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DOE OSTI2019

Folding and Assembly of Short α, β, γ -Hybrid Peptides: Minor Variations in Sequence and Drastic Differences in Higher-Level Structures

Multilevel protein structures typically involve polypeptides of sufficient lengths. Here we report the folding and assembly of seven short tetrapeptides sharing the same types of α-, β-, and aromatic γ-amino acid residues. These are two sets of hybrid peptides, with three members in one set and four in the other, having complementary hydrogen-bonding sequences that were hypothesized to pair into linear H-bonded duplexes. However, instead of undergoing the anticipated pairing, the initially examined three oligomers, 1 and 2a or 2b, differing only in their central αβ hybrid dipeptide sequence, do not associate with each other and exhibit distinctly different folding behavior. Experiments based on NMR and mass spectrometry, along with computational studies and systematic inference, reveal that oligomer 1 folds into an expanded β-turn containing an unusual hybrid α/β-amino acid sequence composed of glycine and β-alanine, two α- and β-amino acid residues that are conformationally most flexible, and peptides 2a and 2b adopt a noncanonical, extended helical conformation and dimerize into double helices undergoing rapid conformational exchange or helix inversion. The different central dipeptide sequences, αβ vs βα, result in drastically different intramolecular H-bonding patterns that are responsible for the observed folding behavior of 1 and 2. The revealed turn and double helix have few natural or synthetic counterparts, and provide novel and unique folding prototypes based on which chiral α- and β-amino acids are incorporated. The resultant derivatives 1a, 1b, 2c, and 2d follow the same folding and assembling behavior and demonstrate the generality of this system with the formation of expanded β-turns and double helices with enhanced folding stabilities, hampered helix inversion, as well as defined and dominant helical sense. This work has demonstrated the unique capability of synthetic foldamers in generating structures with fascinating folding and assembling behavior. As a result, the revealed systems offer ample opportunity for further structural optimization and applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1975

NASTRAN maintenance and enhancement experiences

The current capability is described which includes isoparametric elements, optimization of grid point sequencing, and eigenvalue routine. Overlay and coding errors were corrected for cyclic symmetry, transient response, and differential stiffness rigid formats. Error corrections and program enhancements are discussed along with developments scheduled for the current year and a brief description of analyses being performed using the program.

Schmitz, R. P.↗

DOE OSTI2023

DeCOIL: Optimization of Degenerate Codon Libraries for Machine Learning-Assisted Protein Engineering

With advances in machine learning (ML)-assisted protein engineering, models based on data, biophysics, and natural evolution are being used to propose informed libraries of protein variants to explore. Synthesizing these libraries for experimental screens is a major bottleneck, as the cost of obtaining large numbers of exact gene sequences is often prohibitive. Degenerate codon (DC) libraries are a cost-effective alternative for generating combinatorial mutagenesis libraries where mutations are targeted to a handful of amino acid sites. However, existing computational methods to optimize DC libraries to include desired protein variants are not well suited to design libraries for ML-assisted protein engineering. To address these drawbacks, we present DEgenerate Codon Optimization for Informed Libraries (DeCOIL), a generalized method which directly optimizes DC libraries to be useful for protein engineering: to sample protein variants that are likely to have both high fitness and high diversity in the sequence search space. Using computational simulations and wet-lab experiments, we demonstrate that DeCOIL is effective across two specific case studies, with potential to be applied to many other use cases. DeCOIL offers several advantages over existing methods, as it is direct, easy-to-use, generalizable, and scalable. With accompanying software, DeCOIL can be readily implemented to generate desired informed libraries.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Heterophase fcc-2H-fcc gold nanorods

