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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Universality of Shallow Global Quenches in Critical Spin Chains

Measuring universal data in the strongly correlated regime of quantum critical points remains a fundamental objective for quantum simulators. In foundational work, Calabrese and Cardy demonstrated how these data govern the dynamics of certain global quenches to 1+1-dimensional conformal field theories. While the quasiparticle picture they introduce has been widely successful in both theory and experiment, their seminal prediction that the critical exponents are simply encoded in the relaxation rates of local observables is challenging to investigate experimentally. In this Letter, we examine the critical quench dynamics of local observables from two types of readily accessible initial conditions: ground states and finite-temperature ensembles. Here, we identify universal scaling collapses and scaling functions, utilizing a combination of conformal perturbation theory and tensor network numerics. For the finite-temperature quenches, we determine a regime in which the conformal field theory results are recovered, thereby allowing universal quantum critical data to be extracted from realistic quenches.

Quantum many-body systems↗
DOE OSTI2024

Multiscale Modeling of Vinyl-Addition Polynorbornenes: The Effect of Stereochemistry

Vinyl-addition polynorbornenes are candidates for designing high-performance polymers due to unique characteristics, which include a high glass transition temperature associated with a rigid backbone. Recent studies have established that the processability and properties of these polymers can be fine-tuned by using targeted substitutions. However, synthesis with different catalysts results in materials with distinct properties, potentially due to the presence of various stereoisomers that are difficult to quantify experimentally. Herein, we develop all-atom models of polynorbornene oligomers based on classical force fields and density functional theory. To establish the relationship between chemical architecture, chain conformations, and melt structure, we perform detailed molecular dynamics simulations with the fine-tuned atomistic force field and propose simpler coarse-grained descriptions to address the high molecular weight limit. All-atom simulations of oligomers suggest high glass transition temperatures in the range of 550–600 K. In the melt state (800 K), meso chains form highly rigid extended coils (C∞≈11) with amorphous structural characteristics similar to the X-ray diffraction data observed in the literature. In contrast, simulations with racemo chains predict highly helical tubular chain conformations that could promote assembly into crystalline structures.

Polymer Science↗
DOE OSTI2023

Interplay of molecular dynamics and radiative decay of a TADF emitter in a glass-forming liquid

Herein we investigate the role of molecular dynamics in the luminescent properties of a prototypical thermally activated delayed fluorescence (TADF) emitter, NAI-DMAC, in solution using a combination of temperature dependent time-resolved photoluminescence and absorption spectroscopies. We use a glass forming liquid, 2-methylfuran, to introduce an abrupt change in the temperature dependent diffusion dynamics of the solvent and examine the influence this has on the emission intensity of NAI-DMAC molecules. Comparison of experiment with first principles molecular dynamics simulations reveals that the emission intensity of NAI-DMAC molecules follows the temperature-dependent self-diffusion dynamics of the solvent. A marked reduction of emission intensity is observed as the temperature decreases toward the glass transition because the rate at which NAI-DMAC molecules can access emissive molecular conformations is greatly reduced. Below the glass transition, the diffusion dynamics of the solvent changes more slowly with temperature, which causes the emission intensity to decrease more slowly as well. The combination of experiment and computation suggests a pathway by which TADF emitters may transiently access a distribution of conformational states and avoid the need for an average conformation that strikes a balance between lower singlet–triplet energy splittings versus higher emission probabilities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Dynamical Signatures of Thermotoga maritima Maltose-Binding Proteins Affected by Ligand Binding

Functional segregation among protein isoforms depends on the interplay of their overall structures and the molecular dynamics of these structures. Thermotoga maritima maltose-binding protein (tmMBP) isoforms show size-dependent differential binding of maltose and malto-oligomers while maintaining remarkable fold conservation. This differential behavior needs detailed characterization in native-like aqueous conditions to understand the effects of protein dynamics on ligand binding and recognition. Small-angle neutron scattering (SANS), neutron spin echo (NSE) spectroscopy, and dynamic light scattering (DLS) were used in conjunction with previously published computational molecular dynamics (MD) simulations to understand the dynamic behavior of tmMBPs experimentally. SANS provided information on the overall structure of the molecules, while NSE was used to determine the dynamics in the nanosecond time scale. Both tmMBP2 and tmMBP3 have a bidomain architecture linked with a flexible hinge, with the binding pocket sitting in the cleft between the two domains. tmMBP2 and tmMBP3 showed different solution dynamics, with the translational and rotational components dominating the dynamics of both systems, resulting in a clear differentiation of their diffusion pattern. A faster dynamics component was also observed and was attributed to segmental dynamics. Differences observed between the ligand-free (apo) and ligand-bound (holo) states of the two proteins are attributed to conformational entropy. Our results highlight the intricacies of how structure and dynamics can together shape binding to a repertoire of substrates in structurally similar proteins.

