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At least 145 records · Page 8

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DOE OSTI2026

Many roads to the seam: How conformational flexibility drives nonadiabatic relaxation in a prototypical tetrapyrrolic chromophore

Large and structurally flexible chromophores pose challenges for in silico modeling of photodeactivation due to the many vibrational modes that can funnel the system toward energy degeneracy. In this work, we examine how the multiple degrees of freedom in biliverdin, a prototypical tetrapyrrolic chromophore, cooperate to drive access to the S 1 /S 0 intersection seam in vacuo. We begin by mapping the ground-state potential energy surface to identify representative biliverdin conformers relevant to photoexcitation. We then use a CASSCF-based framework to map the excited-state landscape and characterize the intersection seam, identifying distinct conical-intersection types. Finally, we employ ab initio multiple spawning to resolve the dynamical pathways by which the system accesses these regions. DFT potential-energy and free-energy mappings indicate that, although several conformers are relevant, the “locked-helix” ZsZsZs conformer predominates in the ground state. The intersection seam comprises numerous geometrically distinct regions characterized by varying degrees and combinations of dihedral torsion, pyramidalization, and bond-length alternation. Yet only select regions lie within energetic reach, and moderate barriers separate them from the S 1 minimum. Nonadiabatic dynamics combined with multivariate analyses show that, despite extensive mode coupling during deactivation that guides the system toward multiple regions of the seam, a single dihedral torsion, together with bond-length alternation, predominantly drives energy degeneracy. This work offers new insight into biliverdin’s intrinsic photochemical response and underscores a general feature of flexible chromophores: many modes may participate during photorelaxation, but only a limited subset ultimately dictates seam accessibility.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Conformation-specific synthetic intrabodies modulate mTOR signaling with subcellular spatial resolution

Subcellular compartmentalization is integral to the spatial regulation of mechanistic target of rapamycin (mTOR) signaling. However, the biological outputs associated with location-specific mTOR signaling events are poorly understood and challenging to decouple. Here, we engineered synthetic intracellular antibodies (intrabodies) that are capable of modulating mTOR signaling with genetically programmable spatial resolution. Epitope-directed phage display was exploited to generate high affinity synthetic antibody fragments (Fabs) against the FKBP12–Rapamycin binding site of mTOR (mTOR FRB ). We determined high-resolution crystal structures of two unique Fabs that discriminate distinct conformational states of mTOR FRB through recognition of its substrate recruitment interface. By leveraging these conformation-specific binders as intracellular probes, we uncovered the structural basis for an allosteric mechanism governing mTOR complex 1 (mTORC1) stability mediated by subtle structural adjustments within mTOR FRB . Furthermore, our results demonstrated that synthetic binders emulate natural substrates by employing divergent yet complementary hydrophobic residues at defined positions, underscoring the broad molecular recognition capability of mTOR FRB . Intracellular signaling studies showed differential time-dependent inhibition of S6 kinase 1 and Akt phosphorylation by genetically encoded intrabodies, thus supporting a mechanism of inhibition analogous to the natural product rapamycin. Finally, we implemented a feasible approach to selectively modulate mTOR signaling in the nucleus through spatially programmed intrabody expression. These findings establish intrabodies as versatile tools for dissecting the conformational regulation of mTORC1 and should be useful to explore how location-specific mTOR signaling influences disease progression.

Science & Technology - Other Topics↗

DOE OSTI2026

Conformalized-KANs: Uncertainty Quantification with Coverage Guarantees for Kolmogorov-Arnold Networks (KANs) in Scientific Machine Learning

This paper explores uncertainty quantification (UQ) methods in the context of Kolmogorov–Arnold Networks (KANs). We apply an ensemble approach to KANs to obtain a heuristic measure of UQ, enhancing interpretability and robustness in modeling complex functions. Building on this, we introduce Conformalized-KANs, which integrate conformal prediction, a distribution-free UQ technique, with KAN ensembles to generate calibrated prediction intervals with guaranteed coverage.} Extensive numerical experiments are conducted to evaluate the effectiveness of these methods, focusing particularly on the robustness and accuracy of the prediction intervals under various hyperparameter settings. We show that the conformal KAN predictions can be applied to recent extensions of KANs, including Finite Basis KANs (FBKANs) and multifideilty KANs (MFKANs). The results demonstrate the potential of our approaches to significantly improve the reliability and applicability of KANs in scientific machine learning.

