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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Hidden conformal symmetry of the discrete series scalars in dS 2

In D dimensional de Sitter space, a scalar field has an infinite tower of special tachyonic mass values at which enhanced shift symmetries appear. After modding out by these shift symmetries, these fields correspond to the unitary irreducible representations of the de Sitter group known as the discrete series. We show that in D = 2 these theories have global conformal symmetry. In all but the massless case, these theories have no stress tensor and the conformal symmetry does not act in the usual way on the scalar field. We find the conformal symmetry by explicitly computing the correlators of the shift invariant local operators and showing that they take conformally invariant forms. We also demonstrate how these fields are self-dual in D = 2 , and dual to the shift invariant massive vector fields, which are therefore also conformally invariant. Published by the American Physical Society 2025

Farnsworth, Kara (ORCID:000000020200078X)↗
DOE OSTI2021

Conformer-specific photochemistry imaged in real space and time

Conformation-dependent dynamics play an important role in organic chemistry syntheses such as electrocyclic reactions, as well as in biological processes such as protein folding. However, current time-resolved experimental methods struggle to distinguish conformers from each other, and conformational isomerism is usually analyzed through reactant and product distributions. Using a combination of mega–electron volt ultrafast electron diffraction and quantum wave packet simulations, Champenois et al. directly followed the photochemical electrocyclic ring opening of the molecule α-phellandrene with femtosecond time resolution and confirmed that the transformation of a specific molecular conformer follows the famous Woodward-Hoffmann rules. The proposed method is potentially a powerful tool to follow conformer specificity in various organic and biological systems in real time.

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

Towards interpretable Cryo-EM: disentangling latent spaces of molecular conformations

Molecules are essential building blocks of life and their different conformations (i.e., shapes) crucially determine the functional role that they play in living organisms. Cryogenic Electron Microscopy (cryo-EM) allows for acquisition of large image datasets of individual molecules. Recent advances in computational cryo-EM have made it possible to learn latent variable models of conformation landscapes. However, interpreting these latent spaces remains a challenge as their individual dimensions are often arbitrary. The key message of our work is that this interpretation challenge can be viewed as an Independent Component Analysis (ICA) problem where we seek models that have the property of identifiability. That means, they have an essentially unique solution, representing a conformational latent space that separates the different degrees of freedom a molecule is equipped with in nature. Thus, we aim to advance the computational field of cryo-EM beyond visualizations as we connect it with the theoretical framework of (nonlinear) ICA and discuss the need for identifiable models, improved metrics, and benchmarks. Moving forward, we propose future directions for enhancing the disentanglement of latent spaces in cryo-EM, refining evaluation metrics and exploring techniques that leverage physics-based decoders of biomolecular systems. Moreover, we discuss how future technological developments in time-resolved single particle imaging may enable the application of nonlinear ICA models that can discover the true conformation changes of molecules in nature. The pursuit of interpretable conformational latent spaces will empower researchers to unravel complex biological processes and facilitate targeted interventions. This has significant implications for drug discovery and structural biology more broadly. More generally, latent variable models are deployed widely across many scientific disciplines. Thus, the argument we present in this work has much broader applications in AI for science if we want to move from impressive nonlinear neural network models to mathematically grounded methods that can help us learn something new about nature.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Extending Conformal Prediction to Hidden Markov Models with Exact Validity via de Finetti’s Theorem for Markov Chains

Conformal prediction is a widely used method to quantify uncertainty in settings where the data is independent and identically distributed (IID), or more generally, exchangeable. Conformal prediction takes in a pre-trained classifier and a calibration dataset as inputs, and returns a function which maps feature vectors to subsets of classes. The output of the returned function for a new feature vector is guaranteed to contain the true class with a pre-specified confidence. Despite its success and usefulness in IID settings, extending conformal prediction to non-exchangeable (e.g., Markovian) data in a manner that provably preserves all desirable theoretical properties has largely remained an open problem. As a solution, we extend conformal prediction to the setting of a Hidden Markov Model (HMM) with unknown parameters. The key idea behind the proposed method is to partition the non-exchangeable Markovian data from the HMM into exchangeable blocks by exploiting the de Finetti’s Theorem for Markov Chains discovered by Diaconis and Freedman (1980). The permutations of the exchangeable blocks are then viewed as randomizations of the observed Markovian data from the HMM. The proposed method provably retains all desirable theoretical guarantees offered by the classical conformal prediction framework and is general enough to be useful in many sequential prediction problems.

