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

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At least 127 records · Page 7

Three-dimensional structure-guided evolution of a ribosome with tethered subunits

We report RNA-based macromolecular machines, such as the ribosome, have functional parts reliant on structural interactions spanning sequence-distant regions. These features limit evolutionary exploration of mutant libraries and confound three-dimensional structure-guided design. To address these challenges, we describe Evolink (evolution and linkage), a method that enables high-throughput evolution of sequence-distant regions in large macromolecular machines, and library design guided by computational RNA modeling to enable exploration of structurally stable designs. Using Evolink, we evolved a tethered ribosome with a 58% increased activity in orthogonal protein translation and a 97% improvement in doubling times in SQ171 cells compared to a previously developed tethered ribosome, and reveal new permissible sequences in a pair of ribosomal helices with previously explored biological function. The Evolink approach may enable enhanced engineering of macromolecular machines for new and improved functions for synthetic biology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ab Initio Many Body Quantum Embedding and Local Correlation in Crystalline Materials using Interpolative Separable Density Fitting

We present an efficient implementation of ab initio many-body quantum embedding and local correlation methods for infinite periodic systems through translational symmetry adapted interpolative separable density fitting, an approach which reduces the scaling of the calculations to only linear with the number of k-points. Employing this methodology, we compute correlated ground-state coupled cluster energies within density matrix embedding and local natural orbital correlation frameworks for both weakly and strongly correlated solids, using up to 1000 k-points. By extrapolating the local correlation domains and k-point sampling we further obtain estimates of the full coupled cluster with singles, doubles, and perturbative triples ground-state energies in the thermodynamic limit.

Chemical Physics (physics.chem-ph)↗

CFL Optimized Forward–Backward Runge–Kutta Schemes for the Shallow-Water Equations

Abstract We present the formulation and optimization of a Runge–Kutta-type time-stepping scheme for solving the shallow-water equations, aimed at substantially increasing the effective allowable time step over that of comparable methods. This scheme, called FB-RK(3,2), uses weighted forward–backward averaging of thickness data to advance the momentum equation. The weights for this averaging are chosen with an optimization process that employs a von Neumann–type analysis, ensuring that the weights maximize the admittable Courant number. Through a simplified local truncation error analysis and numerical experiments, we show that the method is at least second-order in time for any choice of weights and exhibits low dispersion and dissipation errors for well-resolved waves. Further, we show that an optimized FB-RK(3,2) can take time steps up to 2.8 times as large as a popular three-stage, third-order strong stability-preserving Runge–Kutta method in a quasi-linear test case. In fully nonlinear shallow-water test cases relevant to oceanic and atmospheric flows, FB-RK(3,2) outperforms SSPRK3 in admittable time step by factors roughly between 1.6 and 2.2, making the scheme approximately twice as computationally efficient with little to no effect on solution quality. Significance Statement The purpose of this work is to develop and optimize time-stepping schemes for models relevant to oceanic and atmospheric flows. Specifically, for the shallow-water equations we optimize for schemes that can take time steps as large as possible while retaining solution quality. We find that our optimized schemes can take time steps between 1.6 and 2.2 times larger than schemes that cost the same number of floating point operations, translating directly to a corresponding speedup. Our ultimate goal is to use these schemes in climate-scale simulations.

54 ENVIRONMENTAL SCIENCES↗

Logic-based analysis of gene expression data predicts association between TNF, TGFB1 and EGF pathways in basal-like breast cancer

