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DOE OSTI2024

Network of epistatic interactions in an enzyme active site revealed by large-scale deep mutational scanning

Cooperative interactions between amino acids are critical for protein function. A genetic reflection of cooperativity is epistasis, which is when a change in the amino acid at one position changes the sequence requirements at another position. To assess epistasis within an enzyme active site, we utilized CTX-M β-lactamase as a model system. CTX-M hydrolyzes β-lactam antibiotics to provide antibiotic resistance, allowing a simple functional selection for rapid sorting of modified enzymes. We created all pairwise mutations across 17 active site positions in the β-lactamase enzyme and quantitated the function of variants against two β-lactam antibiotics using next-generation sequencing. Context-dependent sequence requirements were determined by comparing the antibiotic resistance function of double mutations across the CTX-M active site to their predicted function based on the constituent single mutations, revealing both positive epistasis (synergistic interactions) and negative epistasis (antagonistic interactions) between amino acid substitutions. The resulting trends demonstrate that positive epistasis is present throughout the active site, that epistasis between residues is mediated through substrate interactions, and that residues more tolerant to substitutions serve as generic compensators which are responsible for many cases of positive epistasis. Additionally, we show that a key catalytic residue (Glu166) is amenable to compensatory mutations, and we characterize one such double mutant (E166Y/N170G) that acts by an altered catalytic mechanism. These findings shed light on the unique biochemical factors that drive epistasis within an enzyme active site and will inform enzyme engineering efforts by bridging the gap between amino acid sequence and catalytic function.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Cell‐type‐specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems

SUMMARY Bioenergy sorghum is a low‐input, drought‐resilient, deep‐rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4–5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell‐type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell‐type‐specific and cell‐preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell‐type‐specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell‐specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data ( https://mc‐lab.shinyapps.io/lcm‐dataset/ ).

09 BIOMASS FUELS↗

DOE OSTI2020

TEAL

TEAL is a financial performance calculator plugin for the RAVEN code, framework, resolving around the computation of Net Present Value and associated financial metrics. TEAL can make use of inflation rates, taxation, escalation factors, capital expenditure economy of scale scaling factors. The unique feature of TEAL is the capability to be linked with RAVEN external models and build corresponding cash flows using the variables computed by those external models. In addition to be able to use the capability to generate cash flows derived from complex physical models generated by RAVEN, another distinctive feature of TEAL is the capability to provide financial risk/probabilistic metrics that can empower RAVEN to perform optimization/analysis driven by financial risk augmentations. Optimization, robust optimization, parametric studies, large parallel simulations, sensitivity analysis, data mining, etc. are just some of the capabilities that can be leveraged.

Alfonsi, Andrea↗

DOE OSTI2023

Fabrication of single color centers in sub-50 nm nanodiamonds using ion implantation

Diamond color centers have been widely studied in the field of quantum optics. The negatively charged silicon vacancy (SiV – ) center exhibits a narrow emission linewidth at the wavelength of 738 nm, a high Debye–Waller factor, and unique spin properties, making it a promising emitter for quantum information technologies, biological imaging, and sensing. In particular, nanodiamond (ND)-based SiV – centers can be heterogeneously integrated with plasmonic and photonic nanostructures and serve as in vivo biomarkers and intracellular thermometers. Out of all methods to produce NDs with SiV – centers, ion implantation offers the unique potential to create controllable numbers of color centers in preselected individual NDs. However, the formation of single color centers in NDs with this technique has not been realized. We report the creation of single SiV– centers featuring stable high-purity single-photon emission through Si implantation into NDs with an average size of ~20 nm. We observe room temperature emission, with zero-phonon line wavelengths in the range of 730–800 nm and linewidths below 10 nm. Our results offer new opportunities for the controlled production of group-IV diamond color centers with applications in quantum photonics, sensing, and biomedicine.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Round 3 Update of Stress Testing Results for Organic Light-Emitting Diode Panels and Luminaires

Organic light-emitting diode (OLED) sources are a potential solid-state lighting technology for use in indoor lighting applications. Some of the advantages offered by OLEDs include thin profiles, low glare, diffuse lighting, and unique form factors. The U.S. Department of Energy (DOE) has released six technical reports focused on OLED technologies to provide information and analysis to the lighting industry. These reports include the evaluation of two different field deployment sites, a market analysis, a tear-down analysis, and two independent assessments of the performance of select commercially available OLED products. This report builds on earlier DOE efforts with OLED technology by updating information about previously benchmarked commercial OLED products. Specifically, this report provides updated findings about the robustness and reliability of commercial OLED products.