The crystal phase-based heterostructures of noble metal nanomaterials are of great research interest for various applications, such as plasmonics and catalysis. However, the synthesis of unusual crystal phases of noble metals still remains a great challenge, making the construction of heterophase noble metal nanostructures difficult. Here, we report a one-pot wet-chemical synthesis of well-defined heterophase fcc-2H-fcc gold nanorods (fcc: face-centred cubic; 2H: hexagonal close-packed with stacking sequence of "AB") at mild conditions. Single particle-level experiments and theoretical investigations reveal that the heterophase gold nanorods demonstrate a distinct optical property compared to that of the conventional fcc gold nanorods. Moreover, the heterophase gold nanorods possess superior electrocatalytic activity for the carbon dioxide reduction reaction over their fcc counterparts under ambient conditions. First-principles calculations suggest that the boosted catalytic performance stems from the energetically favourable adsorption of reaction intermediates, endowed by the unique heterophase characteristic of gold nanorods.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Cut site preference allows influenza A virus PA-X to discriminate between host and viral mRNAs

Many viruses block host gene expression to take over the infected cell. This process, termed host shutoff, is thought to promote viral replication by preventing antiviral responses and redirecting cellular resources to viral processes. Several viruses from divergent families accomplish host shutoff through RNA degradation by endoribonucleases. However, viruses also need to ensure expression of their own genes. The influenza A virus endoribonuclease PA-X solves this problem by sparing viral mRNAs and some host RNAs necessary for viral replication. Here, to understand how PA-X distinguishes between RNAs, we characterized PA-X cut sites transcriptome-wide using 5' rapid amplification of complementary DNA ends coupled to high-throughput sequencing. This analysis, along with RNA structure predictions and validation experiments using reporters, shows that PA-Xs from multiple influenza strains preferentially cleave RNAs at GCUG tetramers in hairpin loops. Importantly, GCUG tetramers are enriched in the human but not the influenza transcriptome. Moreover, optimal PA-X cut sites inserted in the influenza A virus genome are quickly selected against during viral replication in cells. This finding suggests that PA-X evolved these cleavage characteristics to preferentially target host over viral mRNAs in a manner reminiscent of cellular self versus non-self discrimination.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations

Subsurface microbial communities mediate the transformation and fate of redox sensitive materials including organic matter, metals and radionuclides. Few studies have explored how changing geochemical conditions influence the composition of groundwater microbial communities over time. We temporally monitored alterations in abiotic forces on microbial community structure using 1L in-field bioreactors receiving background and contaminated groundwater at the Oak Ridge Reservation, TN. Planktonic and biofilm microbial communities were initialized with background water for 4 days to establish communities in triplicate control reactors and triplicate test reactors and then fed filtered water for 14 days. On day 18, three reactors were switched to receive filtered groundwater from a contaminated well, enriched in total dissolved solids relative to the background site, particularly chloride, nitrate, uranium, and sulfate. Biological and geochemical data were collected throughout the experiment, including planktonic and biofilm DNA for 16S rRNA amplicon sequencing, cell counts, total protein, anions, cations, trace metals, organic acids, bicarbonate, pH, Eh, DO, and conductivity. We observed significant shifts in both planktonic and biofilm microbial communities receiving contaminated water. This included a loss of rare taxa, especially amongst members of the Bacteroidetes, Acidobacteria, Chloroflexi, and Betaproteobacteria, but enrichment in the Fe- and nitrate- reducing Ferribacterium and parasitic Bdellovibrio. These shifted communities were more similar to the contaminated well community, suggesting that geochemical forces substantially influence microbial community diversity and structure. These influences can only be captured through such comprehensive temporal studies, which also enable more robust and accurate predictive models to be developed.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Microreactor Assembly Transportation Cask Model Description for Criticality Safety Validation Basis Assessment

