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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 OSTI2021

DFT Mechanism Studies: Biomimetic 1,4-NADH Chemoselective, Co-factor Regeneration with [Cp*Rh(bpy)H] + , in Tandem with the Biocatalysis Pathways of a Core Model of the (HLADH)-Zn(II) Mediated Enzyme, in the Enantioselective Reduction of Achiral Ketones to Chiral S-Alcohols

In this study, Quantum Chemical (QC) calculations, utilizing Density Functional Theory (DFT), were performed to investigate the mechanistic aspects of the chemoselective catalyzed reaction of [Cp*Rh(bpy)H] + with the biomimetic NAD + analogues, N-benzylnicotinamide triflate, 1, and β-nicotinamide ribose-5'-methyl phosphate, 2, in the conversion to their 1,4-NADH analogues, 1,4-dihydro-N-benzylnicotinamide, 4, and β-1,4-dihydronicotinamide-5'-ribose methyl phosphate, 5. This reaction was in tandem with the 1,4-NADH dependent HLADH-Zn(II)- catalyzed reduction of achiral ketones to chiral S-alcohols. The [Cp*Rh(bpy)H] + complex, and not its equilibrium tautomer, [η 4 -Cp*HRh(bpy)] + , was found to control the hydride transfer during the biomimetic NAD + /1,4-NADH conversion, through the non-covalent interactions of the biomimetic co-factors with [Cp*Rh(bpy)H] + . The thermodynamics and kinetics for the chiral reduction of the Zn(II) bound ketones, 2-pentanone and 4-phenyl-2-butanone, with co-factor, 4, catalyzed by Zn(SCH 3 ) 2 (Imidazole), a core model of the Zn(II)-based catalytic center of HLADH, was also investigated by the evaluation of two possible reaction pathways: (1) formation of a ZnH from the C4-H hydride transfer of co-factor, 4, followed by reaction of the postulated ZnH with the bound 2-pentanone or 4-phenyl-2-butanone substrate, and (2), the direct C4-H transfer to the bound achiral ketone substrates, to provide the dominant chiral alcohols, S-2-pentanol or S-4-phenyl-2-butanol. The latter pathway was found most viable, and DFT calculations also revealed an essential η 2 -coordination of the 5,6 double bond of co-factor, 4, to the HLADH-Zn(II) metal ion center, upon imidazole decomplexation, providing an asymmetric differentiation of S-η 2 -5,6-1,4-NADH-Zn(II) binding. A proposed new paradigm for the Zn(II)'s non-innocent role in the HLADH-Zn(II) biocatalysis reduction mechanism, for enantioselective hydride transfer to a Zn(II) bound ketone, providing S-alcohols.

1,4 NADH co-factors↗
DOE OSTI2020

Low-energy magnons in the chiral ferrimagnet Cu 2 OSeO 3 : A coarse-grained approach

We report a comprehensive neutron scattering study of low energy magnetic excitations in the breathing pyrochlore helimagnetic Cu2OSeO3. Fully documenting the four lowest energy magnetic modes that leave the ferrimagnetic configuration of the “strong tetrahedra” intact (| ℏ ω| < 13 meV), we find gapless quadratic dispersion at the Γ point for energies above 0.2 meV, two doublets separated by 1.6(2) meV at the R point, and a bounded continuum at the X point. Our constrained rigid spin cluster model relates these features to Dzyaloshinskii-Moriya (DM) interactions and the incommensurate helical ground state. Combining conventional spin wave theory with a spin cluster form factor accurately reproduces the measured equal time structure factor through multiple Brillouin zones. An effective spin Hamiltonian describing complex anisotropic intercluster interactions is obtained.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1987

The purification and subunit structure of a membrane-bound ATPase from the Archaebacterium Halobacterium saccharovorum

The procedure for the isolation and 70-fold purification of membrane-bound cold-sensitive ATPase from Halobacterium saccharovorum is described. Upon exposure to cold, the enzyme dissociates into two major subunits, I (87 kDa) and II (60 kDa), and two minor subunits, III (29 kDa) and IV (20 kDa). The stoichiometry of the enzyme is proposed to be I2.II2.III.IV; the molecular mass of such a complex would be 343 kDa, which is in good agreement with the value of 350 kDa obtained by gel filtration. The structure of the ATPase from H. saccharovorum makes it unlike any previously described ATPase.

