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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

CryoTRANS: predicting high-resolution maps of rare conformations from self-supervised trajectories in cryo-EM

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.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Searching for Conformity Across Cosmic Time with Local Group and Local Volume Star Formation Histories

Conformity denotes the correlation of properties between pairs of galaxies as a function of separation. Correlations between properties such as the star formation rate (SFR), stellar mass, and specific star formation rate (sSFR) have implications for the impact of environment upon galaxy formation and evolution. Conformity between primary galaxies and satellites within the same dark matter halo has been well documented in simulations and observations. However, the existence of conformity at greater distances—known as two-halo conformity—remains uncertain. We investigate whether galaxies in the Local Volume to a distance of 4 Mpc show conformity by examining the SFR, sSFR, stellar mass, and quenched fraction as a function of physical separation. Making use of the star formation histories of these galaxies, we then extend this analysis back in time to offer the first probe of conformity inside our past light cone. At the present day, we find that the stellar mass or sSFR of a galaxy correlates with the median SFR of neighboring galaxies at a separation of 2–3 Mpc. At a lookback time of 1 Gyr, we find a correlation with the quenched fraction of neighboring galaxies, again at a 2–3 Mpc separation. These signals of conformity likely arise from the differences between the recent star formation histories of Local Group dwarf galaxies and those outside the Local Group. As current and future missions including JWST, Rubin, and Roman expand the sample of Local Volume galaxies, tests of conformity using star formation histories will provide an important tool for exploring spatiotemporal correlations between galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS2009

Assemblies of Conformal Tanks

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.

DeLay, Tom↗
DOE OSTI2023

Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes

Understanding the impact of extractant functionalization on metal-binding energetics in liquid-liquid extraction is essential to guide the development of better separation processes. Traditionally, computational extractant design uses electronic structure calculations on metal-ligand clusters to determine the metal-binding energy of the lowest energy state. Although highly accurate, this approach does not account for all of the relevant physics encountered under experimental conditions. Such methodologies often neglect entropic contributions such as temperature effects and ligand flexibility, in addition to approximating solvent-extractant interactions with implicit solvent models. In this study, we use classical molecular dynamics simulations with an advanced sampling method, metadynamics, to map out extractant molecule conformational free energies in the condensed phase. Here we generate the complete conformational landscape in solution for a family of bidentate malonamide-based extractants with different functionalizations of the headgroup and the side chains. In particular, we show how such alkyl functionalization reshapes the free energy landscape, affecting the free energy penalty of organizing the extractant into the cis-like metal-binding conformation from the trans-like conformation of the free extractant in solution. Specifically, functionalizing alkyl tails to the center of the headgroup has a greater influence on increasing molecular rigidity and disfavoring the binding conformation than functionalizing side chains. These findings are consistent with trends in metal-binding energetics based on experimentally reported distribution ratios. We also consider a different bidentate extractant molecule, carbamoylmethylphosphine oxide, and show how the choice of solvent can further reshape the conformational energetic landscape. This study demonstrates the feasibility of using molecular dynamics simulations with advanced sampling techniques to investigate extractant conformational energetics in solution, which, more broadly, will enable extractant design that accounts for entropic effects and explicit solvation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

The microwave spectra of the conformers of $\mathcal{n}$-butyl nitrate

We report the microwave spectrum of n-butyl nitrate was recorded in the 5 to 20 GHz frequency range using broadband chirp and narrowband pulse excitation molecular jet Fourier transform microwave spectrometers. A quantum chemistry structural analysis yielded thirteen stable conformers. Among them, the five most energetically stable conformers were observed in the experimental spectra. The most stable conformer features a butyl chain with an anti-gauche-anti conformation (AGA) where the γ-carbon atom is about 64° out of the nitrate plane. For this conformer, spectra of all 13 C and 15 N minor isotopologues could be measured. The conformer with a straight butyl chain (AAA), and three other conformers (GAA, GGA, and AGG) were also observed. Accurate rotational constants, centrifugal distortion constants, and 14 N nuclear quadrupole coupling constants could be deduced and compared to the theoretical values.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Computational remodeling of an enzyme conformational landscape for altered substrate selectivity

