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DOE OSTI2022

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future

Abstract As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.

Burley, Stephen K. (ORCID:0000000224879713)↗

NASA NTRS1983

The Galileo spacecraft system design

The Galileo Orbiter differs markedly from its Mariner, Viking and Voyager predecessors in many aspects of its design, as dictated by its unique mission characteristics. Novel design features include a dual spin configuration, long life bipropellant propulsion, radioisotope thermoelectric generators, and a star scanner. Other major changes are related to Space Shuttle Orbiter compatibility. The selection of a distributed data system employing a high speed data bus represents a major advance over Voyager systems. The command, control and data handling functions for the Orbiter are merged into a single software-controlled subsystem. The paramount importance of software development in the design of Galileo subsystems is noted, in view of the requirement for total engineering and science data acquisition process reprogrammability.

Jones, C. P.↗

NASA NTRS1981

Application of an ultrasonic focusing radiator for acoustic levitation of submillimeter samples

An acoustic apparatus has been specifically developed to handle samples of submillimeter size in a gaseous medium. This apparatus consists of an acoustic levitation device, deployment devices for small liquid and solid samples, heat sources for sample heat treatment, acoustic alignment devices, a cooling system and data-acquisition instrumentation. The levitation device includes a spherical aluminum dish of 12 in. diameter and 0.6 in. thickness, 130 pieces of PZT transducers attached to the back side of the dish and a spherical concave reflector situated in the vicinity of the center of curvature of the dish. The three lowest operating frequencies for the focusing-radiator levitation device are 75, 105 and 163 kHz, respectively. In comparison with other levitation apparatus, it possesses a large radiation pressure and a high lateral positional stability. This apparatus can be used most advantageously in the study of droplets and spherical shell systems, for instance, for fusion target applications.

Lee, M. C.↗

DOE OSTI2020

A Generic High Bandwidth Data Acquisition Card for Physics Experiments

In high energy physics and nuclear physics experiments particularly the ones based on particle accelerator, the data rate from the detector is usually in the order of Terabytes per second. This high throughput data from detector front-end electronics need to be transmitted to the back-end computing farm for high level event selection and building. A Data Acquisition (DAQ) system with features of high-density, scalable, easily upgradeable is crucial to simplify the readout architecture of whole experiment. This paper will introduce the design of a generic high bandwidth PCIe card which can be used as the important input output card in a scalable DAQ system. It can factorize front-end electronics from data handling, and reduce amount of custom hardware in favor of scalable detectorindependent commercial hardware and software. Besides the 48 channels of bidirectional high speed fiber optical links with frontends, it also supports to synchronize with the experiment timing system, and to fanout the clock and trigger information with a fixed latency to the front-end electronics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS1992

The ADAM environment and transputers

The ADAM environment is both used for data analysis by Starlink and for data acquisition by the UK-involved observatories in Australia, Hawaii, and the Canary Islands. ADAM was originally hosted under VAX/VMS but is now at an advanced stage of a Unix port. ADAM comprises a parameter system, hierarchical data system, noticeboard system, error handling system, and other components. Originally a multi-tasking single processor environment, it has been enhanced to a multiprocessor environment using local or wide area networking. The Royal Observatory Edinburgh is producing a transputer version of the ADAM kernel to allow instruments which make use of transputers for data acquisition/control to integrate more closely with the ADAM software running at the telescopes. Communication into the transputer system is based on Ethernet carrying TCP/IP, which eases development toward a network of mixed VMS/Unix/transputer Telescope systems. The transputer system is being applied to instruments under development for the UKIRT and JCMT telescopes.

