimate ground cover or green vegetation density in the absence of ground information. The four plant parameters; leaf area index, plant population, plant cover, and plant height explained 87 to 93% of the variability in band 6 digital counts and from 59 to 90% of the variation in bands 4 and 5. A ground area 2244 acres in size was classified on a pixel by pixel basis using simultaneously acquired aircraft support and ERTS-1 data. Overall recognition for vegetables, immature crops and mixed shrubs, and bare soil categories was 64.5% for aircraft and 59.6% for spacecraft data, respectively. Overall recognition results on a per field basis were 61.8% for aircraft and 62.8% for ERTS-1 data.

Wiegand, C. L.↗

Analytical and Computational Properties of Distributed Approaches to MDO

Historical evolution of engineering disciplines and the complexity of the MDO problem suggest that disciplinary autonomy is a desirable goal in formulating and solving MDO problems. We examine the notion of disciplinary autonomy and discuss the analytical properties of three approaches to formulating and solving MDO problems that achieve varying degrees of autonomy by distributing the problem along disciplinary lines. Two of the approaches-Optimization by Linear Decomposition and Collaborative Optimization-are based on bi-level optimization and reflect what we call a structural perspective. The third approach, Distributed Analysis Optimization, is a single-level approach that arises from what we call an algorithmic perspective. The main conclusion of the paper is that disciplinary autonomy may come at a price: in the bi-level approaches, the system-level constraints introduced to relax the interdisciplinary coupling and enable disciplinary autonomy can cause analytical and computational difficulties for optimization algorithms. The single-level alternative we discuss affords a more limited degree of autonomy than that of the bi-level approaches, but without the computational difficulties of the bi-level methods. Key Words: Autonomy, bi-level optimization, distributed optimization, multidisciplinary optimization, multilevel optimization, nonlinear programming, problem integration, system synthesis

Alexandrov, Natalia M.↗

Transfer function analysis of the autonomic response to respiratory activity during random interval breathing

We report a new method for the noninvasive characterization of the frequency response of the autonomic nervous system (ANS) in mediating fluctuations in heart rate (HR). The approach entails computation of the transfer function magnitude and phase between instantaneous lung volume and HR. Broad band fluctuations in lung volume were initiated when subjects breathed on cue to a sequence of beeps spaced randomly in time. We studied 10 subjects in both supine and standing positions. The transfer function, averaged among all the subjects, showed systematic differences between the two postures, reflecting the differing frequency responses of the sympathetic and parasympathetic divisions of the ANS.

Non-NASA Center↗

Argonne Bubble Experiment Thermal Model Development II

This report describes the continuation of the work reported in “Argonne Bubble Experiment Thermal Model Development”. The experiment was performed at Argonne National Laboratory (ANL) in 2014. A rastered 35 MeV electron beam deposited power in a solution of uranyl sulfate, generating heat and radiolytic gas bubbles. Irradiations were performed at three beam power levels, 6, 12 and 15 kW. Solution temperatures were measured by thermocouples, and gas bubble behavior was observed. This report will describe the Computational Fluid Dynamics (CFD) model that was developed to calculate the temperatures and gas volume fractions in the solution vessel during the irradiations. The previous report described an initial analysis performed on a geometry that had not been updated to reflect the as-built solution vessel. Here, the as-built geometry is used. Monte-Carlo N-Particle (MCNP) calculations were performed on the updated geometry, and these results were used to define the power deposition profile for the CFD analyses, which were performed using Fluent, Ver. 16.2. CFD analyses were performed for the 12 and 15 kW irradiations, and further improvements to the model were incorporated, including the consideration of power deposition in nearby vessel components, gas mixture composition, and bubble size distribution. The temperature results of the CFD calculations are compared to experimental measurements.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Spatial intratumoral heterogeneity of proliferation in immunohistochemical images of solid tumors

