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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The Phenix‐AlphaFold webservice: Enabling AlphaFold predictions for use in Phenix

Abstract Advances in machine learning have enabled sufficiently accurate predictions of protein structure to be used in macromolecular structure determination with crystallography and cryo‐electron microscopy data. The Phenix software suite has AlphaFold predictions integrated into an automated pipeline that can start with an amino acid sequence and data, and automatically perform model‐building and refinement to return a protein model fitted into the data. Due to the steep technical requirements of running AlphaFold efficiently, we have implemented a Phenix‐AlphaFold webservice that enables all Phenix users to run AlphaFold predictions remotely from the Phenix GUI starting with the official 1.21 release. This webservice will be improved based on how it is used by the research community and the future research directions for Phenix.

Poon, Billy K.↗
DOE OSTI2021

Chimera Spectrum Diagnostics for Peptides Using Two-Dimensional Partial Covariance Mass Spectrometry

The rate of successful identification of peptide sequences by tandem mass spectrometry (MS/MS) is adversely affected by the common occurrence of co-isolation and co-fragmentation of two or more isobaric or isomeric parent ions. This results in so-called `chimera spectra’, which feature peaks of the fragment ions from more than a single precursor ion. The totality of the fragment ion peaks in chimera spectra cannot be assigned to a single peptide sequence, which contradicts a fundamental assumption of the standard automated MS/MS spectra analysis tools, such as protein database search engines. This calls for a diagnostic method able to identify chimera spectra to single out the cases where this assumption is not valid. Here, we demonstrate that, within the recently developed two-dimensional partial covariance mass spectrometry (2D-PC-MS), it is possible to reliably identify chimera spectra directly from the two-dimensional fragment ion spectrum, irrespective of whether the co-isolated peptide ions are isobaric up to a finite mass accuracy or isomeric. We introduce ‘3-57 chimera tag’ technique for chimera spectrum diagnostics based on 2D-PC-MS and perform numerical simulations to examine its efficiency. We experimentally demonstrate the detection of a mixture of two isomeric parent ions, even under conditions when one isomeric peptide is at one five-hundredth of the molar concentration of the second isomer.

47 OTHER INSTRUMENTATION↗
NASA NTRS1989

Experiences with the JPL telerobot testbed: Issues and insights

The Jet Propulsion Laboratory's (JPL) Telerobot Testbed is an integrated robotic testbed used to develop, implement, and evaluate the performance of advanced concepts in autonomous, tele-autonomous, and tele-operated control of robotic manipulators. Using the Telerobot Testbed, researchers demonstrated several of the capabilities and technological advances in the control and integration of robotic systems which have been under development at JPL for several years. In particular, the Telerobot Testbed was recently employed to perform a near completely automated, end-to-end, satellite grapple and repair sequence. The task of integrating existing as well as new concepts in robot control into the Telerobot Testbed has been a very difficult and timely one. Now that researchers have completed the first major milestone (i.e., the end-to-end demonstration) it is important to reflect back upon experiences and to collect the knowledge that has been gained so that improvements can be made to the existing system. It is also believed that the experiences are of value to the others in the robotics community. Therefore, the primary objective here will be to use the Telerobot Testbed as a case study to identify real problems and technological gaps which exist in the areas of robotics and in particular systems integration. Such problems have surely hindered the development of what could be reasonably called an intelligent robot. In addition to identifying such problems, researchers briefly discuss what approaches have been taken to resolve them or, in several cases, to circumvent them until better approaches can be developed.

Stone, Henry W.↗
NASA NTRS1991

A strongly goal-directed close-range vision system for spacecraft docking

In this presentation, we will propose a strongly goal-oriented stereo vision system to establish proper docking approach motions for automated rendezvous and capture (AR&C). From an input sequence of stereo video image pairs, the system produces a current best estimate of: contact position; contact vector; contact velocity; and contact orientation. The processing demands imposed by this particular problem and its environment dictate a special case solution; such a system should necessarily be, in some sense, minimalist. By this we mean the system should construct a scene description just sufficiently rich to solve the problem at hand and should do no more processing than is absolutely necessary. In addition, the imaging resolution should be just sufficient. Extracting additional information and constructing higher level scene representations wastes energy and computational resources and injects an unnecessary degree of complexity, increasing the likelihood of malfunction. We therefore take a departure from most prior stereopsis work, including our own, and propose a system based on associative memory. The purpose of the memory is to immediately associate a set of motor commands with a set of input visual patterns in the two cameras. That is, rather than explicitly computing point correspondences and object positions in world coordinates and trying to reason forward from this information to a plan of action, we are trying to capture the essence of reflex behavior through the action of associative memory. The explicit construction of point correspondences and 3D scene descriptions, followed by online velocity and point of impact calculations, is prohibitively expensive from a computational point of view for the problem at hand. Learned patterns on the four image planes, left and right at two discrete but closely spaced instants in time, will be bused directly to infer the spacecraft reaction. This will be a continuing online process as the docking collar approaches.