Kelly, B. D.↗

NASA NTRS2015

OSIRIS-REx, Returning the Asteroid Sample

This paper addresses the technical aspects of the sample return system for the upcoming Origins, Spectral Interpretation, Resource Identification, and Security-Regolith Explorer (OSIRIS-REx) asteroid sample return mission. The overall mission design and current implementation are presented as an overview to establish a context for the technical description of the reentry and landing segment of the mission.The prime objective of the OSIRIS-REx mission is to sample a primitive, carbonaceous asteroid and to return that sample to Earth in pristine condition for detailed laboratory analysis. Targeting the near-Earth asteroid Bennu, the mission launches in September 2016 with an Earth reentry date of September 24, 2023.OSIRIS-REx will thoroughly characterize asteroid Bennu providing knowledge of the nature of near-Earth asteroids that is fundamental to understanding planet formation and the origin of life. The return to Earth of pristine samples with known geologic context will enable precise analyses that cannot be duplicated by spacecraft-based instruments, revolutionizing our understanding of the early Solar System. Bennu is both the most accessible carbonaceous asteroid and one of the most potentially Earth-hazardous asteroids known. Study of Bennu addresses multiple NASA objectives to understand the origin of the Solar System and the origin of life and will provide a greater understanding of both the hazards and resources in near-Earth space, serving as a precursor to future human missions to asteroids.This paper focuses on the technical aspects of the Sample Return Capsule (SRC) design and concept of operations, including trajectory design and reentry retrieval. Highlights of the mission are included below.The OSIRIS-REx spacecraft provides the essential functions for an asteroid characterization and sample return mission: attitude control propulsion power thermal control telecommunications command and data handling structural support to ensure successful rendezvous with Bennu characterization of Bennus properties delivery of the sampler to the surface, and return of the spacecraft to the vicinity of the Earth sample collection, performed by the Touch-and-Go Sample Acquisition Mechanism (TAGSAM), to acquire a regolith sample from the surface Earth re-entry and SRC recovery. Following sample collection, OSIRIS-REx drifts away from Bennu until the Asteroid Departure Maneuver is commanded on March 4, 2021, sending OSIRIS-REx on a ballistic return cruise to Earth. No additional large deterministic maneuvers are required to return the SRC to Earth. During the cruise, tracking and trajectory correction maneuvers (TCMs) are performed as necessary to precisely target the entry corridor. As OSIRIS-REx approaches Earth, the reentry plans are reviewed starting about a year before arrival, and preparations begin. The spacecraft is targeted away from the Earth until 7 days before entry. The final two trajectory correction maneuvers bring the spacecraft on target toward the Utah Test and Training Range (UTTR), with sufficient time for contingency resolution. The SRC releases 4 hours prior to atmospheric entry interface and, using the Stardust capsule heritage design, employs a traditional drogue and main parachute descent system for a soft touchdown.

reentry↗

NASA NTRS1993

Mars aqueous chemistry experiment

The Mars Aqueous Chemistry Experiment (MACE) is designed to conduct a variety of measurements on regolith samples, encompassing mineral phase analyses, chemical interactions with H2O, and physical properties determinations. From these data, much can be learned or inferred regarding the past weathering environment, the contemporaneous soil micro-environments, and the general chemical and physical state of the Martian regolith. By analyzing both soil and duricrust samples, the nature of the latter may become more apparent. Sites may be characterized for comparative purposes and criteria could be set for selection of high priority materials on future sample return missions. Progress for the first year MACE PIDDP is reported in two major areas of effort: (1) fluids handling concepts, definition, and breadboard fabrication and (2) aqueous chemistry ion sensing technology and test facility integration. A fluids handling breadboard was designed, fabricated, and tested at Mars ambient pressure. The breadboard allows fluid manipulation scenarios to be tested under the reduced pressure conditions expected in the Martian atmosphere in order to validate valve operations, orchestrate analysis sequences, investigate sealing integrity, and to demonstrate efficacy of the fluid handling concept. Additional fluid manipulation concepts have also been developed based on updated MESUR spacecraft definition. The Mars Aqueous Chemistry Experiment Ion Selective Electrode (ISE) facility was designed as a test bed to develop a multifunction interface for measurements of chemical ion concentrations in aqueous solution. The interface allows acquisition of real time data concerning the kinetics and heats of salt dissolution, and transient response to calibration and solubility events. An array of ion selective electrodes has been interfaced and preliminary calibration studies performed.

Clark, Benton C.↗

NASA NTRS1977

Infrared Imagery of Shuttle (IRIS). Task 1

Assessment of available IR sensor technology showed that the four aerothermodynamic conditions of interest during the entry trajectory of space shuttle can be accommodated by an aircraft flying parallel to the orbiter reentry ground track. Thermal information from the sides of the vehicle can be obtained with degraded performance (temperatures below 800 K) by flying the C-141 aircraft on the opposite side of the shuttle ground track and in the direction opposite that which is optimum for lower surface viewing. An acquisition system using a 6.25-cm aperture telescope and a single indium antimonide detector were designed to meet the acquisition requirements and interface with the 91.5-cm telescope with minimum modification. An image plane system using 600 indium antimonide detectors in two arrays which requires no modification to the existing telescope was also designed. Currently available components were used in a data handling system with interfaces with the experimentors station and the HP2100 computer.

Chocol, C. J.↗

NASA NTRS1981

Meteorology impact on ATC system design

The impact of meteorology on air traffic control (ATC) system design for designs, and for cost benefit evaluations is discussed. The myriad of choices for implementation is a problem of great magnitude, given the economic climate of today. Cost versus benefit requires greater emphasis. Expanding and improving weather data acquisition, increasing the speed of weather data transmission and automating those actions that lend themselves to standardization for automated data processing are outlined. Three programs are mentioned: (1) automated weather observations, (2) weather radar and improvements to the national airspace system as related to the handling of weather data; and (3) products.