Hochstein, Lawrence I.↗
DOE OSTI2020

Photoelectron spectroscopy and computational investigations of the electronic structures and noncovalent interactions of cyclodextrin-closo-dodecaborate anion complexes x-CD·B12X122- (x = a, ß, y; X = H, F)

We report a joint negative ion photoelectron spectroscopy (NIPES) and computational study on the electronic structures and noncovalent interactions of a series of cyclodextrin-closo-dodecaborate dianion complexes, ?-CD·B12X122- (? = a, ß, ?; X = H, F). The measured vertical / adiabatic detachment energies (VDEs / ADEs) are 1.15/0.93, 3.55/3.20, 3.90/3.60, and 3.85/3.60 eV for B12H122- and its a-, ß-, ?-CD complexes, respectively; while the corresponding values are 1.90/1.70, 4.00/3.60, 4.33/3.95, and 4.30/3.85 eV for the X = F case. These results show that the inclusion of B12X122- into the CD cavities greatly increase the electronic stability of the dianions. The effect of electronic stabilization for ß-CD is roughly the same as for ?-CD, both being considerably stronger than that for a-CD. Density functional theory (DFT) based geometry optimization reveals that B12X122- are inserted into CDs increasingly deeper from a-CD to ?-CD. The calculated VDEs and ADEs agree with the experiments well, particularly, reproducing the electron binding energy (EBE) trends. The molecular orbital analyses indicate that the most loosely bound photodetached electrons origin from the guest B12X122- moieties. In addition to a shift of all signals to larger EBE, significant changes in the signal patterns are observed. At low EBE, this is due to the splitting of highly degenerate B12X122- orbitals, while at high EBE, photodetachment from CD oxygens contributes to the new bands. The guest B12X122- and host CD nocovalent, size-specific interaction based on the independent gradient model (IGM) and energy decomposition analysis (EDA), is dominated by electrostatic interactions. The analysis further unravels unambiguiously the existence of dihydrogen bonding and how it affects the total energy that stabilizes the host-guest complexes of CDs·B12H122- compared to the general hydrogen bonding interaction in CDs·B12F122-. This work clearly exhibits strong influences on the electronic structures of dodecaborates upon clustering with CDs, with both size (a-, ß-, ?-) and molecular (X = H or F) specificities, thus providing critical molecular-level information on the cyclodextrin-closo-dodecaborate interactions of interest to medical applications, e.g. Boron neutron capature therapy. The NIPES experiments done at PNNL were supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Bioscience (X.-B.W.) and was performed at the EMSL, a national scientific user facility sponsored by DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. H.S. and Z.S. acknowledge the funding support of National Natural Science Foundation of China (Nos.11727810, 61720106009 and 21603074), the Science and Technology Commission of Shanghai Municipality (Nos. 19JC1412200), and the Program of Introducing Talents of Discipline to Universities 111 project (B12024). Z. L. thanks the China Scholarship Council (CSC) for financial support. We acknowledge the ECNU Multifunctional Platform for Innovation (001) and HPC Research Computing Team for providing computational and storage resources. J.W. acknowledges support from the Alexander von Humboldt foundation (Feodor Lynen Fellowship and Rückkehrerstipendium), a Freigeist fellowship of the Volkswagenfoundation and Prof. Vladimir A. Azov for helpful discussions.

