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At least 505 records · Page 28

rcsb-api : Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.

FAIR principles↗

Cool GTL for the Conversion of Biogas to Jet Fuel

Cool GTL is a new process under development for conversion of biogas from digestors or CO2 +H2 to high quality drop in jet fuel. Cool GTL is designed to be a streamlined simplified low cost process which can be cost effective for small scale biogas applications. Cool GTL has the advantage that it uses a high activity bi-reforming catalyst, in a streamlined electric reformer design, to make the synthesis gas for a high conversion slurry fischer Tropsch process followed by a trailing wax cracking reactor. In this way high quality jet fuel can be directly produced. Recent experimental test data will be presented showing product quality. The life cycle analysis LCA will also be presented as well.

09 BIOMASS FUELS↗

Advanced stability analysis for laminar flow control

Five classes of problems are addressed: (1) the extension of the SALLY stability analysis code to the full eighth order compressible stability equations for three dimensional boundary layer; (2) a comparison of methods for prediction of transition using SALLY for incompressible flows; (3) a study of instability and transition in rotating disk flows in which the effects of Coriolis forces and streamline curvature are included; (4) a new linear three dimensional instability mechanism that predicts Reynolds numbers for transition to turbulence in planar shear flows in good agreement with experiment; and (5) a study of the stability of finite amplitude disturbances in axisymmetric pipe flow showing the stability of this flow to all nonlinear axisymmetric disturbances.

Orszag, S. A.↗

Virtual Mission Operation Framework (VMOF)

The Virtual Mission Operation Framework (VMOF) is one of the project lifecycle engineering process improvement efforts initiated by the institutional technology infrastructure program at JPL. The VMOF is composed of three frameworks: a model integration framework, a simulation framework, and a visualization framework. The model integration framework interfaces with spacecraft system design, mission design, and structure design. The simulation framework interfaces with the operation scenario design, environmental phenomena science, and science payload system design. The visualization framework interfaces with the flight system testbed, the ground system, and the science analysis. The three frameworks of the VMOF collaborate to create a comprehensive virtual mission operation that enables a "validation-in-the-loop" system design process and lifecycle-continuous science-return validation.This paper discusses the technical approaches for each framework implementation, challenges and approaches involved in streamlining mission information access, and on-going activities toward enabling Model-Based Engineering Design in a collaborative distributed environment.

virtual mission operations↗

Demonstration and Evaluation of a Non-Invasive, Low-Cost, Strap-On Sensor for Natural Gas Meters

The U.S. General Services Administration (GSA) is interested in installing internet-connected, gas submeters to better understand gas consumption in its portfolio of buildings. The GSA in partnership with the National Renewable Energy Laboratory conducted a demonstration to assess a specific submeter technology. This technology was implemented at two GSA separate facilities located in Dallas, Texas. This demonstration evaluated hardware and software installations and integrations, data integrity and accuracy, and included an economic analysis. This demonstration evaluated a gas submeter technology provided by the vendor Vata Verks, who produces a non-invasive strap-on submeter. The company was founded with a mission to conserve water (and eventually gas) cheaply and simply, as explained on its website. The product intends to streamline submeter deployments for gas and water by eliminating most hardware costs while allowing for easy integration of submetered data into other systems such as the Building Automation System and removing tenant and building disruption This demonstration evaluated the product features when used on a gas utility meter.

03 NATURAL GAS↗

High-throughput physiochemical and biogeochemical characterization for coastal soils and waters

Coastal environments span large biogeochemical gradients and provide critical ecosystem services worldwide, thereby having a disproportionately larger influence on global biogeochemical cycles and greenhouse gas fluxes than their geographical extent suggests. Despite this, cohesive quantitative tools to understand and describe these environments, including scalable, standardized field and laboratory methodologies are lacking. In this work, we advanced the streamlining and standardizing of quantitative approaches to measure and understand coastal physiochemical properties and biogeochemical processes across systems and scales. Outcomes of this work includes workflows for multiple complementary and in-line analyses, from basic physiochemical datasets to targeted molecular approaches and proof of concept through manipulation and analysis of coastal soils and waters with varying salinity, minerology, and biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗

Benchtop Antigen Detection Technique using Nanofiltration and Fluorescent Dyes

The designed benchtop technique is primed to detect bacteria and viruses from antigenic surface marker proteins in solutions, initially water. This inclusive bio-immunoassay uniquely combines nanofiltration and near infrared (NIR) dyes conjugated to antibodies to isolate and distinguish microbial antigens, using laser excitation and spectrometric analysis. The project goals include detecting microorganisms aboard the International Space Station, space shuttle, Crew Exploration Vehicle (CEV), and human habitats on future Moon and Mars missions, ensuring astronaut safety. The technique is intended to improve and advance water contamination testing both commercially and environmentally as well. Lastly, this streamlined technique poses to greatly simplify and expedite testing of pathogens in complex matrices, such as blood, in hospital and laboratory clinics.