Criticality safety analyses are completed on a transportation cask used for microreactor assembly shipment to provide an example of model and analysis to industry for reproducing this type of study on their microreactor fuel shipment. The fuel assembly considered is based on a gas-cooled microreactor (GC-MR), which utilizes HALEU fuel in the form of TRISO particles and utilizes various design options considered in industry designs. Various versions of this GC-MR assembly were studied, with and without YH2 moderator, providing similar conclusions. The shipment cask design is revised based on an existing design ES-3100, developed by Y-12 for the transport of highly enriched uranium (HEU), but is enlarged to hold the GC-MR fuel assembly. Criticality safety analysis for the cask/GC-MR fuel assembly package was performed using the CSAS6 sequence of SCALE6.3.2, utilizing the ENDF/B-VII.1 based continuous energy neutron library, and the analysis strictly follows the guideline from NRC reference reports. Different scenarios, e.g. normal operation, undamaged cask with water flooded, damaged cask with optimal water moderation, have been analyzed and it could be concluded the package would always have a large margin of subcriticality even packed in an infinite array. Sensitivity and similarity analyses are also performed using the TSUNAMI sequence of SCALE6.3.2, and the similarity analysis uses all the experiments from the ICSBEP Handbook with Intermediate and Mixed Enriched Uranium (IEU) and Low Enriched Uranium (LEU) systems together with additional ones that are sponsored by the DNCSH program. These similarity analyses indicate that dry cases have no similar benchmark experiments (ck values greater than 0.8), which may become problematic if more assemblies are shipped together (or a fully loaded core is shipped) and margin to criticality is reduced. However, the damaged cask models with flooded assemblies exhibited similarities to many experiments with ck values greater than 0.8.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2026

Microreactor Assembly Transportation Cask Model Description for Criticality Safety Validation Basis Assessment (Rev. 3)

Criticality safety analyses are completed on a transportation cask used for microreactor assembly shipment to provide an example of model and analysis to industry for reproducing this type of study on their microreactor fuel shipment. The fuel assembly considered is based on a gas-cooled microreactor (GC-MR), which utilizes HALEU fuel in the form of TRISO particles and utilizes various design options considered in industry designs. Various versions of this GC-MR assembly were studied, with and without YH 2 moderator, providing similar conclusions. The shipment cask design is revised based on an existing ES-3100 design, developed by Y-12 for the transport of highly enriched uranium (HEU), but is enlarged to hold the GC-MR fuel assembly. Criticality safety analysis for the cask/GC-MR fuel assembly package was performed using the CSAS6 sequence of SCALE6.3.2, utilizing the ENDF/B-VII.1 based continuous energy neutron library, and the analysis strictly follows the guideline from NRC reference reports. Different scenarios, e.g. normal operation, undamaged cask with water flooded, damaged cask with optimal water moderation, have been analyzed and it could be concluded the package would always have a large margin of subcriticality even packed in an infinite array. Sensitivity and similarity analyses are also performed using the TSUNAMI sequence of SCALE6.3.2, and the similarity analysis uses all the experiments from the ICSBEP Handbook with Highly Enriched Uranium (HEU), Intermediate and Mixed Enriched Uranium (IEU) and Low Enriched Uranium (LEU) systems, together with additional ones that are sponsored by the DNCSH program, and selected IRPhEP experiments using TRISO fuel and graphite moderator. These similarity analyses indicate that the dry nominal design has no similar benchmark experiments (ck values greater than 0.8), which may become problematic if more assemblies are shipped together (or a fully loaded core is shipped) and margin to criticality is reduced. However, the cask models with flooded assemblies exhibited similarities to many experiments with c k values greater than 0.8.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

NASA NTRS1980

Automation of the Mark 3 field system

The software and hardware components which will enable hands off operation are described. The operation of the field system begins with the scheduling of observations. An interactive program, SKED, provides displays of mutual visibility, automatic calculation of telescope slewing times, and the ability to list and edit the schedule. The output of SKED is a schedule file containing commands in the Standard Notation for Astronomy Procedures (SNAP) language which the field system uses for controlling events during the experiment. The most important features of SNAP include sophisticated time sequencing of events, automatic logging of all commands and responses, and the ability to define often used sequences of commands as procedures. A control program, BOSS, running in an HP 1000 minicomputer, reads the SNAP commands from a schedule file and interprets them in terms of commands and requests to devices. Interactive command input is possible through the operator's display terminal. Communication with all of the Mark 3 electronics modules is done via a small general purpose interface board (a microprocessor based ASCII transceiver) which has been installed in each module. Additional devices are controlled and monitored using the IEEE 488 General Purpose Interface Bus.

