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NASA NTRS2011

High Level Architecture Distributed Space System Simulation for Simulation Interoperability Standards Organization Simulation Smackdown

Modeling and Simulation plays a very important role in mission design. It not only reduces design cost, but also prepares astronauts for their mission tasks. The SISO Smackdown is a simulation event that facilitates modeling and simulation in academia. The scenario of this year s Smackdown was to simulate a lunar base supply mission. The mission objective was to transfer Earth supply cargo to a lunar base supply depot and retrieve He-3 to take back to Earth. Federates for this scenario include the environment federate, Earth-Moon transfer vehicle, lunar shuttle, lunar rover, supply depot, mobile ISRU plant, exploratory hopper, and communication satellite. These federates were built by teams from all around the world, including teams from MIT, JSC, University of Alabama in Huntsville, University of Bordeaux from France, and University of Genoa from Italy. This paper focuses on the lunar shuttle federate, which was programmed by the USRP intern team from NASA JSC. The shuttle was responsible for provide transportation between lunar orbit and the lunar surface. The lunar shuttle federate was built using the NASA standard simulation package called Trick, and it was extended with HLA functions using TrickHLA. HLA functions of the lunar shuttle federate include sending and receiving interaction, publishing and subscribing attributes, and packing and unpacking fixed record data. The dynamics model of the lunar shuttle was modeled with three degrees of freedom, and the state propagation was obeying the law of two body dynamics. The descending trajectory of the lunar shuttle was designed by first defining a unique descending orbit in 2D space, and then defining a unique orbit in 3D space with the assumption of a non-rotating moon. Finally this assumption was taken away to define the initial position of the lunar shuttle so that it will start descending a second after it joins the execution. VPN software from SonicWall was used to connect federates with RTI during testing and the Smackdown event. HLA software from Pitch Technology and MAK Technology were used to edit and extend FOM and provide HLA services for federation execution. The SISO Smackdown event for 2011 was held in Boston, Massachusetts. The federation execution lasted for one hour, and the event was very successful in catching the attention of university students and faculties.

Li, Zuqun↗
NASA NTRS2024

Enabling the Assimilation of CrIS Shortwave Infrared Observations in Global NWP at NOAA. Part I: Background and Methods

Radiance observations from Earth-observing satellites have a significant positive impact on numerical weather prediction (NWP) forecasts, but some spectral regions are not fully exploited. Observations from hyperspectral infrared (IR) sounders in the longwave region (650-1100 cm -1 ), for instance, are routinely assimilated in many NWP models, but observations in the shortwave region (2155-2550 cm -1 ) are not. Each of these regions provides information on the temperature structure of the atmosphere, but the shortwave IR (SWIR) region is considered challenging to assimilate due to noise equivalent delta temperature (NEDT) that is highly variable depending on scene brightness temperature and to phenomena that are difficult to model, like non-Local Thermodynamic Equilibrium (NLTE) and solar reflectance. With recent advances in small-satellite technology, SWIR temperature sounders may provide an agile and cost-effective complement to the current constellation of IR sounders. Therefore, a better understanding of the use and impact of SWIR observations in data assimilation for NWP is warranted. In part one of this study, as presented here, the amount of unique information (as determined by Empirical Orthogonal Decomposition (EOD)) made available to a data assimilation system by Cross-track Infrared Sounder (CrIS) SWIR observations is reviewed, recent advancements to the Community Radiative Transfer Model (CRTM) for the simulation of CrIS shortwave radiances are tested, and enhancements to NOAA’s Global Data Assimilation System (GDAS) for the assimilation of CrIS SWIR observations are implemented and evaluated. Part two of this study, which seeks to assess the value of assimilating shortwave IR observations in global NWP, is also introduced.