For breast cancer, clinically important subtypes are well characterized at the molecular level in terms of gene expression profiles. In addition, signaling pathways in breast cancer have been extensively studied as therapeutic targets due to their roles in tumor growth and metastasis. However, it is challenging to put signaling pathways and gene expression profiles together to characterize biological mechanisms of breast cancer subtypes since many signaling events result from post-translational modifications, rather than gene expression differences. We designed a logic-based computational framework to explain the differences in gene expression profiles among breast cancer subtypes using Pathway Logic and transcriptional network information. Pathway Logic is a rewriting-logic-based formal system for modeling biological pathways including post-translational modifications. Our method demonstrated its utility by constructing subtype-specific path from key receptors (TNFR, TGFBR1 and EGFR) to key transcription factor (TF) regulators (RELA, ATF2, SMAD3 and ELK1) and identifying potential association between pathways via TFs in basal-specific paths, which could provide a novel insight on aggressive breast cancer subtypes. Lastly, codes and results are available at http://epigenomics.snu.ac.kr/PL/.

59 BASIC BIOLOGICAL SCIENCES↗

IBM Open Science Price - SWAP Gate Challenge

On November 30, 2020, IBM announced an open science price competition aimed at improving the fidelity of a SWAP gate on their 7 qubit Quantum system named ”Casablanca”. The details of the SWAP gate problem was outlined in a Jupyter notebook, which utilizes the IBM developed open source package Qiskit. The participants were allowed to work in teams with up to five people and restricted to only use open source software in solving the problem. Their results were due on April 16, 2021. Our approach to solving the SWAP gate challenge is based on the quantum optimal control techniques implemented in our open source packages Juqbox.jl and Quandary. The results from the optimal control approach is only as good as the accuracy in the description of the quantum system dynamics, characterized by a Hamiltonian model that was provided by IBM. Based on the calibrated control pulses IBM provide for the standard gate set, we developed a reverse engineering approach to calibrate our computational model. Techniques were developed to translate between Qiskit’s pulse representation and the B-spline formulation used in Juqbox and Quandary. The fidelity of the optimized pulse sequences were estimated using Qiskit’s randomized bench marking techniques.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Thermal Protection System to Enable Ice Giant Aerocapture Mission for Delivering Both an Orbiter and an In Situ Probe

