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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Semi-Dirac Fermions in a Topological Metal

Topological semimetals with massless Dirac and Weyl fermions represent the forefront of quantum materials research. In two dimensions, a peculiar class of fermions that are massless in one direction and massive in the perpendicular direction was predicted 16 years ago. These highly exotic quasiparticles—the semi-Dirac fermions—ignited intense theoretical and experimental interest but remain undetected. Using magneto-optical spectroscopy, we demonstrate the defining feature of semi-Dirac fermions— B 2 / 3 scaling of Landau levels—in a prototypical nodal-line metal ZrSiS. In topological metals, including ZrSiS, nodal lines extend the band degeneracies from isolated points to lines, loops, or even chains in the momentum space. With calculations and theoretical modeling, we pinpoint the observed semi-Dirac spectrum to the crossing points of nodal lines in ZrSiS. Crossing nodal lines exhibit a continuum absorption spectrum but with singularities that scale as B 2 / 3 at the crossing. Our work sheds light on the hidden quasiparticles emerging from the intricate topology of crossing nodal lines and highlights the potential to explore quantum geometry with linear optical responses. Published by the American Physical Society 2024

Shao, Yinming (ORCID:0000000228910028)↗
NASA NTRS1980

Rationale for evaluating a closed food chain for space habitats

Closed food cycles for long duration space flight and space habitation are examined. Wash water for a crew of six is economically recyclable after a week, while a total closed loop water system is effective only if the stay exceeds six months' length. The stoichiometry of net plant growth is calculated and it is shown that the return of urine, feces, and inedible plant parts to the food chain, along with the addition of photosynthesis, closes the food chain loop. Scenarios are presented to explore the technical feasibility of achieving a closed loop system. An optimal choice of plants is followed by processing, waste conversion, equipment specifications, and control requirements, and finally, cost-effectiveness.

Modell, M.↗
NASA NTRS1992

Structure of a human monoclonal antibody Fab fragment against gp41 of human immunodeficiency virus type

The three-dimensional structure of a human monoclonal antibody (Fab), which binds specifically to a major epitope of the transmembrane protein gp41 of the human immunodeficiency virus type 1, has been determined by crystallographic methods to a resolution of 2.7 A. It has been previously determined that this antibody recognizes the epitope SGKLICTTAVPWNAS, belongs to the subclass IgG1 (kappa), and exhibits antibody-dependent cellular cytotoxicity. The quaternary structure of the Fab is in an extended conformation with an elbow bend angle between the constant and variable domains of 175 degrees. Structurally, four of the hypervariable loops can be classified according to previously recognized canonical structures. The third hypervariable loops of the heavy (H3) and light chain (L3) are structurally distinct. Hypervariable loop H3, residues 102H-109H, is unusually extended from the surface. The complementarity-determining region forms a hydrophobic binding pocket that is created primarily from hypervariable loops L3, H3, and H2.

He, X. M.↗
NASA NTRS1992

Structure of a human monoclonal antibody Fab fragment against gp41 of human immunodeficiency virus type 1

The three-dimensional structure of a human monoclonal antibody (Fab), which binds specifically to a major epitope of the transmembrane protein gp41 of the human immunodeficiency virus type 1, has been determined by crystallographic methods to a resolution of 2.7 A. It has been previously determined that this antibody recognizes the epitope SGKLICTTAVPWNAS, belongs to the subclass IgG1 (kappa), and exhibits antibody-dependent cellular cytotoxicity. The quaternary structure of the Fab is in an extended conformation with an elbow bend angle between the constant and variable domains of 175 deg. Structurally, four of the hypervariable loops can be classified according to previously recognized canonical structures. The third hypervariable loops of the heavy (H3) and light chain (L3) are structurally distinct. Hypervariable loop H3, residues 102H-109H, is unusually extended from the surface. The complementarity-determining region forms a hydrophobic binding pocket that is created primarily from hypervariable loops L3, H3, and H2.