Li, Zhipeng↗
DOE OSTI2021

Analysis and prediction of reaction kinetics using the degree of rate control

“Degree of rate control” (DRC) analysis provides a quantitative approach for analysing the kinetics of multi-step reaction mechanisms that has been widely applied to both heterogeneous and homogeneous catalysis research, as well as electrocatalysis. The DRC of any given transition state or intermediate is defined as a partial derivative such that it approximately equals the fractional increase in net rate to the product of interest per differential decrease in its standard-state free energy for that species (÷RT), holding constant the standard-state free energies of all other transition states and intermediates. Even very complex mechanisms usually have only a few species with non-zero DRCs and are thus the species whose interactions with the catalyst most strongly affect the net rate. These key DRC values thus offer a simple and intuitive route to optimize catalyst materials, especially with the assistance of computational methods like density functional theory (DFT). These high-DRC species are also the species whose energetics must be most accurately measured or calculated to achieve an accurate kinetic model for any reaction mechanism. In simple cases with a single “rate-determining step”, the DRC for its transition state (TS) is + 1. Catalyst-bound intermediates, on the other hand, often have negative DRCs equal to a small integer times their fractional occupancy of catalyst sites. The apparent activation energy equals a weighted average of the standard-state enthalpies (relative to reactants) of all the species (intermediates, transition states and products) in the reaction mechanism, each weighted by its DRC (+RT). It has been shown that the apparent transfer coefficient in electrocatalysis, an inverted form of the Tafel slope, is a weighted average of the number of electrons transferred to generate each intermediate or product species in the mechanism, weighted again by the DRC. Quantitative analysis of kinetic isotope effects (KIEs, or the ratio of net rates for different reactant isotopes) in complex mechanisms has shown that the logarithm of the KIE equals the weighted average over all species in the mechanism of the difference between the two isotopes in their standard-state free energies (÷RT), again weighted by the DRC. The reaction orders with respect to fluid-phase concentrations of reactants, products and intermediates have also been proven to be directly related to DRCs. Thus, there are numerous experimental observables which equate to short linear combinations of DRCs, so that combinations of experimental measurements might provide access to DRC values. Since its invention for transition states in 1994 and its generalization to include intermediates in 2009, the DRC has thus far mainly been calculated for microkinetic models based either entirely on DFT or on DFT with the key energies (i.e., those for high-DRC species) being fine-tuned to match experiments. The relationships summarized in this work provide new opportunities for using experiments earlier in the development and optimization of microkinetic models that require input from computational catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Quantum computational phase transition in combinatorial problems

Quantum Approximate Optimization algorithm (QAOA) aims to search for approximate solutions to discrete optimization problems with near-term quantum computers. As there are no algorithmic guarantee possible for QAOA to outperform classical computers, without a proof that bounded-error quantum polynomial time (BQP) ≠ nondeterministic polynomial time (NP), it is necessary to investigate the empirical advantages of QAOA. We identify a computational phase transition of QAOA when solving hard problems such as SAT—random instances are most difficult to train at a critical problem density. We connect the transition to the controllability and the complexity of QAOA circuits. Moreover, we find that the critical problem density in general deviates from the SAT-UNSAT phase transition, where the hardest instances for classical algorithms lies. Then, we show that the high problem density region, which limits QAOA’s performance in hard optimization problems (reachability deficits), is actually a good place to utilize QAOA: its approximation ratio has a much slower decay with the problem density, compared to classical approximate algorithms. Indeed, it is exactly in this region that quantum advantages of QAOA over classical approximate algorithms can be identified.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

GHB analogs confer neuroprotection through specific interaction with the CaMKIIα hub domain

Ca 2+ /calmodulin-dependent protein kinase II alpha subunit (CaMKIIα) is a key neuronal signaling protein and an emerging drug target. The central hub domain regulates the activity of CaMKIIα by organizing the holoenzyme complex into functional oligomers, yet pharmacological modulation of the hub domain has never been demonstrated. Here, using a combination of photoaffinity labeling and chemical proteomics, we show that compounds related to the natural substance γ-hydroxybutyrate (GHB) bind selectively to CaMKIIα. By means of a 2.2-Å x-ray crystal structure of ligand-bound CaMKIIα hub, we reveal the molecular details of the binding site deep within the hub. Furthermore, we show that binding of GHB and related analogs to this site promotes concentration-dependent increases in hub thermal stability believed to alter holoenzyme functionality. Selectively under states of pathological CaMKIIα activation, hub ligands provide a significant and sustained neuroprotection, which is both time and dose dependent. This is demonstrated in neurons exposed to excitotoxicity and in a mouse model of cerebral ischemia with the selective GHB analog, HOCPCA (3-hydroxycyclopent-1-enecarboxylic acid). Together, our results indicate a hitherto unknown mechanism for neuroprotection by a highly specific and unforeseen interaction between the CaMKIIα hub domain and small molecule brain-penetrant GHB analogs. This establishes GHB analogs as powerful tools for investigating CaMKII neuropharmacology in general and as potential therapeutic compounds for cerebral ischemia in particular.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Learning to classify quantum phases of matter with a few measurements

