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DOE OSTI2018

Structure of HIV-1 reverse transcriptase cleaving RNA in an RNA/DNA hybrid

HIV-1 reverse transcriptase (RT) contains both DNA polymerase and RNase H activities to convert the viral genomic RNA to dsDNA in infected host cells. Here we report the 2.65-Å resolution structure of HIV-1 RT engaging in cleaving RNA in an RNA/DNA hybrid. A preferred substrate sequence is absolutely required to enable the RNA/DNA hybrid to adopt the distorted conformation needed to interact properly with the RNase H active site in RT. Substituting two nucleotides 4 bp upstream from the cleavage site results in scissile-phosphate displacement by 4 Å. Here, we also have determined the structure of HIV-1 RT complexed with an RNase H-resistant polypurine tract sequence, which adopts a rigid structure and is accommodated outside of the nuclease active site. Based on this newly gained structural information and a virtual drug screen, we have identified an inhibitor specific for the viral RNase H but not for its cellular homologs.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1973

Pressurized panel

Large area pressurized meteoroid penetration detector panels with maximum inherent structural rigidity are provided. The panels measure directly the penetration rate in materials to be used in spacecraft. Panel structure include an interconnected cellular configuration in which the cells have spaced periphery welds and tufts in their centers. A spot weld is made at the center point joining the panels.

White, E. C.↗

NASA NTRS2002

Mechanical Testing of IN718 Lattice Block Structures

Lattice block construction produces a flat, structurally rigid panel composed of thin ligaments of material arranged in a three-dimensional triangulated truss-like structure. Low-cost methods of producing cast metallic lattice block panels are now available that greatly expand opportunities for using this unique material system in today's high-performance structures. Additional advances are being made in NASA's Ultra Efficient Engine Technology (UEET) program to extend the lattice block concept to superalloy materials. Advantages offered by this combination include high strength, light weight, high stiffness, and elevated temperature capabilities. Recently under UEET, the nickel-based superalloy Inconel 718 (IN718) was investment cast into lattice block panels with great success. To evaluate casting quality and lattice block architecture merit, individual ligaments, and structural subelement specimens were extracted from the panels. Tensile tests, structural compression, and bending strength tests were performed on these specimens. Fatigue testing was also completed for several bend test specimens. This paper first presents metallurgical and optical microscopy analysis of the castings. This is followed by mechanical test results for the tensile ligament tests and the subelement compression and bending strength tests, as well as for the fatigue tests that were performed. These tests generally showed comparable properties to base IN718 with the same heat treatment, and they underscored the benefits offered by lattice block materials. These benefits might be extended with improved architecture such as face sheets.

Krause, David L.↗

DOE OSTI2021

Observation of Stepwise Ultrafast Crystallization Kinetics of Donor–Acceptor Conjugated Polymers and Correlation with Field Effect Mobility

The semicrystalline microstructures of donor-acceptor conjugated polymers strongly impact their optoelectronic properties. The control of the microstructure relies on the understandings of the crystallization processes in these polymers, from packing structures to crystallization kinetics. How fast these conjugated polymer chains crystallize and how their chemical structures and pre-existing microstructure history influence their crystallization have so far remained unclear, due to the fast crystallization rate caused by chain rigid structures and strong interactions. Here, ultrafast scanning calorimetry (FSC) is employed to reveal the crystallization behaviors of high perform- ance diketopyrrolopyrrole (DPP)-based conjugated polymers with scanning rates up to 500 000 K/s. Through elaborately designed nonisothermal and isothermal crystallization studies, we probed the fast crystallization kinetics and extracted the two-step crystallization process of these polymers quantitatively. We found that both the rigidity of the chain backbones and the preinduced crystalline microstructures can influence the crystallization rate over an order of magnitude at the same degree of undercooling. We further demonstrated the manipulated crystallization kinetics in the DPP-based polymer films with different amounts of preinduced crystallites and correlate it to the polymers’ charge transport mobility.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Electron Redistributed S-Doped Nickel Iron Phosphides Derived from One-Step Phosphatization of MOFs for Significantly Boosting Electrochemical Water Splitting

