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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Modular Commutators in Conformal Field Theory

The modular commutator is a recently discovered entanglement quantity that quantifies the chirality of the underlying many-body quantum state. In this Letter, we derive a universal expression for the modular commutator in conformal field theories in 1 + 1 dimensions and discuss its salient features. We show that the modular commutator depends only on the chiral central charge and the conformal cross ratio. We test this formula for a gapped (2 + 1)-dimensional system with a chiral edge, i.e., the quantum Hall state, and observe excellent agreement with numerical simulations. Furthermore, we propose a geometric dual for the modular commutator in certain preferred states of the AdS/CFT correspondence. Finally, for these states, we argue that the modular commutator can be obtained from a set of crossing angles between intersecting Ryu-Takayanagi surfaces.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Conformer-Specific Dissociation Dynamics in Dimethyl Methylphosphonate Radical Cation

The dynamics of the dimethyl methylphosphonate (DMMP) radical cation after production by strong field adiabatic ionization have been investigated. Pump-probe experiments using strong field 1300 nm pulses to adiabatically ionize DMMP and a 800 nm non-ionizing probe induce coherent oscillations of the parent ion yield with a period of about 45 fs. The yields of two fragments, PO 2 C 2 H 7 + and PO 2 CH 4 + , oscillate approximately out of phase with the parent ion, but with a slight phase shift relative to each other. We use electronic structure theory and nonadiabatic surface hopping dynamics to understand the underlying dynamics. The results show that while the cation oscillates on the ground state along the P=O bond stretch coordinate, the probe excites population to higher electronic states that can lead to fragments PO 2 C 2 H 7 + and PO 2 CH 4 + . The computational results combined with the experimental observations indicate that the two conformers of DMMP that are populated under experimental conditions exhibit different dynamics after being excited to the higher electronic states of the cation leading to different dissociation products. These results highlight the potential usefulness of these pump-probe measurements as a tool to study conformer-specific dynamics in molecules of biological interest.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Conformational Control of DNA Origami by DNA Oligomers, Intercalators and UV Light

DNA origami has garnered great attention due to its excellent programmability and precision. It offers a powerful means to create complex nanostructures which may not be possible by other methods. The macromolecular structures may be used as static templates for arranging proteins and other molecules. They are also capable of undergoing structural transformation in response to external signals, which may be exploited for sensing and actuation at the nanoscale. Such on-demand reconfigurations are executed mostly by DNA oligomers through base-pairing and/or strand displacement, demonstrating drastic shape changes between two different states, for example, open and close. Recent studies have developed new mechanisms to modulate the origami conformation in a controllable, progressive manner. Here we present several methods for conformational control of DNA origami nanostructures including chemical adducts and UV light as well as widely applied DNA oligomers. The detailed methods should be useful for beginners in the field of DNA nanotechnology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states

Full-length Bruton’s tyrosine kinase (BTK) has been refractory to structural analysis. The nearest full-length structure of BTK to date consists of the autoinhibited SH3–SH2–kinase core. Precisely how the BTK N-terminal domains (the Pleckstrin homology/Tec homology [PHTH] domain and proline-rich regions [PRR] contain linker) contribute to BTK regulation remains unclear. We have produced crystals of full-length BTK for the first time but despite efforts to stabilize the autoinhibited state, the diffraction data still reveal only the SH3–SH2–kinase core with no electron density visible for the PHTH–PRR segment. Cryo-electron microscopy (cryoEM) data of full-length BTK, on the other hand, provide the first view of the PHTH domain within full-length BTK. CryoEM reconstructions support conformational heterogeneity in the PHTH–PRR region wherein the globular PHTH domain adopts a range of states arrayed around the autoinhibited SH3–SH2–kinase core. On the way to activation, disassembly of the SH3–SH2–kinase core opens a new autoinhibitory site on the kinase domain for PHTH domain binding that is ultimately released upon interaction of PHTH with phosphatidylinositol (3,4,5)-trisphosphate. Membrane-induced dimerization activates BTK and we present here a crystal structure of an activation loop swapped BTK kinase domain dimer that likely represents the conformational state leading to trans-autophosphorylation. Together, these data provide the first structural elucidation of full-length BTK and allow a deeper understanding of allosteric control over the BTK kinase domain during distinct stages of activation.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2015