Structural plasticity of enzymes dictates their function. Yet, our ability to rationally remodel enzyme conformational landscapes to tailor catalytic properties remains limited. Here, we report a computational procedure for tuning conformational landscapes that is based on multistate design of hinge-mediated domain motions. Using this method, we redesign the conformational landscape of a natural aminotransferase to preferentially stabilize a less populated but reactive conformation and thereby increase catalytic efficiency with a non-native substrate, resulting in altered substrate selectivity. Steady-state kinetics of designed variants reveals activity increases with the non-native substrate of approximately 100-fold and selectivity switches of up to 1900-fold. Structural analyses by room-temperature X-ray crystallography and multitemperature nuclear magnetic resonance spectroscopy confirm that conformational equilibria favor the target conformation. Our computational approach opens the door to targeted alterations of conformational states and equilibria, which should facilitate the design of biocatalysts with customized activity and selectivity.

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

Matrix-formation dynamics dictate methyl nitrite conformer abundance

Methyl nitrite has two stable conformational isomers resulting from rotation about the primary C–O–N–O dihedral angle: cis-CH 3 ONO and trans-CH 3 ONO, with cis being more stable by ∼5 kJ/mol. Here, the barrier to rotational interconversion (∼45 kJ/mol) is too large for isomerization to occur under ambient conditions. This paper presents evidence of a change in conformer abundance when dilute CH 3 ONO is deposited onto a cold substrate; the relative population of the freshly deposited cis conformer is seen to increase compared to its gas-phase abundance, measured by in situ infrared spectroscopy. We observe abundance changes depending on the identity of the bath gas (N 2 , Ar, and Xe) and deposition angle. The observations indicate that the surface properties of the growing matrix influence conformer abundance—contrary to the widely held assumption that conformer abundance in matrices reflects gas-phase abundance. We posit that differences in the angle-dependent host-gas deposition dynamics affect the growing surfaces, causing changes in conformer abundances. Quantum chemistry calculations of the binding energies between CH 3 ONO and a single bath-gas component reveal that significant energetic stabilization is not observed in 1:1 complexes of N 2 :CH 3 ONO, Ar:CH 3 ONO, or Xe:CH 3 ONO. From our results, we conclude that the growing surface plays a significant role in trapping cis-CH 3 ONO more effectively than trans-CH 3 ONO, likely because cis-CH 3 ONO is more compact. Taken together, the observations highlight the necessity for careful characterization of conformers in matrix-isolated systems, emphasizing a need for further study into the deposition dynamics and surface structure of chemically inert matrices.

Hockey, Emily K.↗
DOE OSTI2024

Scale and conformal invariance on (A)dS spacetimes

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

Astronomy & Astrophysics↗
NASA NTRS2013

Testing of Advanced Conformal Ablative TPS

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.

Gasch, Matthew↗
DOE OSTI2024

Data-Efficient Generation of Protein Conformational Ensembles with Backbone-to-Side-Chain Transformers

Excitement at the prospect of using data-driven generative models to sample configurational ensembles of biomolecular systems stems from the extraordinary success of these models on a diverse set of high-dimensional sampling tasks. Unlike image generation or even the closely related problem of protein structure prediction, there are currently no data sources with sufficient breadth to parametrize generative models for conformational ensembles. To enable discovery, a fundamentally different approach to building generative models is required: models should be able to propose rare, albeit physical, conformations that may not arise in even the largest data sets. Here, in this work, we introduce a modular strategy to generate conformations based on “backmapping” from a fixed protein backbone that (1) maintains conformational diversity of the side chains and (2) couples the side-chain fluctuations using global information about the protein conformation. Our model combines simple statistical models of side-chain conformations based on rotamer libraries with the now ubiquitous transformer architecture to sample with atomistic accuracy. Together, these ingredients provide a strategy for rapid data acquisition and hence a crucial ingredient for scalable physical simulation with generative neural networks.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Uncovering Backbone Conformation for Rigid DPP-Based Donor–Acceptor Conjugated Polymer Using Deuterium Labeling and Neutron Scattering

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.