Nonprecious transition metal-organic frameworks (MOFs) are one of the most promising precursors for developing electrocatalysts with high porosity and structural rigidity. This study reports the synthesis of high efficiency electrocatalysts based on S-doped NiFeP. MOF-derived S-doped NiFeP structure is synthesized by a one-step phosphorization process with using S-doped MOFs as the precursor, which is more convenient and environment friendly, and also helps retain the samples’ framework. The oxygen evolution reaction (OER) and hydrogen evolution reaction (HER) performance of the NiFeP catalysts can be improved after partially replacing P by S due to the tunable electronic structure. The optimized CCS-NiFeP-10 reaches a current density of 10 mA cm –2 for OER with an overpotential of 201 mV and outperforms most NiFe-based catalysts. The S doping plays an important role in tuning the ΔG values for intermediates formation in Ni atoms to a suitable value and exhibits a pronouncedly improved the OER performance. CCS-NiFeP-20 sample presents excellent HER performance due to the d-band center downshifting from the Fermi level. When the voltage of the electrolytic cell is 1.50 V, a current density of 10 mA cm –2 can be obtained. This strategy paves the way for designing highly active none-noble metal catalysts.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Physics makes the difference: Bayesian optimization and active learning via augmented Gaussian process

Abstract Both experimental and computational methods for the exploration of structure, functionality, and properties of materials often necessitate the search across broad parameter spaces to discover optimal experimental conditions and regions of interest in the image space or parameter space of computational models. The direct grid search of the parameter space tends to be extremely time-consuming, leading to the development of strategies balancing exploration of unknown parameter spaces and exploitation towards required performance metrics. However, classical Bayesian optimization (BO) strategies based on the Gaussian process (GP) do not readily allow for the incorporation of the known physical behaviors or past knowledge. Here we explore a hybrid optimization/exploration algorithm created by augmenting the standard GP with a structured probabilistic model of the expected system’s behavior. This approach balances the flexibility of the non-parametric GP approach with a rigid structure of physical knowledge encoded into the parametric model. The fully Bayesian treatment of the latter allows additional control over the optimization via the selection of priors for the model parameters. The method is demonstrated for a noisy version of a standard univariate test function used to evaluate optimization algorithms and further extended to physical lattice models. This methodology is expected to be universally suitable for injecting prior knowledge in the form of physical models and past data in the BO framework.

42 ENGINEERING↗

DOE OSTI2021

A conserved epitope III on hepatitis C virus E2 protein has alternate conformations facilitating cell binding or virus neutralization

Epitope III, a highly conserved amino acid motif of 524 APTYSW 529 on the hepatitis C virus (HCV) E2 glycoprotein, resides in the critical loop that binds to the host receptor CD81, thus making it one of the most important antibody targets for blocking HCV infections. Here, we have determined the X-ray crystal structure of epitope III at a 2.0-Å resolution when it was captured by a site-specific neutralizing antibody, monoclonal antibody 1H8 (mAb1H8). The snapshot of this complex revealed that epitope III has a relatively rigid structure when confined in the binding grooves of mAb1H8, which confers the residue specificity at both ends of the epitope. Such a high shape complementarity is reminiscent of the “lock and key” mode of action, which is reinforced by the incompatibility of an antibody binding with an epitope bearing specific mutations. By subtly positioning the side chains on the three residues of Tyr 527 , Ser 528 , and Trp 529 while preserving the spatial rigidity of the rest, epitope III in this cocrystal complex adopts a unique conformation that is different from previously described E2 structures. With further analyses of molecular docking and phage display–based peptide interactions, we recognized that it is the arrangements of two separate sets of residues within epitope III that create these discrete conformations for the epitope to interact selectively with either mAb1H8 or CD81. These observations thus raise the possibility that local epitope III conformational dynamics, in conjunction with sequence variations, may act as a regulatory mechanism to coordinate “mAb1H8-like” antibody-mediated immune defenses with CD81-initiated HCV infections.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1990

State-variable models of structures having rigid-body modes

In cases where the equations of motion of a structure having rigid-body freedom are cast in state-variable form, generalized state rigid-body modes may be needed. It is possible to find a linearly-independent set of generalized vectors which transform an n x n matrix into the almost-diagonal Jordan form. Attention is presently given to equations governing these generalized eigenvectors, together with illustrative examples of the damped and undamped structure cases.