Scardelletti, Maximilian C.↗

Streamlining Payload Integration

Payload integration onto space transport vehicles and the International Space Station (ISS) is a complex process. Yet, cargo transport is the sole reason for any space mission, be it for ferrying humans, science, or hardware. As the largest such effort in history, the ISS offers a wide variety of payload experience. However, for any payload to reach the Space Station under the current process, Payload Developers face a list of daunting tasks that go well beyond just designing the payload to the constraints of the transport vehicle and its stowage topology. Payload customers are required to prove their payload s functionality, structural integrity, and safe integration - including under less than nominal situations. They must also plan for or provide training, procedures, hardware labeling, ground support, and communications. In addition, they must deal with negotiating shared consumables, integrating software, obtaining video, and coordinating the return of data and hardware. All the while, they must meet export laws, launch schedules, budget limits, and the consensus of more than 12 panel and board reviews. Despite the cost and infrastructure overhead, payload proposals have increased. Just in the span from FY08 to FY09, the NASA Payload Space Station Support Office budget rose from $78M to $96M in attempt to manage the growing manifest, but the potential number of payloads still exceeds available Payload Integration Management manpower. The growth has also increased management difficulties due to the fact that payloads are more frequently added to a flight schedule late in the flow. The current standard ISS template for payload integration from concept to payload turn-over is 36 months, or 18 months if the payload already has a preliminary design. Customers are increasingly requiring a turn-around of 3 to 6-months to meet market needs. The following paper suggests options for streamlining the current payload integration process in order to meet customer schedule needs and reduce costs for both the integration support teams and the developers, without reducing quality or compromising safety. Issues for the key integration areas of planning, training, verification, and safety are presented in a Root-Cause Analysis study, with plausible solutions provided that involve technology and tools already available to the ISS community. Although based upon the ISS process, the payload integration techniques outlined herein also offer an integration template for any space transport endeavor.

Lufkin, Susan N.↗

An MBSE Approach to Space Suit Development

The EVA/Space Suit Development Office (ESSD) Systems Engineering and Integration (SE&I) team has utilized MBSE in multiple programs. After developing operational and architectural models, the MBSE framework was expanded to link the requirements space to the system models through functional analysis and interfaces definitions. By documenting all the connections within the technical baseline, ESSD experienced significant efficiency improvements in analysis and identification of change impacts. One of the biggest challenges presented to the MBSE structure was a program transition and restructuring effort, which was completed successfully in 4 months culminating in the approval of a new EVA Technical Baseline. During this time three requirements sets spanning multiple DRMs were streamlined into one NASA-owned Systems Requirement Document (SRD) that successfully identified requirements relevant to the current hardware development effort while remaining extensible to support future hardware developments. A capability-based hierarchy was established to provide a more flexible framework for future space suit development that can support multiple programs with minimal rework of basic EVA/Space Suit requirements. This MBSE approach was most recently applied for generation of an EMU Demonstrator technical baseline being developed for an ISS DTO. The relatively quick turnaround of operational concepts, architecture definition, and requirements for this new suit development has allowed us to test and evolve the MBSE process and framework in an extremely different setting while still offering extensibility and traceability throughout ESSD projects. The ESSD MBSE framework continues to be evolved in order to support integration of all products associated with the SE&I engine.

Cordova, Lauren↗

Assessment of MSFCs Process for the Development and Activation of Space Act Agreements

A Space Act Agreement (SAA) is a contractual vehicle that NASA utilizes to form partnerships with non-NASA entities to stimulate cutting-edge innovation within the science and technology communities while concurrently supporting the NASA missions. SAAs are similar to traditional contracts in that they involve the commitment of Agency resources but allow more flexibility and are more cost effective to implement than traditional contracts. Consequently, the use of SAAs to develop partnerships has greatly increased over the past several years. To facilitate this influx of SAAs, Marshall Space Flight Center (MSFC) developed a process during a kaizen event to streamline and improve the quality of SAAs developed at the Center level. This study assessed the current SAA process to determine if improvements could be implemented to increase productivity, decrease time to activation, and improve the quality of deliverables. Using a combination of direct procedural observation, personnel interviews, and statistical analysis, elements of the process in need of remediation were identified and potential solutions developed. The findings focus primarily on the difficulties surrounding tracking and enforcing process adherence and communication issues among stakeholders. Potential solutions include utilizing customer relationship management (CRM) software to facilitate process coordination and co-locating or potentially merging the two separate organizations involved in SAA development and activation at MSFC.