He, Xiao M.↗
DOE OSTI2019

Proximity to Graphene Dramatically Alters Polymer Dynamics

Proximity to graphene has an extraordinary effect on the dynamics of entangled chains, as evidenced by strong slowing of thermally stimulated fluctuations at the surface of a thin supported film of polystyrene (PS) when a single layer of graphene is placed between the supporting substrate and the PS film. Furthermore, this slowing is due to a layer of highly viscous polymer next to the substrate being thicker for graphene (75 nm or 7.5 R g ) than for silicon (13 nm or 1.3 R g ). Molecular dynamics simulations of unentangled PS chain melts on silicon and on multiple layers of graphene show the work of adhesion with graphene is roughly four times larger than that with silicon. In addition, PS chains adjacent to silicon readily form “loops”, with phenyl rings pointing predominantly toward the substrate. Chains adjacent to graphene more readily form trains, with the phenyl rings predominantly parallel to the graphene.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Dynamic, structural and thermodynamic basis of insulin-like growth factor 1 kinase allostery mediated by activation loop phosphorylation

Despite the importance of kinases' catalytic activity regulation in cell signaling, detailed mechanisms underlying their activity regulation are poorly understood. Herein, using insulin-like growth factor 1 receptor kinase (IGF-1RK) as a model, the mechanisms of kinase regulation by its activation loop (A-loop) phosphorylation were investigated through molecular dynamics (MD) and alchemical free energy simulations. Analyses of the simulation results and free energy landscapes determined for the entire catalytic cycle of the kinase revealed that A-loop phosphorylation affects each step in the IGF-1RK catalytic cycle, including conformational change, substrate binding/product release and catalytic phosphoryl transfer. Specifically, the conformational equilibrium of the kinase is shifted by 13.2 kcal mol –1 to favor the active conformation after A-loop phosphorylation, which increases substrate binding affinity of the activated kinase. This free energy shift is achieved primarily via destabilization of the inactive conformation. The free energy of the catalytic reaction is also changed by 3.3 kcal mol –1 after the phosphorylation and in the end, facilitates product release. Analyses of MD simulations showed that A-loop phosphorylation produces these energetic effects by perturbing the side chain interactions around each A-loop tyrosine. These interaction changes are propagated to the remainder of the kinase to modify the orientations and dynamics of the αC-helix and A-loop, and together yield the observed free energy changes. Furthermore, since many protein kinases share similar interactions identified in this work, the mechanisms of kinase allostery and catalysis unraveled here can be applicable to them.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Chain-End Controlled Depolymerization Selectivity in α,α-Disubstituted Propionate PHAs with Dual Closed-Loop Recycling and Record-High Melting Temperature

In this article, within the large poly(3-hydroxyalkanoate) (PHA) family, C3 propionates are much less studied than C4 butyrates, with the exception of α,α-disubstituted propionate PHAs, particularly poly(3-hydroxy-2,2-dimethylpropionate), P3H(Me) 2 P, due to its high melting temperature (T m ~ 230 °C) and crystallinity (~76%). However, inefficient synthetic routes to its monomer 2,2-dimethylpropiolactone [(Me) 2 PL] and extreme brittleness of P3H(Me) 2 P largely hinder its broad applications. Here, we introduce simple, efficient step-growth polycondensation (SGP) of a hydroxyacid or methyl ester to afford P3H(Me) 2 P with low to medium molar mass, which is then utilized to produce lactones through base-catalyzed depolymerization. The ring-opening polymerization (ROP) of the 4-membered lactone leads to high-molar-mass P3H(Me) 2 P, which can be depolymerized by hydrolysis to the hydroxyacid in 99% yield or methanolysis to the hydroxyester in 91% yield, achieving closed-loop recycling via both SGP and ROP routes. Intriguingly, the chain end of the SGP-P3H(Me) 2 P determines the depolymerization selectivity toward 4- or 12-membered lactone formation, while both can be repolymerized back to P3H(Me) 2 P. Through the formation of copolymers P3H(Me/R) 2 P (R = Et, n Pr), PHAs with high tensile strength and ductility, coupled with high barriers to water vapor and oxygen, have been created. Notably, the PHA structure–property study led to P3H( n Pr) 2 P with a record-high T m of 266 °C within the PHA family.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Structural and Dynamical Roles of Bound Polymer Chains in Rubber Reinforcement