Purpose: The interactions of neoplastic cells with each other and the microenvironment are complex. To understand intratumoral heterogeneity, subtle differences should be quantified. Main factors contributing to heterogeneity include the gradient ischemic level within neoplasms, action of microenvironment, mechanisms of intercellular transfer of genetic information, and differential mechanisms of modifications of genetic material/proteins. This may reflect on the expression of biomarkers in the context of prognosis/stratification. Hence, a rigorous approach for assessing the spatial intratumoral heterogeneity of histological biomarker expression with accuracy and reproducibility is required, since patterns in immunohistochemical images can be challenging to identify and describe. Methods: A quantitative method that is useful for characterizing complex irregular structures is lacunarity; it is a multiscale technique that exhaustively samples the image, while the decay of its index as a function of window size follows characteristic patterns for different spatial arrangements. In histological images, lacunarity provides a useful measure for the spatial organization of a biomarker when a sampling scheme is employed and relevant features are computed. The proposed approach quantifies the segmented proliferative cells and not the textural content of the histological slide, thus providing a more realistic measure of heterogeneity within the sample space of the tumor region. The aim is to investigate in whole sections of primary pancreatic neuroendocrine neoplasms (pNENs), using whole-slide imaging and image analysis, the spatial intratumoral heterogeneity of Ki-67 immunostains. Unsupervised learning is employed to verify that the approach can partition the tissue sections according to distributional heterogeneity. Results: The architectural complexity of histological images has shown that single measurements are often insufficient. Inhomogeneity of distribution depends not only on percentage content of proliferation phase but also on how the phase fills the space. Lacunarity curves demonstrate variations in the sampled image sections. Since the spatial distribution of proliferation in each case is different, the width of the curves changes too. Image sections that have smaller numerical variations in the computed features correspond to neoplasms with spatially homogeneous proliferation, while larger variations correspond to cases where proliferation shows various degrees of clumping. Grade 1 (uniform/nonuniform: 74%/26%) and grade 3 (uniform: 100%) pNENs demonstrate a more homogeneous proliferation with grade 1 neoplasms being more variant, while grade 2 tumor regions render a more diverse landscape (50%/50%). Hence, some cases show an increased degree of spatial heterogeneity comparing to others with similar grade. Whether this is a sign of different tumor biology and an association with a more benign/malignant clinical course needs to be investigated further. The extent and range of spatial heterogeneity has the potential to be evaluated as a prognostic marker. Conclusions: The association with tumor grade as well as the rationale that the methodology reflects true tumor architecture supports the technical soundness of the method. This reflects a general approach which is relevant to other solid tumors and biomarkers. Drawing upon the merits of computational biomedicine, the approach uncovers salient features for use in future studies of clinical relevance.

60 APPLIED LIFE SCIENCES↗

Two-Flux and Green's Function Method for Transient Radiative Transfer in a Semi-Transparent Layer

A method using a Green's function is developed for computing transient temperatures in a semitransparent layer by using the two-flux method coupled with the transient energy equation. Each boundary of the layer is exposed to a hot or cold radiative environment, and is heated or cooled by convection. The layer refractive index is larger than one, and the effect of internal reflections is included with the boundaries assumed diffuse. The analysis accounts for internal emission, absorption, heat conduction, and isotropic scattering. Spectrally dependent radiative properties are included, and transient results are given to illustrate two-band spectral behavior with optically thin and thick bands. Transient results using the present Green's function method are verified for a gray layer by comparison with a finite difference solution of the exact radiative transfer equations; excellent agreement is obtained. The present method requires only moderate computing times and incorporates isotropic scattering without additional complexity. Typical temperature distributions are given to illustrate application of the method by examining the effect of strong radiative heating on one side of a layer with convective cooling on the other side, and the interaction of strong convective heating with radiative cooling from the layer interior.

Siegel, Robert↗

Ray tracing optical analysis of offset solar collector for space station solar dynamic system

OFFSET, a detailed ray tracing computer code, was developed at NASA Lewis Research Center to model the offset solar collector for the Space Station solar dynamic electric power system. This model traces rays from 50 points on the face of the Sun to 10 points on each of the 456 collector facets. The triangular facets are modeled with spherical, parabolic, or toroidal reflective surface contour and surface slope errors. The rays are then traced through the receiver aperture to the walls of the receiver. Images of the collector and of the Sun within the receiver produced by this code provide insight into the collector receiver interface. Flux distribution on the receiver walls, plotted by this code, is improved by a combination of changes to aperture location and receiver tilt angle. Power loss by spillage at the receiver aperture is computed and is considerably reduced by using toroidal facets.