Daugherty, Rachel A.↗

Scaling Retro-Commissioning to Small Commercial Buildings: A Turnkey Automated Hardware-Software Solution

In the United States, small commercial buildings represent 51% of total floor space of all commercial buildings and consume nearly 3 quadrillion Btu (3.2 quintillion joule) of site energy annually, presenting an enormous opportunity for energy savings. Retro-commissioning (RCx), the process through which professional energy service providers identify and correct operational problems, has proven to be a cost-effective means to achieve median energy savings of 16%. However, retro-commissioning is not typically conducted at scale throughout the commercial stock. Very few small commercial buildings are retro-commissioned because utility expenses are relatively modest, margins are tighter, and capital for improvements is limited. In addition, small buildings do not have in-house staff with the expertise to identify improvement opportunities. In response, a turnkey hardware-software solution was developed to enable cost-effective, monitoring-based RCx of small commercial buildings. This highly tailored solution enables non-commissioning providers to identify energy and comfort problems, as well as associated cost impacts and remedies. It also facilitates scale by offering energy service providers the means to streamline their existing processes and reduce costs by more than half. The turnkey RCx sensor suitcase consists of two primary components: a suitcase of sensors for short-term building data collection that guides users through the process of deploying and retrieving their data and a software application that automates analysis of sensor data, identifies problems and generates recommendations. This paper presents the design and testing of prototype models, including descriptions of the hardware design, analysis algorithms, performance testing, and plans for dissemination.

Lin, Guanjing↗

Design Load Analysis for Wave Energy Converters: Preprint

This study demonstrates a systematic methodology for establishing the design loads of a wave energy converter (WEC). The proposed design load methodology incorporates existing design guidelines, where they exist, and follows a typical design progression; namely, advancing from many, quick, order-of-magnitude accurate, conceptual stage design computations to a few, computationally intensive, high-fidelity, design validation simulations. The goal of the study is to streamline and document this process based on quantitative evaluations of the design loads' accuracy at each design step and consideration for the computational efficiency of the entire design process. For the WEC, loads, and site conditions considered, this study demonstrates an efficient and accurate methodology of evaluating the design loads.

16 TIDAL AND WAVE POWER↗

A high-performance workflow system for subsurface simulation

Subsurface modeling applications typically neglect uncertainty in the conceptual models, past or future scenarios, and attribute most or all uncertainty to errors in model parameters. In this contribution, uncertainty in technetium-99 transport in a heterogeneous, deep vadose zone is explored with respect to the conceptual model using a next generation user environment called Akuna. Akuna provides a range of tools to manage environmental modeling projects, from managing simulation data to visualizing results from high-performance computational simulators. Core toolsets accessible through the user interface include model setup, grid generation, parameter estimation, and uncertainty quantification. The BC Cribs site at Hanford in southeastern Washington State is used to demonstrate Akuna capabilities. At the BC Cribs site, conceptualization of the system is highly uncertain because only sparse information is available for the geologic conceptual model, the physical and chemical properties of the sediments, and the history of waste disposal operations. Using the Akuna toolset to perform an analysis of conservative solute transport, significant prediction uncertainty in simulated concentrations is demonstrated by conceptual model variation. This demonstrates that conceptual model uncertainty is an important consideration in sparse data environments such as BC Cribs. It is also demonstrated that Akuna and the underlying toolset provides an integrated modeling environment that streamlines model setup, parameter optimization, and uncertainty analyses for high-performance computing applications.