The addition of nanofillers to rubber matrices is a powerful route to improve the mechanical properties. Here, we focus on a molecular understanding of basic mechanisms that are important for the reinforcement in rubbers. The key role in this process is ascribed to bound rubber (BR) that engages with the matrix as well as with adjacent nanofillers. To date, this understanding has been impeded by the lack of experimental tools to directly probe the BR chains buried in a polymer matrix composed of the same polymer. To tackle this challenge, we combine neutron scattering/spectroscopy techniques with isotope-labeling and molecular dynamics simulations. The system is a simplified carbon-black-filled polybutadiene. The combined experimental and computational results provide new insights into the local structural and dynamical heterogeneities of BR chains and their interactions with the matrix polymer, highlighting (i) the structural partition of the bound chains into three components (i.e., trains, loops, and tails) and their fractions; (ii) their dynamical hierarchies, i.e., the trains that remain immobile on the filler surface, the loops that are fairly large and hence allow the interdigitation of matrix chains, and the tails with their unique characteristics to reach far out into the matrix and entangle with matrix chains. These multiple roles of the constituent components of the BR chains promote the formation of a well-developed adhesive polymer–filler interface, enhancing the elastic property of a filled rubber. Finally, the comprehensive understanding derived and validated by the model rubber will be translatable to many other polymer nanocomposites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1982

Constrained multibody system dynamics: An automated approach

The governing equations for constrained multibody systems are formulated in a manner suitable for their automated, numerical development and solution. The closed loop problem of multibody chain systems is addressed. The governing equations are developed by modifying dynamical equations obtained from Lagrange's form of d'Alembert's principle. The modifications is based upon a solution of the constraint equations obtained through a zero eigenvalues theorem, is a contraction of the dynamical equations. For a system with n-generalized coordinates and m-constraint equations, the coefficients in the constraint equations may be viewed as constraint vectors in n-dimensional space. In this setting the system itself is free to move in the n-m directions which are orthogonal to the constraint vectors.

Kamman, J. W.↗
DOE OSTI2021

A structural explanation for the mechanism and specificity of plant branching enzymes I and IIb

Branching enzymes (BEs) are essential in the biosynthesis of starch and glycogen and play critical roles in determining the fine structure of these polymers. The substrates of these BEs are long carbohydrate chains that interact with these enzymes via multiple binding sites on the enzyme’s surface. By controlling the branched-chain length distribution, BEs can mediate the physiological properties of starch and glycogen moieties; however, the mechanism and structural determinants of this specificity remain mysterious. In this study, we identify a large dodecaose binding surface on rice BE I (BEI) that reaches from the outside of the active site to the active site of the enzyme. Mutagenesis activity assays confirm the importance of this binding site in enzyme catalysis, from which we conclude that it is likely the acceptor chain binding site. Comparison of the structures of BE from Cyanothece and BE1 from rice allowed us to model the location of the donor-binding site. We also identified two loops that likely interact with the donor chain and whose sequences diverge between plant BE1, which tends to transfer longer chains, and BEIIb, which transfers exclusively much shorter chains. When the sequences of these loops were swapped with the BEIIb sequence, rice BE1 also became a short-chain transferring enzyme, demonstrating the key role these loops play in specificity. Taken together, these results provide a more complete picture of the structure, selectivity, and activity of BEs.

