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At least 1,009 records · Page 56

eSHAFTS: Integrated and graphical drug design software based on 3D molecular similarity

With the development of computer technology, computer‐aided drug design (CADD) has become an important means for drug research and development, and its representative method is virtual screening. Various virtual screening platforms have emerged in an endless stream and play great roles in the field of drug discovery. With the increasing number of compound molecules, virtual screening platforms face two challenges: low fluency and low visibility of software operations. In this article, we present an integrated and graphical drug design software eSHAFTS based on three‐dimensional (3D) molecular similarity to overcome these shortcomings. Compared with other software, eSHAFTS has four main advantages, which are integrated molecular editing and drawing, interactive loading and analysis of proteins, multithread and multimode 3D molecular similarity calculation, and multidimensional information visualization. Experiments have verified its convenience, usability, and reliability. By using eSHAFTS, various tasks can be submitted and visualized in one desktop software without locally installing any dependent plug‐ins or software. The software installation package can be downloaded for free at http://lilab.ecust.edu.cn/home/resource.html . © 2019 Wiley Periodicals, Inc.

He, Gaoqi↗

In operando cryo-STEM of pulse-induced charge density wave switching in TaS 2

The charge density wave material 1T-TaS 2 exhibits a pulse-induced insulator-to-metal transition, which shows promise for next-generation electronics such as memristive memory and neuromorphic hardware. However, the rational design of TaS 2 devices is hindered by a poor understanding of the switching mechanism, the pulse-induced phase, and the influence of material defects. Here, we operate a 2-terminal TaS 2 device within a scanning transmission electron microscope at cryogenic temperature, and directly visualize the changing charge density wave structure with nanoscale spatial resolution and down to 300 μs temporal resolution. We show that the pulse-induced transition is driven by Joule heating, and that the pulse-induced state corresponds to the nearly commensurate and incommensurate charge density wave phases, depending on the applied voltage amplitude. With our in operando cryogenic electron microscopy experiments, we directly correlate the charge density wave structure with the device resistance, and show that dislocations significantly impact device performance. This work resolves fundamental questions of resistive switching in TaS 2 devices, critical for engineering reliable and scalable TaS 2 electronics.

36 MATERIALS SCIENCE↗

Using indium tin oxide material to implement the imaging of microwave plasma ignition process

In this paper, a method is introduced to get global observation of microwave plasma ignition process at high pressure. A microwave resonator was designed with an indium tin oxide coated glass at bottom. Microwave plasma ignition was implemented in methane and air mixture at 10 bars by a 2 ms-3 kW-2.45 GHz microwave pulse, and the high speed images of the ignition process were obtained. The images visually proved that microwave plasma ignition could lead to a multi-point ignition. The system may also be applied to obtain Schlieren images, which is commonly used to observe the development of flame kernel in an ignition process.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Data mining for better material synthesis: The case of pulsed laser deposition of complex oxides

The pursuit of more advanced electronics, and finding solutions to energy needs often hinges upon the discovery and optimization of new functional materials. However, the discovery rate of these materials is alarmingly low. Much of the information that could drive this rate higher is scattered across tens of thousands of papers in the extant literature published over several decades but is not in an indexed form, and cannot be used in entirety without substantial effort. Many of these limitations can be circumvented if the experimentalist has access to systematized collections of prior experimental procedures and results. Here, we investigate the property-processing relationship during growth of oxide films by pulsed laser deposition. To do so, we develop an enabling software tool to (1) mine the literature of relevant papers for synthesis parameters and functional properties of previously studied materials, (2) enhance the accuracy of this mining through crowd sourcing approaches, (3) create a searchable repository that will be a community-wide resource enabling material scientists to leverage this information, and (4) provide through the Jupyter notebook platform, simple machine-learning-based analysis to learn the complex interactions between growth parameters and functional properties. Here, the results allow visualization of growth windows, trends and outliers, which can serve as a template for analyzing the distribution of growth conditions, provide starting points for related compounds and act as a feedback for first-principles calculations. Such tools will comprise an integral part of the materials design schema in the coming decade.