Jefferies, Kent S.↗

Ray tracing optical analysis of offset solar collector for Space Station solar dynamic system

OFFSET, a detailed ray tracing computer code, was developed at NASA Lewis Research Center to model the offset solar collector for the Space Station solar dynamic electric power system. This model traces rays from 50 points on the face of the sun to 10 points on each of the 456 collector facets. The triangular facets are modeled with spherical, parabolic, or toroidal reflective surface contour and surface slope errors. The rays are then traced through the receiver aperture to the walls of the receiver. Images of the collector and of the sun within the receiver produced by this code provide insight into the collector receiver interface. Flux distribution on the receiver walls, plotted by this code, is improved by a combination of changes to aperture location and receiver tilt angle. Power loss by spillage at the receiver aperture is computed and is considerably reduced by using toroidal facets.

Jefferies, Kent S.↗

An Investigation of Thermal Properties of 2D Materials [Dissertation]

Studying the thermal conductivity of 2D materials is important due to the applications of 2D materials in fields such as thermal management, thermoelectricity, renewable energy, and sensors. As such, measurements of the thermal conductivity of these 2D materials become important to measure. Thermal conductivity is often difficult to measure for 2D materials due to their atomically thin nature and many experimental methods for doing so requiring contact with the sample, which can alter the thermal properties. A non-contact method for calculating the thermal conductivity of 2D materials supported on substrates in order to model the thermal conductivity of 2D materials for devices, is proposed and experimentally performed in this dissertation. The optothermal Raman technique is a useful non-contact diagnostic technique useful in determining the thermal conductivity of 2D materials. The optothermal Raman typically does not account for heat losses due to convection or radiation or substrate resistance, which are shown to be important factors to consider when developing an optothermal Raman model. Additionally, the calculation of the interfacial thermal conductance between the bottom surface of the sample and the top surface of the substrate, plays an important role in determining the final value of the thermal conductivity of a supported sample, and will yield differing results based on whether or not the conductance is calculated using an approach such as the Diffuse Mismatch Model (DMM) or calculated directly by varying the laser heating profile (usually done by changing the laser objective). This is shown to be the case for both graphene on Ni, graphene on Cu, and SnSe 2 on Cu. In addition to experimentally calculating the thermal conductivity of a 2D material with the optothermal Raman technique, the thermal conductivity of 2D materials can also be calculated using computational methods. The three-phonon method is a method which can be used to simulate phonon scattering processes and determine the thermal conductivity of semiconductors, wherein phonon scattering is the dominant mechanism which determines the thermal conductivity. The three-phonon method uses relaxation times for phonon scattering with other phonons, electrons, and other material system elements, such as isotopes or material defects, in order to create a single-mode relaxation time approximation (SMRTA), which is used to calculate the final value of the thermal conductivity. An important consideration when determining the thermal conductivity of a 2D material using this method is the device geometry, which is reflected in this work as the phonon-boundary scattering relaxation time. This inclusion is important along with the inclusion of phonon-electron scattering in accurately determining the thermal conductivity of a 2D material. In both the optothermal Raman experiments and the three-phonon method computations, strain is shown to have a demonstrable effect on the thermal conductivity of 2D materials. When a 1.1% strain was applied to the mechanical properties of SnSe, the three-phonon processes yielded a lower thermal conductivity than the no-strain case. For the optothermal Raman experiments, the strain induced in the Cu substrate and transferred to a single-layer graphene (SLG) sample yields a trend where the thermal conductivity of the SLG decreases with respect to strain applied. In the case where the interfacial thermal conductance was calculated directly, the conductance increased with respect to strain applied. This presents strain as a reliable and viable method for tuning the thermal properties of 2D materials for device applications.