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

Discovery of Marburg virus neutralizing antibodies from virus-naïve human antibody repertoires using large-scale structural predictions

Marburg virus (MARV) disease is lethal, with fatality rates up to 90%. Neutralizing antibodies (Abs) are promising drug candidates to prevent or treat the disease. Current efforts are focused in part on vaccine development to induce such MARV-neutralizing Abs. We analyzed the antibody repertoire from healthy unexposed and previously MARV-infected individuals to assess if naïve repertoires contain suitable precursor antibodies that could become neutralizing with a limited set of somatic mutations. Here, we computationally searched the human Ab variable gene repertoire for predicted structural homologs of the neutralizing Ab MR78 that is specific to the receptor binding site (RBS) of MARV glycoprotein (GP). Eight Ab heavy-chain complementarity determining region 3 (HCDR3) loops from MARV-naïve individuals and one from a previously MARV-infected individual were selected for testing as HCDR3 loop chimeras on the MR78 Ab framework. Three of these chimerized antibodies bound to MARV GP. We then tested a full-length native Ab heavy chain encoding the same 17-residue-long HCDR3 loop that bound to the MARV GP the best among the chimeric Abs tested. Despite only 57% amino acid sequence identity, the Ab from a MARV-naïve donor recognized MARV GP and possessed neutralizing activity against the virus. Crystallization of both chimeric and full-length native heavy chain-containing Abs provided structural insights into the mechanism of binding for these types of Abs. Our work suggests that the MARV GP RBS is a promising candidate for epitope-focused vaccine design to induce neutralizing Abs against MARV.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2011

Scatterometer-Calibrated Stability Verification Method

The requirement for scatterometer-combined transmit-receive gain variation knowledge is typically addressed by sampling a portion of the transmit signal, attenuating it with a known-stable attenuation, and coupling it into the receiver chain. This way, the gain variations of the transmit and receive chains are represented by this loop-back calibration signal, and can be subtracted from the received remote radar echo. Certain challenges are presented by this process, such as transmit and receive components that are outside of this loop-back path and are not included in this calibration, as well as the impracticality for measuring the transmit and receive chains stability and post fabrication separately, without the resulting measurement errors from the test set up exceeding the requirement for the flight instrument. To cover the RF stability design challenge, the portions of the scatterometer that are not calibrated by the loop-back, (e.g., attenuators, switches, diplexers, couplers, and coaxial cables) are tightly thermally controlled, and have been characterized over temperature to contribute less than 0.05 dB of calibration error over worst-case thermal variation. To address the verification challenge, including the components that are not calibrated by the loop-back, a stable fiber optic delay line (FODL) was used to delay the transmitted pulse, and to route it into the receiver. In this way, the internal loopback signal amplitude variations can be compared to the full transmit/receive external path, while the flight hardware is in the worst-case thermal environment. The practical delay for implementing the FODL is 100 s. The scatterometer pulse width is 1 ms so a test mode was incorporated early in the design phase to scale the 1 ms pulse at 100-Hz pulse repetition interval (PRI), by a factor of 18, to be a 55 s pulse with 556 s PRI. This scaling maintains the duty cycle, thus maintaining a representative thermal state for the RF components. The FODL consists of an RF-modulated fiber-optic transmitter, 20 km SMF- 28 standard single-mode fiber, and a photodetector. Thermoelectric cooling and insulating packaging are used to achieve high thermal stability of the FODL components. The chassis was insulated with 1-in. (.2.5-cm) thermal isolation foam. Nylon rods support the Micarta plate, onto which are mounted four 5-km fiber spool boxes. A copper plate heat sink was mounted on top of the fiber boxes (with thermal grease layer) and screwed onto the thermoelectric cooler plate. Another thermal isolation layer in the middle separates the fiberoptics chamber from the RF electronics components, which are also mounted on a copper plate that is screwed onto another thermoelectric cooler. The scatterometer subsystem fs overall stability was successfully verified to be calibratable to within 0.1 dB error in thermal vacuum (TVAC) testing with the fiber-optic delay line, while the scatterometer temperature was ramped from 10 to 30 C, which is a much larger temperature range than the worst-case expected seasonal variations.

