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Small-angle neutron scattering shows that electron transfer flavoprotein in solution populates extended conformations that are distinct from crystal structures. Extended conformations could mediate conformation changes that gate electron transfer.
A critical comparison of two basic formulations in three-dimensional elastostatics, using conforming and nonconforming boundary elements, is presented. The basic structure of the boundary element method is developed. The peculiarities that both types of boundary elements present in relation to the numerical implementation are discussed. Through selected examples, key issues such as the computational advantages and disadvantages of both formulations, mesh discretization and accuracy questions, and optimal location of the collocation nodes in the case of nonconforming elements are addressed. It is shown that conforming elements are able to produce more accurate results than nonconforming ones, with substantial economy in the final size of the system equations.
High-quality uncertainty quantification (UQ) is a critical component of enabling trust in deep learning (DL) models and is especially important if DL models are to be deployed in high-consequence applications. Conformal prediction (CP) methods represent an emerging nonparametric approach for producing UQ that is easily interpretable and, under weak assumptions, provides a guarantee regarding UQ quality. This report describes the research outputs of an Exploratory Express Laboratory Directed Research and Development (LDRD) project at Sandia National Laboratories. This project focused on how best to implement CP methods for DL models. This report introduces new methodology for obtaining high-quality UQ from DL models using CP methods, describes a novel system of assessing UQ quality, and provides experimental results that demonstrate the quality of the new methodology and utility of the UQ quality assessment system. Avenues for future research and discussion of potential impacts at Sandia and in the wider research community are also given.
A T-cell clone specific to apomyoglobin was generated. It was prepared from a T-cell culture obtained by in vitro driving of lymph node cells with apomyoglobin from SJL mice that have been primed in vivo with apomyoglobin. In proliferative assays, the T-cell clone responded to apomyoglobin but did not recognize native myoglobin or any of the synthetic peptides corresponding to the six T sites of myoglobin. The demonstration that a T-cell clone can be isolated, whose specificity is directed entirely to apomyoglobin and not to its counterpart myoglobin, with an identical amino acid composition, indicates the importance of the three-dimensional structure in the presentation of the protein to T cells.
A compositionally tunable series of AuCu films is active for electrocatalytic urea generation from carbon dioxide and nitrate.
Enzymes catalyze chemical reactions with remarkable rate enhancements and selectivity. Supramolecular catalysis seeks to understand and emulate these outcomes, leveraging noncovalent interactions, electric fields, and controlled active site microenvironments to enhance catalysis in an enzyme-like fashion. The effects of conformational dynamics on supramolecular catalysts and assemblies are, however, relatively unexplored, despite their crucial role in enzyme rate enhancement. Here, we elucidate the conformational landscape of a model M4L4 supramolecular host through a rational approach: stabilizing a high-energy conformer through distal ligand modification and a transient intermediate state through symmetry-matched guest encapsulation, as well as tuning the conformer distribution through same-charge metal exchange at the host vertices. Each of these structural modifications induces a substantial shift in the host's conformational landscape, offering insights into the rational design of conformationally dynamic cages and enzymes. Although the thermodynamic properties of the dynamic Ga4L412- cage can be influenced by temperature, solvent, and guest binding, we find that conformational change occurs on a time scale that renders it rate-limiting in a model catalytic reaction, precluding rate enhancement through conformational selection. This concept is illustrated by locking the catalytically inactive conformer to a high-energy conformer that is catalytically competent. These findings demonstrate that precise modulation of the conformational landscape of supramolecular hosts provides an effective strategy for controlling their catalytic activity and binding.