We study the identification of quantum phases of matter, at zero temperature, when only part of the phase diagram is known in advance. Following a supervised learning approach, we show how to use our previous knowledge to construct an observable capable of classifying the phase even in the unknown region. By using a combination of classical and quantum techniques, such as tensor networks, kernel methods, generalization bounds, quantum algorithms, and shadow estimators, we show that, in some cases, the certification of new ground states can be obtained with a polynomial number of measurements. An important application of our findings is the classification of the phases of matter obtained in quantum simulators, e.g. cold atom experiments, capable of efficiently preparing ground states of complex many-particle systems and applying simple measurements, e.g. single qubit measurements, but unable to perform a universal set of gates.

quantum machine learning↗
DOE OSTI2021

The N-terminus of varicella-zoster virus glycoprotein B has a functional role in fusion

Varicella-zoster virus (VZV) is a medically important alphaherpesvirus that induces fusion of the virion envelope and the cell membrane during entry, and between cells to form polykaryocytes within infected tissues during pathogenesis. All members of the Herpesviridae , including VZV, have a conserved core fusion complex composed of glycoproteins, gB, gH and gL. The ectodomain of the primary fusogen, gB, has five domains, DI-V, of which DI contains the fusion loops needed for fusion function. We recently demonstrated that DIV is critical for fusion initiation, which was revealed by a 2.8Å structure of a VZV neutralizing mAb, 93k, bound to gB and mutagenesis of the gB-93k interface. To further assess the mechanism of mAb 93k neutralization, the binding site of a non-neutralizing mAb to gB, SG2, was compared to mAb 93k using single particle cryogenic electron microscopy (cryo-EM). The gB-SG2 interface partially overlapped with that of gB-93k but, unlike mAb 93k, mAb SG2 did not interact with the gB N-terminus, suggesting a potential role for the gB N-terminus in membrane fusion. The gB ectodomain structure in the absence of antibody was defined at near atomic resolution by single particle cryo-EM (3.9Å) of native, full-length gB purified from infected cells and by X-ray crystallography (2.4Å) of the transiently expressed ectodomain. Both structures revealed that the VZV gB N-terminus (aa72-114) was flexible based on the absence of visible structures in the cryo-EM or X-ray crystallography data but the presence of gB N-terminal peptides were confirmed by mass spectrometry. Notably, N-terminal residues 109 KSQD 112 were predicted to form a small α-helix and alanine substitution of these residues abolished cell-cell fusion in a virus-free assay. Importantly, transferring the 109 AAAA 112 mutation into the VZV genome significantly impaired viral propagation. These data establish a functional role for the gB N-terminus in membrane fusion broadly relevant to the Herpesviridae .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Analysis of the Trusted Inertial Terrain-Aided Navigation Measurement Function

The trusted inertial terrain-aided navigation (TITAN) algorithm leverages an airborne vertical synthetic aperture radar to measure the range to the closest ground points along several prescribed iso-Doppler contours. These TITAN minimum-range, prescribed-Doppler measurements are the result of a constrained nonlinear optimization problem whose optimization function and constraints both depend on the radar position and velocity. Owing to the complexity of this measurement definition, analysis of the TITAN algorithm is lacking in prior work. This publication offers such an analysis, making the following three contributions: (1) an analytical solution to the TITAN constrained optimization measurement problem, (2) a derivation of the TITAN measurement function Jacobian, and (3) a derivation of the Cramér-Rao lower bound on the estimated position and velocity error covariance. These three contributions are verified via Monte Carlo simulations over synthetic terrain, which further reveal two remarkable properties of the TITAN algorithm: (1) the along-track positioning errors tend to be smaller than the cross-track positioning errors, and (2) the cross-track positioning errors are independent of the terrain roughness.

