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At least 415 records · Page 23

Improved Mobilome Delineation in Fragmented Genomes

The mobilome of a microbe, i.e., its set of mobile elements, has major effects on its ecology, and is important to delineate properly in each genome. This becomes more challenging for incomplete genomes, and even more so for metagenome-assembled genomes (MAGs), where misbinning of scaffolds and other losses can occur. Genomic islands (GIs), which integrate into the host chromosome, are a major component of the mobilome. Our GI-detection software TIGER, unique in its precise mapping of GI termini, was applied to 74,561 genomes from 2,473 microbial species, each species containing at least one MAG and one isolate genome. A species-normalized deficit of ∼1.6 GIs/genome was measured for MAGs relative to isolates. To test whether this undercount was due to the higher fragmentation of MAG genomes, TIGER was updated to enable detection of split GIs whose termini are on separate scaffolds or that wrap around the origin of a circular replicon. This doubled GI yields, and the new split GIs matched the quality of single-scaffold GIs, except that highly fragmented GIs may lack central portions. Cross-scaffold search is an important upgrade to GI detection as fragmented genomes increasingly dominate public databases. TIGER2 better captures MAG microdiversity, recovering niche-defining GIs and supporting microbiome research aims such as virus-host linking and ecological assessment.

54 ENVIRONMENTAL SCIENCES↗

Normal mode analysis of macromolecular systems with the mobile block Hessian method

Until recently, normal mode analysis (NMA) was limited to small proteins, not only because the required energy minimization is a computationally exhausting task, but also because NMA requires the expensive diagonalization of a 3N{sub a}×3N{sub a} matrix with N{sub a} the number of atoms. A series of simplified models has been proposed, in particular the Rotation-Translation Blocks (RTB) method by Tama et al. for the simulation of proteins. It makes use of the concept that a peptide chain or protein can be seen as a subsequent set of rigid components, i.e. the peptide units. A peptide chain is thus divided into rigid blocks with six degrees of freedom each. Recently we developed the Mobile Block Hessian (MBH) method, which in a sense has similar features as the RTB method. The main difference is that MBH was developed to deal with partially optimized systems. The position/orientation of each block is optimized while the internal geometry is kept fixed at a plausible - but not necessarily optimized - geometry. This reduces the computational cost of the energy minimization. Applying the standard NMA on a partially optimized structure however results in spurious imaginary frequencies and unwanted coordinate dependence. The MBH avoids these unphysical effects by taking into account energy gradient corrections. Moreover the number of variables is reduced, which facilitates the diagonalization of the Hessian. In the original implementation of MBH, atoms could only be part of one rigid block. The MBH is now extended to the case where atoms can be part of two or more blocks. Two basic linkages can be realized: (1) blocks connected by one link atom, or (2) by two link atoms, where the latter is referred to as the hinge type connection. In this work we present the MBH concept and illustrate its performance with the crambin protein as an example.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Data collection in IMS: It's not as easy as it looks

Data collection in Ion Mobility Spectrometry (IMS) is not as easy an endeavor as it appears. Despite the advent of high speed personal computers and fast analog-to-digital converters (ADC's), care must be taken to ensure that reliable data are obtained in a timely fashion. This is especially true in hyphenated techniques, e.g. GC-IMS, where the amount of data increases dramatically when gas chromatography-ion mobility spectrometry (GC-IMS) data is being collected. Using the Graseby GC-IMS, with a gate repetition rate of 33 Hz, it is theoretically possible to collect 33 spectra per second. This collection rate is not realistically obtained due to a number of factors. Among these factors are inaccuracy of the timing signal from the IMS, the necessity to store the data, disk input/output limitations, disk operating system limitations, and program overhead. Taking these factors into account, we have achieved a data collection rate of 20 spectra per second. This paper will describe these problems, demonstrate the practical effects these problems present, and present methods for minimizing these effects.

Davis, Dennis M.↗

Interplay between microstructure, defect states, and mobile charge generation in transition metal dichalcogenide heterojunctions

Two-dimensional transition metal dichalcogenides (2D-TMDCs) have gained attention for their promise in next-generation energy-harvesting and quantum computing technologies, but realizing these technologies requires a greater understanding of TMDC properties that influence their photophysics. To this end, we discuss here the interplay between TMDC microstructure and defects with the charge generation yield, lifetime, and mobility. As a model system, we compare monolayer-only and monolayer-rich MoS 2 grown by chemical vapor deposition, and we employ the TMDCs in Type-II charge-separating heterojunctions with semiconducting single-walled carbon nanotubes (s-SWCNTs). Our results suggest longer lifetimes and higher yields of mobile carriers in samples containing a small fraction of defect-rich multilayer islands on predominately monolayer MoS 2 . Compared to the monolayer-only heterojunctions, the carrier lifetimes increase from 0.73 μs to 4.71 μs, the hole transfer yield increases from 23% to 34%, and the electron transfer yield increases from 39% to 59%. We reach these conclusions using a unique combination of microwave photoconductivity (which probes only mobile carriers) along with transient absorption spectroscopy (which identifies spectral signatures unique to each material and type of photoexcited quasiparticle, but does not probe mobility). Overall, our results highlight the substantial changes in photophysics that can occur from small changes in TMDC microstructure and defect density, where the presence of defects does not necessarily preclude improvements in charge generation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Project LASER