Erin Jones↗
DOE OSTI2023

Barium stars as tracers of s -process nucleosynthesis in AGB stars: II. Using machine learning techniques on 169 stars

Barium (Ba) stars are characterised by an abundance of heavy elements made by the slow neutron capture process (s-process). This peculiar observed signature is due to the mass transfer from a stellar companion, bound in a binary stellar system, to the Ba star observed today. The signature is created when the stellar companion is an asymptotic giant branch (AGB) star. We aim to analyse the abundance pattern of 169 Ba stars using machine learning techniques and the AGB final surface abundances predicted by the FRUITY and Monash stellar models. We developed machine learning algorithms that use the abundance pattern of Ba stars as input to classify the initial mass and metallicity of each Ba star’s companion star using stellar model predictions. We used two algorithms. The first exploits neural networks to recognise patterns, and the second is a nearest-neighbour algorithm that focuses on finding the AGB model that predicts the final surface abundances closest to the observed Ba star values. In the second algorithm, we included the error bars and observational uncertainties in order to find the best-fit model. The classification process was based on the abundances of Fe, Rb, Sr, Zr, Ru, Nd, Ce, Sm, and Eu. We selected these elements by systematically removing s-process elements from our AGB model abundance distributions and identifying the elements whose removal had the biggest positive effect on the classification. We excluded Nb, Y, Mo, and La. Our final classification combined the output of both algorithms to identify an initial mass and metallicity range for each Ba star companion. With our analysis tools, we identified the main properties for 166 of the 169 Ba stars in the stellar sample. The classifications based on both stellar sets of AGB final abundances show similar distributions, with an average initial mass of M = 2.23 M ⊙ and 2.34 M ⊙ and an average [Fe/H] = –0.21 and –0.11, respectively. We investigated why the removal of Nb, Y, Mo, and La improves our classification and identified 43 stars for which the exclusion had the biggest effect. We found that these stars have statistically significant and different abundances for these elements compared to the other Ba stars in our sample. We discuss the possible reasons for these differences in the abundance patterns.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2022

Simultaneous Retrievals of Biomass Burning Aerosols and Trace Gases From the Ultraviolet to Near-Infrared Over Northern Thailand During the 2019 Pre-Monsoon Season

With the advent of spaceborne spectroradiometers in a geostationary constellation, measuring high spectral resolution ultraviolet–visible (UV-VIS) and selected near-/shortwave-infrared (NIR/SWIR) radiances can enable the probing of the life cycle of key atmospheric trace gases and aerosols at higher temporal resolutions over the globe. The UV-VIS measurements are important for retrieving several key trace gases (e.g., O 3 , SO 2 , NO 2 , and HCHO) and particularly for deriving aerosol characteristics (e.g., aerosol absorption and vertical profile). This study examines the merit of simultaneous retrievals of trace gases and aerosols using a ground-based spectroradiometer covering the UV-NIR to monitor their physicochemical processes and to obtain reliable aerosol information for various applications. During the 2019 pre-monsoon season over northern Thailand, we deployed a ground-based SMART–s (Spectral Measurements for Atmospheric Radiative Transfer–spectroradiometer) instrument, which is an extended-range Pandora with reliable radiometric calibration in the 330–820 nm range, to retrieve remotely sensed chemical and aerosol properties for the first time near biomass burning sources. The high spectral resolution (∼ 1.0 nm full width half maximum with ∼ 3.7 × oversampling) of sun and sky measurements from SMART–s provides several key trace gases (e.g., O 3 , NO 2 , and H 2 O) and aerosol properties covering the UV where significant light absorption occurs by the carbonaceous particles. During the measurement period, highly correlated total column amounts of NO 2 and aerosol optical thickness (т aer ) retrieved from SMART–s (correlation coefficient, R=0.74) indicated their common emissions from biomass burning events. The SMART–s retrievals of the spectral single scattering albedo (ω 0 ) of smoke aerosols showed an abrupt decrease in the UV, which is an important parameter dictating photochemical processes in the atmosphere. The values of ω 0 and column precipitable water vapor (H 2 O) gradually increase with the mixing of biomass burning smoke particles and higher water vapor concentrations when approaching the monsoon season. The retrieved ω 0 and weighted mean radius of fine-mode aerosols from SMART–s showed positive correlations with the H 2 O (R=0.81 for ω 0 at 330 nm and 0.56 for the volume-weighted mean radius), whereas the real part of the refractive index of fine-mode aerosol (n f ) showed negative correlations (R = -0.61 at 330 nm), which suggest that aerosol aging processes including hygroscopic growth (e.g., humidification and cloud processing) can be a major factor affecting the temporal trends of aerosol optical properties. Retrieved n f and ω 0 were closer to those of the water droplet (i.e., n f of about 1.33 and ω 0 of about 1.0) under lower amounts of NO 2 during the measurement period; considering that the NO 2 amounts in the smoke may indicate the aging of the plume after emission due to its short lifetime, the tendency is also consistent with active hygroscopic processes of the aerosols over this area. Retrieved UV aerosol properties from SMART–s generally support the assumed smoke aerosol models (i.e., the spectral shape of aerosol absorption) used in NASA's current satellite algorithms, and their spectral ω 0 retrievals from ground and satellites showed good agreements (R = 0.73–0.79). However, temporal and spectral variabilities in the aerosol absorption properties in the UV emphasize the importance of a realistic optical model of aerosols for further improvements in satellite retrievals.