Boyer, Kim L.↗
NASA NTRS2012

Agile Science Operations: A New Approach for Primitive Exploration Bodies

Primitive body exploration missions such as potential Comet Surface Sample Return or Trojan Tour and Rendezvous would challenge traditional operations practices. Earth-based observations would provide only basic understanding before arrival and many science goals would be defined during the initial rendezvous. It could be necessary to revise trajectories and observation plans to quickly characterize the target for safe, effective observations. Detection of outgassing activity and monitoring of comet surface activity are even more time constrained, with events occurring faster than round-trip light time. "Agile science operations" address these challenges with contingency plans that recognize the intrinsic uncertainty in the operating environment and science objectives. Planning for multiple alternatives can significantly improve the time required to repair and validate spacecraft command sequences. When appropriate, time-critical decisions can be automated and shifted to the spacecraft for immediate access to instrument data. Mirrored planning systems on both sides of the light-time gap permit transfer of authority back and forth as needed. We survey relevant science objectives, identifying time bottlenecks and the techniques that could be used to speed missions' reaction to new science data. Finally, we discuss the results of a trade study simulating agile observations during flyby and comet rendezvous scenarios. These experiments quantify instrument coverage of key surface features as a function of planning turnaround time. Careful application of agile operations techniques can play a significant role in realizing the Decadal Survey plan for primitive body exploration

Agile science↗
NASA NTRS2021

Sailing Towards an Expressive Scheduling Language for Europa Clipper

The mission planners for NASA's Europa Clipper deep-space mission use automated scheduling software to generate activity plans and command sequences for multiple instruments and subsystems before sending the sequences for execution on board. Both science and engineering planners must translate their intents into expressions of mission constraints, goals, and preferences that the scheduling engine understands. This paper describes the ongoing development of a dedicated domain-specific java-embedded language that can efficiently and accurately capture such concerns for the Europa Clipper mission, along with a user-interface companion for the language.

Schaffer, Steve↗
DOE OSTI2023

Automated methods for scalable, parallelized enzymatic biopolymer synthesis and modification using microfluidic devices

Methods for the automated template-free synthesis of user-defined sequence controlled biopolymers using microfluidic devices are described. The methods facilitate simultaneous synthesis of up to thousands of uniquely addressed biopolymers from the controlled movement and combination of regents as fluid droplets using microfluidic and EWOD-based systems. In some forms, biopolymers including nucleic acids, peptides, carbohydrates, and lipids are synthesized from step-wise assembly of building blocks based on a user-defined sequence of droplet movements. In some forms, the methods synthesize uniquely addressed nucleic acids of up to 1,000 nucleotides in length. Methods for adding, removing and changing barcodes on biopolymers are also provided. Biopolymers synthesized according to the methods, and libraries and databases thereof are also described. Modified biopolymers, including chemically modified nucleotides and biopolymers conjugated to other molecules are described.

Banal, James↗
DOE OSTI2020

Genetic circuit design automation for yeast

Cells can be programmed to monitor and react to their environment using genetic circuits. Design automation software maps a desired circuit function to a DNA sequence, a process that requires units of gene regulation (gates) that are simple to connect and behave predictably. This poses a challenge for eukaryotes due to their complex mechanisms of transcription and translation. To this end, we have developed gates for yeast (Saccharomyces cerevisiae) that are connected using RNA polymerase flux as the signal carrier and are insulated from each other and host regulation. They are based on minimal constitutive promoters (~120 base pairs), for which rules are developed to insert operators for DNA-binding proteins. Using this approach, in this work we constructed nine NOT/NOR gates with nearly identical response functions and 400-fold dynamic range. In circuits, they are transcriptionally insulated from each other by placing ribozymes downstream of terminators to block nuclear export of messenger RNAs resulting from RNA polymerase readthrough. Based on these gates, Cello 2.0 was used to build circuits with up to 11 regulatory proteins. A simple dynamic model predicts the circuit response over days. Genetic circuit design automation for eukaryotes simplifies the construction of regulatory networks as part of cellular engineering projects, whether it be to stage processes during bioproduction, serve as environmental sentinels or guide living therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2010

