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At least 847 records · Page 47

Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities

Contemporary microbial ecology studies usually employ one or more omics approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other meta-omic approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool.

mass spectrometry↗

Accelerating Optical Absorption Spectra and Exciton Energy Computation via Interpolative Separable Density Fitting

© Springer International Publishing AG, part of Springer Nature 2018. We present an efficient way to solve the Bethe–Salpeter equation (BSE), a method for the computation of optical absorption spectra in molecules and solids that includes electron–hole interactions. Standard approaches to construct and diagonalize the Bethe–Salpeter Hamiltonian require at least (Formula Presented) operations, where Neis the number of electrons in the system, limiting its application to smaller systems. Our approach is based on the interpolative separable density fitting (ISDF) technique to construct low rank approximations to the bare exchange and screened direct operators associated with the BSE Hamiltonian. This approach reduces the complexity of the Hamiltonian construction to (Formula Presented) with a much smaller pre-constant, and allows for a faster solution of the BSE. Here, we implement the ISDF method for BSE calculations within the Tamm–Dancoff approximation (TDA) in the BerkeleyGW software package. We show that this novel approach accurately reproduces exciton energies and optical absorption spectra in molecules and solids with a significantly reduced computational cost.

Hu, W↗

Confidence intervals with a priori parameter bounds

We review the methods of constructing confidence intervals that account for a priori information about one-sided constraints on the parameter being estimated. We show that the so-called method of sensitivity limit yields a correct solution of the problem. Derived are the solutions for the cases of a continuous distribution with non-negative estimated parameter and a discrete distribution, specifically a Poisson process with background. For both cases, the best upper limit is constructed that accounts for the a priori information. A table is provided with the confidence intervals for the parameter of Poisson distribution that correctly accounts for the information on the known value of the background along with the software for calculating the confidence intervals for any confidence levels and magnitudes of the background (the software is freely available for download via Internet).

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Envision Charlotte Project Final Report

The Envision Charlotte Project (EC Project), supported by partners at the Center for Climate and Energy Solutions, the University of North Carolina at Charlotte’s Center for Sustainably Integrated Buildings and Sites and the City of Charlotte, has successfully demonstrated that existing buildings can benefit from operations improvements and low-cost efficiency upgrades, and that behavioral change campaigns can be effectively designed for measurability, longevity and impact. Support from this grant gave Envision Charlotte and its partners the resources and flexibility to demonstrate a variety of approaches to improve coordination with stakeholders in the implementation of programs to reduce the consumption of energy, water and waste. The project team also gained insights into the motivations and abilities that influence stakeholder engagement in sustainability initiatives at multiple levels. Importantly, as this report describes, strong partnerships between nonprofits, industry partners and research institutions can produce tangible impacts and replicable results in building efficiency. Further, building operators working alongside student researchers can form productive relationships that can advance building energy management goals. Key Findings of the EC Project This project focused on advancing solutions to energy efficiency in U.S. commercial buildings. The Building Re-Tuning™ Training (BRT) developed by the U.S. DOE’s Pacific Northwest National Lab (PNNL), designed to detect energy savings opportunities and implement improvements with resources and online tools, provided the starting point for the curriculum developed by stakeholders in the EC Project. Although the project partners encountered some issues with data consistency, the overall project outcomes fell short of the energy savings stated in the original proposal, and the total participating building targets were lower than anticipated, important findings, outcomes and lessons learned were achieved. EC Project grantees observed that the PNNL BRT, as currently written, was not compatible with the skills of average frontline mechanical personnel in the Charlotte region where the grant program was performed. Frontline staff are not, typically, energy managers, engineers or building commissioning agents, but they can play a key role in building performance. As detailed in this report, the grantees therefore focused on changes to the BRT that improved the level of training and competency of the frontline workers in this region. Among the technical observations related to improving the BRT that were observed in the EC Project: centralized facilities management often has an impact on building performance; operators can be overly reliant on service contracts; individual behaviors matter, and technology cannot be viewed as a crutch; current Building Automation Systems (BAS) are often too complex to support building efficiency optimization, but BAS coupled with appropriate training can support better outcomes; the “perfectly optimized” building is not a near-term possibility, but better education, especially of executives and managers, on the role of behavioral intervention is a promising direction the building science community can and should pursue; a lack of standards and protocols, and competition between proprietary software from service contracts, remain challenges for this industry. These technical observations, in turn, informed the EC Project’s overall findings, which were: Accomplishing building efficiency is a process of education for all involved in the building design, construction and operation supply chain. Building operators, as a professional class, have an opportunity for further training and education that will lead to better on-the-job performance. An updated Building Re-Tuning™ Training curriculum, based on the findings of this report, could be an avenue for these operators’ professional development.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Hybrid Solid Oxide Fuel Cell/Gas Turbine Model Development for Electric Aviation