Nettasinghe, Don Buddhika Wijayantha↗
DOE OSTI2022

Conformal conserved currents in embedding space

We study conformal conserved currents in arbitrary irreducible representations of the Lorentz group using the embedding space formalism. With the help of the operator product expansion, we first show that conservation conditions can be fully investigated by considering only two- and three-point correlation functions. We then find an explicitly conformally-covariant differential operator in embedding space that implements conservation based on the standard position space operator product expansion differential operator ∂μ, although the latter does not uplift to embedding space covariantly. The differential operator in embedding space that imposes conservation is the same differential operator $D_{ijA}$ used in the operator product expansion in embedding space. We provide several examples including conserved currents in irreducible representations that are not symmetric and traceless. With an eye on four-point conformal bootstrap equations for four conserved vector currents $\langle JJJJ\rangle$ and four energy-momentum tensors $\langle TTTT\rangle$, we mostly focus on conservation conditions for $\langle JJ\mathcal{O}\rangle$ and $\langle TT\mathcal{O}\rangle$. Finally, we reproduce and extend the consequences of conformal Ward identities at coincident points by determining three-point coefficients in terms of charges.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Resurgence, conformal blocks, and the sum over geometries in quantum gravity

In two dimensional conformal field theories the limit of large central charge plays the role of a semi-classical limit. Certain universal observables, such as conformal blocks involving the exchange of the identity operator, can be expanded around this classical limit in powers of the central charge c. This expansion is an asymptotic series, so — via the same resurgence analysis familiar from quantum mechanics — necessitates the existence of non-perturbative effects. In the case of identity conformal blocks, these new effects have a simple interpretation: the CFT must possess new primary operators with dimension of order the central charge. This constrains the data of CFTs with large central charge in a way that is similar to (but distinct from) the conformal bootstrap. We study this phenomenon in three ways: numerically, analytically using Zamolodchikov’s recursion relations, and by considering non-unitary minimal models with large (negative) central charge. In the holographic dual to a CFT2, the expansion in powers of c is the perturbative loop expansion in powers of ћ. So our results imply that the graviton loop expansion is an asymptotic series, whose cure requires the inclusion of new saddle points in the gravitational path integral. In certain cases these saddle points have a simple interpretation: they are conical excesses, particle-like states with negative mass which are not in the physical spectrum but nevertheless appear as non-manifold saddle points that control the asymptotic behaviour of the loop expansion. This phenomenon also has an interpretation in SL(2, R) Chern-Simons theory, where the non-perturbative effects are associated with the non-Teichmüller component of the moduli space of flat connections.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Geometry of conformal manifolds and the inversion formula

Families of conformal field theories are naturally endowed with a Riemannian geometry which is locally encoded by correlation functions of exactly marginal operators. We show that the curvature of such conformal manifolds can be computed using Euclidean and Lorentzian inversion formulae, which combine the operator content of the conformal field theory into an analytic function. Analogously, operators of fixed dimension define bundles over the conformal manifold whose curvatures can also be computed using inversion formulae. These results relate curvatures to integrated four-point correlation functions which are sensitive only to the behavior of the theory at separated points. We apply these inversion formulae to derive convergent sum rules expressing the curvature in terms of the spectrum of local operators and their three-point function coefficients. We further show that the curvature can smoothly diverge only if a conserved current appears in the spectrum, or if the theory develops a continuum. We verify our results explicitly in 2d examples. In particular, for 2d (2,2) superconformal field theories we derive a lower bound on the scalar curvature, which is saturated by free theories when the central charge is a multiple of three.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Level-set topology optimization with PDE generated conformal meshes

This paper presents a level-set topology optimization approach that uses conformal meshes for the analysis of the displacement field. The structure’s boundary is represented by the iso-contour of a level-set field discretized on a fixed background design mesh. The conformal mesh is updated for each design iteration via a PDE based mesh morphing process that identifies the set of facets in the background mesh that are homeomorphic to the boundary and relaxes the homeomorphic mesh to conform to the structure’s boundary and ensure high element quality. The conformal mesh allows for a more accurate computation of the response versus density and some level-set based methods which interpolate material properties using the volume fraction. Numerical examples illustrate the proposed approach by optimizing linear-elastic two- and three-dimensional structures, wherein insight into the performance of the mesh morphing process is provided. The examples also highlight the scalability of the approach.