The Office of Chief Technologist, NASA identified the need for research and technology development in part from NASAs Strategic Goal 3.3 of the NASA Strategic Plan to develop and demonstrate the critical technologies that will make NASAs exploration, science, and discovery missions more affordable and more capable. Furthermore, the Game Changing Development Program is a primary avenue to achieve the Agencys 2011 strategic goal to Create the innovative new space technologies for our exploration, science, and economic future. The National Research Council (NRC) Space Technology Roadmaps and Priorities report highlights six challenges and they are: Mass to Surface, Surface Access, Precision Landing, Surface Hazard Detection and Avoidance, Safety and Mission Assurance, and Affordability. In order for NASA to meet these challenges, the report recommends immediate focus on Rigid and Flexible Thermal Protection Systems. Rigid TPS systems such as Avcoat or SLA are honeycomb based and PICA is in the form of tiles. The honeycomb systems are manufactured using techniques that require filling of each (38 cell) by hand, and in a limited amount of time all of the cells must be filled and the heatshield must be cured. The tile systems such as PICA pose a different challenge as the low strain-to-failure and manufacturing size limitations require large number of small tiles with gap-fillers between the tiles. Recent investments in flexible ablative systems have given rise to the potential for conformal ablative TPS. A conformal TPS over a rigid aeroshell has the potential to solve a number of challenges faced by traditional rigid TPS materials. The high strain-to-failure nature of the conformal ablative materials will allow integration of the TPS with the underlying aeroshell structure much easier and enable monolithic-like configuration and larger segments (or parts) to be used. By reducing the overall part count, the cost of installation (based on cost comparisons between blanket and tile materials on shuttle) should be significantly reduced. The conformal ablator design will include a simplified design of seams between gore panels, which should eliminate the need for gap filler design, and should accommodate a wider range of allowable carrier structure imperfections when compared to a rigid material such as PICA.The Conformal TPS development project leverages the past investments made by earlier projects with a goal to develop and deliver a TRL 5 conformal TPS capable of 250 Wcm2 for missions such as MSL or COTS missions. The capabilities goal for the conformal TPS is similar to an MSL design reference mission (250 Wcm2) with matching pressures and shear environments. Both conformal and flexible carbon-felt based materials were successfully tested in stagnation aerothermal environments above 500 Wcm2 under earlier programs. Results on a myriad of materials developed during FY11 were used to determine which materials to start with in FY12. In FY12, the conformal TPS element focused on establishing materials requirements based on MSL-type and COTS Low Earth orbit (LEO) conditions (q 250 Wcm2) to develop and deliver a Conformal Ablative TPS. In FY13, development and refining metrics for mission utilization of conformal ablator technology along with assessment for potential mission stakeholders will be carried out.
This presentation will update the community on the development of conformal ablative TPS. As described at IPPW-10, in FY12, the CA-TPS element focused on establishing materials requirements based on MSL-type and COTS Low Earth orbit (LEO) conditions (q 250 Wcm2) to develop and deliver a conformal ablative TPS. This involved downselecting, manufacturing and testing two of the best candidate materials, demonstrating uniform infiltration of resins into baseline 2-cm thick carbon felt, selecting a primary conformal material formulation based on novel arc jet and basic material properties testing, developing and demonstrating instrumentation for felt-based materials and, based on the data, developing a low fidelity material response model so that the conformal ablator TPS thickness for missions could be established. In addition, the project began to develop Industry Partnerships. Since the nominal thickness of baseline carbon felts was only 2-cm, a partnership with a rayon felt developer was made in order to upgrade equipment, establish the processes required and attempt to manufacture 10-cm thick white goods. A partnership with a processing house was made to develop the methodology to carbonize large pieces of the white goods into 7.5-cm thick carbon felt.In FY13, more advanced testing and modeling of the downselected conformal material was performed. Material thermal properties tests and structural properties tests were performed. The first 3 and 4-point bend tests were performed on the conformal ablator as well as PICA for comparison and the conformal ablator had outstanding behavior compared to PICA. Arc jet testing was performed with instrumented samples of both the conformal ablator and standard PICA at heating rates ranging from 40 to 400 Wcm2 and shear as high as 600 Pa. The results from these tests showed a remarkable improvement in the thermal penetration through the conformal ablator when compared to PICAs response. The data from these tests were used to develop a mid-fidelity thermal response model. Additional arc jet testing in the same conditions on various seam designs were very successful in showing that the material could be joined with a minimum of adhesive and required no complicated gap and gap filler design for installation. In addition, the partnership with industry to manufacture thicker rayon felt was very successful. The vendor made a 2-m wide by 30-m long sample of 10-cm thick rayon felt. When carbonized, the resulting thickness was over 7.5-cm thick, nearly 4 times the thickest off-the-shelf carbon felt. In FY14, the project has initiated a partnership with another vendor to begin the scale-up manufacturing effort. This year, the vendor will duplicate the process and manufacture at the current scale for comparison with NASA-processed materials. Properties testing and arc jet testing will be performed on the vendor-processed materials. Planning for manufacturing large, 1-m x 1-m, panels will begin as well. In FY15, the vendor will then manufacture large panels and the project will build a 2-m x 2-m Manufacturing Demonstration Unit (MDU).