biomass burning↗
NASA NTRS2004

NASA's global differential GPS system and the TDRSS augmentation service for satellites

NASA is planning to launch a new service for Earth satellites providing them with precise GPS differential corrections and other ancillary information enabling decimeter level orbit determination accuracy, and nanosecond time-transfer accuracy, onboard, in real-time. The TDRSS Augmentation Service for Satellites (TASS) will broadcast its message on the S-band multiple access channel of NASA's Tracking and Data Relay Satellite System (TDRSS). The satellite's phase array antenna has been configured to provide a wide beam, extending coverage up to 1000 km altitude over the poles. Global coverage will be ensured with broadcast from three or more TDRSS satellites. The GPS differential corrections are provided by the NASA Global Differential GPS (GDGPS) System, developed and operated by NASA's Jet Propulsion Laboratory. The GDGPS System employs a global ground network of more than 70 GPS receivers to monitor the GPS constellation in real time. The system provides real-time estimates of the GPS satellite states, as well as many other real-time products such as differential corrections, global ionospheric maps, and integrity monitoring. The unique multiply redundant architecture of the GDGPS System ensures very high reliability, with 99.999% demonstrated since the inception of the system in Early 2000. The estimated real time GPS orbit and clock states provided by the GDGPS system are accurate to better than 20 cm 3D RMS, and have been demonstrated to support sub-decimeter real time positioning and orbit determination for a variety of terrestrial, airborne, and spaceborne applications. In addition to the GPS differential corrections, TASS will provide real-time Earth orientation and solar flux information that enable precise onboard knowledge of the Earth-fixed position of the spacecraft, and precise orbit prediction and planning capabilities. TASS will also provide 5 seconds alarms for GPS integrity failures based on the unique GPS integrity monitoring service of the GDGPS System.

Global Postitioning Satellite (GPS)↗
NASA NTRS2017

Hemispherical Optical Dome for Underwater Communication

For many years, acoustic systems have been used as the primary method for underwater communication; however, the data transfer rate of such systems is low because sound propagates slowly through the water. A higher throughput can be achieved using visible light to transmit data underwater. The first issue with using this approach is that there is generally a large loss of the light signal due to scattering and absorption in water even though there is an optimal wavelength for transmission in the blue or green wavelengths of the visible spectrum. The second issue is that a simple system consisting only of a highly directional source/transmitter and small optical detector/receiver has a very narrow field of view. The goal of this project is to improve an optical, underwater communication system by increasing the effective field of view of the receiving optics. To this end, we make two changes to the simple system: (1) An optical dome was added near the receiver. An array of lenses is placed radially on the surface of the dome, reminiscent of the compound eye of an insect. The lenses make the source and detector planes conjugate, and each lens adds a new region of the source plane to the instrument's total field of view. (2) The receiver was expanded to include multiple photodiodes. With these two changes, the receiver has much more tolerance to misalignments (in position and angle) of the transmitter.Two versions of the optical dome (with 6 and 8 diameters) were designed using the CREO CAD software and modeled using the CODE V optical design software. A series of these transparent hemispherical domes, with both design diameters, were manufactured using a 5-axis mill. The prototype was then retrofitted with lenses and compared with the computer-generated model to demonstrate the effectiveness of this solution. This work shows the dome design improves the optical field of view of the underwater communication system considerably. Furthermore, with the experimental test results, a geometric optimization model was derived providing insights to the design performance limits.