42 ENGINEERING↗

DOE OSTI2022

Emerging Role of Exosomal Long Non-coding RNAs in Spaceflight-Associated Risks in Astronauts

During spaceflight, astronauts are exposed to multiple unique environmental factors, particularly microgravity and ionizing radiation, that can cause a range of harmful health consequences. Over the past decades, increasing evidence demonstrates that the space environment can induce changes in gene expression and RNA processing. Long non-coding RNA (lncRNA) represent an emerging area of focus in molecular biology as they modulate chromatin structure and function, the transcription of neighboring genes, and affect RNA splicing, stability, and translation. They have been implicated in cancer development and associated with diverse cardiovascular conditions and associated risk factors. However, their role on astronauts’ health after spaceflight remains poorly understood. In this perspective article, we provide new insights into the potential role of exosomal lncRNA after spaceflight. We analyzed the transcriptional profile of exosomes isolated from peripheral blood plasma of three astronauts who flew on various Shuttle missions between 1998–2001 by RNA-sequencing. Computational analysis of the transcriptome of these exosomes identified 27 differentially expressed lncRNAs with a Log 2 fold change, with molecular, cellular, and clinical implications.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1984

An invariant derivation of flame stretch

The flame stretch factor is derived using an invariant formulation in a consistent manner. The derived generalized expression has two terms and completely describes the flame area evolution with its movement. One term represents the stretch due to the nonuniform tangential velocity field and the other represents the effect of the curvature of the propagating flame. The effect of curvature for stationary flames is implicitly included in the former term through variations of the tangential velocity. The flame sheet assumption, and thereby the stretch factor, are uniquely defined. Another expression is derived under the assumption that the tangential velocity of the flame equals the tangential component of the fluid velocity.

Chung, S. H.↗

NASA NTRS1992

Implications of isotopic compositions of N and Ne in the Martian atmosphere to temporal evolution of its atmosphere and regolith

The isotopic compositions of N and Ne in the Martian atmosphere are governed by several factors, principal among which are the temporal evolution in (1) the absolute surface pressure of oxygen, (2) the physicochemical characteristics of the regolith, and finally (3) the N-15 enrichment expected due to preferential hydrodynamical escape of N-14 (due to solar wind bombardment). Each of these factors is unique to Mars. In fact, no other planet offers the uniquely favorable situations for N-15 and Ne-21 enrichments. The cosmogenic production of N-15 is, in particular, unique. It promises to provide very valuable constraints on the temporal evolution of the martian CO2 and H2O, both in the atmosphere and regolith. The rate of production of cosmogenic (spallation) N-15 is dependent on the surface pressure of oxygen, the principal target element for formation of N-15. In view of the relatively high O/N ratio in the martian atmosphere, relatively high N-15/N ratio are expected to arise from cosmogenic reactions. The added bonus comes from the fact that an appreciable production of N-15 is expected in the martian regolith because of its thin atmosphere. From model calculations it is shown that if accurate isotopic composition data become available for N and Ne, it should be possible to put robust constraints on the time averages martian oxygen surface pressure and subsurface water in the upper layers.