The Ice Giants have been identified as high priority science destinations in the last Decadal Survey [1] and could benefit from aerocapture as the primary method for orbit insertion [2]. A mass-efficient aerocapture system will enable the delivery of an orbiter along with an atmospheric probe (for in situ measurements to anchor global data collected by the orbiter) and possibly a lander at Triton [3]. Aerocapture could be executed either using low L/D rigid aeroshell with lift modulation (LMA) [4] or using deployable aeroshell using drag modulation (DMA) [3]. Nearly two decades ago, a NASA-funded team performed Neptune-Triton aerocapture studies with a mid-L/D lifting configuration [5] for achieving orbit using LMA. This study showed aerocapture challenges. Due to very high peak entry conditions combined with very high heat-load, a suite of TPS materials was required and this suite was deemed problematic from a qualification perspective, due test facility limitations. In the past 20 years, progress made in GN&C for lift-guided entry missions such as MSL, Orion EFT1, Mars 2020 and the upcoming Artemis missions, and the expertise in blunt body aerodynamics at large scale (~ 5m) has led the EDL community to conclude that aerocapture is a “go do” engineering activity and most technologies are in hand to propose missions with aerocapture [6] [7]. Aerocapture using DMA, currently in development, is an option for Ice Giant Missions. While DMA is simpler in some sense, due to ballistic entry and no need for lift-guided maneuvering, it has challenges and it’s maturity is lower. LMA and DMA both require one or more ablative Thermal Protection System (TPS) materials for the rigid aeroshell element. The ablative TPS needs to be robust and mass efficient due to the high heat loads and size of the rigid aeroshell. Currently, there are capable ablative thermal protection materials, e.g., Heatshield for Extreme Entry Environments Technology (HEEET), 3-D woven Mid-Density Carbon- Phenolic (3MDCP), and PICA (Phenolic-Impregnated Carbon Ablator) that are mature, i.e., at TRL 6 or higher. NASA also invested in Conformal PICA that was matured to TRL 5. Our goal is to evaluate the applicability of high TRL TPS and consider other design options. We first establish bounding aerocapture trajectories for a wide range of arrival conditions and the associated aerothermal environment. Based on the environments, we then determine the predicted TPS mass for the aeroshell [4]. In this presentation, we will outline the process by which we establish bounding aerocapture trajectories for hyperbolic excess velocities ranging from 27 km/s to 35 km/s, which are shown to be a range of velocities that can reduce the trip time from ~14 years to 8 years. The above velocity range translates to ~12 km/s to ~24 km/s arrival velocities at the planetary entry interface [2]. The velocity reduction required to achieve orbit ranges between ~2.5 km/s to 9.5 km/s for both Neptune and Triton. Propulsive insertion alone, due to the amount of fuel required to achieve the required velocity reduction, limits the science returned [2]. We establish the bounding aerocapture trajectories for a low L/D (~ 0.4) configuration for three different ballistic coefficients. The ballistic coefficient range is determined from three different aeroshell diameters of 3m, 4m and 5m and with an entry system mass of 2200 kg. With the above range of design parameters, we then determine conservative/bounding estimates of aerothermal environments by using a combination of CFD simulations and stagnation point heating estimates [7]. This engineering approach allows us to first assess the TPS need vs. TPS capability and determine the applicability of existing TPS. Once an applicable suite of TPS is determined, the TPS thickness and mass are computed. We show that the TPS mass fraction can be as low as 5% to as high as 20%, depending on total trip time reduction and other design parameters for a range of TPS. This is a large range for TPS mass fraction. We show PICA and HEEET can indeed enable aerocapture missions, but the missions incur a mass penalty. TPS mass savings, can be further reduced with the use of conformal PICA. Advancing the development of Conformal PICA to make it robust across the entire aerothermal environment (peak heat-flux, pressure and shear) range will result in TPS mass fractions of < 10% for Ice Giant aerocapture missions such as the Neptune-Triton mission. Aerocapture allows for not only shortening the trip time but enables larger mass to be placed in orbit. Furthermore, probes deployed from orbit will benefit in reduced entry environments allowing for a lower risk TPS implementation as compared to mission designs where the probe is released prior to orbit insertion. One of the challenges for the Ice Giant community is to ensure mission designs that maximize science and allow flexibility in the placement of the entry probe. The traditional approach to release the probe ahead of the orbiter may not optimize returned science. In this presentation, we will make the case for mature TPS such as HEEET and PICA. While these materials can enable aerocapture missions, completing the development of conformal PICA and extending Conformal PICA to be more robust, will have significant impact to TPS mass efficiency and significantly enhance science return for future Gas- and Ice-Giant missions.

E Venkatapathy↗

Cooperative Research and Development Agreement With Georgetown University Report: National Institutes of Health, National Center for Advancing Translational Sciences Clinical and Translational Science Award