Underwater↗
NASA NTRS1986

ICE navigation support

The International Cometary Explorer (ICE) encounter with Comet Giacobini-Zinner took place 7 years after the spacecraft's original launch on 12 August 1978 as the International Sun Earth Explorer 3 (ISEE-3), part of a three-spacecraft project to study the interaction between the solar wind and the Earth's magnetosphere. Transfer to an interplanetary trajectory was performed via a 119-km-altitute, gravity-assist, lunar swingby on December 1983. Navigation support during interplanetary cruise and comet encounter was provided by orbit determination utilizing radio metric data from the DSN 64-meter antennas in Goldstone, California and Madrid, Spain. Orbit solutions yielding predictions of 50-km geocentric delivery accuracy in the target aim plane were achieved during interplanetary cruise and at comet encounter using 6-to-12-week data arcs between periodic attitude-change maneuvers. One-sigma two-way range and range rate residuals were consistently 40 meters and 0.2 mm/s or better, respectively. Non-gravitational forces affected the comet's motion during late August and early September 1985 and caused a 2300-km shift in the orbit of the comet relative to the spacecraft. This necessitated a final ICE orbit trim maneuver 3 days prior to encounter. Near-real-time assessment of two-way 2-GHz (S-band) Doppler pseudo-residuals during the June and July 1985 trajectory change maneuvers aided in calibration of the spacecraft's thrusters in preparation for this final critical maneuver. Post-flight analysis indicates tail centerline passage was achieved within 10 seconds of the predicted time and geocentric position uncertainty at encounter was less than 40 km.

Efron, L.↗
NASA NTRS1999

From the Rocket Equation to Maxwell's Equations: Electrodynamic Tether Propulsion Nears Space Test

The US space program is facing a growing challenge to its decades-long, global leadership position, as current launch costs consume valuable resources and limit achievements in science, exploration, and commercial development. More than 40% of projected launches over the next 10 years have payloads with intended destinations beyond low-Earth orbit. Therefore, more cost-effective upper stages and on-board propulsion systems are critical elements in reducing total space transportation costs. A new type of space propulsion, using electrodynamic tethers, may be capable of performing multiple sequential missions without resupply and have a potential usable lifetime of several years. They may provide an in-space infrastructure that has a very low life cycle cost and greatly enhanced mission flexibility, thus supporting the goal of reducing the cost of access to space. Electrodynamic tether thrusters work by virtue of the force the Earth's magnetic field exerts on a wire carrying an electrical current. The effect is the basis for electric motors and generators. The Propulsive Small Expendable Deployer System (ProSEDS) experiment, planned for launch in the summer of 2000, will demonstrate the use electrodynamic tether thrust by lowering the altitude of a Delta-H rocket's upper stage on which it will be flying. Applications of the technology include a passive deorbit system for spacecraft at their end-of-life, reusable Orbit Transfer Vehicles, propellantless reboost of the International Space Station, and propulsion and power generation for future missions to Jupiter.

Johnson, Les↗
NASA NTRS2017

Hemispherical Optical Dome for Underwater Communication

For many years, acoustic systems have been used as the primary method for underwater communication; however, the data transfer rate of such systems is low because sound propagates slowly through the water. A higher throughput can be achieved using visible light to transmit data underwater. The first issue with using this approach is that there is generally a large loss of the light signal due to scattering and absorption in water even though there is an optimal wavelength for transmission in the blue or green wavelengths of the visible spectrum. The second issue is that a simple system consisting only of a highly directional source transmitter and small optical detector receiver has a very narrow field of view. The goal of this project is to improve an optical, underwater communication system by increasing the effective field of view of the receiving optics. To this end, we make two changes to the simple system: (1) An optical dome was added near the receiver. An array of lenses is placed radially on the surface of the dome, reminiscent of the compound eye of an insect. The lenses make the source and detector planes conjugate, and each lens adds a new region of the source plane to the instrument's total field of view. (2) The receiver was expanded to include multiple photodiodes. With these two changes, the receiver has much more tolerance to misalignments (in position and angle) of the transmitter.Two versions of the optical dome (with 6 and 8 diameters) were designed using the CREO CAD software and modeled using the CODE V optical design software. A series of these transparent hemispherical domes, with both design diameters, were manufactured using a 5-axis mill. The prototype was then retrofitted with lenses and compared with the computer-generated model to demonstrate the effectiveness of this solution. This work shows the dome design improves the optical field of view of the underwater communication system considerably. Furthermore, with the experimental test results, a geometric optimization model was derived providing insights to the design performance limits.