NASA formally launched Project LASER (Learning About Science, Engineering and Research) in March 1990, a program designed to help teachers improve science and mathematics education and to provide 'hands on' experiences. It featured the first LASER Mobile Teacher Resource Center (MTRC), is designed to reach educators all over the nation. NASA hopes to operate several MTRCs with funds provided by private industry. The mobile unit is a 22-ton tractor-trailer stocked with NASA educational publications and outfitted with six work stations. Each work station, which can accommodate two teachers at a time, has a computer providing access to NASA Spacelink. Each also has video recorders and photocopy/photographic equipment for the teacher's use. MTRC is only one of the five major elements within LASER. The others are: a Space Technology Course, to promote integration of space science studies with traditional courses; the Volunteer Databank, in which NASA employees are encouraged to volunteer as tutors, instructors, etc; Mobile Discovery Laboratories that will carry simple laboratory equipment and computers to provide hands-on activities for students and demonstrations of classroom activities for teachers; and the Public Library Science Program which will present library based science and math programs.

Source record↗

Alkali‐Ion‐Assisted Activation of ε‐VOPO 4 as a Cathode Material for Mg‐Ion Batteries

Abstract Rechargeable multivalent‐ion batteries are attractive alternatives to Li‐ion batteries to mitigate their issues with metal resources and metal anodes. However, many challenges remain before they can be practically used due to the low solid‐state mobility of multivalent ions. In this study, a promising material identified by high‐throughput computational screening is investigated, ε‐VOPO 4 , as a Mg cathode. The experimental and computational evaluation of ε‐VOPO 4 suggests that it may provide an energy density of >200 Wh kg −1 based on the average voltage of a complete cycle, significantly more than that of well‐known Chevrel compounds. Furthermore, this study finds that Mg‐ion diffusion can be enhanced by co‐intercalation of Li or Na, pointing at interesting correlation dynamics of slow and fast ions.

25 ENERGY STORAGE↗

Security vulnerabilities of connected vehicle streams and their impact on cooperative driving

Autonomous vehicles capable of navigating unpredictable real-world environments with little human feedback are a reality today. Such systems rely heavily on onboard sensors such as cameras, radar/LIDAR, and GPS as well as capabilities such as 3G/4G connectivity and V2V/V2I communication to make real-time maneuvering decisions. Autonomous vehicle control imposes very strict requirements on the security of the communication channels used by the vehicle to exchange information as well as the control logic that performs complex driving tasks such as adapting vehicle velocity or changing lanes. This research presents a first look at the effects of security attacks on the communication channel as well as sensor tampering of a connected vehicle stream equipped to achieve CACC. Our simulation results show that an insider attack can cause significant instability in the CACC vehicle stream. We also outline how different countermeasures, such as downgrading to ACC mode, could potentially be used to improve the security and safety of the connected vehicle streams.

42 ENGINEERING↗

Electrodynamics payloads for small rockets

Totally integrated design facilitates electrical cleanliness and light weight, which are necessary in subsonic parachute-borne payloads for electrodynamics investigations. 'Blunt' probes measure ion conductivity, as do Gerdien condensers. Recent finite-element computer analyses combining flow and electrodynamics have resolved problems in determining ion densities and mobilities from Gerdien data. Three-axis electric fields are measured with deployable boom-mounted electrodes from dc through VLF. Splitting the cylindrical payload with an insulator and measuring the current between halves has provided a vertical Maxwell current detector mechanically rigid enough to measure, at ELF, energy related to coupling. A nose tip 'Smith' probe turbulence measurement is usually performed on ascent. Other instrumentation, such as photo-ionization sources and X-ray detectors, can also be included. These electrodynamic measurement payloads are about one meter in length and have a mass of about 9 kg. They can be launched with an Orion-class or smaller vehicle.