• Artificial intelligence (AI) / machine learning ↗

DOE OSTI2023

Dissect two-halo galactic conformity effect for central galaxies: the dependence of star formation activities on the large-scale environment

We investigate the two-halo galactic conformity effect for central galaxies, which is the spatial correlation of the star formation activities for central galaxies to several Mpcs, by studying the dependence of the star formation activities of central galaxies on their large-scale structure in our local Universe using the SDSS data. Here we adopt a novel environment metric using only central galaxies quantified by the distance to the nth nearest central galaxy. This metric measures the environment within an aperture from ∼1 to ≳ 10 Mpc, with a median value of ∼4 Mpc. We found that two kinds of conformity effects in our local Universe. The first one is that low-mass central galaxies are more quenched in high-density regions, and we found that this effect mainly comes from low-mass centrals that are close to a more massive halo. A similar trend is also found in the IllustrisTNG simulation, which can be entirely explained by backsplash galaxies. The second conformity effect is that massive central galaxies in low-density regions are more star-forming. This population of galaxies also possesses a higher fraction of spiral morphology and lower central stellar velocity dispersion, suggesting that their low quiescent fraction is due to less-frequent major merger events experienced in the low-density regions and, as a consequence, less-massive bulges and central black holes.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Mass-induced confinement near the sill of the conformal window

We revisit standard arguments for hyperscaling of the spectrum when a nonzero fermion mass is introduced to a gauge-fermion theory which is conformal in the infrared limit. With some general assumptions, we argue that the induced confinement scale will be significantly enhanced near the edge of the conformal to confining transition. This enhancement can allow for the fermion mass to be arbitrarily small compared to the confinement scale. This scale separation may allow for apparent spontaneous breaking of chiral symmetry within the conformal window, which may be of interest for construction of dilaton effective field theories in this regime.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Applied nonrelativistic conformal field theory: Scattering-length and effective-range corrections to rate of production of three neutrons at low relative momenta

Due to an accidentally large s-wave scattering length, in a relatively wide range of energy, neutrons are approximately described by the nonrelativistic conformal field theory of unitarity fermions, perturbed by one relevant and an infinite number of irrelevant operators. We develop a formalism which provides a nonperturbative definition of local operators in that nonrelativistic conformal field theory. We compute the scattering-length and effective-range corrections to the two-point functions of primary charge-three operators using the technique of conformal perturbation theory. These calculations allow us to find the first corrections to the scale-invariant behavior of the rate of nuclear reactions with three neutrons in the final state in the regime when the neutrons have small relative momenta.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Trace Anomaly as Signature of Conformality in Neutron Stars

We discuss an interpretation that a peak in the sound velocity in neutron star matter, as suggested by the observational data, signifies strongly coupled conformal matter. Here, the normalized trace anomaly is a dimensionless measure of conformality leading to the derivative and the nonderivative contributions to the sound velocity. We find that the peak in the sound velocity is attributed to the derivative contribution from the trace anomaly that steeply approaches the conformal limit. Smooth continuity to the behavior of high-density QCD implies that the matter part of the trace anomaly may be positive definite. We discuss a possible implication of the positivity condition of the trace anomaly on the M–R relation of the neutron stars.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Conformal duality of the nonlinear Schrödinger equation: Theory and applications to parameter estimation

The nonlinear Schrödinger equation (NLSE) in one spatial dimension has stationary solutions similar to those of the linear Schrödinger equation (LSE) as well as more exotic solutions such as solitary waves and quantum droplets. Here, we present a newly discovered conformal duality which unifies the stationary and time-dependent traveling-wave solutions of the one-dimensional cubic-quintic NLSE, the cubic NLSE and LSE. Any two systems that are classified by the same single number called the cross ratio are related by this symmetry. Notably, the conformal duality can also be adapted in Newtonian mechanics and serves as a powerful tool for investigating physical systems that otherwise cannot be directly accessed in experiments. Further, we show that the conformal symmetry is a valuable resource to substantially improve NLSE parameter estimation from noisy empirical data by introducing an optimization afterburner. The new method therefore has far reaching practical applications for nonlinear physical systems. Published by the American Physical Society 2025

Reinhardt, David B. (ORCID:0009000409812838)↗

DOE OSTI2023

True molecular conformation and structure determination by three-dimensional electron diffraction of PAH by-products potentially useful for electronic applications