Oak Ridge National Laboratory (ORNL) is participating with Georgetown University (GU) as a subrecipient in response to the National Institutes of Health (NIH), National Center for Advancing Translational Sciences (NCATS) Clinical and Translational Science Award (CTSA) (U54 Clinical Trial Optional) funding opportunity announcement. This Cooperative Research and Development Agreement is put in to place to facilitate the development and implementation of clinical interventions that demonstrably improve human health is currently a complex, recursive, and inefficient process that leads to delays of years or decades before discoveries in biomedical research result in health benefits for patients and communities. NCATS conducts and supports research in the science of translation, to discover the mechanistic and operational principles of the intervention development and dissemination process, thereby providing the scientific foundation for improvements in translational efficiency that will accelerate the realization of interventions that improve human health. Under NCATS’ leadership, the CTSA Program supports a national network of medical research institutions called hubs. GU is the lead institution in one of the NIH hubs that was created as a result of a previous NIH CTSA. The missions of the GU have historically included the advancement of health through research in the clinical and biomedical sciences, the education of future leaders in medical and nursing practice and academia, and the provision of compassionate and scientifically competent patient care and service to the Washington, DC community and the nation. GU is the lead institution for the Georgetown-Howard Universities Center for Clinical and Translational Science (GHUCCTS), a multi-institutional partnership of medical research institutions forged from a desire to promote clinical research and translational science. Through multiple collaborations among these institutions, GHUCCTS is transforming clinical research and translational science in order to bring new scientific advances to health care. Oak Ridge National Laboratory is the Department of Energy's (DOE) largest science and energy laboratory. Managed since April 2000 by a partnership of the University of Tennessee and Battelle, ORNL was established in 1943 as a part of the secret Manhattan Project to pioneer a method for producing and separating plutonium. During the 1950s and 1960s, ORNL became an international center for the study of nuclear energy and related research in the physical and life sciences. With the creation of DOE in the 1970s, ORNL's mission broadened to include a variety of energy technologies and strategies. Today the laboratory supports the nation with a peacetime science and technology mission that is just as important as, but very different from, its role during the Manhattan Project. ORNL is home to the world's premier center for high performance supercomputing to enable scientific discovery. ORNL has extensive expertise in various areas of computer science that are uniquely situated to support GU. Additionally, ORNL’s leading computational user facilities present a unique opportunity to leverage the largest scale machines for open science in support of the stated mission of the NCATS CTSA. ORNL's partnership with GU will offer unparalleled opportunity in data analytics, deep-learning, artificial intelligence, and urban dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

Towards understanding particle rigid-body motion during solid-state sintering

A quantitative understanding of particle rigid body (RB) motion that inherently accompanies grain boundary (GB) diffusion is highly desirable to understand and control the dynamic interplay between coarsening and densification during solid state sintering. In this work, by computer simulation using a multi-phase-field approach, we analyze systematically the roles played by each of these processes at different stages of the shrinkage of the internal pore in a three-particle green body as a function of particle size as well as thermodynamic and kinetic factors of interfaces. We demonstrate that particle RB translation promotes both neck growth, and pore rounding and shrinkage. Moreover, the forces acting at GBs and pulling neighboring particles towards one another dynamically evolve as particles fuse. In contrast, particle RB rotation has no contribution to pore shrinkage. The translational force acting on an individual particle varies with not only its size, but also the number and sizes of its neighboring particles.

36 MATERIALS SCIENCE↗

Influence of Data Acquisition Algorithms on X-ray Phase Contrast Imaging Computed Tomography

X-ray phase contrast imaging (XPCI) is a non-destructive evaluation technique that enables high-contrast detection of low-attenuation materials that are largely transparent in traditional radiography. Extending a grating based Talbot-Lau XPCI system to three- dimensional imaging with computed tomography (CT) imposes two motion requirements: the analyzer grating must translate transverse to the optical axis to capture image sets for XPCI reconstruction, and the sample must rotate to capture angular data for CT reconstruction. The acquisition algorithm choice determines the order of movement and positioning of the two stages. The choice of image acquisition algorithm for XPCI CT is instrumental to collecting high fidelity data for reconstruction. We investigate how data acquisition influences XPCI CT by comparing two simple data acquisition algorithms and determine that capturing a full phase-stepping image set for a CT projection before rotating the sample results in higher quality data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A Web of Data Analytics Services

Cloud Computing has become the ubiquitous approach to our Big Data challenge. However, one will quickly discover that moving (a.k.a. forklifting) existing on-premise data analytics solutions to the Cloud doesn’t always translate to costing saving and performance boost. The Cloud’s elasticity, its availability, and its wide selection of computing options and selections of costing models making Cloud an attractive environment to tackle our Big Data challenge. The fact is Cloud, on its own, is not the silver bullet to our daunting challenge need for analyze and derive scientific inferences through vast collections of multi-sensor measurements. We would like to have all scientific data in one easy to access environment, but getting the world of scientific data in one analytic system is immensely difficult to achieve. This paper describes the data analytics web architecture NASA is developing by infusing instances of Integrated Data Analytics systems next to the data. The goal is to minimize unnecessary data movement through collection of data access and analytics webservices for researchers to interact with and analyze measurements without have to download data to their local computer. These services are RESTful and provisioned by the data centers with the help from subject matter and science experts. These services encapsulate the physical computing infrastructure, which could local computing cluster, on-premise or public Cloud environment.