TITAN↗
DOE OSTI2024

High-Fidelity and High-Performance Computational Simulations for Rapid Design Optimization of Sulfur Thermal Energy Storage

Industrial process heating (IPH) accounts for approximately 70% of US manufacturing energy use and is primarily produced by fossil fuel combustion. Approximately 1500 TWht (approximately 60%) of IPH demand is in the temperature range of 100-300. Industrial applications in this temperature range include drying, hydrothermal processing, thermal enhanced oil recovery, food and beverage, bioethanol production, etc. Cost-effective thermal energy storage (TES) that increases the utilization of waste and renewable heat (solar, geothermal, etc.) could provide significant energy savings and reliable heat sources, decrease emissions, and increase US manufacturing competitiveness through reductions in fuel consumption. TES development has historically been dominated by technologies suitable for deployment with concentrating solar power (CSP). State-of-the-art thermal storage deployed commercially with power tower CSP plants uses a 60%/40% NaNO3/KNO3 molten salt and operates between temperatures of approximately 280 degrees Celsius and 570 degrees Celsius using a two-tank configuration. However, these nitrate salts are unsuitable for operation outside of this temperature range due to a high freezing point of approximately 220 degrees Celsius, and limits on high-temperature salt stability and corrosion resistance of containment alloys. Other materials being investigated for TES include those based on: (1) sensible energy storage (various molten salt compositions, inert solid particles, rocks or pebble beds, sulfur, water, concrete, graphite, etc.), (2) latent energy storage in materials that undergo solid-liquid phase change at relevant temperatures (organic materials for low-temperature applications, inorganic salts and/or metals for high-temperature applications), or (3) thermochemical energy storage (hydrides, hydroxides, carbonates, metal oxides, etc.). The application temperature and challenges pertaining to storage material and/or containment cost, energy density, long-term thermal and cyclic stability, and charge/discharge heat transfer effectiveness drive material selection for a given IPH or electricity generation application. Sulfur is a cheap commodity at $80/ton compared to $1100 - 1300/ton for conventional salts. When using a metric of storage cost per kWh, sulfur costs around 2-3 $/kWh. Previous sulfur TES development focused on high temperature (>600 degrees) concentrated solar power applications with sulfur encapsulated in pipes and flow of gaseous HTF (air) in the shell side. However, for lower-temperature IPH applications in the range of approximately 100-300 degrees Celsius Element 16 adopted a compact and scalable TES design with molten sulfur in the shell and HTF pipes submerged in the molten sulfur bath. The low-cost molten sulfur TES for dispatchable IPH has deployment potential for broad applications. The spatial and temporal evolution of the HTF and sulfur temperature is critical to the TES system performance, and thus detailed modeling can improve understanding of the performance and facilitate design improvements. Using high performance computing and computational fluid dynamics (CFD) a low-cost molten sulfur thermal energy storage (TES) system for industrial process heating (IPH) applications was developed. The unique challenges in CFD modeling of sulfur TES are the sharp property changes of sulfur relevant to the working temperatures. Above 159, liquid sulfur undergoes polymerization, and the viscosity of sulfur rapidly increases by several orders of magnitude between 159 degrees Celsius and 188 degrees Celsius, followed by a decrease in viscosity beyond 188 degrees Celsius due to thermal bound dissociation. In addition, various concentrations of H2S impurities can also modify sulfur viscosity. This numerical challenge is especially relevant to transient simulation of the sulfur TES charging and discharging processes as the extreme property variations limit the applicability of traditional heat transfer correlations. Transient CFD simulations including the temperature-dependent sulfur properties and geometric complexity of the TES design were used to predict the effect of natural convection during charging and discharging on the heat transfer process, sulfur temperature uniformity, charge/discharge rates, and performance of the storage devices. The CFD model was validated with experimental results for a full charge and discharge cycle. The work will show 3D and 2D simulation comparisons aimed to facilitate rapid design iterations and a machine learning based design optimization approach.