The true molecular conformation and the crystal structure of benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene, 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene and 7,16-diphenylnaphtho[1,2,3,4-cde]helianthrene were determined ab initio by 3D electron diffraction. All three molecules are remarkable polycyclic aromatic hydrocarbons. The molecular conformation of two of these compounds could not be determined via classical spectroscopic methods due to the large size of the molecule and the occurrence of multiple and reciprocally connected aromatic rings. The molecular structure of the third molecule was previously considered provisional. These compounds were isolated as by-products in the synthesis of similar products and were at the same time nanocrystalline and available only in very limited amounts. 3D electron diffraction data, taken from submicrometric single crystals, allowed for direct ab initio structure solution and the unbiased determination of the internal molecular conformation. Detailed synthetic routes and spectroscopic analyses are also discussed. Based on many-body perturbation theory simulations, benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene may be a promising candidate for triplet–triplet annihilation and 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene may be a promising candidate for intermolecular singlet fission in the solid state.

36 MATERIALS SCIENCE↗

DOE OSTI2021

A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure

Viruses require multifunctional structured RNAs to hijack their host’s biochemistry, but their mechanisms can be obscured by the difficulty of solving conformationally dynamic RNA structures. Using cryo–electron microscopy (cryo-EM), we visualized the structure of the mysterious viral transfer RNA (tRNA)–like structure (TLS) from the brome mosaic virus, which affects replication, translation, and genome encapsidation. Structures in isolation and those bound to tyrosyl-tRNA synthetase (TyrRS) show that this ~55-kilodalton purported tRNA mimic undergoes large conformational rearrangements to bind TyrRS in a form that differs substantially from that of tRNA. Our study reveals how viral RNAs can use a combination of static and dynamic RNA structures to bind host machinery through highly noncanonical interactions, and we highlight the utility of cryo-EM for visualizing small, conformationally dynamic structured RNAs.

Science & Technology - Other Topics↗

DOE OSTI2025

Conformational ensembles reveal the origins of serine protease catalysis

Enzymes exist in ensembles of states that encode the energetics underlying their catalysis. Conformational ensembles built from 1231 structures of 17 serine proteases revealed atomic-level changes across their reaction states. By comparing the enzymatic and solution reaction, we identified molecular features that provide catalysis and quantified their energetic contributions to catalysis. Serine proteases precisely position their reactants in destabilized conformers, creating a downhill energetic gradient that selectively favors the motions required for reaction while limiting off-pathway conformational states. The same catalytic features have repeatedly evolved in proteases and additional enzymes across multiple distinct structural folds. In conclusion, our ensemble-function analyses revealed previously unknown catalytic features, provided quantitative models based on simple physical and chemical principles, and identified motifs recurrent in nature that may inspire enzyme design.

Du, Siyuan [Stanford Univ., CA (United States)] (O↗

DOE OSTI2025

Multiscale Molecular Dynamics Simulations: Accelerating Conformational Sampling of Biomolecular Systems by Iterating All-Atom and Coarse-Grained Simulations

We developed the atomistic-coarse-grained multiscale MD simulation method in the OpenMM simulation package by iterating between the all-atom (AA) and coarse-grained (CG) MD simulations to enhance the sampling of biomolecular conformations. As the free energy surfaces are flattened during CG MD simulations, we can accelerate the transitions between different low-energy conformations. The AA-CG-AA cycles are repeated, facilitating the accelerated sampling of biomolecular conformations at a CG level, while the finer atomistic interactions are refined with AA simulators.

Do, Hung Nguyen↗

DOE OSTI2025

Conformational heterogeneity in the dGsw purine riboswitch: role of Mg²⁺ and 2’-dG in aptamer folding

Recent advancements in RNA structural biology have focused on unraveling the complexities of non-coding mRNA elements like riboswitches. These cis-acting regulatory regions undergo structural changes in response to specific cellular metabolites, leading to up or downregulation of downstream genes. The purine riboswitch family regulates many prokaryotic genes involved in purine degradation and biosynthesis. They feature an aptamer domain organized around a 3-way helical junction, where ligand encapsulation occurs at the junctional core. In our study, we chemically probed the aptamer domain of the 2’-dG-sensing purine riboswitch from Mesoplasma florum (dGsw) under various solution conditions to understand how Mg²⁺ and 2’-dG influence riboswitch folding. Here, we find that efficient 2’-dG binding strongly depends on Mg²⁺, indicating that Mg²⁺ is essential for priming dGsw for ligand interactions. We identified a previously undescribed sequence in the 5’ tail of dGsw that is complementary to a conserved helix. The inclusion of this region in a construct led to intramolecular competition between the alternate helix, Palt, and P1. Mutational analysis confirmed that 5’ flanking end of the aptamer domain forms an alternate helix in the absence of ligand. Molecular dynamics simulations revealed that this alternative conformation is stable. This helix may, therefore, facilitate the formation of an anti-terminator helix by opening the 3-way junction surrounding the 2’-dG binding site. Our study further establishes the importance of a closed terminal P1 helix conformation for metabolite binding and suggests that the delicate interplay between P1 and Palt may fine-tune downstream gene regulation. These insights offer a new perspective on riboswitch structure and enhance our understanding of the role that a conformational ensemble plays in riboswitch activity and regulation.

