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DOE OSTI2023

Probing single-chain conformation and its impact on the optoelectronic properties of donor–accepter conjugated polymers

The chain conformation of donor–acceptor conjugated polymers (D–A CPs) is critical to their optical and electronic properties. However, probing the conformation of D–A CPs (e.g., persistence length and contour length) at a single-chain level is challenging due to the formation of aggregates in dilute solution, even in a good solvent. In this work, we studied the chain conformation and corresponding optical spectra for high-performance D–A CPs in the single-chain state by multimodal variable-temperature scattering and spectroscopy techniques, as well as by molecular dynamics simulations. Here we found a critical role of the side-chain length and branch point in the persistence length and optical absorption due to steric effects. Hence, it is important to consider both the chain rigidity and coplanarity of the polymer backbone to achieve desirable optoelectronic properties. Our findings bridge the fundamental knowledge gaps to design new CPs with desired optoelectronic properties via molecular engineering for next-generation electronic devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Solvent effects on extractant conformational energetics in liquid–liquid extraction: a simulation study of molecular solvents and ionic liquids

Extractant design in liquid–liquid extraction (LLE) is a research frontier of metal ion separations that typically focuses on the direct extractant–metal interactions. However, a more detailed understanding of energetic drivers of separations beyond primary metal coordination is often lacking, including the role of solvent in the extractant phase. In this work, we propose a new mechanism for enhancing metal-complexant energetics with nanostructured solvents. Using molecular dynamics simulations with umbrella sampling, we find that the organic solvent can reshape the energetics of the extractant's intramolecular conformational landscape. Here, we calculate free energy profiles of different conformations of a representative bidentate extractant, n-octyl(phenyl)-N,N-diisobutyl carbamoyl methyl phosphinoxide (CMPO), in four different solvents: dodecane, tributyl phosphate (TBP), and dry and wet ionic liquid (IL) 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM][Tf 2 N]). By promoting reorganization of the extractant molecule into its binding conformation, our findings reveal how particular solvents can ameliorate this unfavorable step of the metal separation process. In particular, the charge alternating nanodomains formed in ILs substantially reduce the free energy penalty associated with extractant reorganization. Importantly, using alchemical free energy calculations, we find that this stabilization persists even when we explicitly include the extracted cation. These findings provide insight into the energetic drivers of metal ion separations and potentially suggest a new approach to designing effective separations using a molecular-level understanding of solvent effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme

Droplet injection strategies are a promising tool to reduce the large amount of sample consumed in serial femtosecond crystallography (SFX) measurements at X-ray free electron lasers (XFELs) with continuous injection approaches. Here, we demonstrate a new modular microfluidic droplet injector (MDI) design that was successfully applied to deliver microcrystals of the human NAD(P)H:quinone oxidoreductase 1 (NQO1) and phycocyanin. We investigated droplet generation conditions through electrical stimulation for both protein samples and implemented hardware and software components for optimized crystal injection at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Stanford Linac Coherent Light Source (LCLS). Under optimized droplet injection conditions, we demonstrate that up to 4-fold sample consumption savings can be achieved with the droplet injector. In addition, we collected a full data set with droplet injection for NQO1 protein crystals with a resolution up to 2.7 Å, leading to the first room-temperature structure of NQO1 at an XFEL. NQO1 is a flavoenzyme associated with cancer, Alzheimer's and Parkinson's disease, making it an attractive target for drug discovery. Further, our results reveal for the first time that residues Tyr128 and Phe232, which play key roles in the function of the protein, show an unexpected conformational heterogeneity at room temperature within the crystals. These results suggest that different substates exist in the conformational ensemble of NQO1 with functional and mechanistic implications for the enzyme's negative cooperativity through a conformational selection mechanism. Our study thus demonstrates that microfluidic droplet injection constitutes a robust sample-conserving injection method for SFX studies on protein crystals that are difficult to obtain in amounts necessary for continuous injection, including the large sample quantities required for time-resolved mix-and-inject studies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions

Determining collective variables (CVs) for conformational transitions is crucial to understanding their dynamics and targeting them in enhanced sampling simulations. Often, CVs are proposed based on intuition or prior knowledge of a system. However, the problem of systematically determining a proper reaction coordinate (RC) for a specific process in terms of a set of putative CVs can be achieved using committor analysis (CA). Identifying essential degrees of freedom that govern such transitions using CA remains elusive because of the high dimensionality of the conformational space. Various schemes exist to leverage the power of machine learning (ML) to extract an RC from CA. Here, we extend these studies and compare the ability of 17 different ML schemes to identify accurate RCs associated with conformational transitions. We tested these methods on an alanine dipeptide in vacuum and on a sarcosine dipeptoid in an implicit solvent. Our comparison revealed that the light gradient boosting machine method outperforms other methods. In order to extract key features from the models, we employed Shapley Additive exPlanations analysis and compared its interpretation with the “feature importance” approach. For the alanine dipeptide, our methodology identifies ϕ and θ dihedrals as essential degrees of freedom in the C7ax to C7eq transition. For the sarcosine dipeptoid system, the dihedrals ψ and ω are the most important for the cisαD to transαD transition. We further argue that analysis of the full dynamical pathway, and not just endpoint states, is essential for identifying key degrees of freedom governing transitions.

Chemistry↗

DOE OSTI2024

Initial data for first-order causal viscous conformal fluids in general relativity

We solve the Einstein constraint equations for a first-order causal viscous relativistic hydrodynamic theory in the case of a conformal fluid. For such a theory, a direct application of the conformal method does not lead to a decoupling of the equations, even for constant-mean curvature initial data. We combine the conformal method applied to a background perfect fluid theory with a perturbative argument in order to obtain the result.

Disconzi, Marcelo (ORCID:0000000234497778)↗

DOE OSTI2025

Repetitive proteins that undergo large conformational changes evade structural prediction algorithms

Protein structure prediction algorithms, such as AlphaFold, have accelerated protein design and advanced the understanding of the relationship between amino acid sequence and protein structure. However, these algorithms are limited in their ability to predict the structures of conformationally dynamic, intrinsically disordered, and stimuli-responsive proteins. To evaluate sequence-to-structure predictions of such challenging proteins, we explored a class of conformationally dynamic, repeats-in-toxin (RTX) proteins. RTX proteins adopt intrinsically disordered conformations in the absence of calcium and undergo reversible folding into β-roll structures upon binding to calcium. RTX proteins are characterized by tandem repeats of the sequence GGXGXDXUX, in which X can be any amino acid and U is an aliphatic amino acid. We designed RTX sequence variants with global substitutions of nonconserved amino acids, tandem repeats of consensus sequences GGAGXDTLY, and tandem repeats of scrambled sequences GGAGXDTYL. AlphaFold2 and AlphaFold3 predicted that all of these RTX variants adopt β-roll structures, characteristic of wild-type RTX bound to calcium. However, modeling the predicted structures with molecular dynamics simulations and characterizing the protein variants with circular dichroism spectroscopy, small-angle x-ray scattering, and x-ray crystallography revealed that variants adopt diverse, sequence-dependent structures in the absence and presence of calcium. To better design proteins for applications in biotechnology and sustainability, it is critical to build predictive tools that consider intrinsically disordered protein states and validate these tools with multi-mode, multi-scale experimental data.

Chang, Marina P. [Stanford Univ., CA (United State↗

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↗