Vandemark, F. E.↗

NASA NTRS1981

Study of a Tracking and Data Acquisition System (TDAS) in the 1990's

Progress in concept definition studies, operational assessments, and technology demonstrations for the Tracking and Data Acquisition System (TDAS) is reported. The proposed TDAS will be the follow-on to the Tracking and Data Relay Satellite System and will function as a key element of the NASA End-to-End Data System, providing the tracking and data acquisition interface between user accessible data ports on Earth and the user's spaceborne equipment. Technical activities of the "spacecraft data system architecture' task and the "communication mission model' task are emphasized. The objective of the first task is to provide technology forecasts for sensor data handling, navigation and communication systems, and estimate corresponding costs. The second task is concerned with developing a parametric description of the required communication channels. Other tasks with significant activity include the "frequency plan and radio interference model' and the "Viterbi decoder/simulator study'.

Source record↗

NASA NTRS1990

Near earth tracking/data exploration

The future challenges facing NASA's data acquisition program are examined, with emphasis on the near-earth exploration activity and the associated data systems. It is noted that the process that is being followed is an evolutionary one: new technologies are being gradually integrated into currently operating systems. For example, advanced handling is already being introduced into such programs as the Space Telescope and the Gamma Ray Source Observatory System.

Spearing, Robert↗

DOE OSTI2022

Status of the data acquisition, trigger, and slow control systems of the Mu2e experiment at Fermilab

The Mu2e experiment at the Fermilab will search for a coherent neutrinoless conversion of a muon into an electron in the field of an aluminum nucleus with a sensitivity improvement by a factor of 10,000 over existing limits. In this work, the Mu2e Trigger and Data Acquisition System (TDAQ) uses otsdaq framework as the online Data Acquisition System (DAQ) solution. Developed at Fermilab, otsdaq integrates several framework components — an artdaq-based DAQ, an art-based event processing, and an EPICS-based detector control system (DCS), and provides a uniform multi-user interface to its components through a web browser. Data streams from the Mu2e tracker and calorimeter are handled by the artdaq-based DAQ and processed by a one-level software trigger implemented within the art framework. Events accepted by the trigger have their data combined, post-trigger, with the separately read out data from the Mu2e Cosmic Ray Veto system. Foundation of the Mu2e DCS, EPICS – an Experimental Physics and Industrial Control System – is an open-source platform for monitoring, controlling, alarming, and archiving. A prototype of the TDAQ and the DCS systems has been built and tested over the last three years at Fermilab’s Feynman Computing Center, and now the production system installation is underway. This work presents their status and focus on the installation plans and procedures for racks, workstations, network switches, gateway computers, DAQ hardware, slow controls implementation, and testing.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

NASA NTRS2012

Mar's Science Laboratory : Qualification Model Dirty Testing (QMDT) Support

The Martian missions of Spirit, Opportunity, and many others have sparked high interest in Mars which has led to Curiosity to answer questions that we have sought after for years. Has life ever existed on Mars? Through the collection and analyzation of samples, it will help to answer questions about the possibilities of life that may have existed on Mars, and we will gain valuable data about the planet Mars.

Qualification Model Dirty Testing (QMDT)↗

NASA NTRS2007

NASA Tech Briefs, March 2007

Topics include: Advanced Systems for Monitoring Underwater Sounds; Wireless Data-Acquisition System for Testing Rocket Engines; Processing Raw HST Data With Up-to-Date Calibration Data; Mobile Collection and Automated Interpretation of EEG Data; System for Secure Integration of Aviation Data; Servomotor and Controller Having Large Dynamic Range; Digital Multicasting of Multiple Audio Streams; Translator for Optimizing Fluid-Handling Components; AIRSAR Web-Based Data Processing; Pattern Matcher for Trees Constructed From Lists; Reducing a Knowledge-Base Search Space When Data Are Missing; Ground-Based Correction of Remote-Sensing Spectral Imagery; State-Chart Autocoder; Pointing History Engine for the Spitzer Space Telescope; Low-Friction, High-Stiffness Joint for Uniaxial Load Cell; Magnet-Based System for Docking of Miniature Spacecraft; Electromechanically Actuated Valve for Controlling Flow Rate; Plumbing Fixture for a Microfluidic Cartridge; Camera Mount for a Head-Up Display; Core-Cutoff Tool; Recirculation of Laser Power in an Atomic Fountain; Simplified Generation of High-Angular-Momentum Light Beams; Imaging Spectrometer on a Chip; Interferometric Quantum-Nondemolition Single-Photon Detectors; Ring-Down Spectroscopy for Characterizing a CW Raman Laser; Complex Type-II Interband Cascade MQW Photodetectors; Single-Point Access to Data Distributed on Many Processors; Estimating Dust and Water Ice Content of the Martian Atmosphere From THEMIS Data; Computing a Stability Spectrum by Use of the HHT; Theoretical Studies of Routes to Synthesis of Tetrahedral N4; Estimation Filter for Alignment of the Spitzer Space Telescope; Antenna for Measuring Electric Fields Within the Inner Heliosphere; Improved High-Voltage Gas Isolator for Ion Thruster; and Hybrid Mobile Communication Networks for Planetary Exploration.