A thermodynamic model was developed and validated to analyze a high-performance solid oxide fuel cell and gas turbine (SOFC-GT) hybrid power system for electric aviation. This study used a process simulation software package (ProMax) to study the role of SOFC design and operation on the feasibility and performance of the hybrid system. Standard modules, including compressor, turbine, heat exchanger, reforming reactor, and combustor were used from the ProMax tool suite while a custom module was created to simulate the SOFC stack. The model used an SOFC test data set as an input. Additional SOFC stack performance effects, such as pressure, temperature, and utilization of air and fuel, were added from open source data. System performance predictors were SOFC specific power, fuel-to-electricity conversion efficiency, and hybrid system efficiency. Using these input data and predictors, a static thermodynamic performance model was created that can be modified for different system configurations and operating conditions. Prior to creating the final aircraft performance model, initial demonstration models were developed to validate output results. We used the NASA SOFC model as a benchmark, which was created with their Numerical Propulsion System Simulator (NPSS) software framework. Our output results matched within 1% of both the NASA model and open source SOFC performance data. With confidence gained in the accuracy of this model, a 1-MW SOFC-GT hybrid power system was constructed for an aircraft propulsion concept. Overall hybrid system efficiencies of > 75% FTE were observed during standard 36,000 feet cruise flight conditions.

30 DIRECT ENERGY CONVERSION↗

Distributed systems and Ada

Viewgraphs of two briefings designed to provide information to the Software I and V Study Group to help complete the I and V study task are given. The information is taken from the areas of Ada real-time processing support, Ada run-time environments, Ada program construction, object oriented design, and Ada/UNIX/POSIX interfaces. Also covered are the development, integration, and verification of Ada systems; fault tolerance and Ada; and Ada programming standards, techniques, and tools.

Source record↗

Attenuation of Gas Turbulence by a Nearly Stationary Dispersion of Fine Particles

