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At least 325 records · Page 18

UnigeneFinder: An Automated Pipeline for Gene Calling From Transcriptome Assemblies Without a Reference Genome

ABSTRACT For most species, transcriptome data are much more readily available than genome data. Without a reference genome, gene calling is cumbersome and inaccurate because of the high degree of redundancy in de novo transcriptome assemblies. To simplify and increase the accuracy of de novo transcriptome assembly in the absence of a reference genome, we developed UnigeneFinder. Combining several clustering methods, UnigeneFinder substantially reduces the redundancy typical of raw transcriptome assemblies. This pipeline offers an effective solution to the problem of inflated transcript numbers, achieving a closer representation of the actual underlying genome. UnigeneFinder performs comparably or better, compared with existing tools, on plant species with varying genome complexities. UnigeneFinder is the only available transcriptome redundancy solution that fully automates the generation of primary transcript, coding region, and protein sequences, analogous to those available for high‐quality reference genomes. These features, coupled with the pipeline’s cross‐platform implementation, focus on automation, and an accessible, user‐friendly interface, make UnigeneFinder a useful tool for many downstream sequence‐based analyses in nonmodel organisms lacking a reference genome, including differential gene expression analysis, accurate ortholog identification, functional enrichments, and evolutionary analyses. UnigeneFinder also runs efficiently both on high‐performance computing (HPC) systems and personal computers, further reducing barriers to use.

Xue, Bo [Plant Resilience Institute Michigan State↗

A Python Module for Storing CCD Images with openPMD (openPMD-CCD) v0.1.0

openPMD is an open meta-data schema that provides meaning and self-description to data sets in science and engineering. The openPMD-CCD software module adds interfaces to organize camera (CCD) images in hierarchical data files. This software provides modern I/O storage formats from high-performance computing and provides bindings for integration into experimental control systems, e.g. via Python 3 and LabView 2020.

Gonsalves, AnthonyJ↗

HAL/SM language specification

A programming language is presented for the flight software of the NASA Space Shuttle program. It is intended to satisfy virtually all of the flight software requirements of the space shuttle. To achieve this, it incorporates a wide range of features, including applications-oriented data types and organizations, real time control mechanisms, and constructs for systems programming tasks. It is a higher order language designed to allow programmers, analysts, and engineers to communicate with the computer in a form approximating natural mathematical expression. Parts of the English language are combined with standard notation to provide a tool that readily encourages programming without demanding computer hardware expertise. Block diagrams and flow charts are included. The semantics of the language is discussed.

Williams, G. P. W., Jr.↗

Organization and use of a Software/Hardware Avionics Research Program (SHARP)

The organization and use is described of the software/hardware avionics research program (SHARP) developed to duplicate the automatic portion of the STOLAND simulator system, on a general-purpose computer system (i.e., IBM 360). The program's uses are: (1) to conduct comparative evaluation studies of current and proposed airborne and ground system concepts via single run or Monte Carlo simulation techniques, and (2) to provide a software tool for efficient algorithm evaluation and development for the STOLAND avionics computer.

Karmarkar, J. S.↗

Satellite on-board processing for earth resources data

Results of a survey of earth resources user applications and their data requirements, earth resources multispectral scanner sensor technology, and preprocessing algorithms for correcting the sensor outputs and for data bulk reduction are presented along with a candidate data format. Computational requirements required to implement the data analysis algorithms are included along with a review of computer architectures and organizations. Computer architectures capable of handling the algorithm computational requirements are suggested and the environmental effects of an on-board processor discussed. By relating performance parameters to the system requirements of each of the user requirements the feasibility of on-board processing is determined for each user. A tradeoff analysis is performed to determine the sensitivity of results to each of the system parameters. Significant results and conclusions are discussed, and recommendations are presented.

Bodenheimer, R. E.↗

Development of a systems theoretical procedure for evaluation of the work organization of the cockpit crew of a civil transport airplane

To achieve optimum design for the man machine interface with aircraft, a description of the interaction and work organization of the cockpit crew is needed. The development of system procedure to evaluate the work organization of pilots while structuring the work process is examined. Statistical data are needed to simulate sequences of pilot actions on the computer. Investigations of computer simulation and applicability for evaluation of crew concepts are discussed.