Diffusion↗
DOE OSTI2026

Single-Molecule Electron Transport in Peptoids

Peptoids are structural analogs of peptides in which side chains are appended to the backbone nitrogen rather than the α-carbon. The sequence-defined modularity of peptoids enables precise control over structure−function relationships, enabling applications in energy storage and biomedical materials. Despite recent progress, the role of sequence and conformation on electron transport in peptoid molecules is not fully understood. Here, we synthesize a library of peptoid oligomers and characterize their molecular electronic properties using the scanning tunneling microscope-break junction (STM-BJ) technique. Our results show well-defined electron transport behavior for peptoid sequences containing aromatic side groups lacking hydrogen bonds (H-bonds) and without chemical substitutions at the N−C α position. This behavior fundamentally differs from electron transport in peptides, where H-bond interactions give rise to higher conductance states. All-atom molecular dynamics (MD) simulations are used to understand the conformational heterogeneity of peptoids, and molecular conformations obtained from MD simulations are used in quantum mechanical calculations based on the nonequilibrium Green’s function−density functional theory (NEGF-DFT) formalism. In all cases, computational results are in reasonable qualitative agreement with experiments. Our work demonstrates that the conductance behavior of peptoids depends on monomer identity, including side-chain aromaticity and substitution at the N−C α position. Overall, this work provides new insights into the structure−function relationships governing electron transport in peptoid-based materials and establishes design rules for peptoid-based molecular junctions.

Charge transport↗
DOE OSTI2023

Solution Structure and Scaling Laws of Cylindrical and Tapered Bottlebrush Polymers

Bottlebrush polymers are a unique class of macromolecular architectures with a plethora of potential industrial and pharmaceutical applications that critically depend on the bottlebrush shape and dimensions. Here, a systematic series of 12 cylindrical and 12 cone-shaped (tapered) bottlebrush polymers with poly(tert-butyl acrylate) (PtBA) or polystyrene (PS) side chains were synthesized using the sequential addition of macromonomers ring-opening metathesis polymerization (SAM-ROMP) grafting-through method. Small-angle neutron scattering (SANS) studies on dilute solutions of the two types of bottlebrush polymers provided noninvasive characterization of their structural dimensions and chain conformations. Simulated SANS traces, generated using coarse-grained molecular dynamics simulations, reproduced the distinctive features observed in the experimental SANS signals and provided necessary validation for data modeling. The combined analysis of experimental and simulated SANS signals yielded key structural and conformational parameters, including the bottlebrush radius, length, and Kuhn length as well as the excluded volume parameter and the correlation length of the polymer side chains. Importantly, the obtained structural parameters followed well-defined scaling laws as a function of the backbone and side chain degrees of polymerization, as predicted by mean field theories. In conclusion, these findings provide clear experimental and computational evidence of the interdependence of structural and conformational properties in an important class of polymer architectures.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Structural and dynamic effects of paraoxon binding to human acetylcholinesterase by X-ray crystallography and inelastic neutron scattering

Organophosphorus (OP) compounds, including nerve agents and some pesticides, covalently bind to the catalytic serine of human acetylcholinesterase (hAChE), thereby inhibiting acetylcholine hydrolysis necessary for efficient neurotransmission. Oxime antidotes can reactivate the OP-conjugated hAChE, but reactivation efficiency can be low for pesticides, such as paraoxon (POX). Understanding structural and dynamic determinants of OP inhibition and reactivation can provide insights to design improved reactivators. Here, in this study, X-ray structures of hAChE with unaged POX, with POX and oximes MMB4 and RS170B, and with MMB4 are reported. A significant conformational distortion of the acyl loop was observed upon POX binding, being partially restored to the native conformation by oximes. Neutron vibrational spectroscopy combined with molecular dynamics simulations showed that picosecond vibrational dynamics of the acyl loop soften in the ~20–50 cm –1 frequency range. The acyl loop structural perturbations may be correlated with its picosecond vibrational dynamics to yield more comprehensive template for structure-based reactivator design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The Role of Hydrophobic Nodes in the Dynamics of Class A β-Lactamases