A Comparison Between Orion Automated and Space Shuttle Rendezvous Techniques

The Orion spacecraft will replace the space shuttle and will be the first human spacecraft since the Apollo program to leave low earth orbit. This vehicle will serve as the cornerstone of a complete space transportation system with a myriad of mission requirements necessitating rendezvous to multiple vehicles in earth orbit, around the moon and eventually beyond . These goals will require a complex and robust vehicle that is, significantly different from both the space shuttle and the command module of the Apollo program. Historically, orbit operations have been accomplished with heavy reliance on ground support and manual crew reconfiguration and monitoring. One major difference with Orion is that automation will be incorporated as a key element of the man-vehicle system. The automated system will consist of software devoted to transitioning between events based on a master timeline. This effectively adds a layer of high level sequencing that moves control of the vehicle from one phase to the next. This type of automated control is not entirely new to spacecraft since the shuttle uses a version of this during ascent and entry operations. During shuttle orbit operations however many of the software modes and hardware switches must be manually configured through the use of printed procedures and instructions voiced from the ground. The goal of the automation scheme on Orion is to extend high level automation to all flight phases. The move towards automation represents a large shift from current space shuttle operations, and so these new systems will be adopted gradually via various safeguards. These include features such as authority-to-proceed, manual down modes, and functional inhibits. This paper describes the contrast between the manual and ground approach of the space shuttle and the proposed automation of the Orion vehicle. I will introduce typical orbit operations that are common to all rendezvous missions and go on to describe the current Orion automation architecture and contrast it with shuttle rendezvous techniques and circumstances. The shuttle rendezvous profile is timed to take approximately 3 days from orbit insertion to docking at the International Space Station (ISS). This process can be divided into 3 phases: far-field, mid-field and proximity operations. The far-field stage is characterized as the most quiescent phase. The spacecraft is usually too far to navigate using relative sensors and uses the Inertial Measurement Units (IMU s) to numerically solve for its position. The maneuvers are infrequent, roughly twice per day, and are larger than other burns in the profile. The shuttle uses this opportunity to take extensive ground based radar updates and keep high fidelity orbit states on the ground. This state is then periodically uplinked to the shuttle computers. The targeting solutions for burn maneuvers are also computed on the ground and uplinked. During the burn the crew is responsible for setting the shuttle attitude and configuring the propulsion system for ignition. Again this entire process is manually driven by both crew and ground activity. The only automatic processes that occur are associated with the real-time execution of the burn. The Orion automated functionality will seek to relieve the workload of both the crew and ground during this phase

Ruiz, Jose O,↗
NASA NTRS1980

An automated approach to the design of decision tree classifiers

The classification of large dimensional data sets arising from the merging of remote sensing data with more traditional forms of ancillary data is considered. Decision tree classification, a popular approach to the problem, is characterized by the property that samples are subjected to a sequence of decision rules before they are assigned to a unique class. An automated technique for effective decision tree design which relies only on apriori statistics is presented. This procedure utilizes a set of two dimensional canonical transforms and Bayes table look-up decision rules. An optimal design at each node is derived based on the associated decision table. A procedure for computing the global probability of correct classfication is also provided. An example is given in which class statistics obtained from an actual LANDSAT scene are used as input to the program. The resulting decision tree design has an associated probability of correct classification of .76 compared to the theoretically optimum .79 probability of correct classification associated with a full dimensional Bayes classifier. Recommendations for future research are included.

Argentiero, P.↗
NASA NTRS1986

Artificial intelligence planning applications for space exploration and space robotics

Mission sequencing involves the plan for actuation of the experiments to be conducted aboard a spacecraft; automation is under study by NASA as a means to reduce time and manpower costs in mission planning and in robotic implementation. The development of a mission sequence is conditioned by the limited duration of advantageous spacecraft encounters with objects of study, more research requests than can be satisfied, and requested changes in objectives. Autonomous robot development is hampered by the absence of task-level programming languages, the existence of anomalies in real-world interactions, and a lack of required capabilities in current sensor technology.