Design↗
DOE OSTI2020

Early Career Paths at Los Alamos National Laboratory

We represent a selection of early career staff at LANL with backgrounds in mathematics. There are many possible paths to a position at LANL. The lab has very active graduate research and postdoctoral programs, and it is not uncommon for graduate students to become postdocs, who can then be “converted” to staff. Conversion from being a postdoc is not the only route to a position at LANL, nor is it a guarantee, but most of us did postdocs here before becoming staff. Being a postdoc here also gives you an idea of whether you’d like living in northern New Mexico, a rugged, beautiful, and somewhat remote area. It is important to say here that citizenship is not a requirement for many of the positions at the lab. The lab historically and currently welcomes investigators from all over the world. LANL offers a broad spectrum of mathematical challenges that are largely problem driven. Particularly to those who feel that academic mathematics can be stove-piped, with a focus on deep but not necessarily broad expertise, the LANL environment gives the flexibility to move and grow in many different directions. The lab encourages a team-based approach to problems, which not only enhances the breadth of our approach to solving problems, but also gives team members access to new fields. From the outside (academia), however, it can be difficult to see how fields map between academia and the lab. This is one of the reasons that having interaction with the lab as a graduate student or postdoc can be helpful in understanding if the environment would be a good match for you. An important advantage of working at the lab is our high visibility both in academia, as well as in industry and the government. Because of its mission-driven projects, LANL, and more broadly the Department of Energy Laboratories, help set research directions that are picked up by researchers in academia. For this reason, many lab staff have worked at LANL for a number of years, then have transferred into academia after having set the agenda for their field of expertise. Below, we will share some of our experiences, opinions, and reflections in order to give the reader a feel for our own early career experiences.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2014

Biomechanics of the Treadmill Locomotion on the International Space Station

Exercise prescriptions completed by International Space Station (ISS) crewmembers are typically based upon evidence obtained during ground-based investigations, with the assumption that the results of long-term training in weightlessness will be similar to that attained in normal gravity. Coupled with this supposition are the assumptions that exercise motions and external loading are also similar between gravitational environments. Normal control of locomotion is dependent upon learning patterns of muscular activation and requires continual monitoring of internal and external sensory input [1]. Internal sensory input includes signals that may be dependent on or independent of gravity. Bernstein hypothesized that movement strategy planning and execution must include the consideration of segmental weights and inertia [2]. Studies of arm movements in microgravity showed that individuals tend to make errors but that compensation strategies result in adaptations, suggesting that control mechanisms must include peripheral information [3-5]. To date, however, there have been no studies examining a gross motor activity such as running in weightlessness other than using microgravity analogs [6-8]. The objective of this evaluation was to collect biomechanical data from crewmembers during treadmill exercise before and during flight. The goal was to determine locomotive biomechanics similarities and differences between normal and weightless environments. The data will be used to optimize future exercise prescriptions. This project addresses the Critical Path Roadmap risks 1 (Accelerated Bone Loss and Fracture Risk) and 11 (Reduced Muscle Mass, Strength, and Endurance). Data were collected from 7 crewmembers before flight and during their ISS missions. Before launch, crewmembers performed a single data collection session at the NASA Johnson Space Center. Three-dimensional motion capture data were collected for 30 s at speeds ranging from 1.5 to 9.5 mph in 0.5 mph increments with a 12-camera system. During flight, each crewmember completed up to 6 data collection sessions spread across their missions, performing their normal exercise prescription for the test day, resulting in varying data collection protocols between sessions. Motion data were collected by a single HD video camera positioned to view the crewmembers' left side, and tape markers were placed on their feet, legs, and neck on specific landmarks. Before data collection, the crewmembers calibrated the video camera. Video data were collected during the entire exercise session at 30 Hz. Kinematic data were used to determine left leg hip, knee, and ankle range of motion and contact time, flight time, and stride time for each stride. 129 trials in weightlessness were analyzed. Mean time-normalized strides were found for each trial, and cross-correlation procedures were used to examine the strength and direction of relationships between segment movement pattern timing in each gravitational condition. Cross-correlation analyses between gravitational conditions revealed highly consistent movement patterns at each joint. Peak correlation coefficients occurred at 0% phase, indicating there were no lags in movement timing. Joint ranges of motion were similar between gravitational conditions, with some slight differences between subjects. Motion patterns in weightlessness were highly consistent at a given speed with those occurring in 1G, indicating that despite differing sensory input, subjects maintain running kinematics. The data suggest that individuals are capable of compensating for loss of limb weight when creating movement strategies. These results have important implications for creating training programs for use in weightlessness as practitioners can have greater confidence in running motions transferring across gravitational environments. Furthermore, these results have implications for use by researchers investigating motor control mechanisms and investigating hypotheses related to movement strategies when using sensory input that is dependent upon gravity.