Fricke, M.↗

A parallel data management system for large-scale NASA datasets

The past decade has experienced a phenomenal growth in the amount of data and resultant information generated by NASA's operations and research projects. A key application is the reprocessing problem which has been identified to require data management capabilities beyond those available today (PRAT93). The Intelligent Information Fusion (IIF) system (ROEL91) is an ongoing NASA project which has similar requirements. Deriving our understanding of NASA's future data management needs based on the above, this paper describes an approach to using parallel computer systems (processor and I/O architectures) to develop an efficient parallel database management system to address the needs. Specifically, we propose to investigate issues in low-level record organizations and management, complex query processing, and query compilation and scheduling.

Srivastava, Jaideep↗

Evaluation of Model-Based Training for Vertical Guidance Logic

This paper will summarize the results of a study which introduces a structured, model based approach to learning how the automated vertical guidance system works on a modern commercial air transport. The study proposes a framework to provide accurate and complete information in an attempt to eliminate confusion about 'what the system is doing'. This study will examine a structured methodology for organizing the ideas on which the system was designed, communicating this information through the training material, and displaying it in the airplane. Previous research on model-based, computer aided instructional technology has shown reductions in the amount of time to a specified level of competence. The lessons learned from the development of these technologies are well suited for use with the design methodology which was used to develop the vertical guidance logic for a large commercial air transport. The design methodology presents the model from which to derive the training material, and the content of information to be displayed to the operator. The study consists of a 2 X 2 factorial experiment which will compare a new method of training vertical guidance logic and a new type of display. The format of the material used to derive both the training and the display will be provided by the Operational Procedure Methodology. The training condition will compare current training material to the new structured format. The display condition will involve a change of the content of the information displayed into pieces that agree with the concepts with which the system was designed.

Feary, Michael↗

Benchmark Problems Used to Assess Computational Aeroacoustics Codes

The field of computational aeroacoustics (CAA) encompasses numerical techniques for calculating all aspects of sound generation and propagation in air directly from fundamental governing equations. Aeroacoustic problems typically involve flow-generated noise, with and without the presence of a solid surface, and the propagation of the sound to a receiver far away from the noise source. It is a challenge to obtain accurate numerical solutions to these problems. The NASA Glenn Research Center has been at the forefront in developing and promoting the development of CAA techniques and methodologies for computing the noise generated by aircraft propulsion systems. To assess the technological advancement of CAA, Glenn, in cooperation with the Ohio Aerospace Institute and the AeroAcoustics Research Consortium, organized and hosted the Fourth CAA Workshop on Benchmark Problems. Participants from industry and academia from both the United States and abroad joined to present and discuss solutions to benchmark problems. These demonstrated technical progress ranging from the basic challenges to accurate CAA calculations to the solution of CAA problems of increasing complexity and difficulty. The results are documented in the proceedings of the workshop. Problems were solved in five categories. In three of the five categories, exact solutions were available for comparison with CAA results. A fourth category of problems representing sound generation from either a single airfoil or a blade row interacting with a gust (i.e., problems relevant to fan noise) had approximate analytical or completely numerical solutions. The fifth category of problems involved sound generation in a viscous flow. In this case, the CAA results were compared with experimental data.

Dahl, Milo D.↗

GIS Methodology for Planning Planetary-Rover Operations

A document describes a methodology for utilizing image data downlinked from cameras aboard a robotic ground vehicle (rover) on a remote planet for analyzing and planning operations of the vehicle and of any associated spacecraft. Traditionally, the cataloging and presentation of large numbers of downlinked planetary-exploration images have been done by use of two organizational methods: temporal organization and correlation between activity plans and images. In contrast, the present methodology involves spatial indexing of image data by use of the computational discipline of geographic information systems (GIS), which has been maturing in terrestrial applications for decades, but, until now, has not been widely used in support of exploration of remote planets. The use of GIS to catalog data products for analysis is intended to increase efficiency and effectiveness in planning rover operations, just as GIS has proven to be a source of powerful computational tools in such terrestrial endeavors as law enforcement, military strategic planning, surveying, political science, and epidemiology. The use of GIS also satisfies the need for a map-based user interface that is intuitive to rover-activity planners, many of whom are deeply familiar with maps and know how to use them effectively in field geology.