Croskey, C. L.↗

Integrated Computational Fluid Dynamics and Thermal Desktop Thermal Modeling for Assessment of the EMU in Support of ISS EVA 80

Following the reports of water accumulation in the Extravehicular Mobility Unit (EMU) helmet during the ISS US EVA-80, various efforts for mitigation and further understanding of this phenomenon have been undertaken with the goal of prevention and to ensure crew safety in future EVAs. In support of this goal, a combination of Thermal Desktop thermal modeling and Computational Fluid Dynamics (CFD) has been performed in order to characterize the performance of the EMU components, specifically those within the ventilation/cooling water loops. This modeling effort evaluates the dry/wet gas pressure drop and flow distribution through gas and liquid flow paths using CFD, as well as a two-phase flow assessment of condensation production and water separation/removal performance using an integrated Thermal Desktop model of important EMU ventilation loop components. The models assess this overall thermal-fluid performance in comparison with previous existing models, design points, and historical EVA data using their inputs.

Blain Ryan Lancaster↗

Integrated Computational Fluid Dynamics and Thermal Desktop Thermal Modeling for Assessment of the EMU in Support of ISS EVA 80

Following the reports of water accumulation in the Extravehicular Mobility Unit (EMU) helmet during the ISS US EVA-80, various efforts for mitigation and further understanding of this phenomenon have been undertaken with the goal of prevention and to ensure crew safety in future EVAs. In support of this goal, a combination of Thermal Desktop thermal modeling and Computational Fluid Dynamics (CFD) has been performed in order to characterize the performance of the EMU components, specifically those within the ventilation/cooling water loops. This modeling effort evaluates the dry/wet gas pressure drop and flow distribution through gas and liquid flow paths using CFD, as well as a two-phase flow assessment of condensation production and water separation/removal performance using an integrated Thermal Desktop model of important EMU ventilation loop components. The models assess this overall thermal-fluid performance in comparison with previous existing models, design points, and historical EVA data using their inputs.

EVA 80↗

Hardware Architecture for Measurements for 50-V Battery Modules

Energy storage devices, especially batteries, have become critical for several industries including automotive, electric utilities, military and consumer electronics. With the increasing demand for electric and hybrid electric vehicles and the explosion in popularity of mobile and portable electronic devices such as laptops, cell phones, e-readers, tablet computers and the like, reliance on portable energy storage devices such as batteries has likewise increased. Because many of the systems these batteries integrated into are critical, there is an increased need for an accurate in-situ method of monitoring battery state-of-health. Over the past decade the Idaho National Laboratory (INL), Montana Tech of the University of Montana (Tech), and Qualtech Systems, Inc. (QSI) have been developing the Smart Battery Status Monitor (SBSM), an integrated battery management system designed to monitor battery health, performance and degradation and use this knowledge for effective battery management and increased battery life. Key to the success of the SBSM is an in-situ impedance measurement system called the Impedance Measurement Box (IMB). One of the challenges encountered has been development of a compact IMB system that will perform rapid accurate measurements of a battery impedance spectrum working with higher voltage batteries of up to 300 volts. This paper discusses the successful realization of a system that will work up to 50 volts.

25 ENERGY STORAGE↗

AN ADVANCED CALIBRATION PROCEDURE FOR COMPLEX IMPEDANCE SPECTRUM MEASUREMENTS OF ADVANCED ENERGY STORAGE DEVICES

With the increasing demand for electric and hybrid electric vehicles and the explosion in popularity of mobile and portable electronic devices such as laptops, cell phones, e-readers, tablet computers and the like, reliance on portable energy storage devices such as batteries has likewise increased. The concern for the availability of critical systems in turn drives the availability of battery systems and thus the need for accurate battery health monitoring has become paramount. Over the past decade the Idaho National Laboratory (INL), Montana Tech of the University of Montana (Tech), and Qualtech Systems, Inc. (QSI) have been developing the Smart Battery Status Monitor (SBSM), an integrated battery management system designed to monitor battery health, performance and degradation and use this knowledge for effective battery management and increased battery life. Key to the success of the SBSM is an in-situ impedance measurement system called the Impedance Measurement Box (IMB). One of the challenges encountered has been development of an accurate, simple, robust calibration process. This paper discusses the successful realization of this process.

25 ENERGY STORAGE↗

Piezoelectric Electron-Phonon Interaction from Ab Initio Dynamical Quadrupoles: Impact on Charge Transport in Wurtzite GaN

First-principles calculations of $\textit{e}$-ph interactions are becoming a pillar of electronic structure theory. However, the current approach is incomplete. The piezoelectric (PE) $\textit{e}$-ph interaction, a long-range scattering mechanism due to acoustic phonons in noncentrosymmetric polar materials, is not accurately described at present. Current calculations include short-range $\textit{e}$-ph interactions (obtained by interpolation) and the dipolelike Frölich long-range coupling in polar materials, but lack important quadrupole effects for acoustic modes and PE materials. Here we derive and compute the long-range $\textit{e}$-ph interaction due to dynamical quadrupoles, and apply this framework to investigate $\textit{e}$-ph interactions and the carrier mobility in the PE material wurtzite GaN. In this work, we show that the quadrupole contribution is essential to obtain accurate $\textit{e}$-ph matrix elements for acoustic modes and to compute PE scattering. Our work resolves the outstanding problem of correctly computing $\textit{e}$-ph interactions for acoustic modes from first principles, and enables studies of $\textit{e}$-ph coupling and charge transport in PE materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Automated Work Package: Initial Wireless Communication Platform Design, Development, and Evaluation