Biochemistry & Molecular Biology↗

DOE OSTI2022

Structure and conformational dynamics of Clostridioides difficile toxin A

Clostridioides difficile toxin A and B (TcdA and TcdB) are two major virulence factors responsible for diseases associated with C. difficile infection (CDI). Here, we report the 3.18-Å resolution crystal structure of a TcdA fragment (residues L843–T2481), which advances our understanding of the complete structure of TcdA holotoxin. Our structural analysis, together with complementary single molecule FRET and limited proteolysis studies, reveal that TcdA adopts a dynamic structure and its CROPs domain can sample a spectrum of open and closed conformations in a pH-dependent manner. Furthermore, a small globular subdomain (SGS) and the CROPs protect the pore-forming region of TcdA in the closed state at neutral pH, which could contribute to modulating the pH-dependent pore formation of TcdA. A rationally designed TcdA mutation that trapped the CROPs in the closed conformation showed drastically reduced cytotoxicity. Taken together, these studies shed new lights into the conformational dynamics of TcdA and its roles in TcdA intoxication.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

The DESI One-Percent Survey: A Concise Model for the Galactic Conformity of Emission-line Galaxies

Galactic conformity is the phenomenon whereby a galaxy of a certain physical property is correlated with its neighbors of the same property, implying a possible causal relationship. Here, the observed auto correlations of emission-line galaxies (ELGs) from the highly complete DESI One-Percent Survey exhibit a strong clustering signal on small scales, providing clear evidence for the conformity effect of ELGs. Building upon the original subhalo abundance-matching (SHAM) method developed by Gao et al., we propose a concise conformity model to improve the ELG–halo connection. In this model, the number of satellite ELGs is boosted by a factor of ~5 in the halos whose central galaxies are ELGs. We show that the mean ELG satellite number in such central halos is still smaller than 1 and that the model does not significantly increase the overall satellite fraction. With this model, we can well recover the ELG auto correlations to the smallest scales explored with the current data (i.e., r p > 0.03 Mpc h –1 in real space and at s > 0.3 Mpc h –1 in redshift space), while the cross correlations between luminous red galaxies and ELGs are nearly unchanged. Although our SHAM model has only eight parameters, we further verify that it can accurately describe the ELG clustering in the entire redshift range from z = 0.8 to 1.6. We therefore expect that this method can be used to generate high-quality ELG lightcone mocks for DESI.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1973

A conformal head-up display for the visual approach

The degree of conformity used in matching a superimposed display to its visual background is considered in relation to the information available for vertical guidance and control during a purely visual approach. The information may be represented by individual symbols or combined in a single symbol, and the relative merits of these methods are discussed. A fully conformal display format is developed for the purpose of showing both the position and direction of the flight path, with provision for the effects of disturbances, ILS compatibility, and control needs. The field of view needed for all conditions and phases of the visual approach with a fully conformal display is studied in relation to the limitations of conventional collimator systems. Methods are discussed which depend on deviation of the sight line, and on windshield reflection of the uncollimated image of a simple pointer. Limited flight tests show some promise for the uncollimated method.

Naish, J. M.↗

NASA NTRS1985

Monte Carlo lattice models for adsorbed polymer conformation

The adhesion between a polymer film and a metal surface is of great technological interest. However, the prediction of adhesion and wear properties of polymer coated metals is quite difficult because a fundamental understanding of the polymer surface interaction does not yet exist. A computer model for the conformation of a polymer molecule adsorbed on a surface is discussed. The chain conformation is assumed to be described by a partially directed random walk on a three dimensional simple cubic lattice. An attractive surface potential is incorporated into the model through the use of a random walk step probability distribution that is anisotropic in the direction normal to the attractive surface. The effects of variations in potential characteristics are qualitatively included by varying both the degree of anisotropy of the step distribution and the range of the anisotropy. Polymer conformation is characterized by the average end to end distance, average radius of gyration, and average number of chain segments adsorbed on the surface.

Good, B. S.↗