Lal, D.↗

NASA NTRS2016

The Cognitive Challenges of Flying a Remotely Piloted Aircraft

A large variety of Remotely Piloted Aircraft (RPA) designs are currently in production or in development. These aircraft range from small electric quadcopters that are flown close to the ground within visual range of the operator, to larger systems capable of extended flight in airspace shared with conventional aircraft. Before RPA can operate routinely and safely in civilian airspace, we need to understand the unique human factors associated with these aircraft. The task of flying an RPA in civilian airspace involves challenges common to the operation of other highly-automated systems, but also introduces new considerations for pilot perception, decision-making, and action execution. RPA pilots participated in focus groups where they were asked to recall critical incidents that either presented a threat to safety, or highlighted a case where the pilot contributed to system resilience or mission success. Ninety incidents were gathered from focus-groups. Human factor issues included the impact of reduced sensory cues, traffic separation in the absence of an out-the-window view, control latencies, vigilance during monotonous and ultra-long endurance flights, control station design considerations, transfer of control between control stations, the management of lost link procedures, and decision-making during emergencies. Some of these concerns have received significant attention in the literature, or are analogous to human factors of manned aircraft. The presentation will focus on issues that are poorly understood, and have not yet been the subject of extensive human factors study. Although many of the reported incidents were related to pilot error, the participants also provided examples of the positive contribution that humans make to the operation of highly-automated systems.

remote pilot station↗

NASA NTRS2016

An Optimized Multicolor Point-Implicit Solver for Unstructured Grid Applications on Graphics Processing Units

In the field of computational fluid dynamics, the Navier-Stokes equations are often solved using an unstructuredgrid approach to accommodate geometric complexity. Implicit solution methodologies for such spatial discretizations generally require frequent solution of large tightly-coupled systems of block-sparse linear equations. The multicolor point-implicit solver used in the current work typically requires a significant fraction of the overall application run time. In this work, an efficient implementation of the solver for graphics processing units is proposed. Several factors present unique challenges to achieving an efficient implementation in this environment. These include the variable amount of parallelism available in different kernel calls, indirect memory access patterns, low arithmetic intensity, and the requirement to support variable block sizes. In this work, the solver is reformulated to use standard sparse and dense Basic Linear Algebra Subprograms (BLAS) functions. However, numerical experiments show that the performance of the BLAS functions available in existing CUDA libraries is suboptimal for matrices representative of those encountered in actual simulations. Instead, optimized versions of these functions are developed. Depending on block size, the new implementations show performance gains of up to 7x over the existing CUDA library functions.

Zubair, Mohammad↗

NASA NTRS2016

The Human Challenges of Remotely Piloted Aircraft Systems

Remotely Piloted Aircraft (RPA) range from small electric quadcopters that are flown close to the ground within visual range of the operator, to larger systems capable of extended flight in airspace shared with conventional aircraft. Before RPA can operate routinely and safely in civilian airspace, we need to understand the unique human factors associated with these aircraft. RPA pilots participated in focus groups where they were asked to recall critical incidents that either presented a threat to safety, or highlighted a case where the pilot contributed to system resilience or mission success. Ninety incidents were gathered from focus-groups. Human factor issues included the impact of reduced sensory cues, traffic separation in the absence of an out-the-window view, control latencies, vigilance during monotonous and ultra-long endurance flights, control station design considerations, transfer of control between control stations, the management of lost link procedures, and decision-making during emergencies. Some of these concerns have received significant attention in the literature, or are analogous to human factors of manned aircraft. Although many of the reported incidents were related to pilot error, the participants also provided examples of the positive contribution that humans make to the operation of highly-automated systems.

Hobbs, Alan↗

NASA NTRSDate not supplied

Cryogenic Insulation Solutions for the Surface of Mars with Its Unique Environments

The surface of Mars provides unique challenges for cryogenic insulation systems and for cryogenic spacecraft traveling there. In order to store cryogenic fluids for propulsion, life support, and other applications on the surface of Mars one must protect the insulation from the array of unique environmental factors that are present. Travel to Mars is a very energy intensive endeavor and landing on the surface requires launching over 200 kg of propellant and spacecraft per kilogram landed. As such, high performance, lightweight insulations are needed for cryogenic systems to be used on the surface. Traditional spacecraft use multilayer insulation that works well in a vacuum, but Mars has an atmospheric of pressure approximately 7 torr, consisting of approximately 95 % carbon dioxide. Based on analysis and trade studies NASA has shown that the mass savings from the higher performance of multilayer insulation with a vacuum jacket saved several hundred kilograms of mass for a typical human Mars ascent stage. Thus NASA, along with several contractors, have been developing a lightweight vacuum jacketed system for the 7 torr environment. This lightweight vacuum jacketed system must survive launch from earth, travel to Mars, and on the surface for several years. On the surface, it must be able to survive landing, natural environmental occurrences such as dust storms, and temperature cycling with minimal if any human maintenance. The insulation systems under development have been exposed to an array of tests to demonstrate their capability to survive these environments while still providing the high performance required to meet mission needs.