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

Bootstrapping smooth conformal defects in Chern-Simons-matter theories

Abstract The expectation value of a smooth conformal line defect in a CFT is a conformal invariant functional of its path in space-time. For example, in largeNholographic theories, these fundamental observables are dual to the open-string partition function in AdS. In this paper, we develop a bootstrap method for studying them and apply it to conformal line defects in Chern-Simons matter theories. In these cases, the line bootstrap is based on three minimal assumptions — conformal invariance of the line defect, largeNfactorization, and the spectrum of the two lowest-lying operators at the end of the line. On the basis of these assumptions, we solve the one-dimensional CFT on the line and systematically compute the defect expectation value in an expansion around the straight line. We find that the conformal symmetry of a straight defect is insufficient to fix the answer. Instead, imposing the conformal symmetry of the defect along an arbitrary curved line leads to a functional bootstrap constraint. The solution to this constraint is found to be unique.

Physics↗
DOE OSTI2026

Noncanonical folding of peptoid oligomers: Formation of a closed conformation in nonpolar solvent

Peptoids provide a versatile platform for foldamer design, yet their conformational behavior in low-dielectric media remains poorly understood. The structural characteristics of N-1-phenylethylglycine (Nspe) homo-oligomers were inves-tigated in chloroform, a solvent that mimics the interior of lipid bilayers, using nuclear magnetic resonance (NMR) spec-troscopy and molecular dynamics (MD) simulations. Nspe7 populated two distinct compact conformations, while Nspe10 adopted a single homogeneous conformation related to the previously reported Nspe9 threaded-loop structure. Integrated experimental and computational analysis reveals that these structures are stabilized by cooperative end-to-end intramo-lecular hydrogen bonding, cis-trans backbone isomerism, and hydrophobic side-chain shielding. The resulting structures minimize exposed polar surface area, demonstrating a closed conformation in the low-dielectric environment. These find-ings establish specific chain-length requirements for achieving well-defined closed conformations. This work provides insights into peptoid folding in nonpolar media, enabling rational design strategies for solvent-directed conformational switching systems.

Oh, Jinyoung↗
DOE OSTI2025

Ligand efficacy shifts a nuclear receptor conformational ensemble between transcriptionally active and repressive states

Abstract Nuclear receptors (NRs) are thought to dynamically alternate between transcriptionally active and repressive conformations, which are stabilized upon ligand binding. Most NR ligand series exhibit limited bias, primarily consisting of transcriptionally active agonists or neutral antagonists, but not repressive inverse agonists—a limitation that restricts understanding of the functional NR conformational ensemble. Here, we report a NR ligand series for peroxisome proliferator-activated receptor gamma (PPARγ) that spans a pharmacological spectrum from repression (inverse agonism) to activation (agonism) where subtle structural modifications switch compound activity. While crystal structures provide snapshots of the fully repressive state, NMR spectroscopy and conformation-activity relationship analysis reveals that compounds within the series shift the PPARγ conformational ensemble between transcriptionally active and repressive conformations that are natively populated in the apo/ligand-free ensemble. Our findings reveal a molecular framework for minimal chemical modifications that enhance PPARγ inverse agonism and elucidate their influence on the dynamic PPARγ conformational ensemble.