Akuna↗

Determining biomolecular structures near room temperature using X-ray crystallography: concepts, methods and future optimization

For roughly two decades, cryocrystallography has been the overwhelmingly dominant method for determining high-resolution biomolecular structures. Competition from single-particle cryo-electron microscopy and micro-electron diffraction, increased interest in functionally relevant information that may be missing or corrupted in structures determined at cryogenic temperature, and interest in time-resolved studies of the biomolecular response to chemical and optical stimuli have driven renewed interest in data collection at room temperature and, more generally, at temperatures from the protein–solvent glass transition near 200 K to ∼350 K. Fischer has recently reviewed practical methods for room-temperature data collection and analysis [Fischer (2021), Q. Rev. Biophys. 54 , e1]. Here, the key advantages and physical principles of, and methods for, crystallographic data collection at noncryogenic temperatures and some factors relevant to interpreting the resulting data are discussed. For room-temperature data collection to realize its potential within the structural biology toolkit, streamlined and standardized methods for delivering crystals prepared in the home laboratory to the synchrotron and for automated handling and data collection, similar to those for cryocrystallography, should be implemented.

59 BASIC BIOLOGICAL SCIENCES↗

drtsans

drtsans is highly modular, allowing users to customize collected data as well as test hypothetical or simulated neutron events data. Instrument scientists can use the advance features of drtsans to calibrate their instruments and reduced large quantities of datasets in a streamlined mode. Users can correct the collected data with dark current subtraction and normalization by neutron flux, detector sensitivity, solid angle subtended by the detectors, and scaling to absolute units. Conversion from time-of-flight and/or wavelength to 1D or 2D momentum transfer renders the final scattering quantities amenable to analysis.

Bilheux, JeanC↗

Deploying and Operating CephFS for Scientific Applications at Fermilab

Fermilab has been running a Ceph cluster in production for several years to support high-throughput scientific computing. Our primary use case is CephFS, which serves interactive data analysis workloads, with growing interest in using RGW for scalable object storage of scientific datasets. In this talk, we'll share lessons learned from successfully deploying and maintaining our Ceph cluster with cephadm, including challenges faced, performance tuning, and operational practices. We'll also present custom tools we've developed to streamline monitoring and management and discuss how Ceph fits into our broader storage architecture for large-scale scientific research.

Peisker, Alison [Fermilab]↗

Numerical studies of porous airfoils in transonic flow

A numerical tool is constructed to examine the effects of a porous surface on transonic airfoil performance and to help understand the flow structure of passive shockwave/boundary layer interactions. The porous region is located near the shock with a cavity underneath it. This study is composed of two parts. Solved in the first part, with an inviscid-flow approach, is the transonic full-potential equation associated with transpiration boundary conditions which are obtained from porosity modeling. The numerical results indicate that a porous airfoil has a wave drag lower than that of a solid airfoil. The observed lambda-shock structure in the wind-tunnel testing can be predicted. Furthermore, the lift could be increased with an appropriate porosity distribution. In the second part of this work, the modified version of either an interactive boundary layer (IBL) algorithm or a thin-layer Navier-Stokes (TLNS) algorithm is used to study the outer flow, while a stream-function formulation is used to model the inner flow in the shallow cavity. The coupling procedure at the porous surface is based on Darcy's law and the assumption of a constant total pressure in the cavity. In addition, a modified Baldwin-Lomax turbulence model is used to describe the transpired turbulent boundary layer in the TLNS approach, while the Cebeci turbulence model is used in the IBL approach. According to the present analysis, a porous surface can reduce the wave drag appreciably, but can also increase the viscous losses. As has been observed experimentally, the numerical results indicate that the total drag is reduced at higher Mach numbers and increased at lower Mach numbers when the angles of attack are small. Furthermore, the streamline pattern of passive shock/boundary layer interaction are revealed.

Chow, C. Y.↗

Computation of viscous transonic flow over porous airfoils

The viscous effects on transonic flow past an airfoil which contains a shallow cavity beneath a porous surface are studied numerically. The porous region occupies a small portion of the total airfoil surface, and is located near the shock. Both an interactive boundary layer (IBL) algorithm and a thin-layer Navier-Stokes (TLNS) algorithm have been modified for use in studying the outer flow, whereas a stream-function formulation has been used to model the inner flow in the small cavity. The coupling procedure at the porous surface is based on Darcy's law and on the assumption of a constant total presusre in the cavity. In addition, a modified Baldwin-Lomax turbulence model is used to consider the transpired turbulent boundary layer in the TLNS approach, and the Cebeci-Smith turbulence model is used in the IBL approach. According to the present analysis, a porous surface can reduce the wave drag appreciably, but it can also increase viscous losses. As has been observed experimentally, the numerical results indicate that the total drag is reduced at higher Mach numbers and increased at lower Mach numbers when the angles of attack are small. Furthermore, the streamline patterns of passive-shock and boundary-layer interaction are revealed in this study.

Chow, Chuen-Yen↗