Class A β-lactamases are known for being able to rapidly gain broad spectrum catalytic efficiency against most β-lactamase inhibitor combinations as a result of elusively minor point mutations. The evolution in class A β-lactamases occurs through optimisation of their dynamic phenotypes at different timescales. At long-timescales, certain conformations are more catalytically permissive than others while at the short timescales, fine-grained optimisation of free energy barriers can improve efficiency in ligand processing by the active site. Free energy barriers, which define all coordinated movements, depend on the flexibility of the secondary structural elements. The most highly conserved residues in class A β-lactamases are hydrophobic nodes that stabilize the core. To assess how the stable hydrophobic core is linked to the structural dynamics of the active site, we carried out adaptively sampled molecular dynamics (MD) simulations in four representative class A β-lactamases (KPC-2, SME-1, TEM-1, and SHV-1). Using Markov State Models (MSM) and unsupervised deep learning, we show that the dynamics of the hydrophobic nodes is used as a metastable relay of kinetic information within the core and is coupled with the catalytically permissive conformation of the active site environment. Finally, our results collectively demonstrate that the class A enzymes described here, share several important dynamic similarities and the hydrophobic nodes comprise of an informative set of dynamic variables in representative class A β-lactamases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Determining the Conformation of Supported Complexes Using an 17 O TEDOR-like NMR Experiment

Dynamic nuclear polarization surface-enhanced nuclear magnetic resonance (NMR) spectroscopy has enabled the determination of the three-dimensional configuration of surface sites, in particular supported metal complexes of relevance to single-site heterogeneous catalysis. These approaches have chiefly leveraged the application of NMR double-resonance experiments that either reveal the complex conformation via point-to-point intramolecular distances between spin-labeled atoms or the complex-surface orientation via distances between the spins and the surface plane. Either method typically requires expensive isotope labeling and each reports on different structural features. The application of an experiment that simultaneously reveals both types of distances with chemical resolution would be ideal. Here, in this article, we describe an 17 O{ 1 H} pseudo-3D correlation experiment that achieves this goal. Specifically, Si–O–Si and Si–O–M oxygens are well-resolved by 17 O NMR; therefore, distances can be simultaneously measured radially, between Si– 17 O–M and the 1 H’s of the ligands, and vertically to the Si– 17 O–Si linkages of the silica support. We demonstrate the experiment using supported yttrium and zirconium complexes. Good agreement is obtained when comparing the experimental results to theoretical predictions from density functional theory calculations, highlighting the reliability of this relatively simple experiment.

alkyls↗
NASA NTRS2010

Interactions of Ku70/80 with Double-Strand DNA: Energetic, Dynamics, and Functional Implications

Space radiation is a proficient inducer of DNA damage leading to mutation, aberrant cell signaling, and cancer formation. Ku is among the first responding proteins in nucleus to recognize and bind the DNA double strand breaks (DSBs) whenever they are introduced. Once loaded Ku works as a scaffold to recruit other repair factors of non-homologous end joining and facilitates the following repair processes. The crystallographic study of the Ku70/80 heterodimer indicate the core structure of this protein shows virtually no conformational change after binding with DNA. To investigate the dynamical features as well as the energetic characteristics of Ku-DNA binding, we conduct multi-nanosecond molecular dynamics simulations of a modeled Ku70/80 structure and several complexes with two 24-bp DNA duplexes. Free energy calculations show significant energy differences between the complexes with Ku bound at DSBs and those with Ku associated at an internal site of a chromosome. The results also reveal detailed interactions between different nucleotides and the amino acids along the DNA-binding cradle of Ku, indicating subtle binding preference of Ku at specific DNA sequences. The covariance matrix analyses along the trajectories demonstrate the protein is stimulated to undergo correlated motions of different domains once bound to DNA ends. Additionally, principle component analyses identify these low frequency collective motions suitable for binding with and translocation along duplex DNA. It is proposed that the modification of dynamical properties of Ku upon binding with DSBs may provide a signal for the further recruitment of other repair factors such as DNA-PKcs, XLF, and XRCC4.