Source record↗

NASA NTRS1988

Test data acquisition system for the ESTEC large solar simulator at ESA/ESTEC

A prototype data acquisition system is described. The device characteristics, its performance and the system aspects connected to the integration of the data acquisition system into the space simulator instrumentation and environment are discussed. The data acquisition system has a modular architecture and manifold configuration capability. The input characteristics feature high resolution and accuracy/stability for the measurement of low level (thermocouple originated) analog signals, even in the presence of high common mode and S/N figures. The output is serial digital, compatible with ESA data handling standards. The device is designed to be installed in particularly hostile environments, such as that of a solar simulator.

Buroni, G.↗

DOE OSTI2026

GP Cosmology Surrogate v1.0

GP Cosmology Surrogate is a Python library for building and training a generalized multi-output Gaussian process (GP) framework of @takhtaganov2021cosmic. In this approach, the surrogate is constructed sequentially, guided by a Bayesian optimization acquisition function that targets reduction of emulation error in the regions most consistent with the observational data. This adaptive design concentrates computational resources where they have the greatest impact on inference accuracy. The library supports efficient training for separable GP kernels, which allows the use of Kronecker algebra to handle high-dimensional input spaces and large numbers of correlated outputs. This makes it well suited for applications such as modeling cosmological power spectra, large-scale physical simulations, and multi-output hyperparameter tuning. By combining scalable multi-output GP modeling with data-driven adaptive sampling, GPsurrogate enables parameter inference and optimization with substantially fewer simulations than conventional space-filling designs.

Lukic, Zarija [Lawrence Berkeley National Laborato↗

NASA NTRSDate not supplied

Constraining the Hydration of X-Ray Amorphous and Clay Mineral Phases in Gale Crater, Mars

Clay minerals and salts in the Gale crater stratigraphy investigated by the Mars Science Laboratory (MSL) Curiosity rover preserve information about sediment sources, depositional environment, and post-depositional alteration history. The compositions of amorphous components in samples have bearing on the redox potential, pH, and chemistry of alteration fluids, and on the heterogeneity of these conditions. Interlayer clay hydration in present-day Gale crater could be an indication of high water/rock ratios of late-stage fluid alteration events, which increases the potential habitability of these post-depositional environments. The MSL Dynamic Albedo of Neutrons instrument (DAN) measures bulk hydration and here we attempt to determine the hydration states of both clay minerals and amorphous components throughout the Curiosity traverse to constrain the abundance of individual amorphous phases and determine if clay interlayer water is present today. These implications are also more broadly applicable to similar sedimentary successions outside Gale crater. In this study, we compare hydration results from DAN to mineralogical results from the MSL Chemistry and Mineralogy instrument (CheMin) for 16 different fluvio-lacustrine sample locations. These samples typically contain one or more hydrated crystalline phases, a hydrated X-ray amorphous fraction composed of multiple amorphous phases, and one or more clay mineral phases which CheMin has consistently measured as collapsed (i.e., no interlayer water). However, Gale samples are known to dehydrate during sample acquisition and handling, and because DAN measures hydration to a depth of tens of cm, we can test for the presence of clay interlayer water in situ by comparing DAN bulk hydration to CheMin mineralogy. We can also constrain the hydration of the samples’ amorphous fractions, and with geochemical data from the ChemCam and APXS instruments, this will allow us to better define the phases which compose this fraction.

S Czarnecki↗

NASA NTRS1981

A high performance, continuously variable data rate, digitally implemented BPSK modem for deep space network

This paper describes a high performance, digital, BPSK modem designed to improve the telemetry data handling capability of NASA's Deep Space Network. The data rate is continuously variable from 0.5 Mbps to 30 Mbps. It uses newly designed, high speed digital alogrithms for receive filtering, carrier tracking, bit timing and AGC. The carrier and bit time tracking loops have been designed to provide fast acquisition and low tracking phase jitter at E sub b/N sub 0 as low as -4 dB and bit transition density as low as 10%. The performance of the modem is within 0.65 dB below 10 Mbps, 1.0 dB from 10 Mbps to 20 Mbps, and 1.5 dB above 20 Mbps of theoretical coherent BPSK at a BER of 0.0004.

Paik, W. H.↗