Turbulence attenuation by greater than a factor of two has been observed in many practical gas flows carrying volume fractions as small as 0.01% of dispersed particles. Particles which cause such attenuation usually are smaller than the smallest scales of the turbulence and have time constants 5 to 10 times greater than the time scale of a typical turbulent eddy. That is, strongly attenuating particles usually have Stokes numbers in the range of 5 to 10, indicating that they do not respond to the turbulent fluctuations, but instead just fall through the flow responding only to the mean flow. There are two mechanisms by which free falling particles may attenuate turbulence. First, the unresponsive particles act as a drag on the turbulent eddies, passing energy from the turbulent eddies to the small scale wakes of the particles where it is quickly dissipated by viscosity. The second mechanism is more complicated. Particles falling under gravity convert gravitational potential energy to turbulent velocity fluctuations. If the particles are large, this mechanism increases the overall turbulence level. However, with moderate size particles, the small scale turbulence generated apparently distorts the turbulent eddies leading to more rapid dissipation. Unfortunately, this conclusion is supported only by circumstantial evidence to date. The objectives of the experiment are to use microgravity to separate the two mechanisms. A region of nearly-isotropic decaying turbulence with zero mean flow will be formed in a box in the microgravity environment. Different sets of particles with Stokes numbers in the range of 2 to 20 will be dispersed in the flow. With zero gravity and no mean fluid velocity the particles will have zero mean velocity. With the large Stokes numbers, the fluctuating velocities will also be small. Therefore, the only attenuation mechanism will be the direct action of the particles on the turbulence. Control experiments will also be done in which the particles fall through the measurement volume. Measurements will be acquired using a high resolution image velocimetry (PIV) system being developed specifically for work in particle-laden flows. The measurements will include the decay of the turbulence kinetic energy under various particle loadings. The spatial spectra of the turbulence will also be measured. In a second set of experiments, the interaction of a single eddy with a collection of nearly stationary particles will be examined. The eddy will be a vortex ring emitted by a jet pulse through an orifice. The distortion of the vortex under the influence of the particles will be examined to gain a better understanding of how fine particles can cause such large reductions in turbulence levels. This experiment could not be conducted in terrestrial gravity because the high particle velocities would overwhelm the relatively low speed motion of the vortex ring. This experimental program is just getting underway. The initial challenge is to build a closed facility containing reasonably homogeneous and isotropic turbulence with zero mean velocity. Our approach is to use a set of synthetic jets mounted on the periphery of a transparent plexiglass box to create the turbulence. A synthetic jet is a plenum chamber with an orifice open to the volume of interest. The volume of the chamber fluctuates periodically so alternately a jet is ejected from the volume or flow is drawn back in as a sink. The asymmetry of this situation results in a net transport of momentum and kinetic energy into the volume of interest. The present apparatus includes eight synthetic jets each powered independently by a six inch loudspeaker. The synthetic jets discharge through ejector tubes to increase the scale of the turbulence. Construction of the apparatus is now complete and preliminary flow visualization studies have been conducted. The PIV system is also under development. A compact dual-pulse YAG laser has been acquired as the light source and special software is under development to allow simultaneous measurements of both the particle phase and the fluid phase (marked by fine tracers).

Paris, A. D.↗

Power Station Design

Kuljian Corporation provides design engineering and construction management services for power generating plants in more than 20 countries. They used WASP (Calculating Water and Steam Properties), a COSMIC program to optimize power station design. This enabled the company to substantially reduce lead time and software cost in a recent design project.

Source record↗

Robotic Assembly of Truss Structures for Space Systems and Future Research Plans

Many initiatives under study by both the space science and earth science communities require large space systems, i.e. with apertures greater than 15 m or dimensions greater than 20 m. This paper reviews the effort in NASA Langley Research Center's Automated Structural Assembly Laboratory which laid the foundations for robotic construction of these systems. In the Automated Structural Assembly Laboratory reliable autonomous assembly and disassembly of an 8 meter planar structure composed of 102 truss elements covered by 12 panels was demonstrated. The paper reviews the hardware and software design philosophy which led to reliable operation during weeks of near continuous testing. Special attention is given to highlight the features enhancing assembly reliability.

Doggett, William↗

Comparison of Modal Analysis Methods Applied to a Vibro-Acoustic Test Article

Modal testing of a vibro-acoustic test article referred to as the Aluminum Testbed Cylinder (ATC) has provided frequency response data for the development of validated numerical models of complex structures for interior noise prediction and control. The ATC is an all aluminum, ring and stringer stiffened cylinder, 12 feet in length and 4 feet in diameter. The cylinder was designed to represent typical aircraft construction. Modal tests were conducted for several different configurations of the cylinder assembly under ambient and pressurized conditions. The purpose of this paper is to present results from dynamic testing of different ATC configurations using two modal analysis software methods: Eigensystem Realization Algorithm (ERA) and MTS IDEAS Polyreference method. The paper compares results from the two analysis methods as well as the results from various test configurations. The effects of pressurization on the modal characteristics are discussed.