Cockpit alerting systems monitor potentially hazardous situations, both inside and outside the aircraft. When a hazard is projected to occur, the alerting system displays alerts and/or command decisions to the pilot. However, pilots have been observed to not conform to alerting system commands by delaying their response or by not following the automatic commands exactly. This non-conformance to the automatic alerting system can reduce its benefit. Therefore, a need exists to understand the causes and effects of pilot non-conformance in order to develop automatic alerting systems whose commands the pilots are more likely to follow. These considerations were examined through flight simulator evaluations of the collision avoidance task during closely spaced parallel approaches. This task provided a useful case-study because the effects of non-conformance can be significant, given the time-critical nature of the task. A preliminary evaluation of alerting systems identified non-conformance in over 40% of the cases and a corresponding drop in collision avoidance performance. A follow-on experiment found subjects' alerting and maneuver selection criteria were consistent with different strategies than those used by automatic systems, indicating the pilot may potentially disagree with the alerting system if the pilot attempts to verify automatic alerts and commanded avoidance maneuvers. A final experiment found supporting automatic alerts with the explicit display of its underlying criteria resulted in more consistent subject reactions. In light of these experimental results, a general discussion of pilot non-conformance is provided. Contributing factors in pilot non-conformance include a lack of confidence in the automatic system and mismatches between the alerting system's commands and the pilots' own decisions based on the information available to them. The effects of non-conformance on system performance are discussed. Possible methods of reconciling mismatches are given, and design considerations for alerting systems which alleviate the problem of non-conformance are provided.
NASA’s X-57 Maxwell flight demonstrator has a high-lift system that includes 12 fixed- pitch high-lift propellers located upstream of the wing leading edge for lift augmentation at low speeds. These high-lift propellers are only required at low speeds, and to reduce drag, the propeller blades are folded conformally along the nacelles at other operating conditions. The method of designing the high-lift blades permits several variations of blade cross-section placement along the nacelle surface and a comparative performance analysis was needed to determine if any particular design showed significant benefits. We analyzed the performance of three conformal high-lift propeller designs and compared them to that of a non-conformal baseline propeller to establish both the benefit of stowable blades and the value of each variation. In this study, we first performed a drag analysis of each design in the stowed configuration at the X-57 cruise speed and altitude to determine the drag benefits of each conforming method. Then, among blade designs we compared the thrust, power, and lift for a given input shaft speed to establish any performance losses from the baseline. This analysis shows that the conformal blade designs do not have any appreciable performance losses compared to the baseline blades. Moreover, although the drag in the cruise condition is significantly less than for the non-folding baseline, the drag benefits of each conforming blade approach are similar and the value of each approach largely depends on the ease of integration into the nacelle. This paper presents the results of these studies and discusses the benefits and drawbacks of implementing the conformal blade designs. Specifically, we demonstrate that folding, conformal propeller blades contribute significantly less to cruise drag when compared to windmilling, with an increase relative to a. We also show a less than 1% difference in performance formal, folding propellers and the non-conforming baseline propeller.
We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.