Conformal Ablative Thermal Protection System for Small and Large Scale Missions: Approaching TRL 6 for Planetary and Human Exploration Missions and TRL 9 for Small Probe Missions

In 2011, NASAs Aeronautics Research Mission Directorate (ARMD) funded an effort to develop an ablative thermal protection system (TPS) material that would have improved properties when compared to Phenolic Impregnated Carbon Ablator (PICA) and AVCOAT. Their goal was a conformal material, processed with a flexible reinforcement that would result in similar or better thermal characteristics and higher strain-to-failure characteristics that would allow for easier integration on flight aeroshells than then-current rigid ablative TPS materials. In 2012, NASAs Space Technology Mission Directorate (STMD) began funding the maturation of the best formulation of the game changing conformal ablator, C-PICA. Progress has been reported at IPPW over the past three years, describing C-PICA with a density and recession rates similar to PICA, but with a higher strain-to-failure which allows for direct bonding and no gap fillers, and even more important, with thermal characteristics resulting in half the temperature rise of PICA. Overall, C-PICA should be able to replace PICA with a thinner, lighter weight, less complicated design. These characteristics should be particularly attractive for use as backshell TPS on high energy planetary entry vehicles. At the end of this year, the material should be ready for missions to consider including in their design, in fact, NASAs Science Mission Directorate (SMD) is considering incentivizing the use of C-PICA in the next Discovery Proposal call. This year both scale up of the material to large (1-m) sized pieces and the design and build of small probe heatshields for flight tests will be completed. NASA, with an industry partner, will build a 1-m long manufacturing demonstration unit (MDU) with a shape based on a mid LD lifting body. In addition, in an effort to fly as you test and test as you fly, NASA, with a second industry partner, will build a small probe to test in the Interactive Heating Facility (IHF) arc jet and, using nearly the same design, build the aeroshell and TPS, with instrumentation, for a small probe flight test article, due to fly in 2017. At the end of the year, the C-PICA will be at TRL 5+, and with the flight data in 2017, it will be at TRL 9 for missions needs with C-PICA at a small scale (12 diameter). The scale-up and small probe efforts will be de-scribed in this presentation.

Conformal Ablative↗
NASA NTRS2016

Conformal Ablative Thermal Protection Systems (CA-TPS) for Venus and Saturn Backshells

This poster provides an overview of the work performed to date on the Conformal Ablative TPS (CA-TPS) element of the TPSM project out of GCDP. Under this element, NASA is developing improved ablative TPS materials based on flexible felt for reinforcement rather than rigid reinforcements. By replacing the reinforcements with felt, the resulting materials have much higher strain-to-failure and are much lower in thermal conductivity than their rigid counterparts. These characteristics should allow for larger tile sizes, direct bonding to aeroshells and even lower weight TPS. The conformal phenolic impregnated carbon felt (C-PICA) is a candidate for backshell TPS for both Venus and Saturn entry vehicles.