36 MATERIALS SCIENCE↗

Structural Basis of Pan-Ebolavirus Neutralization by a Human Antibody against a Conserved, yet Cryptic Epitope

ABSTRACT Only one naturally occurring human antibody has been described thus far that is capable of potently neutralizing all five ebolaviruses. Here we present two crystal structures of this rare, pan-ebolavirus neutralizing human antibody in complex with Ebola virus and Bundibugyo virus glycoproteins (GPs), respectively. The structures delineate the key protein and glycan contacts for binding that are conserved across the ebolaviruses, explain the antibody’s unique broad specificity and neutralization activity, and reveal the likely mechanism behind a known escape mutation in the fusion loop region of GP2. We found that the epitope of this antibody, ADI-15878, extends along the hydrophobic paddle of the fusion loop and then dips down into a highly conserved pocket beneath the N-terminal tail of GP2, a mode of recognition unlike any other antibody elicited against Ebola virus, and likely critical for its broad activity. The fold of Bundibugyo virus glycoprotein, not previously visualized, is similar to the fold of Ebola virus GP, and ADI-15878 binds to each virus’s GP with a similar strategy and angle of attack. These findings will be useful in deployment of this antibody as a broad-spectrum therapeutic and in the design of immunogens that elicit the desired broadly neutralizing immune response against all members of the ebolavirus genus and filovirus family. IMPORTANCE There are five different members of the Ebolavirus genus. Provision of vaccines and treatments able to protect against any of the five ebolaviruses is an important goal of public health. Antibodies are a desired result of vaccines and can be delivered directly as therapeutics. Most antibodies, however, are effective against only one or two, not all, of these pathogens. Only one human antibody has been thus far described to neutralize all five ebolaviruses, antibody ADI-15878. Here we describe the molecular structure of ADI-15878 bound to the relevant target proteins of Ebola virus and Bundibugyo virus. We explain how it achieves its rare breadth of activity and propose strategies to design improved vaccines capable of eliciting more antibodies like ADI-15878.

West, Brandyn R. (ORCID:0000000213990117)↗

Thermal Modeling of NUHOMS HSM-15 and HSM-1 Storage Modules at Calvert Cliffs Nuclear Power Station ISFSI

As part of the Used Fuel Disposition Campaign of the Department of Energy (DOE), visual inspections and temperature measurements were performed on two storage modules in the Calvert Cliffs Nuclear Power Station’s Independent Spent Fuel Storage Installation (ISFSI). Detailed thermal models models were developed to obtain realistic temperature predictions for actual storage systems, in contrast to conservative and bounding design basis calculations.

Dry Storage Systems↗

Characterizing Photometric Flicker. Handheld Meters

Temporal light modulation (TLM) is the variation of light output as a function of time and its presence can have adverse effects on health and visual performance (e.g., increased occurrence of migraines, reduced visual-task performance). TLM has been the subject of recent articles primarily associated with flicker in LED lighting. Lighting system characteristics that can affect flicker vary by technology; examples include filament thickness for incandescent sources, phosphor persistence for fluorescent and coated metal halide sources, and circuit designs for electronically ballasted or driven sources. The characterization of flicker, especially in the field, is important to ensure adequate living and working conditions. Today, various types of flicker meters are available, including high-speed and precise benchtop models for laboratory environments and portable handheld meters that can range from simple smartphone applications in an existing smart device to scientific grade meters that have capabilities beyond flicker measurements. In this report, the performance of various handheld meters capable of measuring flicker in the field is compared to a reference benchtop meter chosen based on its performance in the initial round of meter comparisons performed by Pacific Northwest National Laboratory.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