Cryogenic Fluid Management↗

NASA NTRS1982

NECAP 4.1: NASA's Energy Cost Analysis Program thermal response factor routine

A thermal response factor is described and calculation sequences and flowcharts for RESFAC2 are provided. RESFAC is used by NASA's (NECAP) to calculate hourly heat transfer coefficients (thermal response factors) for each unique delayed surface. NECAP uses these response factors to compute each spaces' hourly heat gain/loss.

Weise, M. R.↗

NASA NTRSDate not supplied

Quantitative Analysis of Spaceflight Drug Stability Data to Support a Predictive Pharmaceutical Testing Strategy

To systematically quantify the time-dependent effect of spaceflight on active pharmaceutical ingredient (API) degradation, data were extracted from available published and unpublished spaceflight drug stability studies. Seven studies were identified that investigated the stability of individual medications following storage aboard crewed spacecraft. Medications stored for up to 2.4 years in low earth orbit (LEO) show limited change in API potency that, in all cases, falls within 10% of matched terrestrial controls, and within 5% of controls for the most drugs. This investigation shows that spaceflight is associated with a ~1.5-fold increase in the degradation rate relative to lot-matched terrestrial controls. Spaceflight is associated with an increased probability of drug failure over time; however, the incremental increase in degradation risk associated with spaceflight is minor compared to the baseline risk associated with terrestrial controls. Since most drugs across all NASA-supported studies were repackaged solid oral formulations that had been removed from protective manufacturer packaging, it is likely that prolonged exposure to atmospheric factors during both terrestrial and spaceflight treatments is a key contributor to degradation. Unique spaceflight environmental factors, particularly ionizing radiation and elevated CO2, may contribute to the additional cumulative effect of spaceflight. The results of this study show that the effect of spaceflight on drug stability is minor relative to the terrestrial baseline; however, the degradation rate and time-dependent failure of terrestrial controls highlights an extremely critical need to evaluate the effect of current repackaging methods and development of operationally appropriate methods to protected repackaged solid oral medications from environmental factors that mediate degradation.

J F Reichard↗

NASA NTRS2022

Unique NISTAR-Based Climate GCM Diagnostics of the Earth’s Planetary Albedo and Spectral Absorption Through Longitudinal Data Slicing

Deep Space Climate Observatory (DSCOVR) measurements of Earth’s reflected solar and emitted thermal radiation permit a unique model/data comparison perspective that is not readily available from other satellite data. The key factor is the unique Lissajous orbital viewing geometry from the Lagrangian L1 point, which enables a continuous view of Earth’s sunlit hemisphere. The National Institute of Standards and Technology Advanced Radiometer (NISTAR) is the DSCOVR Mission energy budget instrument, which views the reflected and emitted radiation of the Earth’s sunlit hemisphere by means of single pixel active cavity full-spectrum (Band-A, 0.2–100 μm) and filtered solar wavelength (Band-B, 0.2–4.0 μm; and Band-C, 0.7–4.0 μm) radiometer measurements. An additional solar wavelength photodiode channel (0.3–1.1 μm) provides a calibration reference. The objective of this study is the assessment of climate GCM performance via direct model/data comparisons. Such comparisons are difficult due to quasi-chaotic natural variability present in real-world observational data and in climate GCM simulations. This is where the unique DSCOVR viewing geometry makes possible the longitudinal data slicing methodology for more direct model/data comparison. The key point of the longitudinal slicing approach is that data integration over the entire sunlit hemisphere eliminates the quasi-chaotic meteorological weather-scale noise, while preserving intra-seasonal and planetary-scale variability. The rotation of the Earth that retrieves this climate-style, large-scale longitudinal and seasonal variability. The hemispheric averaging is accomplished automatically in NISTAR measurements with its single-pixel view of the Earth. For climate GCMs, this requires implementing the Sunlit Hemisphere Sampling (SHS) scheme to operate on the GCM run-time output data, utilizing the DSCOVR Satellite Ephemeris data to assure precise viewing geometry between NISTAR measurements and GCM output data, while averaging out the meteorological weather noise. However, GCM generated data are radiative fluxes, while NISTAR (and EPIC) measurements are near-backscattered radiances. Conversing NISTSR measurements into radiative fluxes cannot be accomplished using NISTAR data alone, even with detailed support from conventional satellite data. But the identical viewing geometry of Earth’s sunlit hemisphere, and synergistic analyses of EPIC data make it feasible for this conversion of NISTAR near-backscatter radiances into radiative fluxes.