Saturn↗
NASA NTRSDate not supplied

Conformal PICA TPS– Enabling Future Nasa Planetary Science Missions

Initial development of conformal PICA (C-PICA) ablative TPS occurred under NASA’s Hypersonics Project in the 2000’s and demonstrated very low through the thickness conductivity compared to state-of-the-art PICA. PICA, which was first demonstrated on Stardust, has some inherent limitations that C-PICA improves on, primarily strain to failure. More recently C-PICA has been further matured and a family of C-PICA materials are now ready for consideration as an enabling technology for New Frontiers and other NASA missions. C-PICA has several improvements compared to PICA including: - Higher strain to failure and lower thermal conductivity (up to 55% less than PICA depending on C-PICA variant) - CTE comparable to typical composite carrier structures - Temperature independent mechanical properties - Suited for single piece (up to ~ 1.5m) or tiled configurations - Larger tiles leading to reduced integration complexity compared to tiled PICA - Reduced mass compared to PICA due to reduced thermal conductivity C-PICA has been tested at heating fluxes ranging from 250-1850 W/cm2 with excellent performance. Based on our evaluation, multiple missions listed on the SMD Technology Showcase will potentially need a thermal protection system capable of withstanding entry environments where C-PICA is suited either as a forebody or backshell TPS. We will be highlighting mature conformal PICA variants to support the following missions at the showcase in January 2023.

thermal protection↗
DOE OSTI2023

Boosting Piezoelectricity by 3D Printing PVDF‐MoS 2 Composite as a Conformal and High‐Sensitivity Piezoelectric Sensor

Abstract Additively manufactured flexible and high‐performance piezoelectric devices are highly desirable for sensing and energy harvesting of 3D conformal structures. Herein, the study reports a significantly enhanced piezoelectricity in polyvinylidene fluoride (PVDF) achieved through the in situ dipole alignment of PVDF within PVDF‐2D molybdenum disulfide (2D MoS 2 ) composite by 3D printing. The shear stress‐induced dipole poling of PVDF and 2D MoS 2 alignment are harnessed during 3D printing to boost piezoelectricity without requiring a post‐poling process. The results show a remarkable, more than the eight‐fold increment in the piezoelectric coefficient ( d 33 ) for 3D printed PVDF‐8wt.% MoS 2 composite over cast neat PVDF. The underlying mechanism of piezoelectric property enhancement is attributed to the increased volume fraction of β phase in PVDF, filler fraction, heterogeneous strain distribution around PVDF‐MoS 2 interfaces, and strain transfer to the nanofillers as confirmed by microstructural analysis and finite element simulation. These results provide a promising route to design and fabricate high‐performance 3D piezoelectric devices via 3D printing for next‐generation sensors and mechanical–electronic conformal devices.

2D MoS2↗
DOE OSTI2020

Concurrently Approaching Volumetric and Specific Capacity Limits of Lithium Battery Cathodes via Conformal Pickering Emulsion Graphene Coatings

Abstract To achieve the high energy densities demanded by emerging technologies, lithium battery electrodes need to approach the volumetric and specific capacity limits of their electrochemically active constituents, which requires minimization of the inactive components of the electrode. However, a reduction in the percentage of inactive conductive additives limits charge transport within the battery electrode, which results in compromised electrochemical performance. Here, an electrode design that achieves efficient electron and lithium‐ion transport kinetics at exceptionally low conductive additive levels and industrially relevant active material areal loadings is introduced. Using a scalable Pickering emulsion approach, Ni‐rich LiNi 0.8 Co 0.15 Al 0.05 O 2 (NCA) cathode powders are conformally coated using only 0.5 wt% of solution‐processed graphene, resulting in an electrical conductivity that is comparable to 5 wt% carbon black. Moreover, the conformal graphene coating mitigates degradation at the cathode surface, thus providing improved electrochemical cycle life. The morphology of the electrodes also facilitates rapid lithium‐ion transport kinetics, which provides superlative rate capability. Overall, this electrode design concurrently approaches theoretical volumetric and specific capacity limits without tradeoffs in cycle life, rate capability, or active material areal loading.