INL High-Performance and Sustainable Building Strategy

High-performance buildings are reliable, cost effective, and sustainable structures that minimize energy and water use, reduce solid waste and pollutant emissions, and limit the depletion of natural resources. High-performance buildings also provide a thermally and visually comfortable working environment that increases productivity for building occupants. As Idaho National Laboratory (INL) is the nation’s premier nuclear energy research laboratory, the physical infrastructure requires continual updating and repurposing to help accomplish that mission. INL’s infrastructure must incorporate high-performance sustainable design features to be fiscally responsible and reflect an image of innovation to the public and prospective employees. INL is a large consumer of energy with annual energy costs exceeding $16M. This High-Performance and Sustainable Building Strategy will help engineering and construction project teams design sustainable facilities, reduce life cycle operating costs, and support the INL net-zero plan while providing INL employees with a safe and healthy working environment. With these goals in mind, the recommendations described in this document are intended to form INL’s foundation for sustainable and high-performance building standards. This strategy incorporates the latest federal and Department of Energy (DOE) orders and directives, including DOE Order 436.1A, “Departmental Sustainability,” the DOE Sustainability Plan (SP), the INL Site Sustainability Plan (SSP), and Code of Federal Regulations (CFR). This document identifies the requirements of the “Guiding Principles for Sustainable Federal Buildings” (Guiding Principles) and briefly highlights the Leadership in Energy and Environmental Design (LEED) Gold certification. LEED Gold certification can be used to meet many of the requirements of the Guiding Principles.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

User-defined feature comparison for vector field ensembles

Most of the existing approaches to visualize vector field ensembles are to reveal the uncertainty of individual variables, for example, statistics, variability, etc. However, a user-defined derived feature like vortex or air mass is also quite significant, since they make more sense to domain scientists. In this paper, we present a new framework to extract user-defined derived features from different simulation runs. Specially, we use a detail-to-overview searching scheme to help extract vortex with a user-defined shape. We further compute the geometry information including the size, the geo-spatial location of the extracted vortexes. We also design some linked views to compare them between different runs. At last, the temporal information such as the occurrence time of the feature is further estimated and compared. Results show that our method is capable of extracting the features across different runs and comparing them spatially and temporally.

Comparative visualization↗

A VR-based volumetric medical image segmentation and visualization system with natural human interaction

Volume rendering produces informative two-dimensional (2D) images from a 3-dimensional (3D) volume. It highlights the region of interest and facilitates a good comprehension of the entire data set. However, volume rendering faces a few challenges. First, a high-dimensional transfer function is usually required to differentiate the target from its neighboring objects with subtle variance. Unfortunately, designing such a transfer function is a strenuously trial-and-error process. Second, manipulating/visualizing a 3D volume with a traditional 2D input/output device suffers dimensional limitations. To address all the challenges, we design NUI-VR 2 , a natural user interface-enabled volume rendering system in the virtual reality space. NUI-VR 2 marries volume rendering and interactive image segmentation. It transforms the original volume into a probability map with image segmentation. A simple linear transfer function will highlight the target well in the probability map. More importantly, we set the entire image segmentation and volume rendering pipeline in an immersive virtual reality environment with a natural user interface. NUI-VR 2 eliminates the dimensional limitations in manipulating and perceiving 3D volumes and dramatically improves the user experience.

42 ENGINEERING↗

Industrial Energy Assessment Training Effectiveness Evaluation: An Eye-Tracking Study

It is essential to understand the effectiveness of any training program so it can be improved accordingly. Various studies have applied standard metrics for the evaluation of visual behavior to recognize the areas of interest that attract individuals’ attention as there is a high correlation between attentional behavior and where one is focusing on. However, through reviewing the literature, we believe that studies that applied eye-tracking technologies for training purposes are still limited, especially in the industrial energy assessment training field. In this paper, the effectiveness of industrial energy assessment training was quantitatively evaluated by measuring the attentional allocation of trainees using eye-tracking technology. Moreover, this study identifies the areas that require more focus based on evaluating the performance of subjects after receiving the training. Additionally, this research was conducted in a controlled environment to remove the distractions that may be caused by environmental factors to only concentrate on variables that influence the learning behavior of subjects. The experiment results showed that after receiving the training, the subjects’ performance in energy assessment was significantly improved in two areas: production, and recycling and waste management, and the designed training program enhanced the knowledge of participants in identifying energy-saving opportunities to the knowledge level of experienced participants.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Dynamic fracture of glass fiber-reinforced ductile polymer matrix composites and loading rate effect