36 MATERIALS SCIENCE↗

Computer Programs For Analysis Of Thermally Reactive Tracer Tests In Geothermal Reservoirs

The Tracer Analysis Toolbox (TAT) is a stand-alone executable software package that focuses on reservoir monitoring, using changes in concentration of thermally degrading tracers between and injection well and a production well to reflect the temperature-time histories along flow paths through the reservoir. By conducting such tests periodically, the thermal evolution of the flow paths connecting injection wells to production wells can be monitored. Because this approach is sensitive to temperature along the whole path, it can detect changes well before they occur at the distal end of the path (i.e., the production well). Thus, the thermally degrading tracer method provides early detection of thermal decline before it impacts that well. The goal of TAT is to simplify planning of a reactive tracer monitoring campaign and interpretation of results by providing: (1) tracer test planning and analysis tools to define the necessary kinetic parameters, injection concentrations, and other tracer parameters that are suitable for the expected reservoir residence time and temperature, (2) identification of tracers with suitable characteristics (defined by (1)) and (3) a suite of analysis programs to analyze tracer test results.

Plummer, MitchellAaron [Idaho National Laboratory ↗

Who is marginalized in energy justice? Amplifying community leader perspectives of energy transitions in Ghana

There is a divide in energy access studies, between technologically-focused modeling papers in engineering and economics, and energy justice frameworks and principles grounded in social sciences. Quantitative computational models are necessary when analyzing energy, and more specifically electricity, systems, as they are technologically-complex systems that can diverge from intuitive patterns. To assure energy justice, these models must be reflective of, and informative to, a wide range of stakeholders, including households and communities alongside utilities, governments, and others. Yet, moving from a qualitative understanding of preferences to quantitative modeling is challenging. In this perspective piece, we pilot the use of the value-focused thinking framework to inform stakeholder engagement. The result is a strategic objective hierarchy that highlights the tradeoffs and the social, economic and technological factors that need to be measured in models. We apply the process in Ghana, using a survey, stakeholder workshops, and follow-up interviews to uncover key tradeoffs and stakeholder-derived objectives. We discuss three key areas that have been rarely, if ever, well-represented in energy models: (1) the relationship between the dynamics of electricity end-use and the technology and economic structure of the system; (2) explicit tradeoffs between electricity access, cost, and reliability as defined by stakeholders; and (3) the definition of new objectives, such as minimizing hazards related to theft. We conclude that this model of engagement provides an opportunity to tie together rigorous qualitative analysis and stakeholder engagement with crucial quantitative models of the electricity system.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Structure−Property Relationships in a Series of Hybrid Halopyridinium Ruthenium(IV) Halides

Reported is the synthesis and characterization of a family of hybrid ruthenium halides consisting of haloruthenium octahedra (X = Cl, Br) charge balanced with halopyridinium (XPy; X= H, Cl, Br, I) organic cations which assemble via noncovalent interactions between ion pairs. Diffuse reflectance spectroscopy showed that compounds containing RuBr 6 2- octahedra displayed a lower bandgap (1.05 eV< x < 1.08 eV) compared to compounds with RuCl 6 2- octahedra (1.22 eV < x < 1.43 eV). Additionally, computational density functional theory (DFT) based natural bonding orbital (NBO) analysis and density of state (DOS) methods were used to characterize second-sphere non-covalent interaction strengths and elucidate molecular orbital perturbations to elucidate their influence on Ru-X orbital constructs and in turn rationalize band gap trends. Analyses showed ligand to metal charge transfer is responsible for the small bandgap energies and are unperturbed by second-sphere interactions. Here, this report serves as a platform for probing the relationship between the structural and photophysical properties within the haloruthenium family of low dimensional transition metal halide perovskites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Non-Hermitian wave packet approximation of Bloch optical equations