Park, Kyu‐Young↗
DOE OSTI2020

Membrane Proteins Have Distinct Fast Internal Motion and Residual Conformational Entropy

Abstract The internal motions of integral membrane proteins have largely eluded comprehensive experimental characterization. Here the fast side‐chain dynamics of the α‐helical sensory rhodopsin II and the β‐barrel outer membrane protein W have been investigated in lipid bilayers and detergent micelles by solution NMR relaxation techniques. Despite their differing topologies, both proteins have a similar distribution of methyl‐bearing side‐chain motion that is largely independent of membrane mimetic. The methyl‐bearing side chains of both proteins are, on average, more dynamic in the ps–ns timescale than any soluble protein characterized to date. Accordingly, both proteins retain an extraordinary residual conformational entropy in the folded state, which provides a counterbalance to the absence of the hydrophobic effect. Furthermore, the high conformational entropy could greatly influence the thermodynamics underlying membrane‐protein functions, including ligand binding, allostery, and signaling.

O'Brien, Evan S.↗
DOE OSTI2022

M379A Mutant Tyrosine Phenol–lyase from Citrobacter freundii Has Altered Conformational Dynamics

The M379A mutant of Citrobacter freundii tyrosine phenol-lyase (TPL) has been prepared. M379A TPL is a robust catalyst to prepare a number of tyrosines substituted at the 3-position with bulky groups that cannot be made with wild type TPL. The three dimensional structures of M379A TPL complexed with L-methionine and 3-bromo-DL-phenylalanine have been determined by X-ray crystallography. Methionine is bound as a quinonoid complex in a closed active site in 3 of 4 chains of homotetrameric M379A TPL. M379A TPL reacts with L-methionine about 8-fold slower than wild type TPL. The temperature dependence shows that the slower reaction is due to less positive activation entropy. The structure of the M379A TPL complex of 3-bromo-DL-phenylalanine has a quinonoid complex in two subunits, with an open active site conformation. The effects of the M379A mutation on TPL suggest that the mutant enzyme has altered the conformational dynamics of the active site.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Methyl α‐D‐galactopyranosyl‐(1→3)‐β‐D‐galactopyranoside and methyl β‐D‐galactopyranosyl‐(1→3)‐β‐D‐galactopyranoside: Glycosidic linkage conformation determined from MA'AT analysis

Abstract MA'ATanalysis has been applied to two biologically‐importantO‐glycosidic linkages in two disaccharides, α‐D‐Galp‐(1→3)‐β‐D‐GalpOMe (3) and β‐D‐Galp‐(1→3)‐β‐D‐GalpOMe (4). Using density functional theory (DFT) to obtain parameterized equations relating a group of trans‐O‐glycosidic NMR spin‐couplings to eitherphi(ϕ') orpsi(ψ'), and experimental 3 J COCH , 2 J COC , and 3 J COCC spin‐couplings measured in aqueous solution in 13 C‐labeled isotopomers, probability distributions ofϕ'andψ'in each linkage were determined and compared to those determined by aqueous 1‐μs molecular dynamics (MD) simulation. Good agreement was found between theMA'ATand single‐state MD conformational models of these linkages for the most part, with modest (approximately <15°) differences in the mean values ofϕ'andψ', although the envelope of allowed angles (encoded in circular standard deviations or CSDs) is consistently larger forϕ'determined fromMA'ATanalysis than from MD for both linkages. TheMA'ATmodel of the α‐Galp‐(1→3)‐β‐Galplinkage agrees well with those determined previously using conventional NMR methods ( 3 J COCH values and/or 1 H‐ 1 H NOEs), but some discrepancy was observed for the β‐Galp‐(1→3)‐β‐Galplinkage, which may arise from errors in the conventions used to describe the linkage torsion angles. Statistical analyses of X‐ray crystal structures show ranges ofϕ'andψ'for both linkages that include the mean angles determined fromMA'ATanalyses, although both angles adopt a wide range of values in the crystalline state, withϕ'in β‐Galp‐(1→3)‐β‐Galplinkages showing greater‐than‐expected conformational variability.