42 ENGINEERING↗
DOE OSTI2022

A catalytic dyad modulates conformational change in the CO 2 -fixing flavoenzyme 2-ketopropyl coenzyme M oxidoreductase/carboxylase

2-Ketopropyl-coenzyme M oxidoreductase/carboxylase (2-KPCC) is a member of the flavin and cysteine disulfide containing oxidoreductase family (DSOR) that catalyzes the unique reaction between atmospheric CO 2 and a ketone/enolate nucleophile to generate acetoacetate. However, the mechanism of this reaction is not well understood. Here, we present evidence that 2-KPCC, in contrast to the well-characterized DSOR enzyme glutathione reductase, undergoes conformational changes during catalysis. Using a suite of biophysical techniques including limited proteolysis, differential scanning fluorimetry, and native mass spectrometry in the presence of substrates and inhibitors, we observed conformational differences between different ligand-bound 2-KPCC species within the catalytic cycle. Analysis of site-specific amino acid variants indicated that 2-KPCC-defining residues, Phe501-His506, within the active site are important for transducing these ligand induced conformational changes. We propose that these conformational changes promote substrate discrimination between H + and CO 2 to favor the metabolically preferred carboxylation product, acetoacetate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Designer molecules of the synaptic organizer MDGA1 reveal 3D conformational control of biological function

MDGAs (MAM domain-containing glycosylphosphatidylinositol anchors) are synaptic cell surface molecules that regulate the formation of trans-synaptic bridges between neurexins (NRXNs) and neuroligins (NLGNs), which promote synaptic development. Mutations in MDGAs are implicated in various neuropsychiatric diseases. MDGAs bind NLGNs in cis on the postsynaptic membrane and physically block NLGNs from binding to NRXNs. In crystal structures, the six immunoglobulin (Ig) and single fibronectin III domains of MDGA1 reveal a striking compact, triangular shape, both alone and in complex with NLGNs. Whether this unusual domain arrangement is required for biological function or other arrangements occur with different functional outcomes is unknown. Here, we show that WT MDGA1 can adopt both compact and extended 3D conformations that bind NLGN2. Designer mutants targeting strategic molecular elbows in MDGA1 alter the distribution of 3D conformations while leaving the binding affinity between soluble ectodomains of MDGA1 and NLGN2 intact. In contrast, in a cellular context, these mutants result in unique combinations of functional consequences, including altered binding to NLGN2, decreased capacity to conceal NLGN2 from NRXN1β, and/or suppressed NLGN2-mediated inhibitory presynaptic differentiation, despite the mutations being located far from the MDGA1-NLGN2 interaction site. Thus, the 3D conformation of the entire MDGA1 ectodomain appears critical for its function, and its NLGN-binding site on Ig1-Ig2 is not independent of the rest of the molecule. As a result, global 3D conformational changes to the MDGA1 ectodomain via strategic elbows may form a molecular mechanism to regulate MDGA1 action within the synaptic cleft.

MDGAs↗
DOE OSTI2022

Unmasking the Conformational Stability and Inhibitor Binding to SARS-CoV-2 Main Protease Active Site Mutants and Miniprecursor

We recently demonstrated that inhibitor binding reorganizes the oxyanion loop of a monomeric catalytic domain of SARS CoV-2 main protease (MPro) from an unwound (E) to a wound (active, E*) conformation, independent of dimerization. Here we assess the effect of the flanking N-terminal residues, to imitate the MPro precursor prior to its autoprocessing, on conformational equilibria rendering stability and inhibitor binding. Thermal denaturation (T m ) of C145A mutant, unlike H41A, increases by 6.8 °C, relative to wild-type mature dimer. An inactivating H41A mutation to maintain a miniprecursor containing TSAVL[Q or E] of the flanking nsp4 sequence in an intact form [ (-6) MPro H41A and (-6*) MPro H41A , respectively], and its corresponding mature MPro H41A were systematically examined. While the H41A mutation exerts negligible effect on T m and dimer dissociation constant (K dimer ) of MPro H41A , relative to the wild type MPro, both miniprecursors show a 4–5 °C decrease in T m and > 85-fold increase in K dimer as compared to MPro H41A . The K d for the binding of the covalent inhibitor GC373 to (-6*) MPro H41A increases ~12-fold, relative to MPro H41A , concomitant with its dimerization. While the inhibitor-free dimer exhibits a state in transit from E to E* with a conformational asymmetry of the protomers’ oxyanion loops and helical domains, inhibitor binding restores the asymmetry to mature-like oxyanion loop conformations (E*) but not of the helical domains. Finally, disorder of the terminal residues 1–2 and 302–306 observed in both structures suggest that N-terminal autoprocessing is tightly coupled to the E-E* equilibrium and stable dimer formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Systematic mapping of the conformational landscape and dynamism of soluble fibrinogen

