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Results for “Conformational dynamics”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Insights into distorted lamellar phases with small-angle scattering and machine learning

Lamellar phases are essential in various soft matter systems, with topological defects significantly influencing their mechanical properties. In this report, we present a machine-learning approach for quantitatively analyzing the structure and dynamics of distorted lamellar phases using scattering techniques. By leveraging the mathematical framework of Kolmogorov–Arnold networks, we demonstrate that the conformations of these distorted phases – expressed as superpositions of complex waves – can be reconstructed from small-angle scattering intensities. Through the contour analysis of wave field phase singularities, we obtain the statistics of the spatial distribution of topological defects. Furthermore, we establish that the temporal evolution of these defects can be derived from the time-dependent traveling wave field, informed by the dispersion relation of spectral components. This method opens new avenues for investigating the dynamics of distorted lamellar phases using various dynamic scattering techniques such as neutron spin echo and X-ray photon correlation spectroscopy. These findings enhance our microscopic understanding of how defects influence the physical properties of lamellar materials, with implications for both equilibrium and non-equilibrium states in general lamellar systems.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Advances for QCD and the standard model: color-confining light-front holography and the principle of maximum conformality

Here, I review how the application of superconformal quantum mechanics and light-front holography leads to new insights into the physics of color confinement, the spectroscopy and dynamics of hadrons, as well as surprising supersymmetric relations between the masses of mesons, baryons, and tetraquarks. Spontaneous chiral symmetry breaking is automatically fulfilled by supersymmetric Light-Front QCD. The light-front holographic approach (HLFQCD) also predicts the behavior of the QCD running coupling and other observables from the nonperturbative color-confining domain to the perturbative domain. One can determine the QCD running coupling to high precision from the data of just a single experiment over the entire perturbative regime by using the Principle of Maximum Conformality (PMC). The PMC, which generalizes the conventional Gell-Mann-Low method for scale-setting in perturbative QED to non-Abelian QCD, provides a rigorous method for achieving unambiguous scheme-independent, fixed-order Standard Model predictions, consistent with the principles of the renormalization group. I also briefly review a novel feature of hadronic physics predicted by QCD: intrinsic heavy quarks.

Brodsky, Stanley J. [SLAC National Accelerator Lab↗
DOE OSTI2025

Acetylcholinesterase: Structure, dynamics, and interactions with organophosphorus compounds

Acetylcholinesterase (AChE) is an enzyme that hydrolyzes the neurotransmitter acetylcholine (ACh), removing it from the synaptic cleft after the transmission of an electrical signal, making it an essential component of chemical neurotransmission. AChE is a serine hydrolase, containing a catalytic triad of Ser/His/Glu. AChE is a prime target for pharmaceuticals treating a variety of neurological disorders. It is also the target of synthetic organophosphorus (OP) compounds that have been used as pesticides and chemical warfare agents. OP compounds contain a potent leaving group, such as fluorine, and act by forming a covalent adduct with the catalytic serine of the AChE active site. A wealth of structural information is available for AChE, including over 300 structures, including a subset of structures in complex with drugs as well as OP compounds. This review will highlight the interactions between OP compounds and AChE from a structural and computational perspective, with a discussion of access to the active site, as well as side reactions that lead to dealkylation of the OP-catalytic serine adduct, a process known as aging. We conclude that while the majority of the conformational changes needed to accommodate the OP compounds are localized to the acyl loop in the crystal structures, molecular dynamics simulations highlight the potential for a far more dynamic enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Arbitrary Order Virtual Element Methods for High‐Order Phase‐Field Modeling of Dynamic Fracture

ABSTRACT Accurate modeling of fracture nucleation and propagation in brittle and ductile materials subjected to dynamic loading is important in predicting material damage and failure under extreme conditions. Phase‐field fracture models have garnered a lot of attention in recent years due to their success in representing damage and fracture processes in a wide class of materials and under a variety of loading conditions. Second‐order phase‐field fracture models are by far the most popular among researchers (and increasingly, among practitioners), but fourth‐order models have started to gain broader acceptance since their more recent introduction. The exact solution corresponding to these high‐order phase‐field fracture models has higher regularity. Thus, numerical solutions of the model equations can achieve improved accuracy and higher spatial convergence rates. In this work, we develop a virtual element framework for the high‐order phase‐field model of dynamic fracture. The virtual element method (VEM) can be regarded as a generalization of the classical finite element method. In addition to many other desirable characteristics, the VEM allows computing on polytopal meshes. Here, we use ‐conforming virtual elements and the generalized‐ time integration method for the momentum balance equation, and adopt ‐conforming virtual elements for the high‐order phase‐field equation. We verify our virtual element framework using classical quasi‐static benchmark problems and demonstrate its capabilities with the aid of numerical simulations of dynamic fracture in brittle materials.