Rokey, Mark↗
DOE OSTI2026

DIVA/DeviceEditor v6.1.2

DIVA is an end-to-end DNA design and construction management platform that streamlines how researchers design, build, and receive sequence-verified DNA constructs. Through a web-based BioCAD interface (DeviceEditor), researchers independently design DNA constructs and submit them to a centralized queue with a single action. Designs progress transparently through standardized states which allow researchers to track status and access finished constructs via a central DNA repository. Submitted designs are reviewed by dedicated staff for feasibility and optimization, reducing costly failures and improving downstream execution. Automated DNA assembly software optimizes construction strategies by reusing existing parts where possible and sourcing synthetic DNA only when needed. Standardized, sequence-agnostic assembly methods enable many independent constructs to be built in parallel using lab automation, dramatically increasing throughput. High-throughput next-generation sequencing is used to verify construct accuracy, with flexible platforms selected based on task requirements. Throughout the process, detailed success and failure data are captured and analyzed, enabling continuous improvement of assembly protocols. Compared to traditional, manual DNA construction workflows, DIVA offers higher scalability, transparency, reproducibility, and data-driven optimization.

Plahar, Hector [Lawrence Berkeley National Laborat↗
NASA NTRS1999

The Palomar Testbed Interferometer

The Palomar Testbed Interferometer (PTI) is a long-baseline infrared interferometer located at Palomar Observatory, California. It was built as a testbed for interferometric techniques applicable to the Keck Interferometer. First fringes were obtained in 1995 July. PTI implements a dual-star architecture, tracking two stars simultaneously for phase referencing and narrow-angle astrometry. The three fixed 40 cm apertures can be combined pairwise to provide baselines to 110 m. The interferometer actively tracks the white-light fringe using an array detector at 2.2 microns and active delay lines with a range of +/-38 m. Laser metrology of the delay lines allows for servo control, and laser metrology of the complete optical path enables narrow-angle astrometric measurements. The instrument is highly automated, using a multiprocessing computer system for instrument control and sequencing.

Colavita, M. M.↗
NASA NTRS2011

Automated Miniaturized Instrument for Space Biology Applications and the Monitoring of the Astronauts Health Onboard the ISS

Human space travelers experience a unique environment that affects homeostasis and physiologic adaptation. The spacecraft environment subjects the traveler to noise, chemical and microbiological contaminants, increased radiation, and variable gravity forces. As humans prepare for long-duration missions to the International Space Station (ISS) and beyond, effective measures must be developed, verified and implemented to ensure mission success. Limited biomedical quantitative capabilities are currently available onboard the ISS. Therefore, the development of versatile instruments to perform space biological analysis and to monitor astronauts' health is needed. We are developing a fully automated, miniaturized system for measuring gene expression on small spacecraft in order to better understand the influence of the space environment on biological systems. This low-cost, low-power, multi-purpose instrument represents a major scientific and technological advancement by providing data on cellular metabolism and regulation. The current system will support growth of microorganisms, extract and purify the RNA, hybridize it to the array, read the expression levels of a large number of genes by microarray analysis, and transmit the measurements to Earth. The system will help discover how bacteria develop resistance to antibiotics and how pathogenic bacteria sometimes increase their virulence in space, facilitating the development of adequate countermeasures to decrease risks associated with human spaceflight. The current stand-alone technology could be used as an integrated platform onboard the ISS to perform similar genetic analyses on any biological systems from the tree of life. Additionally, with some modification the system could be implemented to perform real-time in-situ microbial monitoring of the ISS environment (air, surface and water samples) and the astronaut's microbiome using 16SrRNA microarray technology. Furthermore, the current system can be enhanced substantially by combining it with other technologies for automated, miniaturized, high-throughput biological measurements, such as fast sequencing, protein identification (proteomics) and metabolite profiling (metabolomics). Thus, the system can be integrated with other biomedical instruments in order to support and enhance telemedicine capability onboard ISS. NASA's mission includes sustained investment in critical research leading to effective countermeasures to minimize the risks associated with human spaceflight, and the use of appropriate technology to sustain space exploration at reasonable cost. Our integrated microarray technology is expected to fulfill these two critical requirements and to enable the scientific community to better understand and monitor the effects of the space environment on microorganisms and on the astronaut, in the process leveraging current capabilities and overcoming present limitations.