The Department of Energy's Light Water Reactor Sustainability Program is developing the scientific basis to ensure long-term reliability, productivity, safety, and security of the nuclear power industry in the United States. The Instrumentation, Information, and Control (II and C) pathway of the program aims to increase the role of advanced II and C technologies to achieve this objective. One of the pathway efforts at Idaho National Laboratory (INL) is to improve the work packages execution process by replacing the expensive, inefficient, bulky, complex, and error-prone paper-based work orders with automated work packages (AWPs). An AWP is an automated and dynamic presentation of the work package designed to guide the user through the work process. It is loaded on a mobile device, such as a tablet, and is capable of communicating with plant equipment and systems to acquire plant and procedure states. The AWP replaces those functions where a computer is more efficient and reliable than a human. To enable the automatic acquisition of plant data, it is necessary to design and develop a prototype platform for data exchange between the field instruments and the AWP mobile devices. The development of the platform aims to reveal issues and solutions generalizable to large-scale implementation of a similar system. Topics such as bandwidth, robustness, response time, interference, and security are usually associated with wireless communication. These concerns, along with other requirements, are listed in an earlier INL report. Specifically, the targeted issues and performance aspects in this work are relevant to the communication infrastructure from the perspective of promptness, robustness, expandability, and interoperability with different technologies. The development of a prompt system entailed significant performance optimization, including the use of parallel processing, parallel communication, modularity, noise filtering, and frequency tuning. A robust system was achieved by enforcing a persistent continuous data exchange that automatically detects and conveys a failure of any link or component in any part of the system, and that automatically restores the communication once the link or component is restored. An expandable topology was enabled by modularity and load sharing. The number of servers, mobile devices, and field instruments is not limited from a system structure point of view. The system interoperability was achieved by enforcing the independence of the field communication application from the mobile device application. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Twisted fracton models in three dimensions

We study novel three-dimensional gapped quantum phases of matter which support quasiparticles with restricted mobility, including immobile “fracton” excitations. So far, most existing fracton models may be instructively viewed as generalized Abelian lattice gauge theories. Here, by analogy with Dijkgraaf-Witten topological gauge theories, we discover a natural generalization of fracton models, obtained by twisting the gauge symmetries. Introducing generalized gauge transformation operators carrying an extra phase factor depending on local configurations, we construct a plethora of exactly solvable three-dimensional models, which we dub “twisted fracton models.” A key result of our approach is to demonstrate the existence of rich non-Abelian fracton phases of distinct varieties in a three-dimensional system with finite-range interactions. For an accurate characterization of these novel phases, the notion of being inextricably non-Abelian is introduced for fractons and quasiparticles with one-dimensional mobility, referring to their new behavior of displaying braiding statistics that is, and remains, non-Abelian regardless of which quasiparticles with higher mobility are added to or removed from them. We also analyze these models by embedding them on a 3-torus and computing their ground-state degeneracies, which exhibit a surprising and novel dependence on the system size in the non-Abelian fracton phases. Furthermore, as an important advance in the study of fracton order, we develop a general mathematical framework which systematically captures the fusion and braiding properties of fractons and other quasiparticles with restricted mobility.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Hydrotalcite Intercalated siRNA: Computational Characterization of the Interlayer Environment

Using molecular dynamics (MD) simulations, we explore the structural and dynamical properties of siRNA within the intercalated environment of a Mg:Al 2:1 Layered Double Hydroxide (LDH) nanoparticle. An ab initio force field (Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies: COMPASS) is used for the MD simulations of the hybrid organic-inorganic systems. The structure, arrangement, mobility, close contacts and hydrogen bonds associated with the intercalated RNA are examined and contrasted with those of the isolated RNA. Computed powder X-ray diffraction patterns are also compared with related LDH-DNA experiments. As a method of probing whether the intercalated environment approximates the crystalline or rather the aqueous state, we explore the stability of the principle parameters (e.g., the major groove width) that differentiate both A- and A'- crystalline forms of siRNA and contrast this with recent findings for the same siRNA simulated in water. We find the crystalline forms remain structurally distinct when intercalated, whereas this is not the case in water. Implications for the stability of hybrid LDH-RNA systems are discussed.

gene therapy↗