Vandenbere, N. R.↗

NASA NTRS1986

Automation, robotics, and inflight training for manned Mars missions

The automation, robotics, and inflight training requirements of manned Mars missions will be supported by similar capabilities developed for the space station program. Evolutionary space station onboard training facilities will allow the crewmembers to minimize the amount of training received on the ground by providing extensive onboard access to system and experiment malfunction procedures, maintenance procedures, repair procedures, and associated video sequences. Considerable on-the-job training will also be conducted for space station management, mobile remote manipulator operations, proximity operations with the Orbital Maneuvering Vehicle (and later the Orbit Transfer Vehicle), and telerobotics and mobile robots. A similar approach could be used for manned Mars mission training with significant additions such as high fidelity image generation and simulation systems such as holographic projection systems for Mars landing, ascent, and rendezvous training. In addition, a substantial increase in the use of automation and robotics for hazardous and tedious tasks would be expected for Mars mission. Mobile robots may be used to assist in the assembly, test and checkout of the Mars spacecraft, in the handling of nuclear components and hazardous chemical propellent transfer operations, in major spacecraft repair tasks which might be needed (repair of a micrometeroid penetration, for example), in the construction of a Mars base, and for routine maintenance of the base when unmanned.

Holt, Alan C.↗

NASA NTRS1988

Superfluid Helium On-Orbit Transfer (SHOOT) operatons

The in-flight tests and the operational sequences of the Superfluid Helium On-Orbit Transfer (SHOOT) experiment are outlined. These tests include the transfer of superfluid helium at a variety of rates, the transfer into cold and warm receivers, the operation of an extravehicular activity coupling, and tests of a liquid acquisition device. A variety of different types of instrumentation will be required for these tests. These include pressure sensors and liquid flow meters that must operate in liquid helium, accurate thermometry, two types of quantity gauges, and liquid-vapor sensors.

Kittel, P.↗

NASA NTRS1988

The Shuttle Imaging Spectrometer Experiment (SISEX)

The concept of the imaging spectrometer is becoming established as a major new thrust in remote sensing of the earth. For several years, JPL has operated the airborne imaging spectrometer on a NASA C-130; this instrument has demonstrated the direct identification of surface materials using imaging spectrometry. An advanced aircraft instrument, the airborne visible/infrared imaging spectrometer (AVIRIS), began operation on a NASA U-2 in 1987. The Shuttle Imaging Spectrometer Experiment (SISEX) was conceived as the next step in the sequence, and would provide a relatively inexpensive demonstration of the concept in earth orbit. This paper describes the design and development status of SISEX and the status of the enabling technology.

Herring, Mark↗

NASA NTRS1989

Superfluid Helium On-Orbit Transfer (SHOOT) operations

Kittel, P.↗

NASA NTRS1992

In-step Inflatable Antenna Experiment

The topics are presented in viewgraph form and include the following: potential space antenna applications; experiment objectives; experiment technical approach; experiment scenario; spartan services; experiment orbital configuration; experiment canister structure; surface measurement system configuration; and orbital functional sequences.

Veal, G.↗

NASA NTRS1998

PLUM: Parallel Load Balancing for Unstructured Adaptive Meshes

Dynamic mesh adaption on unstructured grids is a powerful tool for computing large-scale problems that require grid modifications to efficiently resolve solution features. Unfortunately, an efficient parallel implementation is difficult to achieve, primarily due to the load imbalance created by the dynamically-changing nonuniform grid. To address this problem, we have developed PLUM, an automatic portable framework for performing adaptive large-scale numerical computations in a message-passing environment. First, we present an efficient parallel implementation of a tetrahedral mesh adaption scheme. Extremely promising parallel performance is achieved for various refinement and coarsening strategies on a realistic-sized domain. Next we describe PLUM, a novel method for dynamically balancing the processor workloads in adaptive grid computations. This research includes interfacing the parallel mesh adaption procedure based on actual flow solutions to a data remapping module, and incorporating an efficient parallel mesh repartitioner. A significant runtime improvement is achieved by observing that data movement for a refinement step should be performed after the edge-marking phase but before the actual subdivision. We also present optimal and heuristic remapping cost metrics that can accurately predict the total overhead for data redistribution. Several experiments are performed to verify the effectiveness of PLUM on sequences of dynamically adapted unstructured grids. Portability is demonstrated by presenting results on the two vastly different architectures of the SP2 and the Origin2OOO. Additionally, we evaluate the performance of five state-of-the-art partitioning algorithms that can be used within PLUM. It is shown that for certain classes of unsteady adaption, globally repartitioning the computational mesh produces higher quality results than diffusive repartitioning schemes. We also demonstrate that a coarse starting mesh produces high quality load balancing, at a fraction of the cost required a fine initial mesh. Results indicate that our parallel load balancing strategy will remain viable on large numbers of processors.