Pritchard, Jocelyn↗

Proceedings of the Second NASA Formal Methods Symposium

This publication contains the proceedings of the Second NASA Formal Methods Symposium sponsored by the National Aeronautics and Space Administration and held in Washington D.C. April 13-15, 2010. Topics covered include: Decision Engines for Software Analysis using Satisfiability Modulo Theories Solvers; Verification and Validation of Flight-Critical Systems; Formal Methods at Intel -- An Overview; Automatic Review of Abstract State Machines by Meta Property Verification; Hardware-independent Proofs of Numerical Programs; Slice-based Formal Specification Measures -- Mapping Coupling and Cohesion Measures to Formal Z; How Formal Methods Impels Discovery: A Short History of an Air Traffic Management Project; A Machine-Checked Proof of A State-Space Construction Algorithm; Automated Assume-Guarantee Reasoning for Omega-Regular Systems and Specifications; Modeling Regular Replacement for String Constraint Solving; Using Integer Clocks to Verify the Timing-Sync Sensor Network Protocol; Can Regulatory Bodies Expect Efficient Help from Formal Methods?; Synthesis of Greedy Algorithms Using Dominance Relations; A New Method for Incremental Testing of Finite State Machines; Verification of Faulty Message Passing Systems with Continuous State Space in PVS; Phase Two Feasibility Study for Software Safety Requirements Analysis Using Model Checking; A Prototype Embedding of Bluespec System Verilog in the PVS Theorem Prover; SimCheck: An Expressive Type System for Simulink; Coverage Metrics for Requirements-Based Testing: Evaluation of Effectiveness; Software Model Checking of ARINC-653 Flight Code with MCP; Evaluation of a Guideline by Formal Modelling of Cruise Control System in Event-B; Formal Verification of Large Software Systems; Symbolic Computation of Strongly Connected Components Using Saturation; Towards the Formal Verification of a Distributed Real-Time Automotive System; Slicing AADL Specifications for Model Checking; Model Checking with Edge-valued Decision Diagrams; and Data-flow based Model Analysis.

Munoz, Cesar↗

Overview of the National Airspace System (NAS) Digital Twin Simulation Environment

The National Airspace System (NAS) Digital Twin is an environment for building and running diverse, realistic simulations of current or future airspace operations. The environment allows for many different types of simulations including both fast-time and real-time operating modes. Playback of historical or live NAS traffic can be combined with simulated aircraft to create a detailed, live, virtual, and constructive environment. These capabilities go together to create an environment that allows for development of concepts through the entire Technology Readiness Levels scale from initial concept to field evaluations. This extended abstract will discuss details of the software-foundations of the NAS Digital Twin environment. Then, several example simulations and analyses will be presented to illustrate the breadth and power of the tool.

airspace simulation, digital twin↗

Overview of the National Airspace System (NAS) Digital Twin Simulation Environment

The National Airspace System (NAS) Digital Twin is an environment for building and running diverse, realistic simulations of current or future airspace operations. The environment allows for many different types of simulations including both fast-time and real-time operating modes. Playback of historical or live NAS traffic can be combined with simulated aircraft to create a detailed, live, virtual, and constructive environment. These capabilities go together to create an environment that allows for development of concepts through the entire Technology Readiness Levels scale from initial concept to field evaluations. This extended abstract will discuss details of the software-foundations of the NAS Digital Twin environment. Then, several example simulations and analyses will be presented to illustrate the breadth and power of the tool.

airspace simulation↗

Performance of an RPM based on Gd-lined plastic scintillator for neutron and gamma detection [ANIMMA--2015-IO-372]