42 ENGINEERING↗
DOE OSTI2024

Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser

Catalysis and translocation of multisubunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near-atomic resolution and precise arrangement of key active site components have been elusive. Here, we present the free-electron laser (FEL) structures of a matched ATP-bound Pol II and the hyperactive Rpb1 T834P bridge helix (BH) mutant at the highest resolution to date. The radiation-damage-free FEL structures reveal the full active site interaction network, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg 2+ , and, more importantly, a putative third (site C) Mg 2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structures indicate that the third Mg 2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/BH interactions induce conformational changes that could allow translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the T834P mutant reveal rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.

Science & Technology - Other Topics↗
DOE OSTI2024

Deciphering the Cofilin Oligomers via Intermolecular Disulfide Bond Formation: A Coarse-Grained Molecular Dynamics Approach to Understanding Cofilin’s Regulation on Actin Filaments

Cofilin, a key actin-binding protein, orchestrates the dynamics of the actomyosin network through its actin-severing activity and by promoting the recycling of actin monomers. Recent experimental work suggests that cofilin also forms functionally distinct oligomers through thiol post-translational modification (PTM) that encourages actin nucleation and assembly. Despite these advances, the structural conformations of cofilin oligomers that modulate actin activity remain elusive because there are combinatorial ways to oxidize thiols in cysteines to form disulfide bonds rapidly. This study employs molecular dynamics simulations to investigate human cofilin 1 as a case study for exploring cofilin dimers via disulfide bond formation. Using the free energy profiling, our simulations unveil a range of probable cofilin dimer structures not represented in current Protein Data Bank entries. These candidate dimers are characterized by their distinct population distributions and relative free energies. Of particular note is a dimer featuring an interface between cysteines 139 and 147 residues, which demonstrates stable free energy characteristics and intriguingly symmetrical geometry. In contrast, the experimentally proposed dimer structure exhibits a less stable free energy profile. Here, we also evaluate frustration quantification based on the energy landscape theory in the protein-protein interactions at the dimer interfaces. Notably, the 39-39 dimer configuration emerges as a promising candidate for forming cofilin tetramers, as substantiated by frustration analysis. Additionally, docking simulations with actin filaments further evaluate the stability of these cofilin dimer-actin complexes. Our findings thus offer a computational framework for understanding the role of thiol post-translational modification cofilin proteins in regulating oligomerization, and the subsequent cofilin-mediated actin dynamics in the actomyosin network.

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

Data-driven equation-free dynamics applied to many-protein complexes: The microtubule tip relaxation

Microtubules (MTs) constitute the largest components of the eukaryotic cytoskeleton and play crucial roles in various cellular processes, including mitosis and intracellular transport. The property allowing MTs to cater to such diverse roles is attributed to dynamic instability, which is coupled to the hydrolysis of GTP (guanosine-5'-triphosphate) to GDP (guanosine-5'-diphosphate) within the β-tubulin monomers. Understanding the equilibrium dynamics and the structural features of both GDP- and GTP-complexed MT tips, especially at an all-atom level, remains challenging for both experimental and computational methods because of their dynamic nature and the prohibitive computational demands of simulating large, many-protein systems. This study employs the “equation-free” multiscale computational method to accelerate the relaxation of all-atom simulations of MT tips toward their putative equilibrium conformation. Using large MT lattice systems (14 protofilaments × 8 heterodimers) comprising ~21-38 million atoms, we applied this multiscale approach to leapfrog through time and nearly double the computational efficiency in realizing relaxed all-atom conformations of GDP- and GTP-complexed MT tips. Commencing from an initial 4 μs unbiased all-atom simulation, we interleave coarse projective “equation-free” jumps with short bursts of all-atom molecular dynamics simulation to realize an additional effective simulation time of 1.875 μs. Our 5.875 μs of effective simulation trajectories for each system expose the subtle yet essential differences in the structures of MT tips as a function of whether β-tubulin monomer is complexed with GDP or GTP, as well as the lateral interactions within the MT tip, offering a refined understanding of features underlying MT dynamic instability. Furthermore, the approach presents a robust and generalizable framework for future explorations of large biomolecular systems at atomic resolution.

Wu, Jiangbo [University of Chicago, IL (United Sta↗
DOE OSTI2024

Light scalar meson and decay constant in SU(3) gauge theory with eight dynamical flavors

The SU(3) gauge theory with N f = 8 nearly massless Dirac fermions has long been of theoretical and phenomenological interest due to the near-conformality arising from its proximity to the conformal window. One particularly interesting feature is the emergence of a relatively light, stable flavor-singlet scalar meson σ ( J P C = 0 + + ) in contrast to the N f = 2 theory QCD. In this work, we study the finite-volume dependence of the σ meson correlation function computed in lattice gauge theory and determine the σ meson mass and decay constant extrapolated to the infinite-volume limit. We also determine the infinite-volume mass and decay constant of the flavor-nonsinglet scalar meson a 0 . Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2026