Huang, Thomas↗

A Geometric Volume of Fluid-Based Multiphase Flow Solver Extension to the Reacting Flow Solver, PeleLM

A new algorithm is presented to simulate multiphase flows with surface tension in a pathway for spray combustion simulation. The algorithm combines capabilities from two open-source packages, including the interface reconstruction library (IRL), a library of computational geometry routines to enable the volume of fluid (VOF) method, and PeleLM, a solver for the reacting Navier-Stokes equations. Additionally, surface tension is implemented using the continuum surface force (CSF) model with an improved height function technique in the volume fraction field. Spurious errors in volume fraction arising from our combined strategy are corrected through a topology-based method that improves both numerical stability and accuracy. Multiple validation simulations are conducted, including (i) translations and rotations of Zalesak's disk, (ii) a stationary circular droplet with surface tension, (iii) an oscillating elliptical droplet, and (iv) three-dimensional deformation of a spherical droplet. Results indicate that the combined scheme retains the favorable properties of each of the component algorithms.

42 ENGINEERING↗

Elucidating Quintet-State Dynamics in Singlet Fission Oligomers and Polymers with Tetracene Pendants

To unlock the potential of molecular engineering for practical quantum sensing and computing, it is essential to create and control pure magnetic states in molecular systems. Singlet fission (SF) in organic materials offers a promising approach by generating pairs of triplet excited states from photoexcited singlets. Here, in this work, we investigate SF in a polymer with strategically positioned tetracene pendant groups along a polynorbornene backbone and its oligomeric counterparts, facilitating intrapolymer through-space coupling. Using continuous-wave and pulsed time-resolved electron paramagnetic resonance (EPR) spectroscopy, we elucidate the spin dynamics and identify key intermediates, including the quintet state, that emerge during SF. Our findings reveal that exciton translational motion along the pendant groups enhances the dissociation of triplet pairs, with oligomer length playing a critical role in modulating spin state interconversion and exciton transport. Our results provide key insights into the SF mechanism in polymeric materials and highlight the role of oligomer length in modulating spin state interconversion and exciton transport. This work advances our understanding of SF in polymers, paving the way for their application in quantum information science and energy conversion technologies.

Bindra, Jasleen K. [Argonne National Laboratory (A↗

Next-generation electronics by co-design with chalcogenide materials

As Moore’s law approaches its limits, chalcogenides offer a promising route to next-generation computing and sensing, thanks to their topological, magnetoelectric, excitonic, and spintronic properties. Yet the same traits that make them appealing, e.g., exotic properties at monolayer thickness, clean van der Waals interfaces, and strong many-body effects, also heighten sensitivity to fabrication, hindering translation into scalable devices. Progress is further constrained by fragmented knowledge across synthesis, processing, and integration, and by the lack of systematic links between fabrication parameters and performance metrics. This Perspective examines key obstacles in controlling chalcogenide heterostructures and stresses the need for an integrated co-design framework, uniting materials growth, processing, and device architecture to accelerate practical technologies.