Human space travelers↗
DOE OSTI2020

Bayesian Approach to Estimation of Water Table Elevations Using Historical Rasters as Prior Information 2019 - 20430

In cases of complex but only partially known geology and a lack of spatial control in observation well locations, water table elevation estimation is very challenging. In some cases, auxiliary information, such as observations of the movement of tracers, operation of injection and extraction wells, and calibration of groundwater models against the historical elevation data, can be combined with expert judgement to estimate flow directions in areas of sparse data and to aid in the production of more reliable contour maps (and associated rasters) than could be produced by relying on sparse well elevation data alone. Given a historical sequence of these raster maps, the question arises how to automate, to the extent possible, the process of producing new raster maps to reflect data from previous times, the current data and the operation of expert judgement. One solution is to adopt a Bayesian point of view and to regard the historical well elevation data, auxiliary information and historical raster maps as prior information. The well elevations for water table wells, as well as those for injection/extraction wells and the data associated with other relevant variables, can be viewed as predictors for the raster surface. From this prior information, we can, conditional on the values of these predictors for a new time period, compute an expected value map and a standard deviation map for the new raster. These then can be taken to specify a prior predictive distribution for the pixels in the new raster map. Then we condition the pixels, corresponding to water level observation wells within the raster, on the observed values in those wells (which in general will differ from the regression estimate) for the new time period. Given the smoothness of the water table surface, we then smooth the surface of deviations from the mean surface, based on the variograms of the historical rasters, and add this smoothed surface to the regression mean surface. The error structure of the produced raster map is defined by the regression error structure and the error due to smoothing based on the estimated variograms. This methodology has been developed and is being further refined for groundwater monitoring and remediation at LANL. It is a very flexible method that can also be applied with a variety of other predictors applied to model the water level wells in the area of interest over the historical record. The smoothness of the spatial process and its possible evolution over time can then be estimated from the residuals from this regression. This can be augmented by expert hydrogeological opinion based on site topography and hydrogeology. (authors)

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1994

Attempt of automated space network operations at ETS-VI experimental data relay system

National Space Development Agency of Japan (NASDA) is to perform experimental operations to acquire necessary technology for the future inter-satellite communications configured with a data relay satellite. This paper intends to overview functions of the experimental ground system which NASDA has developed for the Engineering Test Satellite VI (ETS-VI) Data Relay and Tracking Experiment, and to introduce Space Network System Operations Procedure (SNSOP) method with an example of Ka-band Single Access (KSA) acquisition sequence. To reduce operational load, SNSOP is developed with the concept of automated control and monitor of both ground terminal and data relay satellite. To perform acquisition and tracking operations fluently, the information exchange with user spacecraft controllers is automated by SNSOP functions.

Ishihara, Kiyoomi↗
DOE OSTI2023

Optimizing Cell-based Antimicrobials through Pooled Genomic Libraries

DNA synthesis and assembly technologies ushered in through synthetic biology have great promise for biomanufacturing, bioremediation, and the development of living therapeutics. Unfortunately, predicting sequence to function relationships, including for biosynthetic pathways expressed in a new host organism, is difficult and often requires many iterative cycles of design, construction, and testing. We are working to develop data-driven approaches to identify the genetic determinants of growth defects and productivity for the expression of a cell-based antimicrobial. We assayed the growth, pigment production, and antimicrobial activity of a collection of over 10,000 genetic mutants of the violacein biosynthetic pathway and sequenced the genetic variation of these mutants. Through this project, we have developed an innovative codebase to automate the determination of pigmentation and antimicrobial clearing diameter for tens of thousands of genetic mutants cultivated on agar dishes. Further, we have written DNA sequence analysis code to demultiplex & provide consensus sequences from high-throughput PacBio long-read circular consensus sequencing (CCS) datasets. From this foundation, we plan to map DNA sequence to function to predict an optimal genetic design to maximize antimicrobial activity while minimizing deleterious growth effects. The workflows and algorithms developed through this project can be broadly applied to other engineered functions in microbes, uncovering sequence to function relationships for complex phenotypes where function impacts fitness.

59 BASIC BIOLOGICAL SCIENCES↗