CFD↗
DOE OSTI2022

Structures of Fission Yeast Inositol Pyrophosphate Kinase Asp1 in Ligand-Free, Substrate-Bound, and Product-Bound States

Expression of the fission yeast Schizosaccharomyces pombe phosphate regulon is sensitive to the intracellular level of the inositol pyrophosphate signaling molecule 1,5-IP 8 . IP 8 dynamics are determined by Asp1, a bifunctional enzyme consisting of an N-terminal kinase domain and a C-terminal pyrophosphatase domain that catalyze IP 8 synthesis and catabolism, respectively. Here, we report structures of the Asp1 kinase domain, crystallized with two protomers in the asymmetric unit, one of which was complexed with ligands (ADPNP, ADP, or ATP; Mg 2+ or Mn 2+ ; IP 6 , 5-IP 7 , or 1,5-IP 8 ) and the other which was ligand-free. The ligand-free enzyme adopts an “open” conformation that allows ingress of substrates and egress of products. ADPNP, ADP, and ATP and associated metal ions occupy a deep phospho-donor pocket in the active site. IP 6 or 5-IP 7 engagement above the nucleotide favors adoption of a “closed” conformation, in which surface protein segments undergo movement and a disordered-to-ordered transition to form an inositol polyphosphate-binding site. In a structure mimetic of the kinase Michaelis complex, the anionic 5-IP 7 phosphates are encaged by an ensemble of nine cationic amino acids: Lys43, Arg223, Lys224, Lys260, Arg274, Arg285, Lys290, Arg293, and Lys341. Alanine mutagenesis of amino acids that contact the adenosine nucleoside of the ATP donor underscored the contributions of Asp258 interaction with the ribose 3'-OH and of Glu248 with adenine-N 6 . Changing Glu248 to Gln elicited a gain of function whereby the kinase became adept at using GTP as phosphate donor. Wild-type Asp1 kinase can utilize N 6 -benzyl-ATP as phosphate donor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Human cytochrome P450 17A1 structures with metabolites of prostate cancer drug abiraterone reveal substrate-binding plasticity and a second binding site

Abiraterone acetate is a first-line therapy for castration-resistant prostate cancer. This prodrug is deacetylated in vivo to abiraterone, which is a potent and specific inhibitor of cytochrome P450 17A1 (CYP17A1). CYP17A1 performs two sequential steps that are required for the biosynthesis of androgens that drive prostate cancer proliferation, analogous to estrogens in breast cancer. Abiraterone can be further metabolized in vivo on the steroid A ring to multiple metabolites that also inhibit CYP17A1. Despite its design as an active-site-directed substrate analog, abiraterone and its metabolites demonstrate mixed competitive/noncompetitive inhibition. To understand their binding, we solved the X-ray structures of CYP17A1 with three primary abiraterone metabolites. Despite different conformations of the steroid A ring and substituents, all three bound in the CYP17A1 active site with the steroid core packed against the I helix and the A ring C3 keto or hydroxyl oxygen forming a hydrogen bond with N202 similar to abiraterone itself. The structure of CYP17A1 with 3-keto, 5α-abiraterone was solved to 2.0 Å, the highest resolution to date for a CYP17A1 complex. This structure had additional electron density near the F/G loop, which is likely a second molecule of the inhibitor and which may explain the noncompetitive inhibition. Mutation of the adjacent Asn52 to Tyr positions its side chain in this space, maintains enzyme activity, and prevents binding of the peripheral ligand. Collectively, our findings provide further insight into abiraterone metabolite binding and CYP17A1 function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A minimal motif for sequence recognition by mitochondrial transcription factor A (TFAM)

Abstract Mitochondrial transcription factor A (TFAM) plays a critical role in mitochondrial transcription initiation and mitochondrial DNA (mtDNA) packaging. Both functions require DNA binding, but in one case TFAM must recognize a specific promoter sequence, while packaging requires coating of mtDNA by association with non sequence-specific regions. The mechanisms by which TFAM achieves both sequence-specific and non sequence-specific recognition have not yet been determined. Existing crystal structures of TFAM bound to DNA allowed us to identify two guanine-specific interactions that are established between TFAM and the bound DNA. These interactions are observed when TFAM is bound to both specific promoter sequences and non-sequence specific DNA. These interactions are established with two guanine bases separated by 10 random nucleotides (GN10G). Our biochemical results demonstrate that the GN10G consensus is essential for transcriptional initiation and contributes to facilitating TFAM binding to DNA substrates. Furthermore, we report a crystal structure of TFAM in complex with a non sequence-specific sequence containing a GN10G consensus. The structure reveals a unique arrangement in which TFAM bridges two DNA substrates while maintaining the GN10G interactions. We propose that the GN10G consensus is key to facilitate the interaction of TFAM with DNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Gamow-shell-model description of Li isotopes and their mirror partners