A Radiation Portal Monitor (RPM) was developed by the Istituto Nazionale di Fisica Nucleare (INFN) and Ansaldo Nucleare (ANN) within the FP7 SCINTILLA European project. The system was designed to detect both gamma and neutron radiation with a single technology. It is conceived to monitor vehicle and cargo containers in transits across borders or ports, to find radioactive elements and to avoid illegal trafficking of strategic nuclear materials. The system is based on a {sup 3}He-free neutron detection technology using plastic scintillators coupled to Gadolinium to detect and discriminate gamma from neutron signals. During the 3 years of the SCINTILLA project the construction and test of the first two prototypes drove the definition of the final layout of a full RPM system consisting of two twin pillars as a portal for vehicle and cargo container scan. A custom System Control Software (SCS) manages the electronics of the RPM, the ancillary devices and the data analysis. The combination of the detector layout and of the software functionalities enables both to distinguish neutrons and gammas and to identify the energy range of a detected gamma source. The system was initially characterized via static tests with gamma and neutron sources in the INFN laboratory. These measurements were used to calibrate the detector, evaluate the response of the single pillars as well as of the full system, and optimize the RPM configuration and discrimination algorithm. During this phase, specific tests were performed to study the stability over time of the system, monitoring the measured the neutron and gamma count rates over periods of several weeks. The results allow us to demonstrate the reliability and robustness of the RPM. In a second time the RPM performance was studied via dynamic tests performed during the SCINTILLA test and benchmark campaigns. These measurements took place in the JRC ITRAP+10 facility at Ispra (Varese-Italy). The laboratory is equipped with an experimental set-up for dynamic tests of multiple systems according to international standards. The performed measurements utilized radioactive sources with activities selected according to ANSI and IEC standards to test the detector alarm performances in terms of gamma and neutron response, sensitivity to high gamma fields, sensitivity to moderated neutron sources as well as false alarm rates (FAR). In addition, the RPM was tested in challenging configurations exceeding the requirements set by international standards to determine the real limits of the system. The results obtained during these campaigns demonstrated that the system detection efficiency is not only compliant to international standards for its category, but often exceeds them, demonstrating the validity of the chosen technology and of the implemented layout. The positive performance also showed the effectiveness of the SCS and of its functionalities. To further demonstrate the system capabilities, a test in a real-life environment of the RPM is planned to happen in a near future by installing the detectors in a seaport. In this presentation I will give an overview of the RPM characteristics, of its performances as determined in the test campaign mentioned above and of future plans, to demonstrate how this technology can be an effective choice for the realization of {sup 3}He-free RPM detectors. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Origami-based Composite Space Structures

The main objective of my internship was working on developing a new type of deployable composite for space structures and new method of deployment via use of origami, composites, UV curing resins, and shape memory polymers. My role in the project was to collect an initial literature survey on the subject including origami, the history of deployable space structures, previous issues and problems faced in the field, previous and current research being done on the structural aspect as well as the materials aspect of the subject. I presented this information to our team, where we discussed and determined our research focus and project design specs. We have been making or will make decisions on the project’s purpose, material, origami type, manufacturing method, and testing methods. I am now in charge of the protype design as we enter the design stage of our research. I am using PTC Creo software to design the structural aspects of the first protype so that we can begin small scale testing. I will perform data analysis in order to review the results with our team, so we can make the next design decisions regarding changes or iterations of the design. We hope to renew this project in the next fiscal year in order to increase the TRL of the project so that it can eventually be used in multiple functions in space such as the construction of lunar habitats. In just my brief time with NASA, I have gained so much personally and professionally. I developed my ability to search through and narrow down information when doing research. In the weekly meetings I practiced presenting information to my peers and superiors, and, just as importantly, discussing and adapting to what we were learning. I acquired experience in using technology to my advantage including remote work, new software like PTC Creo, NASA archives, and connecting with others beyond my team to gain help. I enjoyed the immense resource of knowledge that my mentors had to offer, and that they gave me a large amount of responsibility in this research. I truly felt like I was contributing to something bigger than myself and understood how directly I was involved in NASA’s work. This internship has further cemented my love for space and desire to continue in the field. I have a better understanding of the research and development process and am now considering joining a research lab with my university next year.