DeWitt, John↗
DOE OSTI2026

CAHS: Context-Aware Homology Search

Protein homology search is foundational to bioinformatics: it supports annotation transfer, structure/function inference, and evolutionary analysis over rapidly expanding sequence repositories (e.g., UniProtKB). Profile hidden Markov models (pHMMs), as implemented in HMMER, remain the most widely trusted approach because they provide statistically calibrated E-values; however, their gap behavior is fixed once a profile is trained, despite biological evidence that insertion/deletion tolerance varies across flexible loops and intrinsically disordered regions. We present CAHS (Context-Aware Homology Search), a lightweight query-time adapter for pHMM search that incorporates learned and biologically motivated signals without changing HMMER's downstream search pipeline or its calibrated E-value reporting. Given a query sequence, CAHS computes per-residue representations from a protein language model and a disorder predictor, maps these to profile coordinates, and modulates only match-state transition rows (gap-open and gap-extension probabilities) while preserving Plan7 constraints. We comprehensively evaluate CAHS across six structurally diverse protein families and multi-domain architectures against a 570k-sequence target corpus. CAHS expands detection capability, retrieving thousands of additional remote homologs at relaxed thresholds by maintaining alignment quality through flexible regions. For multi-domain proteins, context-aware modulation resolves 94% of fragmented alignments. Crucially, CAHS preserves hit-set invariance at stringent operating points (E<10-10), demonstrating increased statistical confidence without inflating false positives. Furthermore, sharper statistical distinction between homologs and background noise during early filter stages yields up to a 3.87× acceleration in end-to-end wall-clock time on high-performance computing clusters. Overall, CAHS illustrates a practical AI-for-science design pattern: augmenting a trusted probabilistic model with query-specific learned signals to improve interpretable, reproducible inference in data-rich biology.

Bhattaram, Swethasree [Georgia Institute of Techno↗
NASA NTRS2003

Integrated Propulsion/Vehicle System Structurally Optimized

Ongoing research and testing are essential in the development of air-breathing hypersonic propulsion technology, and this year some positive advancement was made at the NASA Glenn Research Center. Recent work performed for GTX, a rocket-based combined-cycle, single-stage-to-orbit concept, included structural assessments of both the engine and flight vehicle. In the development of air-breathing engine technology, it is impractical to design and optimize components apart from the fully integrated system because tradeoffs must be made between performance and structural capability. Efforts were made to control the flight trajectory, for example, to minimize the aerodynamic heating effects. Structural optimization was applied to evaluate concept feasibility and was instrumental in the determination of the gross liftoff weight of the integrated system. Achieving low Earth orbit with even a small payload requires an aggressive approach to weight minimization through the use of lightweight, oxidation-resistant composite materials. Assessing the integrated system involved investigating the flight trajectory to determine where the critical load events occur in flight and then generating the corresponding environment at each of these events. Structural evaluation requires the mapping of the critical flight loads to finite element models, including the combined effects of aerodynamic, inertial, combustion, and other loads. NASA s APAS code was used to generate aerodynamic pressure and temperature profiles at each critical event. The radiation equilibrium surface temperatures from APAS were used to predict temperatures through the thickness. Heat transfer solutions using NASA's MINIVER code and the SINDA code (Cullimore & Ring Technologies, Littleton, CO) were calculated at selective points external to the integrated vehicle system and then extrapolated over the entire exposed surface. FORTRAN codes were written to expedite the finite element mapping of the aerodynamic heating effects for the internal structure.