Craig, Roy R., Jr.↗

DOE OSTI2019

Impact of Rigidity on Molecular Self-Assembly

Rigid, cage-like molecules, like diamondoids, show unique self-assembly behavior, such as templating 1-D nanomaterial assembly via pathways that are typically blocked for such bulky substituents. We investigate molecular forces between diamondoids to explore why molecules with high structural rigidity exhibit these novel assembly pathways. The rigid nature of diamondoids significantly lowers configurational entropy, and we hypothesize that this influences molecular interaction forces. To test this concept, we calculated the distance-dependent impact of entropy on assembly using molecular dynamics simulations. To isolate pairwise entropic and enthalpic contributions to assembly, we considered pairs of molecules in a thermal bath, fixed at set intermolecular separations but otherwise allowed to freely move. By comparing diamondoids to linear alkanes, we draw out the impact of rigidity on the entropy and enthalpy of pairwise interactions. We find that linear alkanes actually exhibit stronger van der Waals interactions than diamondoids at contact, because the bulky structure of diamondoids induces larger net atomic separations. Yet, we also find that diamondoids pay lower entropic penalties when assembling into contact pairs. Thus, the cage-like shape of diamondoids introduces an enthalpic penalty at contact, but the penalty is counterbalanced by entropic effects. Investigating the distance dependence of entropic forces provides a mechanism to explore how rigidity influences molecular assembly. Our results show that low entropic penalties paid by diamondoids can explain the effectiveness of diamondoids in templating nanomaterial assembly. Hence, tuning molecular rigidity can be an effective strategy for controlling the assembly of functional materials, such as biomimetic surfaces and nanoscale materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Holographic entropy inequalities and multipartite entanglement

Abstract We study holographic entropy inequalities and their structural properties by making use of a judicious grouping of terms into certain multipartite information quantities. This allows us to recast cumbersome entropic expressions into much simpler ones which share interestingly rigid structures. By performing a systematic search over some of these structures, we are able to discover more than 1800 novel entropy inequalities for six parties, thereby demonstrating that these recastings provide a fruitful generating technique for uncovering new holographic entropy inequalities. In attempting to interpret the corresponding sign-definite quantities as correlation measures, we also obtain a no-go result: the superbalance property of holographic entropy inequalities turns out to preclude them from being monotonic under partial tracing. In the process, we also comment on the geometrical significance of multipartite information quantities and present various structural relations amongst them.

Physics↗

NASA NTRSDate not supplied

Fluid-Thermal-Structural Interactions in Ramp-Induced Shock-Wave Boundary-Layer Interactions at Mach6

Shock-wave boundary-layer interactions (SWBLI) pose unique challenges for the slender airframes and sharp control surfaces characteristic of high-speed airbreathing aircraft. Spikes in pressure and thermal loading have been shown to occur in SWBLI regions; thus, predicting their location and behavior proves critical for assuring aircraft structural integrity and fatigue resilience. SWBLIs frequently lead to severe turbulent boundary-layer separation and corresponding unsteady motions characterized by a wide range of frequencies. Low-frequency motion has been shown to couple with the structure of a compliant panel, and turbulent boundary layers thus present a particular danger for thin control surfaces. Previous studies have shown that the thermal loading on a compliant panel in a ramp-induced SWBLI may have a signi cant impact on the panel vibrations. A multitude of studies has investigated the heating on rigid structures, but a charactrization of the heating effects on compliant structures is necessary to fully understand the fluid-thermal-structural interactions (FTSI) occurring in ramp-induced SWBLIs. This studuses infrared thermography and high-frequency Kulite pressure transducers to examine the heating loads on rigid and compliant ramps at various angles and flow conditions at Mach 6.

Hypersonic↗

NASA NTRSDate not supplied

Fluid-Thermal-Structural Interactions in Ramp-Induced Shock-Wave Boundary-Layer Interactions at Mach 6

Hypersonic↗

DOE OSTI2018

DNA-binding induced conformational change of c-Myb R2R3 analyzed using diffracted X-ray tracking

Highlights: • DNA-binding protein, c-Myb R2R3, largely fluctuates in solution. • We evaluated structural dynamics of R2R3 using diffracted X-ray tracking (DXT). • The flexibility of R2R3 is decreased upon the DNA binding. • We could determine the DNA-binding energies of R2R3 using DXT. Previous structural analyses have shown that R2R3, the minimum unit of the DNA-binding domain of the transcriptional factor c-Myb, is largely flexible in solution, and changes to a more rigid structure upon DNA binding. In this study, we evaluated the structural dynamics using the diffracted X-ray tracking method, in correlation with DNA-binding abilities under different salt conditions, and compared them with the previous results. The resultant curve of the mean square angular displacements (MSD) clearly showed that the flexibility of R2R3 was decreased upon DNA binding, and the DNA-binding energies determined using the angular diffusion coefficients were in good agreement with those determined using isothermal titration calorimetry. The results of the MSD curves also indicate that the translational length reduces by approximately half upon DNA binding.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2018