Background: Weakly bound and unbound nuclei close to particle drip lines are laboratories of new nuclear structure physics at the extremes of neutron/proton excess. The comprehensive description of these systems requires an open quantum system framework that is capable of treating resonant and nonresonant many-body states on equal footing. Purpose: In this work, we develop the complex-energy configuration interaction approach to describe binding energies and spectra of selected 5 ≤ $\textit{A}$ ≤ 11 nuclei. Method: We employ the complex-energy Gamow shell model (GSM) assuming a rigid 4 He core. The effective Hamiltonian, consisting of a core-nucleon Woods-Saxon potential and a simplified version of the Furutani-Horiuchi-Tamagaki interaction with the mass-dependent scaling, is optimized in the $\textit{sp}$ space. To diagonalize the Hamiltonian matrix, we employ the Davidson method and the Density Matrix Renormalization Group technique. Results: We report our optimized GSM Hamiltonian offers a good reproduction of binding energies and spectra with the root-mean-square (rms) deviation from experiment of 160 keV. Since the model performs well when used to predict known excitations that have not been included in the fit, it can serve as a reliable tool to describe poorly known states. A case in point is our prediction for the pair of unbound mirror nuclei 10 Li – 10 N in which a huge Thomas-Ehrman shift dramatically alters the pattern of low-energy excitations. Conclusion: The new model will enable comprehensive studies of structure and reactions aspects of light drip-line nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS1983

Spectral properties of mixtures of montmorillonite and dark grains - Implications for remote sensing minerals containing chemically and physically adsorbed water

The spectral properties from 0.4 to 3 microns of montmorillonite plus dark carbon grains (called opaques) of various sizes are studied as a function of the weight fraction of opaques present. The reflectance level and band depths of the 1.4-, 1.9-, 2.2-, and 2.8-micron water and/or OH absorption features are analyzed using derived empirical relationships and scattering theory. It is found that the absorption band depths and reflectance level are a very nonlinear function of the weight fraction of opaques present but can be predicted in many cases by simple scattering theory. The 2.8-micron bound water fundamental band is the most difficult absorption feature to suppress. The overtone absorptions are suppressed a greater amount than the fundamental but are still apparent even when 10-20 wt pct opaques are present. The relationships observed and the simple scattering theory presented show that quantitative compositional remote sensing studies are feasible for surfaces containing complex mineral mixtures.

Clark, R. N.↗
NASA NTRS1988

Decentralized adaptive control of robot manipulators with robust stabilization design

Due to geometric nonlinearities and complex dynamics, a decentralized technique for adaptive control for multilink robot arms is attractive. Lyapunov-function theory for stability analysis provides an approach to robust stabilization. Each joint of the arm is treated as a component subsystem. The adaptive controller is made locally stable with servo signals including proportional and integral gains. This results in the bound on the dynamical interactions with other subsystems. A nonlinear controller which stabilizes the system with uniform boundedness is used to improve the robustness properties of the overall system. As a result, the robot tracks the reference trajectories with convergence. This strategy makes computation simple and therefore facilitates real-time implementation.

Yuan, Bau-San↗
NASA NTRS1988

Robustness with real parametric and structured complex uncertainty

The problem of robust stability and performance in feedback control systems with n real (possibly related) uncertain parameters and structured unmodeled dynamics (the latter taking the form of m complex blocks dynamic uncertainties) is considered. A robustness margin rm is defined with respect to such model uncertainty structure and an algorithm is developed to compute it. Robust stability and performance are characterized in terms of r sub m or the structured singular value mu. An iterative procedure using the above algorithm is given to compute tight bounds on k sub m and mu. These bounds are exact for the case m = 3 or less.

Pena, Ricardo S. Sanchez↗