Science & Technology - Other Topics↗
DOE OSTI2026

A curated benchmark for cofolding models on kinase conformational states

Abstract Protein kinases are critical drug targets, requiring therapeutics that can modulate their active and inactive conformational states. While cofolding models can generate global folds directly from kinase sequences and ligand SMILES strings, these models have not yet been tested on their ability to recover ligand-induced-fit conformational states of the kinase proteins. Here, we introduce KinConfBench, a curated benchmark of 2225 high-quality human kinase chains to evaluate the ability of four state-of-the-art cofolding models—Boltz-2, Chai-1, Protenix, and RoseTTAFold-All-Atom—to recover both canonical and rare conformational states. We show that geometric success metrics of a ligand pose in the active site do not correlate strongly with the correct kinase conformational state, motivating a new set of dynamical benchmarks for assessing cofolding models. While all four cofolding models achieve ~60–80% prediction accuracy for kinase conformational classification, they exhibit severe mode collapse when performing multiple inferences, show negligible structural diversity in sampling induced-fit motions, and display a prevalent “apo-drift” in which most cofolding models predominantly predict the kinase to be in its ligand-free state. Our results highlight that capturing ligand-induced protein conformational diversity, not just geometric fit, is critical for next-generation structure-based drug discovery.

Sun, Kunyang↗
DOE OSTI2025

Conformal geometry from entanglement

In a physical system with conformal symmetry, observables depend on cross-ratios, measures of distance invariant under global conformal transformations (conformal geometry for short). We identify a quantum information-theoretic mechanism by which the conformal geometry emerges at the gapless edge of a 2+1D quantum many-body system with a bulk energy gap. We introduce a novel pair of information-theoretic quantities (\mathfrak{c}_{\textrm{tot}}, \eta) ( 𝔠 tot , η ) that can be defined locally on the edge from the wavefunction of the many-body system, without prior knowledge of any distance measure. We posit that, for a topological groundstate, the quantity \mathfrak{c}_{\textrm{tot}} 𝔠 tot is stationary under arbitrary variations of the quantum state, and study the logical consequences. We show that stationarity, modulo an entanglement-based assumption about the bulk, implies (i) \mathfrak{c}_{\textrm{tot}} 𝔠 tot is a non-negative constant that can be interpreted as the total central charge of the edge theory. (ii) \eta η is a cross-ratio, obeying the full set of mathematical consistency rules, which further indicates the existence of a distance measure of the edge with global conformal invariance. Thus, the conformal geometry emerges from a simple assumption on groundstate entanglement. We show that stationarity of \mathfrak{c}_{\textrm{tot}} 𝔠 tot is equivalent to a vector fixed-point equation involving \eta η , making our assumption locally checkable. We also derive similar results for 1+1D systems under a suitable set of assumptions.

Kim, Isaac H.↗
DOE OSTI2026

Continuous Family of Conformal Field Theories and Exactly Marginal Operators

Does a conformal manifold imply the existence of exactly marginal operators? We answer this question affirmatively under the assumption that there exists a conformal interface with certain properties connecting nearby conformal field theories. We show that the exactly marginal operator that connects the conformal field theories can be reconstructed from the interface displacement operator. Our construction is model independent and based on the general principles of conformal symmetry.

conformal field theory↗
DOE OSTI2024

Chain Conformations of TEMPO-Based Organic Radical Polymers with Varying Radical Loading and Temperature in Battery-Relevant Solvents

Poly(2,2,6,6-tetramethylpiperidinyloxy-4-yl methacrylate) (PTMA) is an organic radical polymer that is a promising active material in organic batteries. The proximity of the radical groups impacts the nature of charge transfer, in which closer packing promotes electron exchange; however, the chain conformation of PTMA is not well understood. Here, the conformation of PTMA in, and its thermodynamic interactions with, battery-relevant solvents is determined using small-angle neutron scattering (SANS). N-methyl-2-pyrrolidone (NMP) and 50:50 (wt %) ethylene carbonate/dimethyl carbonate (EC/DMC) mixtures with PTMA of varying radical content (68 vs 98%) and temperature (25 and 60 °C) are examined. Both solvents are theta solvents for PTMA irrespective of radical loading and temperature. PTMA attains an expanded chain conformation in NMP and a more compact polymer chain conformation in EC/DMC. Lastly, the electrochemical performance of PTMA films formed from EC/DMC shows improved performance relative to those cast from NMP, which is interpreted to indicate that the compact conformation of PTMA in EC/DMC enables improved inter- and intrachain charge transfer.

25 ENERGY STORAGE↗