As described at IPPW-10, in FY12, the CA-TPS element focused on establishing materials requirements based on MSL-type and COTS Low Earth orbit (LEO) conditions (q 250 Wcm2) to develop and deliver a conformal ablative TPS. This involved down selecting, manufacturing and testing two of the best candidate materials, demonstrating uniform infiltration of resins into baseline 2-cm thick carbon felt, selecting a primary conformal material formulation based on novel arc jet and basic material properties testing, developing and demonstrating instrumentation for felt-based materials and, based on the data, developing a low fidelity material response model so that the conformal ablator TPS thickness for missions could be established. In addition, the project began to develop Industry Partnerships. Since the nominal thickness of baseline carbon felts was only 2-cm, a partnership with a rayon felt developer was made in order to upgrade equipment, establish the processes required and attempt to manufacture 10-cm thick white goods. A partnership with a processing house was made to develop the methodology to carbonize large pieces of the white goods into 7.5-cm thick carbon felt. In FY13, more advanced testing and modeling of the down selected conformal material was performed. Material thermal properties tests and structural properties tests were performed. The first 3 and 4-point bend tests were performed on the conformal ablator as well as PICA for comparison and the conformal ablator had outstanding behavior compared to PICA. Arc jet testing was performed with instrumented samples of both the conformal ablator and standard PICA at heating rates ranging from 40 to 400 Wcm2 and shear as high as 600 Pa. The results from these tests showed a remarkable improvement in the thermal penetration through the conformal ablator when compared to PICAs response. The data from these tests were used to develop a mid-fidelity thermal response model. Additional arc jet testing in the same conditions on various seam designs were very successful in showing that the material could be joined with a minimum of adhesive and required no complicated gap and gap filler design for installation. In addition, the partnership with industry to manufacture thicker rayon felt was very successful. The vendor made a 2-m wide by 30-m long sample of 10-cm thick rayon felt. When carbonized, the resulting thickness was over 7.5-cm thick, nearly 4 times the thickest off-the-shelf carbon felt. In FY14, the project has initiated a partnership with another vendor to begin the scale-up manufacturing effort. This year, the vendor will duplicate the process and manufacture at the current scale for comparison with NASA-processed materials. Properties testing and arc jet testing will be performed on the vendor-processed materials. Planning for manufacturing large, 1-m x 1-m, panels will begin as well. In FY15, the vendor will then manufacture large panels and the project will build a 2-m x 2-m Manufacturing Demonstration Unit (MDU).
Understanding how a macromolecule’s primary sequence governs its conformational landscape is crucial for elucidating its function, yet these design principles are still emerging for macromolecules with intrinsic disorder. Herein, we introduce a high-throughput workflow that implements a practical colorimetric conformational assay, introduces a semi-automated sequencing protocol using matrix-assisted laser desorption/ionization and tandem mass spectrometry (MALDI-MS/MS), and develops a generalizable sequence-structure algorithm. Using a model system of 20mer peptidomimetics containing polar glycine and hydrophobic N-butylglycine residues, we identified nine classifications of conformational disorder and isolated 122 unique sequences across varied compositions and conformations. Conformational distributions of three compositionally identical library sequences were corroborated through atomistic simulations and ion mobility spectrometry coupled with liquid chromatography. A data-driven strategy was developed using existing sequence variables and data-derived “motifs” to inform a machine-learning algorithm toward conformation prediction. Here, this multifaceted approach enhances our understanding of sequence-conformation relationships and offers a powerful tool for accelerating the discovery of materials with conformational control.
Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.
Assemblies of tanks having shapes that conform to each other and/or conform to other proximate objects have been investigated for use in storing fuels and oxidizers in small available spaces in upper stages of spacecraft. Such assemblies might also prove useful in aircraft, automobiles, boats, and other terrestrial vehicles in which space available for tanks is limited. The basic concept of using conformal tanks to maximize the utilization of limited space is not new in itself: for example, conformal tanks are used in some automobiles to store windshield -washer liquid and coolant that overflows from radiators. The novelty of the present development lies in the concept of an assembly of smaller conformal tanks, as distinguished from a single larger conformal tank. In an assembly of smaller tanks, it would be possible to store different liquids in different tanks. Even if the same liquid were stored in all the tanks, the assembly would offer an advantage by reducing the mechanical disturbance caused by sloshing of fuel in a single larger tank: indeed, the requirement to reduce sloshing is critical in some applications. The figure shows a prototype assembly of conformal tanks. Each tank was fabricated by (1) copper plating a wax tank mandrel to form a liner and (2) wrapping and curing layers of graphite/epoxy composite to form a shell supporting the liner. In this case, the conformal tank surfaces are flat ones where they come in contact with the adjacent tanks. A band of fibers around the outside binds the tanks together tightly in the assembly, which has a quasi-toroidal shape. For proper functioning, it would be necessary to maintain equal pressure in all the tanks.