Hu, Shaowen↗
DOE OSTI2021

Lorentzian dynamics and factorization beyond rationality

We investigate the emergence of topological defect lines in the conformal Regge limit of two-dimensional conformal field theory. We explain how a local operator can be factorized into a holomorphic and an anti-holomorphic defect operator connected through a topological defect line, and discuss implications on analyticity and Lorentzian dynamics including aspects of chaos. We derive a formula relating the infinite boost limit, which holographically encodes the “opacity” of bulk scattering, to the action of topological defect lines on local operators. Leveraging the unitary bound on the opacity and the positivity of fusion coefficients, we show that the spectral radii of a large class of topological defect lines are given by their loop expectation values. Factorization also gives a formula relating the local and defect operator algebras and fusion categorical data. We then review factorization in rational conformal field theory from a defect perspective, and examine irrational theories. On the orbifold branch of the c = 1 free boson theory, we find a unified description for the topological defect lines through which the twist fields are factorized; at irrational points, the twist fields factorize through “non-compact” topological defect lines which exhibit continuous defect operator spectra. Along the way, we initiate the development of a formalism to characterize non-compact topological defect lines.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

cAMP binding to closed pacemaker ion channels is non-cooperative

Electrical activity in the brain and heart depends on rhythmic generation of action potentials by pacemaker ion channels (HCN) whose activity is regulated by cAMP binding. Previous work has uncovered evidence for both positive and negative cooperativity in cAMP binding, but such bulk measurements suffer from limited parameter resolution. Efforts to eliminate this ambiguity using single-molecule techniques have been hampered by the inability to directly monitor binding of individual ligand molecules to membrane receptors at physiological concentrations. Here we overcome these challenges using nanophotonic zero-mode waveguides4 to directly resolve binding dynamics of individual ligands to multimeric HCN1 and HCN2 ion channels. We show that cAMP binds independently to all four subunits when the pore is closed, despite a subsequent conformational isomerization to a flip state at each site. The different dynamics in binding and isomerization are likely to underlie physiologically distinct responses of each isoform to cAMP and provide direct validation of the ligand-induced flip-state model. Furthermore, this approach for observing stepwise binding in multimeric proteins at physiologically relevant concentrations can directly probe binding allostery at single-molecule resolution in other intact membrane proteins and receptors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Ligand-induced transmembrane conformational coupling in monomeric $\mathrm{EGFR}$

Single pass cell surface receptors regulate cellular processes by transmitting ligand-encoded signals across the plasma membrane via changes to their extracellular and intracellular conformations. This transmembrane signaling is generally initiated by ligand binding to the receptors in their monomeric form. While subsequent receptor-receptor interactions are established as key aspects of transmembrane signaling, the contribution of monomeric receptors has been challenging to isolate due to the complexity and ligand-dependence of these interactions. By combining membrane nanodiscs produced with cell-free expression, single-molecule Förster Resonance Energy Transfer measurements, and molecular dynamics simulations, we report that ligand binding induces intracellular conformational changes within monomeric, full-length epidermal growth factor receptor (EGFR). Our observations establish the existence of extracellular/intracellular conformational coupling within a single receptor molecule. We implicate a series of electrostatic interactions in the conformational coupling and find the coupling is inhibited by targeted therapeutics and mutations that also inhibit phosphorylation in cells. Collectively, these results introduce a facile mechanism to link the extracellular and intracellular regions through the single transmembrane helix of monomeric EGFR, and raise the possibility that intramolecular transmembrane conformational changes upon ligand binding are common to single-pass membrane proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Mechanistic insights into a heterobifunctional degrader-induced PTPN2/N1 complex

PTPN2 (protein tyrosine phosphatase non-receptor type 2, or TC-PTP) and PTPN1 are attractive immuno-oncology targets, with the deletion of Ptpn1 and Ptpn2 improving response to immunotherapy in disease models. Targeted protein degradation has emerged as a promising approach to drug challenging targets including phosphatases. We developed potent PTPN2/N1 dual heterobifunctional degraders (Cmpd-1 and Cmpd-2) which facilitate efficient complex assembly with E3 ubiquitin ligase CRL4 CRBN , and mediate potent PTPN2/N1 degradation in cells and mice. To provide mechanistic insights into the cooperative complex formation introduced by degraders, we employed a combination of structural approaches. Our crystal structure reveals how PTPN2 is recognized by the tri-substituted thiophene moiety of the degrader. We further determined a high-resolution structure of DDB1-CRBN/Cmpd-1/PTPN2 using single-particle cryo-electron microscopy (cryo-EM). This structure reveals that the degrader induces proximity between CRBN and PTPN2, albeit the large conformational heterogeneity of this ternary complex. The molecular dynamic (MD)-simulations constructed based on the cryo-EM structure exhibited a large rigid body movement of PTPN2 and illustrated the dynamic interactions between PTPN2 and CRBN. Together, our study demonstrates the development of PTPN2/N1 heterobifunctional degraders with potential applications in cancer immunotherapy. Furthermore, the developed structural workflow could help to understand the dynamic nature of degrader-induced cooperative ternary complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Acoustic force spectroscopy reveals subtle differences in cellulose unbinding behavior of carbohydrate-binding modules