36 MATERIALS SCIENCE↗

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↗

SchrödingerNet: A Universal Neural Network Solver for the Schrödinger Equation

Recent advances in machine learning have facilitated numerically accurate solution of the electronic Schrödinger equation (SE) by integrating various neural network (NN)-based wave function ansatzes with variational Monte Carlo methods. Nevertheless, such NN-based methods are all based on the Born–Oppenheimer approximation (BOA) and require computationally expensive training for each nuclear configuration. In this work, we propose a novel NN architecture, SchrödingerNet, to solve the full electronic-nuclear SE by defining a loss function designed to equalize local energies across the system. This approach is based on a translationally, rotationally and permutationally symmetry-adapted total wave function ansatz that includes both nuclear and electronic coordinates. Furthermore, this strategy not only allows for an efficient and accurate generation of a continuous potential energy surface at any geometry within the well-sampled nuclear configuration space, but also incorporates non-BOA corrections, through a single training process. Comparison with benchmarks of atomic and small molecular systems demonstrates its accuracy and efficiency.

Chemical calculations↗

Structural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch

T-box riboswitches are unique riboregulators where gene regulation is mediated through interactions between two highly structured RNAs. Despite extensive structural insights, how RNA-RNA interactions drive the folding and structural transitions of T-box to achieve functional conformations remains unclear. Here, by combining SAXS, single-molecule FRET and computational modeling, we elaborate the folding energy landscape of a translational T-box aptamer consisting of stems I, II and IIA/B, which Mg 2+ -induced global folding and tRNA binding are cooperatively coupled. smFRET measurements reveal that high Mg 2+ stabilizes IIA/B and its stacking on II, which drives the pre-docking of I and II into a competent conformation, subsequent tRNA binding promotes docking of I and II to form a high-affinity tRNA binding groove, of which the essentiality of IIA/B and S-turn in II is substantiated with mutational analysis. We highlight a delicate balance among Mg 2+ , the intra- and intermolecular RNA-RNA interactions in modulating RNA folding and function.

59 BASIC BIOLOGICAL SCIENCES↗

BASIN-3D Data Integration for Selected ARM Data Field Campaign Report

The purpose of this data services request was to demonstrate integration of the Atmospheric Radiation Measurement (ARM) User Facility’s “met” datastreams with time series data from other earth science data sources using the BASIN-3D data synthesis software tool. BASIN-3D is an open-source Python library that enables researchers to integrate data across configured public and private data sources. It provides a common query language for researchers to request measurement locations and time series data based on specified locations, variables, time period, statistics, aggregation, and data quality. BASIN-3D acquires the data that match the query from each configured data source and translates the results into harmonized vocabularies, thus reducing researchers' data-wrangling effort. In addition, because the queries are executed on demand, researchers can easily regenerate their synthesized data sets as new data and/or data updates become available, eliminating one-off data products. BASIN-3D can output data using a variety of different data structures for end-user applications including Python pandas data frames and hdf5 output formats.

54 ENVIRONMENTAL SCIENCES↗

Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation

Abstract Riboswitches are structured RNA motifs that recognize metabolites to alter the conformations of downstream sequences, leading to gene regulation. To investigate this molecular framework, we determined crystal structures of a preQ1-I riboswitch in effector-free and bound states at 2.00 Å and 2.65 Å-resolution. Both pseudoknots exhibited the elusive L2 loop, which displayed distinct conformations. Conversely, the Shine-Dalgarno sequence (SDS) in the S2 helix of each structure remained unbroken. The expectation that the effector-free state should expose the SDS prompted us to conduct solution experiments to delineate environmental changes to specific nucleobases in response to preQ1. We then used nudged elastic band computational methods to derive conformational-change pathways linking the crystallographically-determined effector-free and bound-state structures. Pathways featured: (i) unstacking and unpairing of L2 and S2 nucleobases without preQ1—exposing the SDS for translation and (ii) stacking and pairing L2 and S2 nucleobases with preQ1—sequestering the SDS. Our results reveal how preQ1 binding reorganizes L2 into a nucleobase-stacking spine that sequesters the SDS, linking effector recognition to biological function. The generality of stacking spines as conduits for effector-dependent, interdomain communication is discussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus ribosome sensor.

59 BASIC BIOLOGICAL SCIENCES↗