Here, the dynamic fracture of S-2 glass fiber-reinforced polymer matrix composites (FRPMCs) was investigated in this study. The matrix ductility was improved by a recently developed network topology modification technique via mixing partially reacted substructures (mPRS). The composite material was manufactured and characterized by micro-CT scanning and scanning electron microscopy (SEM). Dynamic single-edge notched bending (d-SENB) experiments were performed on the composites by using a modified split-Hopkinson pressure bar. Each specimen’s fracture process was visualized by ultrafast X-ray imaging. Such in-situ radiography enabled identifying the damage initiation below 50-micron scale and inspecting its propagation through the internal structures of opaque composites, thereby accurately quantifying the composites’ mechanical properties. Furthermore, the identical d-SENB experiments were designed and the digital image correlation (DIC) was employed to monitor the stress wave propagation on the composite specimens. The force and deflection measurements were modified and correlated to the physical damage processes. Besides, quasi-static SENB experiments were conducted to identify the loading rate effects on the composites’ fracture behaviors. The force and deflection history, bending stiffness, energy dissipation, and fracture toughness at different loading rates were quantified and compared. Finally, post-fracture analysis by micro-CT scanning and SEM provided physical observations on the variation of the fracture morphology by different loading rates.

42 ENGINEERING↗

Controlling thermoelectric transport via native defects in the diamond-like semiconductors Cu 2 HgGeTe 4 and Hg 2 GeTe 4

Diamond like semiconductors (DLS) have emerged as candidates for thermoelectric energy conversion. Towards understanding and optimizing performance, we present a comprehensive investigation of the electronic properties of two DLS phases, quaternary Cu 2 HgGeTe 4 and related ordered vacancy compound Hg 2 GeTe 4 , including thermodynamic stability, defect chemistry, and transport properties. To establish the thermodynamic link between the related but distinct phases, the stability region for both is visualized in chemical potential space. In spite of their similar structure and bonding, we show that the two materials exhibit reciprocal behaviors for dopability. Cu 2 HgGeTe 4 is degenerately p-type in all environments despite its wide stability region, due to the presence of low-energy acceptor defects V Cu and Cu Hg and is resistant to extrinsic n-type doping. Meanwhile Hg 2 GeTe 4 has a narrow stability region and intrinsic behavior due to the relatively high formation energy of native defects, but presents an opportunity for bi-polar doping. While these two compounds have similar structure, bonding, and chemical constituents, the reciprocal nature of their dopability emerges from significant differences in band edge positions. A Brouwer band diagram approach is utilized to visualize the role of native defects on carrier concentrations, dopability, and transport properties. Here this study elucidates the doping asymmetry between two solid-solution forming DLS phases Cu 2 HgGeTe 4 and Hg 2 GeTe 4 by revealing the defect chemistry of each compound, and suggests design strategies for defect engineering of DLS phases.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

pnnl/DPVPROT

Distributed photovoltaics protection software toolkit The code package includes several important functions for design and analysis of new grid protection schemes, for scenarios of distributed photovoltaic (DPV) generation approaching 100% of the peak feeder load, i.e., high-penetration DPV. Convert distribution feeder models, used by planning engineers, to electromagnetic transient (EMT) models that produce waveforms for advanced relay algorithms. Visualize the results of protection scheme operation. Tools to determine distance relay settings on distribution systems. Tools to predict the performance of time-domain, incremental distance relay algorithms

McDermott, Tom↗

VERAView API and Programmer's Guide (Milestone L3:PHI.MQA-1.P19.03)

VERAView's component-based design facilitates extension and integration into other applications and systems. In addition to describing VERAView's architecture and components, this document provides details on the component application programming interfaces (API), illustrates how to use them independently of VERAView itself, and explains how to extend VERAView with custom visualizations.