Oliker, Leonid↗

NASA NTRS1996

Expectancy and Repetition in Task Preparation

We studied the mechanisms of task preparation using a design that pitted task expectancy against task repetition. In one experiment, two simple cognitive tasks were presented in a predictable sequence containing both repetitions and non-repetitions. The typical task sequence was AABBAABB. Occasional violations of this sequence allowed us to measure the effects of valid versus invalid expectancy. With this design, we were able to study the effects of task expectancy, task repetition, and interaction.

Ruthruff, E.↗

NASA NTRS2008

Differences and Similarities in MaCWAVE Summer and Winter Temperatures and Winds

Small meteorological rockets released inflatable falling spheres during the MaCWAVE Campaign. The Mountain and Convective Waves Ascending Vertically Experiment (MaCWAVE) was carried out in two parts, a summer sequence from Andoya Rocket Range (69N) during July 2002 to examine convective initiation of gravity waves and a winter sequence from ESRANGE (68N) during January 2003 to examine mountain-terrain initiated gravity waves. The sphere-tracked data provided significant information about the variation of temperature and wind from 70 km and above. The changes observed may be considered akin to tidal motion; unfortunately the launch activity was restricted to 12-hour periods, thus the observation of a full diurnal cycle was not possible. During summer, temperature variation was smaller than that observed during winter when peak to null differences reached 15-20 K at 80-85 km. Variation in the zonal winds varied up to 100+mps in summer and winter. Examination of the times of peak wind vs altitude showed that the peak zonal wind occurred approximately two hours ahead of the peak meridional wind. We provide details about the measurements and observed variations.

Schmidlin, F. J.↗

DOE OSTI2023

Whole genome sequencing of Mycobacterium bovis directly from clinical tissue samples without culture

Advancement in next generation sequencing offers the possibility of routine use of whole genome sequencing (WGS) for Mycobacterium bovis (M. bovis) genomes in clinical reference laboratories. To date, the M. bovis genome could only be sequenced if the mycobacteria were cultured from tissue. This requirement for culture has been due to the overwhelmingly large amount of host DNA present when DNA is prepared directly from a granuloma. To overcome this formidable hurdle, we evaluated the usefulness of an RNA-based targeted enrichment method to sequence M. bovis DNA directly from tissue samples without culture. Initial spiking experiments for method development were established by spiking DNA extracted from tissue samples with serially diluted M. bovis BCG DNA at the following concentration range: 0.1 ng/μl to 0.1 pg/μl (10 –1 to 10 –4 ). Library preparation, hybridization and enrichment was performed using SureSelect custom capture library RNA baits and the SureSelect XT HS2 target enrichment system for Illumina paired-end sequencing. The method validation was then assessed using direct WGS of M. bovis DNA extracted from tissue samples from naturally (n = 6) and experimentally (n = 6) infected animals with variable Ct values. Direct WGS of spiked DNA samples achieved 99.1% mean genome coverage (mean depth of coverage: 108×) and 98.8% mean genome coverage (mean depth of coverage: 26.4×) for tissue samples spiked with BCG DNA at 10 –1 (mean Ct value: 20.3) and 10 –2 (mean Ct value: 23.4), respectively. The M. bovis genome from the experimentally and naturally infected tissue samples was successfully sequenced with a mean genome coverage of 99.56% and depth of genome coverage ranging from 9.2× to 72.1×. The spoligoyping and M. bovis group assignment derived from sequencing DNA directly from the infected tissue samples matched that of the cultured isolates from the same sample. Our results show that direct sequencing of M. bovis DNA from tissue samples has the potential to provide accurate sequencing of M. bovis genomes significantly faster than WGS from cultures in research and diagnostic settings.

59 BASIC BIOLOGICAL SCIENCES↗