Protein adsorption to solid carbohydrate interfaces is critical to many biological processes, particularly in biomass deconstruction. To engineer more-efficient enzymes for biomass deconstruction into sugars, it is necessary to characterize the complex protein–carbohydrate interfacial interactions. A carbohydrate-binding module (CBM) is often associated with microbial surface-tethered cellulosomes or secreted cellulase enzymes to enhance substrate accessibility. However, it is not well known how CBMs recognize, bind, and dissociate from polysaccharides to facilitate efficient cellulolytic activity, due to the lack of mechanistic understanding and a suitable toolkit to study CBM–substrate interactions. Our work outlines a general approach to study the unbinding behavior of CBMs from polysaccharide surfaces using a highly multiplexed single-molecule force spectroscopy assay. Here, we apply acoustic force spectroscopy (AFS) to probe a Clostridium thermocellum cellulosomal scaffoldin protein (CBM3a) and measure its dissociation from nanocellulose surfaces at physiologically relevant, low force loading rates. An automated microfluidic setup and method for uniform deposition of insoluble polysaccharides on the AFS chip surfaces are demonstrated. The rupture forces of wild-type CBM3a, and its Y67A mutant, unbinding from nanocellulose surfaces suggests distinct multimodal CBM binding conformations, with structural mechanisms further explored using molecular dynamics simulations. Applying classical dynamic force spectroscopy theory, the single-molecule unbinding rate at zero force is extrapolated and found to agree with bulk equilibrium unbinding rates estimated independently using quartz crystal microbalance with dissipation monitoring. However, our results also highlight critical limitations of applying classical theory to explain the highly multivalent binding interactions for cellulose–CBM bond rupture forces exceeding 15 pN.

09 BIOMASS FUELS↗
DOE OSTI2025

Metric isometries, holography, and continuous symmetry operators

In the AdS/CFT correspondence, a topological symmetry operator of the boundary conformal field theory (CFT) is dual to a dynamical brane in the gravitational bulk. Said differently, this predicts a dynamical brane for every global symmetry of the boundary CFT. We analyze this correspondence for continuous symmetries which arise from a consistent truncation of isometries on the “internal” factor 𝑋 of AdS × 𝑋. In the extra-dimensional geometry, these branes are associated with various metric singularities and do not arise from wrapped D-branes. Boosts relate configurations interpreted as topological symmetry operators and heavy defects in the CFT. From the perspective of the AdS factor, with gravity and bulk gauge fields, these are codimension-2 Gukov-Witten-like vortex configurations which are the gravity duals of 0-form symmetry operators. These effective branes come with an asymptotic tension and size which is also fully fixed by bulk dynamics. We use this higher-dimensional perspective to determine properties of the worldvolume theory for these branes. We also discuss how these considerations generalize to more general quantum field theories engineered via string theory which need not possess a semiclassical gravity dual.

anomalies↗
DOE OSTI2025

Structure-Based Design of Small-Molecule Inhibitors of Human Interleukin-6

Human Interleukin-6 (hIL-6) is a pro inflammatory cytokine that binds to its receptor, IL-6Rα followed by binding to gp130 and subsequent dimerization to form a hexamer signaling complex. As a critical inflammation mediator, hIL-6 is associated with a diverse range of diseases and monoclonal antibodies in clinical use that either target IL-6Rα or hIL-6 to inhibit signaling. Here, we perform high-throughput structure-based computational screening using ensemble docking for small-molecule antagonists for which the target conformations were taken from 600 ns long molecular dynamics simulations of the apo protein. Prior knowledge of the contact sites from binary complex studies and experimental work was incorporated into the docking studies. The top 20 scoring ligands from the in silico studies after post analysis were subjected to in vitro functional assays. Among these compounds, the ligand with the second-highest calculated binding affinity experimentally showed an ~84% inhibitory effect on IL6-induced STAT3 reporter activity at 10 μM concentration. This finding may pave the way for designing small-molecule inhibitors of hIL-6 of therapeutic significance.

Human Interleukin-6↗