McWatters, Dalia A.↗
DOE OSTI2020

Structural basis of a shared antibody response to SARS-CoV-2

Molecular understanding of neutralizing antibody responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could accelerate vaccine design and drug discovery. We analyzed 294 anti–SARS-CoV-2 antibodies and found that immunoglobulin G heavy-chain variable region 3-53 (IGHV3-53) is the most frequently used IGHV gene for targeting the receptor-binding domain (RBD) of the spike protein. Co-crystal structures of two IGHV3-53–neutralizing antibodies with RBD, with or without Fab CR3022, at 2.33- to 3.20-angstrom resolution revealed that the germline-encoded residues dominate recognition of the angiotensin I converting enzyme 2 (ACE2)–binding site. This binding mode limits the IGHV3-53 antibodies to short complementarity-determining region H3 loops but accommodates light-chain diversity. These IGHV3-53 antibodies show minimal affinity maturation and high potency, which is promising for vaccine design. Knowledge of these structural motifs and binding mode should facilitate the design of antigens that elicit this type of neutralizing response.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Conformational Dynamics and Catalytic Backups in a Hyper-thermostable Engineered Archaeal Protein Tyrosine Phosphatase

Protein tyrosine phosphatases (PTPs) are a family of enzymes that play important roles in regulating cellular signaling pathways. The activity of these enzymes is regulated by the motion of a catalytic loop that places a critical conserved aspartic acid side chain into the active site for acid–base catalysis upon loop closure. These enzymes also have a conserved phosphate-binding loop that is typically highly rigid and forms a well-defined anion-binding nest. The intimate links between loop dynamics and chemistry in these enzymes make PTPs an excellent model system for understanding the role of loop dynamics in protein function and evolution. In this context, archaeal PTPs, which have often evolved in extremophilic organisms, are highly understudied, despite their unusual biophysical properties. We present here an engineered chimeric PTP (ShufPTP) generated by shuffling the amino acid sequence of five extant hyperthermophilic archaeal PTPs. Despite ShufPTP’s high sequence similarity to its natural counterparts, it presents a suite of unique properties, including high flexibility of the phosphate binding P-loop, facile oxidation of the active-site cysteine, mechanistic promiscuity, and, most notably, hyperthermostability, with a denaturation temperature likely >130 °C (>8 °C higher than the highest recorded growth temperature of any archaeal strain). Our combined structural, biochemical, biophysical, and computational analysis provides insight both into how small steps in evolutionary space can radically modulate the biophysical properties of an enzyme and showcases the tremendous potential of archaeal enzymes for biotechnology, to generate novel enzymes capable of operating under extreme conditions.

archaea↗
DOE OSTI2022

Experimental Setup for Grid Control Device Software Updates in Supply Chain Cyber-Security

Supply chain cyberattacks that exploit insecure third-party software are a growing concern for the security of the electric power grid. These attacks seek to deploy malicious software in grid control devices during the fabrication, shipment, installation, and maintenance stages, or as part of routine software updates. Malicious software on grid control devices may inject bad data or execute bad commands, which can cause blackouts and damage power equipment. This paper describes an experimental setup to simulate the software update process of a commercial power relay as part of a hardware-in-the-loop simulation for grid supply chain cyber-security assessment. The laboratory setup was successfully utilized to study three supply chain cyber-security use cases.