Powell, Mark↗

Recent Advancements in Modeling and Simulation of Entry Systems at NASA

This paper describes recent development of modeling and simulation technologies for entry systems in support of NASA's exploration missions. Mission-tailored research and development in modeling of entry systems occurs across the Agency (e.g., within the Orion and Mars 2020 Programs), however the aim of this paper is to discuss the broad, cross-mission research conducted by NASA's Entry Systems Modeling (ESM) Project, which serves as the Agency's only concerted effort toward advancing entry systems across a range of technical disciplines. Technology development in ESM is organized and prioritized from a system-level perspective, resulting in four broad technical areas of investment: (1) Predictive material modeling, (2) Shock layer kinetics and radiation, (3) Computational and experimental aerosciences, and (4) Guidance, navigation, and control. Investments in thermal protection material modeling are geared toward high-fidelity, predictive models capable of handling complex structures, with an eye toward optimizing design performance and quantifying thermal protection system reliability. New computational tools have been developed to characterize material properties and behavior at the microstructural level, and experimental techniques (molecular beam scattering, micro-computed tomography, among others) have been developed to measure material kinetics, morphology, and other parameters needed to inform and validate detailed simulations. Advancements have also been made in macrostructural simulation capability to enable 3-D system-scale calculations of material response with complex topological features, including differential recession of tile gaps. Research and development in the area of shock layer kinetics has focused on air and CO2-based atmospheres. Capacity and capability of the NASA Ames Electric Arc Shock Tube (EAST) have been expanded in recent years and analysis of resulting data has led to several improvements in kinetic models, while simultaneously reducing uncertainties associated with radiative heat transfer predictions. First-principles calculations of fundamental kinetic, thermodynamic, and transport data, along with state-specific models for non-equilibrium flow regimes, have also yielded new insights and have the potential to vastly improve model fidelity. Aerosciences is a very broad area of interest in entry systems, yet a number of important challenges are being addressed: Coupled fluid-structure simulations of parachute inflation and dynamics; Experimental and computational studies of vehicle dynamics; Multi-phase flow with dust particles to simulate entry environments at Mars during dust storms; Studies of roughness-induced heating augmentation relevant to tiled and woven thermal protection systems; and Advanced numerical methods to optimize computational analyses for desired accuracy versus cost. Guidance and control in the context of entry systems has focused on development of methods for multi-axis control (i.e. pitch and yaw, rather than bank angle alone) of spacecraft during entry and descent. With precision landing requirements driven by Mars human exploration goals, recent efforts have yielded 6-DOF models of multi-axis control with propulsive descent of both inflatable and rigid ellipsled-like architectures.

Barnhardt, Michael D.↗

Recent Advancements in Modeling and Simulation of Entry Systems at NASA

This paper describes recent development of modeling and simulation technologies for entry systems in support of NASA’s exploration missions. Mission-tailored research and development in modeling of entry systems occurs across the Agency (e.g., within the Orion and Mars 2020 Programs), however the aim of this paper is to discuss the broad, cross-mission research conducted by NASA’s Entry Systems Modeling (ESM) Project, which serves as the Agency’s only concerted effort toward advancing entry systems across a range of technical disciplines. Technology development in ESM is organized and prioritized from a system-level perspective, resulting in four broad technical areas of investment: (1) Predictive material modeling, (2) Shock layer kinetics and radiation, (3) Computational and experimental aerosciences, and (4) Guidance, navigation, and control. Investments in thermal protection material modeling are geared toward high-fidelity, predictive models capable of handling complex structures, with an eye toward optimizing design performance and quantifying thermal protection system reliability. New computational tools have been developed to characterize material properties and behavior at the microstructural level, and experimental techniques (molecular beam scattering, micro-computed tomography, among others) have been developed to measure material kinetics, morphology, and other parameters needed to inform and validate detailed simulations. Advancements have also been made in macrostructural simulation capability to enable 3-D system-scale calculations of material response with complex topological features, including differential recession of tile gaps. Research and development in the area of shock layer kinetics has focused on air and CO2-based atmospheres. Capacity and capability of the NASA Ames Electric Arc Shock Tube (EAST) have been expanded in recent years and analysis of resulting data has led to several improvements in kinetic models, while simultaneously reducing uncertainties associated with radiative heat transfer predictions. First-principles calculations of fundamental kinetic, thermodynamic, and transport data, along with state-specificmodels for non-equilibrium flow regimes, have also yielded new insights and have the potential to vastly improve model fidelity. Aerosciences is a very broad area of interest in entry systems, yet a number of important challenges are being addressed: Coupled fluid-structure simulations of parachute inflation and dynamics; Experimental and computational studies of vehicle dynamics; Multi-phase flow with dust particles to simulate entry environments at Mars during dust storms; Studies of roughness-induced heating augmentation relevant to tiled and woven thermal protection systems; and Advanced numerical methods to optimize computational analyses for desired accuracy versus cost. Guidance and control in the context of entry systems has focused on development of methods for multi-axis control (i.e. pitch and yaw, rather than bank angle alone) of spacecraft during entry and descent. With precision landing requirements driven by Mars human exploration goals, recent efforts have yielded 6-DOF models of multi-axis control with propulsive descent of both inflatable and rigid ellipsled-like architectures. Results for both configurations have demonstrated the ability to land within the 50-meter precision requirement demanded by Mars human exploration missions, while also reducing propellant requirements by enabling more efficient control through entry and descent. Ongoing research in GN&C is developing mechanical specifications for the systems and establishing engineering feasibility.