Background: Fibrinogen is a soluble, multisubunit, and multidomain dimeric protein, which, upon its proteolytic cleavage by thrombin, is converted to insoluble fibrin, initiating polymerization that substantially contributes to clot growth. Fibrinogen contains numerous, transiently accessible “cryptic” epitopes for hemostatic and immunologic proteins, suggesting that fibrinogen exhibits conformational flexibility, which may play functional roles in its temporal and spatial interactions. Hitherto, there have been limited integrative approaches characterizing the solution structure and internal flexibility of fibrinogen. Methods: Here, utilizing a multipronged, biophysical approach involving 2 solution-based techniques, temperature-dependent hydrogen-deuterium exchange mass spectrometry and small angle X-ray scattering, corroborated by negative stain electron microscopy, we present a holistic, conformationally dynamic model of human fibrinogen in solution. Results: Our data reveal 4 major and distinct conformations of fibrinogen accommodated by a high degree of internal protein flexibility along its central scaffold. We propose that the fibrinogen structure in the solution consists of a complex, conformational landscape with multiple local minima. This is further supported by the location of numerous point mutations that are linked to dysfibrinogenemia and posttranslational modifications, residing near the identified fibrinogen flexions. Conclusion: Further, this work provides a molecular basis for the structural “dynamism” of fibrinogen that is expected to influence the broad swath of its functionally diverse macromolecular interactions and fine-tune the structural and mechanical properties of blood clots.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Tuning the Double Gyroid Phase Window in Block Copolymers via Polymer Chain Conformation Near the Interface

Block copolymer network morphologies have been proven interesting for applications ranging from mechanical to transport and optical properties. The shape of the polymer chain and its ability to stretch across an interface can be used as handles to target these network morphologies. Here, we show that the double gyroid phase window is broadened when there is a flexible segment near the interface and narrowed when a more constrained segment is placed there by using a series of poly(styrene-b-peptoid) block copolymers in which the polypeptoid block chain conformation can be tuned to adopt either a helical or a coil conformation (NRpe 6 vs Npe 6 ). The double gyroid phase is accessed in both block copolymer series, while the phase boundaries are shifted toward larger polypeptoid volume fractions in the helix-forming PS–(NRpe 6 Nmey) series, due to the more compact helix segment (i.e., the helix segment has the same chain volume as its random coil counterpart but occupies less space). The space-filling difference between the helix and coil segment is further confirmed by the smaller domain spacing of PS–(NRpe 6 Nme 39 ) compared to PS–(Npe 6 Nme 36 ) (13.9 nm vs 14.3 nm) despite the former having a longer polypeptoid block. Furthermore, a broadened double gyroid phase window is accessed in the PS–(Npe 6 Nme y ) series that has a flexible coil segment near the interface. These results demonstrate the possibility of tuning the double gyroid phase in linear block copolymers by chain conformation near the interface alone, highlighting chain conformation as a versatile handle in block copolymer design.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Hydrogen-Bond-Promoted Planar Conformation, Crystallinity, and Charge Transport in Semiconducting Diazaisoindigo Derivatives

Conformational control of π-conjugated molecules using intramolecular noncovalent bonds represents a promising strategy to tailor the solid-state molecular packing and electronic properties of these materials. Here, we report the design and synthesis of two model compounds featuring intramolecular hydrogen bonds formed between a center diazaisoindigo unit (the acceptor) and flanking indole units (the donor). Computational and experimental investigations show that these hydrogen bonds enthalpically stabilize the coplanar molecular conformation by over 10 kcal/mol. The formation of these hydrogen bonds is also slightly favorable in terms of entropy, ensuring high temperature stability of the planar conformation. In this work, thermal annealing of thin films of these compounds imparts high crystallinity and orientation in the solid state, while the non-hydrogen bond control only gave an amorphous solid. Field-effect transistor devices fabricated from these thin films exhibit hole mobilities up to 0.270 cm 2 V -1 s -1 , in contrast to the lack of measurable charge carrier mobility for the non-hydrogen bond control. This work demonstrates an efficient synthetic strategy to incorporate robust intramolecular hydrogen bonds into conjugated π-systems and elucidates the mechanism on how such hydrogen bonds promote the desired molecular conformation, solid-state packing, and electronic performances of conjugated organic materials.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Conformable, Composite Tank for Liquid Hydrogen Storage in Heavy-duty Ground Transportation