Crystal structure of the nicotinamidase/pyrazinamidase PncA from Bacillus subtilis

Highlights: • Crystal structure of B. Subtilis PncA consists of an α/β domain and a subdomain. • The metal-binding site of BsPncA is located at the bottom of a large cavity between the core and the subdomain. • Zinc ion is pentahedrally coordinated within several highly conserved amino acid residues and one water molecule. • Both dimers and tetramers were observed in BsPncA protein crystals, but only dimers were observed in solution. The nicotinamidase/pyrazinamidase PncA is a member of a large family of hydrolase enzymes that catalyze the deamination of nicotinamide to nicotinic acid. PncA also functions as a pyrazinamidase in a wide variety of eubacteria and is an essential coenzyme in many cellular redox reactions in living systems. We report the crystal structure of substrate-free PncA from Bacillus subtilis (BsPncA) at 2.0 Å resolution to improve our understanding of the PncA family. The structure of BsPncA consists of an α/β domain and a subdomain. The subdomain of BsPncA has a different conformation than that of PncA enzymes from other organisms. The B-factor analysis revealed a rigid structure of the α/β domain, while the subdomain is highly flexible. Both dimers and tetramers were observed in BsPncA protein crystals, but only dimers were observed in solution. Our results provide useful information that will further enhance our understanding of the molecular functions of PncA family members.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Ligand-Structure-Dependent Coherent Vibrational Wavepacket Dynamics in Pyrazolate-Bridged Pt(II) Dimers

Bimetallic transition metal complexes have gained increasing attention because of their versatile functions in solar energy conversion and photonics applications arising from inter-metal electronic coupling. In bimetallic platinum (Pt) complexes, electronic communication between the Pt-centered and ligand-centered moieties have been shown to be critical for defining their excited-state dynamic trajectories undergoing either localized ligand centered (LC)/metal-to-ligand-charge-transfer (MLCT) transitions or delocalized metal-metal-to-ligand-charge-transfer (MMLCT) transitions. The branching of the excited-state intersystem crossing (ISC) trajectories are modulated through structural factors that alter the relative energies of the different states. In this study, we investigated the correlation of the structural factors influencing the excited state trajectories. Using femtosecond broadband transient absorption (fs-BBTA) spectroscopy, ultrafast dynamics in the excited state of two select Pt(II) dimers have been mapped out using their coherent vibrational wavepacket signatures in corresponding transient absorption spectra. To examine how the ligand moieties of the Pt(II) dimers influence excited-state dynamics and the coherent vibrational wavepacket behavior, here we carried out comparative studies on two pyrazolate-bridged Pt(II) dimers of the general formula [Pt( t Bu 2 Pz)(N^C)] 2 ( t Bu 2 Pz = 3,5-di-tert-butylpyrazole); N^C = 7,8-benzoquinoline (bzq, 1) or 1-phenylisoquinoline (piq, 2)). We found that photoexcitation into the low energy absorption bands of 1 and 2 respectively induce the formation of 1 MMLCT states from which ultrafast ISC proceeds, resulting in stimulated emission quenching and decoherence of the vibrational wavepacket motions. The results obtained in this study suggest that both energetics and the structural rigidity of the aromatic cyclometalating ligands in 1 and 2 can significantly influence dynamics along the excited state trajectory characterized by dephasing of the coherent oscillations. The collective results provide direct evidence of how ligand structure alters electronic dynamics along excited state trajectories associated with ISC processes, providing insight into using ligand design to steer photochemical processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Reduced Complexity Model Intercomparison Project Phase 2: Synthesizing Earth System Knowledge for Probabilistic Climate Projections