aerothermodynamics↗

Analytical derivatives of the individual state energies in ensemble density functional theory. II. Implementation on graphical processing units (GPUs)

Conical intersections control excited state reactivity, and thus, elucidating and predicting their geometric and energetic characteristics are crucial for understanding photochemistry. Locating these intersections requires accurate and efficient electronic structure methods. Unfortunately, the most accurate methods (e.g., multireference perturbation theories such as XMS-CASPT2) are computationally challenging for large molecules. The state-interaction state-averaged restricted ensemble referenced Kohn–Sham (SI-SA-REKS) method is a computationally efficient alternative. The application of SI-SA-REKS to photochemistry was previously hampered by a lack of analytical nuclear gradients and nonadiabatic coupling matrix elements. We have recently derived analytical energy derivatives for the SI-SA-REKS method and implemented the method effectively on graphical processing units. We demonstrate that our implementation gives the correct conical intersection topography and energetics for several examples. Furthermore, our implementation of SI-SA-REKS is computationally efficient, with observed sub-quadratic scaling as a function of molecular size. This demonstrates the promise of SI-SA-REKS for excited state dynamics of large molecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

TomoPyUI : a user-friendly tool for rapid tomography alignment and reconstruction

The management and processing of synchrotron and neutron computed tomography data can be a complex, labor-intensive and unstructured process. Users devote substantial time to both manually processing their data ( i.e. organizing data/metadata, applying image filters etc. ) and waiting for the computation of iterative alignment and reconstruction algorithms to finish. In this work, we present a solution to these problems: TomoPyUI , a user interface for the well known tomography data processing package TomoPy . This highly visual Python software package guides the user through the tomography processing pipeline from data import, preprocessing, alignment and finally to 3D volume reconstruction. The TomoPyUI systematic intermediate data and metadata storage system improves organization, and the inspection and manipulation tools (built within the application) help to avoid interrupted workflows. Notably, TomoPyUI operates entirely within a Jupyter environment. Herein, we provide a summary of these key features of TomoPyUI , along with an overview of the tomography processing pipeline, a discussion of the landscape of existing tomography processing software and the purpose of TomoPyUI , and a demonstration of its capabilities for real tomography data collected at SSRL beamline 6-2c.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

On the potentially transformative role of auxiliary-field quantum Monte Carlo in quantum chemistry: A highly accurate method for transition metals and beyond

Approximate solutions to the ab initio electronic structure problem have been a focus of theoretical and computational chemistry research for much of the past century, with the goal of predicting relevant energy differences to within “chemical accuracy” (1 kcal/mol). For small organic molecules, or in general, for weakly correlated main group chemistry, a hierarchy of single-reference wave function methods has been rigorously established, spanning perturbation theory and the coupled cluster (CC) formalism. For these systems, CC with singles, doubles, and perturbative triples is known to achieve chemical accuracy, albeit at O(N7) computational cost. In addition, a hierarchy of density functional approximations of increasing formal sophistication, known as Jacob’s ladder, has been shown to systematically reduce average errors over large datasets representing weakly correlated chemistry. However, the accuracy of such computational models is less clear in the increasingly important frontiers of chemical space including transition metals and f-block compounds, in which strong correlation can play an important role in reactivity. A stochastic method, phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC), has been shown to be capable of producing chemically accurate predictions even for challenging molecular systems beyond the main group, with relatively low O(N3 − N4) cost and near-perfect parallel efficiency. Herein, we present our perspectives on the past, present, and future of the ph-AFQMC method. We focus on its potential in transition metal quantum chemistry to be a highly accurate, systematically improvable method that can reliably probe strongly correlated systems in biology and chemical catalysis and provide reference thermochemical values (for future development of density functionals or interatomic potentials) when experiments are either noisy or absent. Finally, we discuss the present limitations of the method and where we expect near-term development to be most fruitful.