Chemistry↗
DOE OSTI2025

Crystal structures of Salmonella enterica FraB deglycase reveal a conformational heterodimer with remarkable structural plasticity at the active site

Abstract Thefralocus ofSalmonella entericaencodes five genes for metabolism of fructose‐asparagine, an Amadori product formed by condensation of asparagine with glucose. In the last step of this pathway, the FraB deglycase cleaves 6‐phospho‐fructose‐aspartate into glucose‐6‐phosphate and aspartate. In homology models, FraB forms a homodimer with two equivalent active sites located at the dimer interface. E214 and H230, two invariant residues essential for catalysis, project into each active site cleft from opposing subunits of the dimer. Here, we have determined six crystal structures of FraB, three of a variant containing an N‐terminal His 6 tag and two mutations needed for crystallization (hereafter referred to as WT′), two with additional mutations to active site residues (E214A and P232A), and one of a variant with C‐terminal residues 313–325 deleted. Surprisingly, in the WT′ FraB structure, the two catalytic residues, E214 (general base) and H230 (general acid), are positioned ~22 Å apart. In the E214A and C‐terminus‐truncated FraB variants, however, a conformational change in the E214‐residing helix brings E214 and H230* to ~7 Å (* indicates residue from the second protomer that creates the inter‐subunit catalytic center). The loop bearing H230 also exhibits significant variation, ranging from being completely disordered to adopting open or closed states, with the nearby P232* residue being eithercisortrans. The C‐terminal residues 313–325 form a flexible “C‐tail” that can be fully disordered, bind in the active site to block access of substrate, or angle across the active site to wrap across the other subunit of the dimer and potentially close over substrate. Collectively, these structures reveal that FraB is a conformational heterodimer with two chemically identical subunits that are constrained to adopt different structures as they come together for catalysis. This plasticity likely involves correlated opening and closure of the two active sites for their respective binding and release of substrates and ligands.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Thiol post-translational modifications modulate allosteric regulation of the OpcA–G6PDH complex through conformational gate control

In cyanobacteria, the redox-sensitive protein OpcA acts as a metabolic switch for G6PDH, enabling rapid adjustment of reducing power generation from glycogen catabolism and thereby precisely regulating carbon flux between anabolic and catabolic pathways. Although redox-sensitive cysteines in OpcA are known to regulate G6PDH, the mechanisms by which redox post-translational modifications (PTMs) on OpcA control G6PDH structure and activity remain unclear. Here, we combine computational modeling with experimental redox proteomics in Synechococcus elongatus PCC 7942 to dissect this mechanism. Experimentally, redox proteome analysis revealed differential redox PTM patterns, particularly on cysteines within the G6PDH-binding site of OpcA. These environmentally sensitive PTM changes at the interface suggest that thiol modifications in this region form a key regulatory node. More broadly, redox proteomics identified site-specific cysteine modifications under light/dark transitions and circadian cycling, linking distinct redox regimes to discrete PTM states. We employed PTM-Psi simulations to show that thiol PTMs near the OpcA–G6PDH interface are critical for allosteric regulation of G6PDH. The thiol PTMs on OpcA affect a putative gate region in G6PDH for substrate ingress and product egress as well as key hydrogen-bond networks within the active site. We infer that PTMs on OpcA tune the conformational landscapes of individual G6PDH subunits toward functionally relevant configurations according to environmental gradients, biasing the enzyme toward catalytically favorable states. Together, our results reveal a molecular mechanism in which thiol PTMs on OpcA modulate G6PDH structure and function through PTM-induced reorganization of conformational dynamics and allosteric communication. These findings demonstrate that PTM-level regulation provides a critical control layer from genotypes to phenotypes that enables cyanobacteria to rapidly adapt to environmental fluctuations through precise metabolic fine-tuning.