Hunter, James E.↗
DOE OSTI2023

Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines

Climate change threatens Earth’s ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea ice conditions. We used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea ice brine, and underlying seawater, recovering 11,088 vOTUs (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg brine viruses were of marine origin yet distinct from either sea ice brine or seawater viruses, while 94% of sea ice brine viruses were also present in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred “active” vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacter in cryopeg and sea ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea ice environment, while many sea ice brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races. Our results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth’s destabilized and rapidly disappearing cryosphere.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Mapping the influence of ligand electronics on the spectroscopic and 1 O 2 sensitization characteristics of Pd( ii ) biladiene complexes bearing phenyl–alkynyl groups at the 2- and 18-positions

Photodynamic therapy (PDT) is a promising treatment for certain cancers that proceeds via sensitization of ground state 3 O 2 to generate reactive 1 O 2 . Classic macrocyclic tetrapyrrole ligand scaffolds, such as porphyrins and phthalocyanines, have been studied in detail for their 1 O 2 photosensitization capabilities. Despite their compelling photophysics, these systems have been limited in PDT applications because of adverse biological side effects. Conversely, the development of non-traditional oligotetrapyrrole ligands metalated with palladium (Pd[DMBil1]) have established new candidates for PDT that display excellent biocompatibility. Herein, the synthesis, electrochemical, and photophysical characterization of a new family of 2,18-bis(phenylalkynyl)-substituted Pd II 10,10-dimethyl-5,15-bis(pentafluorophenyl)-biladiene (Pd[DMBil2-R]) complexes is presented. These second generation biladienes feature extended conjugation relative to previously characterized Pd II biladiene scaffolds (Pd[DMBil1]). We show that these new derivatives can be prepared in good yield and, that the electronic nature of the phenylalkynyl appendages dramatically influence the Pd II biladiene photophysics. Extending the conjugation of the Pd[DMBil1] core through installation of phenylacetylene resulted in a ~75 nm red-shift of the biladiene absorption spectrum into the phototherapeutic window (600–900 nm), while maintaining the Pd II biladiene's steady-state spectroscopic 1 O 2 sensitization characteristics. Varying the electronics of the phenylalkyne groups via installation of electron donating or withdrawing groups dramatically influences the steady-state spectroscopic and photophysical properties of the resulting Pd[DMBil2-R] family of complexes. The most electron rich variants (Pd[DMBil2-N(CH3)2]) can absorb light as far red as ~700 nm but suffer from significantly reduced ability to sensitize formation of 1 O 2 . By contrast, Pd[DMBil2-R] derivatives bearing electron withdrawing functionalities (Pd[DMBil2-CN] and Pd[DMBil2-CF3]) display 1 O 2 quantum yields above 90%. The collection of results we report suggest that excited state charge transfer from more electron-rich phenyl-alkyne appendages to the electron deficient biladiene core circumvents triplet sensitization. The spectral and redox properties, as well as the triplet sensitization efficiency of each Pd[DMBil2-R] derivative is considered in relation to the Hammett value (σp) for each biladiene's R-group. More broadly, the results reported in this study clearly demonstrate that biladiene redox properties, spectral properties, and photophysics can be perturbed greatly by relatively minor alterations to biladiene structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Quantitative and three-dimensional assessment of holdup material

Nuclear material deposited in equipment, transfer lines, and ventilation systems of a processing facility is usually referred to as holdup. Operators need to know the location and amount of holdup in their facility for radiation safety and material accountability. In this work, we propose to use an array of detectors co-axial to the inspected pipe to measure the holdup material. This method is implementable into an automated system capable of crawling on surfaces and pipes of various curvatures, which would enable faster, easier, and more accurate holdup safeguards measurements. We first demonstrated that the current holdup assay procedure could lead to a non-negligible bias in the estimate of special nuclear material mass, due to the simplified assumption of deposited geometry introduced by the Generalized Geometry Holdup (GGH) model. The new approach consists of imaging the inner holdup material by characterizing the detector array’s response and unfolding it from the measured light output. Our experimental proof of principle consists of three NaI(Tl) detectors surrounding an aluminum pipe containing two cesium-137 ( 137 Cs) sources. We derived the source distribution inside the pipe by first calculating the detector response matrix using a method adaptive to the surface geometry of the object containing the measured holdup material. Creating a matrix of the detector array’s measured counts, we then proceed to solve an inverse problem, resulting in an accurately located source position and activity distribution within the response matrix’s spatial resolution. Furthermore, we then developed a simulated model of the envisioned experimental setup, which accurately described both the activity and position of the source in 2D. Finally, we extended our model onto a discretized three-dimensional model of the system, encompassing 36 detectors. The model was simulated to measure the source distribution and activity of multiple sources in pipes of varied geometries, which could then be conveniently translated to a real-time holdup measurement protocol. For the 3D simulation of four different source geometries, the model accurately localized the source position in 3D, while the activity retained a maximum relative error of ±5.32%.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
NASA NTRS2012