We examine the question of scale versus conformal invariance on maximally symmetric curved backgrounds and study general two-derivative conformally invariant free theories of vectors and tensors. For spacetime dimension D > 4 , these conformal theories can be diagonalized into standard massive fields in which unbroken conformal symmetry nontrivially mixes components of different spins. In D = 4 , the tensor case becomes a conformal theory mixing a partially massless spin-2 field with a massless spin-1 field. For massless linearized gravity in D = 4 , we confirm through direct calculation that correlation functions of gauge-invariant operators take the conformally invariant form, despite the absence of standard conformal symmetry at the level of the action. Published by the American Physical Society 2024
In support of the CA250 project, this paper details the results of a test campaign that was conducted at the Ames Arcjet Facility, wherein several novel low density thermal protection (TPS) materials were evaluated in an entry like environment. The motivation for these tests was to investigate whether novel conformal ablative TPS materials can perform under high heat flux and shear environment as a viable alternative to rigid ablators like PICA or Avcoat for missions like MSL and beyond. A conformable TPS over a rigid aeroshell has the potential to solve a number of challenges faced by traditional rigid TPS materials (such as tiled Phenolic Impregnated Carbon Ablator (PICA) system on MSL, and honeycomb-based Avcoat on the Orion Multi Purpose Crew Vehicle (MPCV)). The compliant (high strain to failure) nature of the conformable ablative materials will allow better integration of the TPS with the underlying aeroshell structure and enable monolithic-like configuration and larger segments to be used in fabrication.A novel SPRITE1 architecture, developed by the researchers at NASA Ames was used for arcjet testing. This small probe like configuration with 450 spherecone, enabled us to test the materials in a combination of high heat flux, pressure and shear environment. The heat flux near the nose were in the range of 500-1000 W/sq cm whereas in the flank section of the test article the magnitudes were about 50 of the nose, 250-500W/sq cm range. There were two candidate conformable materials under consideration for this test series. Both test materials are low density (0.28 g/cu cm) similar to Phenolic Impregnated Carbon Ablator (PICA) or Silicone Impregnated Refractory Ceramic Ablator (SIRCA) and are comprised of: A flexible carbon substrate (Carbon felt) infiltrated with an ablative resin system: phenolic (Conformal-PICA) or silicone (Conformal-SICA). The test demonstrated a successful performance of both the conformable ablators for heat flux conditions between 50-500 W/sq cm. The recession and temperature profile for these materials were comparable to PICA proving them to be viable alternatives for TPS technology development for future missions.
The conjugated polymer’s backbone conformation dictates the delocalization of electrons, ultimately affecting its optoelectronic properties. Most conjugated polymers can be viewed as semirigid rods with their backbone embedded among long alkyl side chains. Thus, it is challenging to experimentally quantify the conformation of a conjugated backbone. Here, we performed contrast variation neutron scattering on rigid conjugated donor–acceptor (D–A) diketopyrrolopyrrole (DPP) polymers with selectively deuterated side chains to measure the conjugated backbone conformation. We first synthesized DPPbased polymers with deuterated side chains, confirmed by NMR and FTIR. Using contrast variation neutron scattering, we found that the DPP-based conjugated polymers are much more rigid than poly(3-alkylthiophenes), with persistence length (L p ) at 16–18 nm versus 2–3 nm. More importantly, in contrast to the relatively flexible poly(3-alkylthiophenes) whose backbone is more flexible than the whole polymer, we found that the backbone of DPP-based polymers has the same L p value compared to the whole polymer chain. This indicates that side chain interference on backbone conformation is not present for the semirigid polymer, which is further confirmed by coarse-grained molecular dynamics (CG-MD) simulations. Our work provides a novel protocol to probe polymer’s backbone conformation and paradigm-shifting understanding of the backbone conformation of semirigid conjugated polymers.