Raytheon Technologies Research Center (RTRC), with its partners, Argonne National Labs and University of Dayton Research Institute proposed to design and manufacture a conformable composite tank prototype to store liquid Hydrogen (LH2) for heavy-duty truck applications. A dual-wall tank concept was proposed where an outer shell covers and protects an inner pressure vessel that stores liquid hydrogen. The inner pressure vessel is liner-less and designed with a conformable concept, derived from prior RTRC ARPA-E program where multiple vessels are coalesced into one, maximizing space utilization and reducing surface area for heat leak. The gap between the dual wall is evacuated of air pressure, and filled with multi-layer insulation to minimize radiative heat transfer. Fiber reinforced composites were proposed for light-weighting and conformable shape manufacture. To minimize LH2 leakage, carbon nanotubes-infused composites were proposed, in addition to use of thin plies. The project was divided into two 18-month budget periods (BP), BP1 and BP2, separated by a Go/No-Go gate review. The high-level goal for BP1 was to demonstrate the feasibility of the overall approach, the tank design, material selection, and manufacturing methodology, build and test a prototype tank; and the goal for BP2 was to design and manufacture a conformal tank per DOE requirements (minimum 20 kg of LH2) and perform a successful test of the tank. The program was terminated about two-thirds of the way through BP1. The outcome of this program would have permitted long-haul trucks and construction vehicles to use liquid Hydrogen, reducing the emission of green-house gases. This technology is applicable to other transportation sectors as well.

08 HYDROGEN↗
DOE OSTI2023

Molecular Structure and Conformational Design of Donor‐Acceptor Conjugated Polymers to Enable Predictable Optoelectronic Property

Abstract Tuning the optoelectronic properties of donor‐acceptor conjugated polymers (D‐A CPs) is of great importance in designing various organic optoelectronic devices. However, there remains a critical challenge in precise control of bandgap through synthetic approach, since the chain conformation also affects molecular orbital energy levels. Here, D‐A CPs with different acceptor units are explored that show an opposite trend in energy band gaps with the increasing length of oligothiophene donor units. By investigating their chain conformation and molecular orbital energy, it is found that the molecular orbital energy alignment between donor and acceptor units plays a crucial role in dictating the final optical bandgap of D‐A CPs. For polymers with staggered orbital energy alignment, the higher HOMO with increasing oligothiophene length leads to a narrowing of the optical bandgap despite decreased chain rigidity. On the other hand, for polymers with sandwiched orbital energy alignment, the increased band gap with increasing oligothiophene length originates from the reduction of bandwidth due to more localized charge density distribution. Thus, this work provides a molecular understanding of the role of backbone building blocks on the chain conformation and bandgaps of D‐A CPs for organic optoelectronic devices through the conformation design and segment orbital energy alignment.

Cao, Zhiqiang↗
DOE OSTI2025

Improving Ionic Conformality Across Polymer Electrolyte|Electrode Interfaces

Maintaining uniform ionic transport at electrode|electrolyte interfaces, i.e., ionic conformality, remains challenging in polymer electrolyte (PE)-based solid-state batteries. Morphological conformality does not necessarily imply ionic conformality. In PEs, which typically consist of a mechanically supporting component and distinct ionically conductive components, the rearrangement or depletion of mobile ion-conductive domains at interfaces can disrupt ionic transport pathways. Such localized ionic depletion contributes to interfacial instability and capacity degradation in high-voltage lithium-metal batteries. Herein, an electrolyte design approach aimed at minimizing interfacial heterogeneities is demonstrated through compositional adjustments, characterized by spatially resolved structural and chemical X-ray techniques and NMR diffusometry to elucidate ion transport dynamics. This approach improves ionic conformality at electrode interfaces, enhancing cycling stability in Li||LiNi 0.8 Co 0.1 Mn 0.1 O 2 (NMC811) coin and pouch cells cycled at high voltages. These results contribute to understanding interfacial behaviors in multiphase PEs and inform strategies for improving stability across solid-state battery interfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2024

One- and two-dimensional higher-point conformal blocks as free-particle wavefunctions in $$ {\textrm{AdS}}_3^{\otimes m} $$

Abstract We establish that all of the one- and two-dimensional global conformal blocks are, up to some choice of prefactor, free-particle wavefunctions in tensor products of AdS 3 or limits thereof. Our first core observation is that the six-point comb-channel conformal blocks correspond to free-particle wavefunctions on an AdS 3 constructed directly in cross-ratio space. This construction generalizes to blocks for a special class of diagrams, which are determined as free-particle wavefunctions in tensor products of AdS 3 . Conformal blocks for all the remaining topologies are obtained as limits of the free wavefunctions mentioned above. Our results show directly that the integrable models associated with all one- and two-dimensional conformal blocks can be seen as limits of free theory, and manifest a relation between AdS and CFT kinematics that lies outside of the standard AdS/CFT dictionary. We complete the discussion by providing explicit Feynman-like rules that can be used to work out blocks for all topologies, as well as a Mathematica notebook that allows simple computation of Casimir equations and series expansions for blocks, by requiring just an OPE diagram as input.

Physics↗