97 MATHEMATICS AND COMPUTING↗

Using Machine Learning to Identify Optimum Prospects for Offshore Geologic CO 2 Storage and Enhanced Oil Recovery in the Gulf of Mexico

The SECARB Offshore Partnership is a government-industry partnership focused on assembling the knowledge base required for secure, long-term, large-scale CO 2 subsea storage in saline formations and mature oil reservoirs. The SECARB Offshore Partnership is evaluating potential storage opportunities in the Central and Eastern planning areas of the outer continental shelf (OCS) of the Gulf of Mexico. The evaluation focuses on active and depleted oil and gas fields and potentially associated CO 2 -enhanced oil recovery (CO 2 -EOR), as well as, deep saline storage resources. As part of Subtask 3.0 (Offshore Storage Resources Characterization) and Subtask 4.0 (Risk Assessment, Simulation, and Modeling), Oklahoma State University (OSU) is developing a machine learning system that employs the SAS Institute’s Viya platform with visual data mining and machine learning to identify and characterize optimum prospects for enhanced oil recovery and stacked storage in saline reservoirs. This report summarizes this effort to date and discusses the many variables that can be used to characterize these storage objectives, as well as, the design vision of the Viya machine learning system.

02 PETROLEUM↗

A Multi-band Catalog of 10978 Star Clusters, Associations, and Candidates in the Milky Way

We present a catalog of Galactic star clusters, associations and candidates with 10978 entries. This multi-band catalog was constructed over 20 years, starting with visual inspections on the Digital Sky Survey and incremented with the 2MASS, WISE, VVV, Spitzer, and Herschel surveys. Large and small catalogs, as well as papers on individual objects have been systematically cross-identified. The catalog provides Galactic and equatorial coordinates, angular diameters, and chronologically ordered designations, making it simple to assign discoveries and verify how often the objects were cataloged by different authors, search methods, and/or surveys. Detection in a single band is the minimum constraint to validate an entry. About 3200 objects have measured parameters in the literature. A fundamental contribution of the present study is to present an additional ≈7700 objects for the first analyses of nature, photometry, spectroscopy and structure. The present focus is not to compile or determine fundamental parameters, but to provide a catalog uniformly characterizing the entries. A major result is that now 4234 embedded clusters are cataloged, a factor of ≈1.5 larger than open clusters. In addition to cross-identifications in different references and wavelength domains, we also communicate the discovery of 638 star clusters and similar objects. The present general catalog provides previously studied objects and thousands of additional entries in a homogeneous way, a timely contribution to Gaia-related works.

79 ASTRONOMY AND ASTROPHYSICS↗

Lighting energy savings potential of split-pane electrochromic windows controlled for daylighting with visual comfort

A simulation study was conducted to evaluate lighting energy savings of split-pane electrochromic (EC) windows controlled to satisfy key visual comfort parameters. Using the Radiance lighting simulation software, interior illuminance and luminance levels were computed for a south-facing private office illuminated by a window split into two independently-controlled EC panes. The transmittance of these was optimized hourly for a workplane illuminance target while meeting visual comfort constraints, using a least-squares algorithm with linear inequality constraints. Blinds were successively deployed until visual comfort criteria were satisfied. The energy performance of electrochromics proved to be highly dependent on how blinds were controlled. With hourly blind position adjustments, electrochromics showed significantly higher (62percent and 53percent, respectively without and with overhang) lighting energy consumption than clear glass. With a control algorithm designed to better approximate realistic manual control by an occupant, electrochromics achieved significant savings (48percent and 37percent, respectively without and with overhang). In all cases, energy consumption decreased when the workplace illuminance target was increased. In addition, the fraction of time during which the occupant had an unobstructed view of the outside was significantly greater with electrochromics: 10 months out of the year versus a handful of days for the reference case.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