We introduce a non-Hermitian approximation of Bloch optical equations. This approximation provides a complete description of the excitation, relaxation, and decoherence dynamics of ensembles of coupled quantum systems in weak laser fields, taking into account collective effects and dephasing. In the proposed method, one propagates the wave function of the system instead of a complete density matrix. Relaxation and dephasing are taken into account via automatically adjusted time-dependent gain and decay rates. As an application, we compute the numerical wave packet solution of a time-dependent non-Hermitian Schroedinger equation describing the interaction of electromagnetic radiation with a quantum nano-structure, and compare the calculated transmission, reflection, and absorption spectra with those obtained from the numerical solution of the Liouville-von Neumann equation. It is shown that the proposed wave packet scheme is significantly faster than the propagation of the full density matrix while maintaining small error. We provide the key ingredients for easy-to-use implementation of the proposed scheme and identify the limits and error scaling of this approximation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Theoretical rotation-vibration spectrum of thioformaldehyde

We present a variational calculation of the first comprehensive T = 300 K rovibrational line list for thioformaldehyde, H{sub 2}CS. It covers 41 809 rovibrational levels for states up to J{sub max} = 30 with vibrational band origins up to 5000 cm{sup −1} and provides the energies and line intensities for 547 926 transitions from the ground vibrational state to these levels. It is based on our previously reported accurate ab initio potential energy surface and a newly calculated ab initio dipole moment surface. Minor empirical adjustments are made to the ab initio equilibrium geometry to reduce systematic errors in the predicted intra-band rotational energy levels. The rovibrational energy levels and transition intensities are computed variationally by using the methods implemented in the computer program TROVE. Transition wavelengths and intensities are found to be in excellent agreement with the available experimental data. The present calculations correctly reproduce the observed resonance effects, such as intensity borrowing, thus reflecting the high accuracy of the underlying ab initio surfaces. We report a detailed analysis of several vibrational bands, especially those complicated by strong Coriolis coupling, to facilitate future laboratory assignments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

TH-E-209-00: Radiation Dose Monitoring and Protocol Management

Radiation dose monitoring solutions have opened up new opportunities for medical physicists to be more involved in modern clinical radiology practices. In particular, with the help of comprehensive radiation dose data, data-driven protocol management and informed case follow up are now feasible. Significant challenges remain however and the problems faced by medical physicists are highly heterogeneous. Imaging systems from multiple vendors and a wide range of vintages co-exist in the same department and employ data communication protocols that are not fully standardized or implemented making harmonization complex. Many different solutions for radiation dose monitoring have been implemented by imaging facilities over the past few years. Such systems are based on commercial software, home-grown IT solutions, manual PACS data dumping, etc., and diverse pathways can be used to bring the data to impact clinical practice. The speakers will share their experiences with creating or tailoring radiation dose monitoring/management systems and procedures over the past few years, which vary significantly in design and scope. Topics to cover: (1) fluoroscopic dose monitoring and high radiation event handling from a large academic hospital; (2) dose monitoring and protocol optimization in pediatric radiology; and (3) development of a home-grown IT solution and dose data analysis framework. Learning Objectives: Describe the scope and range of radiation dose monitoring and protocol management in a modern radiology practice Review examples of data available from a variety of systems and how it managed and conveyed. Reflect on the role of the physicist in radiation dose awareness.

60 APPLIED LIFE SCIENCES↗

Ab initio studies of structural, electronic, optical, elastic and thermal properties of CuGaTe{sub 2}

We have performed ab initio calculations for the structural, electronic, optical, elastic and thermal properties of CuGaTe{sub 2}. In this study, we used an accurate full potential linearized augmented plane wave (FP-LAPW) method to find the equilibrium structural parameters and to compute the full elastic tensors. We report electronic and optical properties with the recently developed density functional of Tran and Blaha. Furthermore, optical features such as dielectric functions, refractive indices, extinction coefficient, optical reflectivity, absorption coefficients, optical conductivities, were calculated for photon energies up to 30 eV. The thermodynamical properties such as Debye temperature, entropy and Gruneisen parameter, bulk modulus and hardness were calculated employing the quasi-harmonic Debye model at different temperatures (0–1000 K) and pressures (0–8 GPa) and the silent results were interpreted. Most of the investigated parameters are reported for the first time.

36 MATERIALS SCIENCE↗