deep space climate observatory↗

NASA NTRS2023

Sleep Issues in Aviation and Space

This article describes the factors that cause sleep issues in aviation and spaceflight. There are many causes of sleep disruption that are common to both domains, including, irregular schedules, circadian misalignment, and inadequate sleep environment. There are also factors that are unique to each type of operation that may lead to the manifestation of sleep disorders among these populations. Each of these factors, and their subsequent impact on sleep, are reviewed in this article.

Astronaut↗

NASA NTRS1999

Statistical Analysis of Complexity Generators for Cost Estimation

Predicting the cost of cutting edge new technologies involved with spacecraft hardware can be quite complicated. A new feature of the NASA Air Force Cost Model (NAFCOM), called the Complexity Generator, is being developed to model the complexity factors that drive the cost of space hardware. This parametric approach is also designed to account for the differences in cost, based on factors that are unique to each system and subsystem. The cost driver categories included in this model are weight, inheritance from previous missions, technical complexity, and management factors. This paper explains the Complexity Generator framework, the statistical methods used to select the best model within this framework, and the procedures used to find the region of predictability and the prediction intervals for the cost of a mission.

Rowell, Ginger Holmes↗

NASA NTRS2004

Space Biology and Medicine: Health, Performance, and Safety of Space Crews - Volume 4

Volume IV is devoted to examining the medical and associated organizational measures used to maintain the health of space crews and to support their performance before, during, and after space flight. These measures, collectively known as the medical flight support system, are important contributors to the safety and success of space flight. The contributions of space hardware and the spacecraft environment to flight safety and mission success are covered in previous volumes of the Space Biology and Medicine series. In Volume IV, we address means of improving the reliability of people who are required to function in the unfamiliar environment of space flight as well as the importance of those who support the crew. Please note that the extensive collaboration between Russian and American teams for this volume of work resulted in a timeframe of publication longer than originally anticipated. Therefore, new research or insights may have emerged since the authors composed their chapters and references. This volume includes a list of authors' names and addresses should readers seek specifics on new information. At least three groups of factors act to perturb human physiological homeostasis during space flight. All have significant influence on health, psychological, and emotional status, tolerance, and work capacity. The first and most important of these factors is weightlessness, the most specific and radical change in the ambient environment; it causes a variety of functional and structural changes in human physiology. The second group of factors precludes the constraints associated with living in the sealed, confined environment of spacecraft. Although these factors are not unique to space flight, the limitations they entail in terms of an uncomfortable environment can diminish the well-being and performance of crewmembers in space. The third group of factors includes the occupational and social factors associated with the difficult, critical nature of the crewmembers' work: the risks involved in space flight, changes in circadian rhythms, and intragroup interactions. The physical and emotional stress and fatigue that develop under these conditions also can disturb human health and performance. In addition to these factors, the risk also exists that crewmembers will develop various illnesses during flight. The risk of illness is no less during space flight than on Earth, and may actually be greater for some classes of diseases.

Dietlein, Lawrence F.↗