Chemistry↗

Side chain engineering in indacenodithiophene- co -benzothiadiazole and its impact on mixed ionic–electronic transport properties

Organic semiconductors are increasingly being decorated with hydrophilic solubilising chains to create materials that can function as mixed ionic–electronic conductors, which are promising candidates for interfacing biological systems with organic electronics. While numerous organic semiconductors, including p- and n-type materials, small molecules and polymers, have been successfully tailored to encompass mixed conduction properties, common to all these systems is that they have been semicrystalline materials. Here, we explore how side chain engineering in the nano-crystalline indacenodithiophene-co-benzothiadiazole (IDTBT) polymer can be used to instil ionic transport properties and how this in turn influences the electronic transport properties. This allows us to ultimately assess the mixed ionic–electronic transport properties of these new IDTBT polymers using the organic electrochemical transistor as the testing platform. Using a complementary experimental and computational approach, we find that polar IDTBT derivatives can be infiltrated by water and solvated ions, they can be electrochemically doped efficiently in aqueous electrolyte with fast doping kinetics, and upon aqueous swelling there is no deterioration of the close interchain contacts that are vital for efficient charge transport in the IDTBT system. Despite these promising attributes, mixed ionic–electronic charge transport properties are surprisingly poor in all the polar IDTBT derivatives. Albeit a “negative” result, this finding clearly contradicts established side chain engineering rules for mixed ionic–electronic conductors, which motivated our continued investigation of this system. We eventually find this anomalous behaviour to be caused by increasing energetic disorder in the polymers with increasing polar side chain content. We have investigated computationally how the polar side chain motifs contribute to this detrimental energetic inhomogeneity and ultimately use the learnings to propose new molecular design criteria for side chains that can facilitate ion transport without impeding electronic transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dicyanobenzothiadiazole (DCBT) Organic Dye as a Visible Light Absorbing Strong Photoinduced Oxidant with a 16 Microsecond Long–Lived Excited State

Strong photoinduced oxidants are important to organic synthesis and solar energy conversion, to chemical fuels or electric. For these applications, visible light absorption is important to solar energy conversion and long–lived excited states are needed to drive catalysis. With respect to these desirable qualities, a series of five 5,6–dicyano[2,1,3]benzothiadiazole (DCBT) dyes are examined as organic chromophores that can serve as strong photooxidants in catalytic systems. The series utilizes a DCBT core with aryl groups on the periphery with varying electron donation strengths relative to the core. The dyes are studied via both steady–state and transient absorption and emission studies. Additionally, computational analysis, voltammetry, crystallography, and absorption spectroelectrochemistry are also used to better understand the behavior of these dyes. Ultimately, a strong photooxidant is arrived at with an exceptionally long excited state lifetime for an organic chromophore of 16 µs. Finally, the long–lived excited state photosensitizer is well–suited for use in catalysis, and visible light driven photosensitized water oxidation is demonstrated using a water–soluble photosensitizer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computers formed by the problems rather than problems deformed by the computers.

Description of an approach to computer programming which tries to minimize the time required for retranslation from the computer language into the language of the original process. A notion of a programmable network is introduced which allows the abstract machines that are a model of the processes in the user's mind to be put into a rigorous and simple form. Each process is then modeled as a particular finite-state machine, a circulating page loose system being employed as an architecture for implementing these finite-state machines. An experiment is discussed in which the use of abstract machines as a language for modeling processes, in conjunction with the use of a self-organizing computer, decreases user effort, eliminates the need for compilation, facilitates debugging, and decreases computer time.

Schaffner, M. R.↗