Composite↗

Overview of the DESI Legacy Imaging Surveys

The DESI Legacy Imaging Surveys (http://legacysurvey.org/) are a combination of three public projects (the Dark Energy Camera Legacy Survey, the Beijing–Arizona Sky Survey, and the Mayall z-band Legacy Survey) that will jointly image ≈14,000 deg{sup 2} of the extragalactic sky visible from the northern hemisphere in three optical bands (g, r, and z) using telescopes at the Kitt Peak National Observatory and the Cerro Tololo Inter-American Observatory. The combined survey footprint is split into two contiguous areas by the Galactic plane. The optical imaging is conducted using a unique strategy of dynamically adjusting the exposure times and pointing selection during observing that results in a survey of nearly uniform depth. In addition to calibrated images, the project is delivering a catalog, constructed by using a probabilistic inference-based approach to estimate source shapes and brightnesses. The catalog includes photometry from the grz optical bands and from four mid-infrared bands (at 3.4, 4.6, 12, and 22 μm) observed by the Wide-field Infrared Survey Explorer satellite during its full operational lifetime. The project plans two public data releases each year. All the software used to generate the catalogs is also released with the data. This paper provides an overview of the Legacy Surveys project.

79 ASTRONOMY AND ASTROPHYSICS↗

Update of GRASP/Ada reverse engineering tools for Ada

The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) successfully created and prototyped a new algorithmic level graphical representation for Ada software, the Control Structure Diagram (CSD). The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis was on the automatic generation of the CSD from Ada PDL or source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional pretty printed Ada source code. In Phase 1 of the GRASP/Ada project, the CSD graphical constructs were created and applied manually to several small Ada programs. A prototype CSD generator (Version 1) was designed and implemented using FLEX and BISON running under VMS on a VAX 11-780. In Phase 2, the prototype was improved and ported to the Sun 4 platform under UNIX. A user interface was designed and partially implemented using the HP widget toolkit and the X Windows System. In Phase 3, the user interface was extensively reworked using the Athena widget toolkit and X Windows. The prototype was applied successfully to numerous Ada programs ranging in size from several hundred to several thousand lines of source code. Following Phase 3,e two update phases were completed. Update'92 focused on the initial analysis of evaluation data collected from software engineering students at Auburn University and the addition of significant enhancements to the user interface. Update'93 (the current update) focused on the statistical analysis of the data collected in the previous update and preparation of Version 3.4 of the prototype for limited distribution to facilitate further evaluation. The current prototype provides the capability for the user to generate CSD's from Ada PDL or source code in a reverse engineering as well as forward engineering mode with a level of flexibility suitable for practical application. An overview of the GRASP/Ada project with an emphasis on the current update is provided.

Cross, James H., II↗

PyApprox: A software package for sensitivity analysis, Bayesian inference, optimal experimental design, and multi-fidelity uncertainty quantification and surrogate modeling

PyApprox is a Python-based one-stop-shop for probabilistic analysis of numerical models such as those used in the earth, environmental and engineering sciences. Easy to use and extendable tools are provided for constructing surrogates, sensitivity analysis, Bayesian inference, experimental design, and forward uncertainty quantification. The algorithms implemented represent a wide range of methods for model analysis developed over the past two decades, including recent advances in multi-fidelity approaches that use multiple model discretizations and/or simplified physics to significantly reduce the computational cost of various types of analyses. An extensive set of Benchmarks from the literature is also provided to facilitate the easy comparison of new or existing algorithms for a wide range of model analyses. Here, this paper introduces PyApprox and its various features, and presents results demonstrating the utility of PyApprox on a benchmark problem modeling the advection of a tracer in groundwater.

54 ENVIRONMENTAL SCIENCES↗