Allosteric regulation↗
DOE OSTI2020

Engineering Supramolecular Polymer Conformation for Efficient Carbon Nanotube Sorting

Supramolecular polymer sorting is a promising approach to separating single-walled carbon nanotubes (CNTs) by electronic type. Unlike conjugated polymers, they can be easily removed from the CNTs after sorting by breaking the supramolecular bonds, allowing for isolation of electronically pristine CNTs as well as facile recycling of the sorting polymer. However, little is understood about how supramolecular polymer properties affect CNT sorting. Herein, chain stoppers are used to engineer the conformation of a supramolecular sorting polymer, thereby elucidating the relationship between sorting efficacy and polymer conformation. Through NMR and UV–vis spectroscopy, small-angle X-ray scattering (SAXS), and thermodynamic modeling, it is shown that this supramolecular polymer exhibits ring–chain equilibrium, and that this equilibrium can be skewed toward chains by the addition of chain stoppers. Furthermore, by controlling the stopper–monomer ratio, the sorting yield can be doubled from 7% to 14% without compromising the semiconducting purity (>99%) or properties of sorted CNTs.

42 ENGINEERING↗
DOE OSTI2022

Universally Accessible Structural Data on Macromolecular Conformation, Assembly, and Dynamics by Small Angle X-Ray Scattering for DNA Repair Insights.

Structures provide a critical breakthrough step for biological analyses, and small angle X-ray scattering (SAXS) is a powerful structural technique to study dynamic DNA repair proteins. As toxic and mutagenic repair intermediates need to be prevented from inadvertently harming the cell, DNA repair proteins often chaperone these intermediates through dynamic conformations, coordinated assemblies, and allosteric regulation. By measuring structural conformations in solution for both proteins, DNA, RNA, and their complexes, SAXS provides insight into initial DNA damage recognition, mechanisms for validation of their substrate, and pathway regulation. Here, we describe exemplary SAXS analyses of a DNA damage response protein spanning from what can be derived directly from the data to obtaining super resolution through the use of SAXS selection of atomic models. We outline strategies and tactics for practical SAXS data collection and analysis. Making these structural experiments in reach of any basic and clinical researchers who have protein, SAXS data can readily be collected at government-funded synchrotrons, typically at no cost for academic researchers. In addition to discussing how SAXS complements and enhances cryo-electron microscopy, X-ray crystallography, NMR, and computational modeling, we furthermore discuss taking advantage of recent advances in protein structure prediction in combination with SAXS analysis.

Chinnam, Naga Babu↗
DOE OSTI2023

Conformal freeze-in, composite dark photon, and asymmetric reheating

Large classes of dark sector models feature mass scales and couplings very different from the ones we observe in the Standard Model (SM). Moreover, in the freeze-in mechanism, often employed by the dark sector models, it is also required that the dark sector cannot be populated during the reheating process like the SM. This is the so called asymmetric reheating. Such disparities in sizes and scales often call for dynamical explanations. In this paper, we explore a scenario in which slow evolving conformal field theories (CFTs) offer such an explanation. Building on the recent work on conformal freeze-in (COFI), we focus on a coupling between the Standard Model Hypercharge gauge boson and an anti-symmetric tensor operator in the dark CFT. We present a scenario which dynamically realizes the asymmetric reheating and COFI production. With a detailed study of dark matter production, and taking into account limits on the dark matter (DM) self-interaction, warm DM bound, and constraints from the stellar evolution, we demonstrate that the correct relic abundance can be obtained with reasonable choices of parameters. The model predicts the existence of a dark photon as an emergent composite particle, with a small kinetic mixing also determined by the CFT dynamics, which correlates it with the generation of the mass scale of the dark sector. At the same time, COFI production of dark matter is very different from those freeze-in mediated by the dark photon. This is an example of the physics in which a realistic dark sector model can often be much richer and with unexpected features.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Time dependence of reflected entropy in rational and holographic conformal field theories

We calculate the time dependence of the reflected entropy of two disconnected regions after a global quench in (1 + 1)-dimensional conformal field theories and in large temperature limit. For rational conformal field theories, we find that the time evolution of the reflected entropy is the same as that of the mutual information. We get the same result for holographic theories in the limit where the separation between disconnected regions is much smaller than their respective sizes. We discuss how this result is consistent with the quasi-particle picture of Calabrese and Cardy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