Calculation of the Frequency Distribution of the Energy Deposition in DNA Volumes by Heavy Ions

Radiation quality effects are largely determined by energy deposition in small volumes of characteristic sizes less than 10 nm representative of short-segments of DNA, the DNA nucleosome, or molecules initiating oxidative stress in the nucleus, mitochondria, or extra-cellular matrix. On this scale, qualitatively distinct types of molecular damage are possible for high linear energy transfer (LET) radiation such as heavy ions compared to low LET radiation. Unique types of DNA lesions or oxidative damages are the likely outcome of the energy deposition. The frequency distribution for energy imparted to 1-20 nm targets per unit dose or particle fluence is a useful descriptor and can be evaluated as a function of impact parameter from an ions track. In this work, the simulation of 1-Gy irradiation of a cubic volume of 5 micron by: 1) 450 (1)H(+) ions, 300 MeV; 2) 10 (12)C(6+) ions, 290 MeV/amu and 3) (56)Fe(26+) ions, 1000 MeV/amu was done with the Monte-Carlo simulation code RITRACKS. Cylindrical targets are generated in the irradiated volume, with random orientation. The frequency distribution curves of the energy deposited in the targets is obtained. For small targets (i.e. <25 nm size), the probability of an ion to hit a target is very small; therefore a large number of tracks and targets as well as a large number of histories are necessary to obtain statistically significant results. This simulation is very time-consuming and is difficult to perform by using the original version of RITRACKS. Consequently, the code RITRACKS was adapted to use multiple CPU on a workstation or on a computer cluster. To validate the simulation results, similar calculations were performed using targets with fixed position and orientation, for which experimental data are available [5]. Since the probability of single- and double-strand breaks in DNA as function of energy deposited is well know, the results that were obtained can be used to estimate the yield of DSB, and can be extended to include other targeted or non-target effects.

Plante, Ianik↗
DOE OSTI2021

Realization of a high luminosity muon beam at the Jefferson Lab

The proton is the major component of the visible matter of our universe, so being able to determine its fundamental properties, such as its charge radius, is of vital importance. In recent years, several experiments have been performed for the accurate measurement of the proton radius with different experimental techniques. The main and most common are based on two different techniques: ep scattering and Lamb shift spectroscopy of regular hydrogen atoms. The latter can also be performed on muonic hydrogen atoms with a significant improvement in accuracy. Recent measurements that use this method have highlighted a discrepancy between the results obtained with the diffusion of electrons and those obtained with the spectroscopic technique leading to the so-called ?proton radius puzzle?. The explanation of why this difference between the measured values exists is still a matter of discussion. The last attempt to address the puzzle was the PRad Experiment. It was performed with a unique experimental setup that gave the scientists an excellent control on the systematic errors that are usually present in electron-proton scattering experiments. This has significantly increased the precision of the measurement, bringing it in the same area as the spectroscopic ones done on muonic hydrogen atoms, which are considered the most precise. However, to solve the puzzle once and for all, even more precise electron scattering measurements are needed. Alternatively, new methods can be used, such as eg. muon-proton scattering at low transferred momenta in order to lower the systematic errors that comes with the measurement. This thesis tries to address this problem by studying the set up of an intense muon beam at the Jefferson Laboratory (JLab) that can be used to carry out a high-precision m ? p scattering experiment. Using Montecarlo simulations I studied the muon production resulting from the interaction of the primary electron beam with the beam-dump at JLab Hall-A. The simulations were performed using the FLUKA package via the FLAIR graphical interface. In this study, I modified an existing geometry (built for the ?Beam Dump eXperiment?) and performed several studies in order to optimize the muon beam parameters. In order to estimate the beam intensity, I studied the muon generation and transportation through the concrete bunker surrounding the Hall-A beam-dump. Detailed studies on muon attenuation and dispersion at different depth allowed me to track the beam profile in space and momentum as a function of the distance from the beam-dump. Last, but not least, I studied a possible tagging system for the muon beam. The tagging system will allow us to know with good precision (O(1=1000)) the energy of each muon of the beam. Based on the results obtained, I created an event generator that incorporates the detailed description of the muon beam (energy, position, emittance) useful to define and optimize the experimental setup for a future measurement of the proton radius at the JLab.

Fulci, Antonino↗