Abstract Over the last decades, climate science has evolved rapidly across multiple expert domains. Our best tools to capture state‐of‐the‐art knowledge in an internally self‐consistent modeling framework are the increasingly complex fully coupled Earth System Models (ESMs). However, computational limitations and the structural rigidity of ESMs mean that the full range of uncertainties across multiple domains are difficult to capture with ESMs alone. The tools of choice are instead more computationally efficient reduced complexity models (RCMs), which are structurally flexible and can span the response dynamics across a range of domain‐specific models and ESM experiments. Here we present Phase 2 of the Reduced Complexity Model Intercomparison Project (RCMIP Phase 2), the first comprehensive intercomparison of RCMs that are probabilistically calibrated with key benchmark ranges from specialized research communities. Unsurprisingly, but crucially, we find that models which have been constrained to reflect the key benchmarks better reflect the key benchmarks. Under the low‐emissions SSP1‐1.9 scenario, across the RCMs, median peak warming projections range from 1.3 to 1.7°C (relative to 1850–1900, using an observationally based historical warming estimate of 0.8°C between 1850–1900 and 1995–2014). Further developing methodologies to constrain these projection uncertainties seems paramount given the international community's goal to contain warming to below 1.5°C above preindustrial in the long‐term. Our findings suggest that users of RCMs should carefully evaluate their RCM, specifically its skill against key benchmarks and consider the need to include projections benchmarks either from ESM results or other assessments to reduce divergence in future projections.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2006

Manufacturing Precise, Lightweight Paraboloidal Mirrors

A process for fabricating a precise, diffraction- limited, ultra-lightweight, composite- material (matrix/fiber) paraboloidal telescope mirror has been devised. Unlike the traditional process of fabrication of heavier glass-based mirrors, this process involves a minimum of manual steps and subjective judgment. Instead, this process involves objectively controllable, repeatable steps; hence, this process is better suited for mass production. Other processes that have been investigated for fabrication of precise composite-material lightweight mirrors have resulted in print-through of fiber patterns onto reflecting surfaces, and have not provided adequate structural support for maintenance of stable, diffraction-limited surface figures. In contrast, this process does not result in print-through of the fiber pattern onto the reflecting surface and does provide a lightweight, rigid structure capable of maintaining a diffraction-limited surface figure in the face of changing temperature, humidity, and air pressure. The process consists mainly of the following steps: 1. A precise glass mandrel is fabricated by conventional optical grinding and polishing. 2. The mandrel is coated with a release agent and covered with layers of a carbon- fiber composite material. 3. The outer surface of the outer layer of the carbon-fiber composite material is coated with a surfactant chosen to provide for the proper flow of an epoxy resin to be applied subsequently. 4. The mandrel as thus covered is mounted on a temperature-controlled spin table. 5. The table is heated to a suitable temperature and spun at a suitable speed as the epoxy resin is poured onto the coated carbon-fiber composite material. 6. The surface figure of the optic is monitored and adjusted by use of traditional Ronchi, Focault, and interferometric optical measurement techniques while the speed of rotation and the temperature are adjusted to obtain the desired figure. The proper selection of surfactant, speed or rotation, viscosity of the epoxy, and temperature make it possible to obtain the desired diffraction-limited, smooth (1/50th wave) parabolic outer surface, suitable for reflective coating. 7. A reflective coat is applied by use of conventional coating techniques. 8. Once the final figure is set, a lightweight structural foam is applied to the rear of the optic to ensure stability of the figure.

Hermann, Frederick Thomas↗

NASA NTRS2009

Concepts for Life Cycle Cost Control Required to Achieve Space Transportation Affordability and Sustainability

Cost control must be implemented through the establishment of requirements and controlled continually by managing to these requirements. Cost control of the non-recurring side of life cycle cost has traditionally been implemented in both commercial and government programs. The government uses the budget process to implement this control. The commercial approach is to use a similar process of allocating the non-recurring cost to major elements of the program. This type of control generally manages through a work breakdown structure (WBS) by defining the major elements of the program. If the cost control is to be applied across the entire program life cycle cost (LCC), the approach must be addressed very differently. A functional breakdown structure (FBS) is defined and recommended. Use of a FBS provides the visibifity to allow the choice of an integrated solution reducing the cost of providing many different elements of like function. The different functional solutions that drive the hardware logistics, quantity of documentation, operational labor, reliability and maintainability balance, and total integration of the entire system from DDT&E through the life of the program must be fully defined, compared, and final decisions made among these competing solutions. The major drivers of recurring cost have been identified and are presented and discussed. The LCC requirements must be established and flowed down to provide control of LCC. This LCC control will require a structured rigid process similar to the one traditionally used to control weight/performance for space transportation systems throughout the entire program. It has been demonstrated over the last 30 years that without a firm requirement and methodically structured cost control, it is unlikely that affordable and sustainable space transportation system LCC will be achieved.

Rhodes, Russel E.↗