Keller, Joseph↗
DOE OSTI2025

Is a Malleable Active Site Loop the Key to High Substrate Promiscuity? Hybrid, Biocatalytic Route to Structurally Diverse Taxoid Side Chains with Remarkable Dual Stereocontrol

Abstract These studies reveal the first structure ofClostridium acetobutylicumalcohol dehydrogenase (CaADH), a protein exhibiting remarkable substrate promiscuity and stereochemical fidelity. The CaADH enzyme is utilized here for synthesizing 20 potential aryl isoserine side chains for the Taxotere family of tubulin‐binding chemotherapeutics. The approach involves dynamic reductive kinetic resolution (DYRKR) upon the corresponding α‐chloro‐β‐keto esters, showing high D‐synstereoselectivity, including those leading to the clinically relevant milataxel (Ar = 2‐furyl) and simotaxel (Ar = 2‐thienyl) side chains. Furthermore, various cross‐coupling chemistries performed on thep‐bromophenyl isoserine side chain significantly enhance the structural diversity of the taxoid side chain library obtained (16 additional taxoid side chains). The CaADH structure is notable: (i) the nicotinamide cofactor is bound in ananti‐conformation, with the amide carbonyl occupying the ketone binding pocket, and (ii) a flexible loop near the active site likely contributes to the remarkable substrate promiscuity observed in CaADH. We present our perspective on the dynamic nature of the CaADH active site through molecular dynamics simulation, proposing a halogen bonding model as a potential mechanism for the remarkable selectivity for an (S)‐configured C─Cl bond, in addition to the D‐facial selectivity, demonstrated across 20 diverse substrates by this remarkable short‐chain dehydrogenase enzyme.

Chemistry↗
DOE OSTI2019

Improvement of antibody functionality by structure-guided paratope engraftment

Broadly neutralizing antibodies (bNAbs) represent a promising alternative to antiretroviral drugs for HIV-1 prevention and treatment. Selected antibodies to the CD4-binding site bolster envelope trimer binding via quaternary contacts. Here, we rationally engraft a new paratope, i.e., the extended heavy-chain framework region 3 (FR3) loop of VRC03, which mediates quaternary interaction, onto several potent bNAbs, enabling them to reach an adjacent gp120 protomer. The interactive quaternary surface is delineated by solving the crystal structure of two FR3 loop-chimeric antibodies. Chimerization enhances the neutralizing activity of several potent bNAbs against a majority of global HIV-1 strains. Compared to unmodified antibodies, chimeric antibodies display lower autoreactivity and prolonged in vivo half-life in huFcRn mice and rhesus macaques. Thus, paratope engraftment may be used to expand the epitope repertory of natural antibodies, improving their functionality for disease prevention and treatment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Refining HPCToolkit for application performance analysis at exascale

As part of the US Department of Energy’s Exascale Computing Project (ECP), Rice University has been refining its HPCToolkit performance tools to better support measurement and analysis of applications executing on exascale supercomputers. To efficiently collect performance measurements of GPU-accelerated applications, HPCToolkit employs novel non-blocking data structures to communicate performance measurements between tool threads and application threads. To attribute performance information in detail to source lines, loop nests, and inlined call chains, HPCToolkit performs parallel analysis of large CPU and GPU binaries involved in the execution of an exascale application to rapidly recover mappings between machine instructions and source code. To analyze terabytes of performance measurements gathered during executions at exascale, HPCToolkit employs distributed-memory parallelism, multithreading, sparse data structures, and out-of-core streaming analysis algorithms. To support interactive exploration of profiles up to terabytes in size, HPCToolkit’s hpcviewer graphical user interface uses out-of-core methods to visualize performance data. The result of these efforts is that HPCToolkit now supports collection, analysis, and presentation of profiles and traces of GPU-accelerated applications at exascale. These improvements have enabled HPCToolkit to efficiently measure, analyze and explore terabytes of performance data for executions using as many as 64K MPI ranks and 64K GPU tiles on ORNL’s Frontier supercomputer. HPCToolkit’s support for measurement and analysis of GPU-accelerated applications has been employed to study a collection of open-science applications developed as part of ECP. This paper reports on these experiences, which provided insight into opportunities for tuning applications, strengths and weaknesses of HPCToolkit itself, as well as unexpected behaviors in executions at exascale.

Adhianto, Laksono↗