From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture

Background Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two-dimensional (2D) genome-wide contact maps of chromatin interactions by capturing the spatial proximity between genomic loci, which reveal interaction frequencies but lack the spatial resolution needed to interpret the three-dimensional (3D) genome structure(s). Emerging evidence suggests that epigenetic regulation is closely linked to 3D genome architecture, and that structural changes over time (4D) drive key biological processes in development, disease, and environmental response. Thus, integrating 3D structure with functional data is critical for a more complete understanding of genome regulation. Previous work, most notably the 4DHiC chromosome modeling framework, has shown that physical multi-dimensional modeling approaches rooted in polymer physics and molecular dynamics can resolve these structures at biologically meaningful resolutions by integrating temporal Hi-C data with physical constraints to uncover dynamic chromosome reorganization. Thus, molecular dynamics simulations, constrained by Hi-C contact matrices, can resolve fine-scale structural changes and reveal functionally significant transitions in chromatin conformation. Results Herein, we present the 4D Genome Browser Workflow (4DGBWorkflow) and the 4D Genome Browser (4DGB). The algorithm is based on the 4DHiC method, and the containerized tool is an end-to-end workflow that can transform, filter, and view 4D epigenomics and chromatin datasets, allowing non-specialists to apply three-dimensional modeling principles to diverse datasets and experimental conditions. The software executes on a laptop running macOS, Linux or Windows. From input Hi-C files (.hic), the 4DGBWorkflow produces 3D reconstructions of chromosomes, integrates the reconstruction with track data (e.g., epigenetic marks, transcriptome profiles), and provides comparative visualization of the results in a single workflow. Conclusions The 4DGBWorkflow and 4D Genome Browser are open-source tools for comparative analysis and visualization of 4D chromosome datasets, including chromatin architecture and epigenomic signals. Automatic integration of Hi-C data with molecular dynamics democratizes the construction of time resolved 3D genome structures, simplifying complex simulations and data integration schemes.

3D Genome Browser↗
DOE OSTI2024

The Influence of Alkyl Spacers and Molecular Weight on the Charge Transport and Storage Properties of Oxy‐Bithiophene‐Based Conjugated Polymers

Conjugated polymers (CPs) with polar side chains can conduct electronic and ionic charges simultaneously, making them promising for bioelectronics, electrocatalysis and energy storage. Recent work showed that adding alkyl spacers between CP backbones and polar side chains improved electronic charge carrier mobility, reduced swelling and enhanced stability, without compromising ion transport. However, how alkyl spacers impact polymer backbone conformation and, subsequently, electronic properties remain unclear. In this work, we design two oxy-bithiophene-based CP series, each featuring progressively extended alkyl spacer lengths and two distinct molecular weight (MW) distributions. Using operando characterisations, we evaluate the (spectro)electrochemical and swelling properties of the polymer thin films, and their performance in organic field-effect transistors and organic electrochemical transistors. Surprisingly, alkyl spacers negatively impact the hole mobility of our polymers, with higher MW amplifying this effect. Using molecular dynamics simulations, we show that it is thermodynamically favourable for adjacent non-polar alkyl spacers to aggregate in polar electrolytes, leading to backbone twisting. Further spectroscopic measurements corroborate this prediction. Our findings demonstrate the active interactions between side chain structure, MW and electrolyte/solvent polarity in influencing polymer performance, underscoring the importance of considering solvation environment effects on polymer conformation when designing new mixed conducting CPs for electrochemical applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Role of electron correlation on the adenine dimer interaction for non-equilibrium geometries: a benchmark Quantum Monte Carlo study

The accurate description of non-covalent interactions is critical for understanding the structure, dynamics, and eventual function of biomolecules. The adenine dimer serves as a benchmark system for computational methods due to its role in nucleic acid structures and its rich conformational landscape. In this study, we employ benchmark diffusion quantum Monte Carlo (DMC) methods to investigate the relative energies and role of electron correlation on a set of adenine dimer conformations generated via a search of the potential energy landscape using the global optimizer algorithm. Relative DMC energies are compared against a wide range of density functional theory (DFT) approximation results. We find that although most of the DFT functionals perform well for low-energy structures, their accuracy varies significantly for higher-energy conformations, including stacked and T-shaped structures. A large fraction of the variation is due to the treatment of the van der Waals interaction. BLYP, B3LYP, and PBE0 significantly improve with added D4 dispersion, while the recent r2SCAN-D4 and ωB97M-V functionals show the least scatter and closest agreement with the DMC. These findings highlight the delicate nature of these interactions in biomolecular systems and provide guidance for simulations of their structure and dynamics and for the development of machine learned interatomic potentials.

Washburn, Laurel [ORNL] (ORCID:0000000324179335)↗
DOE OSTI2024

Dynamic structural determinants in bacterial microcompartment shells

Bacterial microcompartments (BMCs) are polyhedral structures that segregate enzymatic cargo from the cytosol via encapsulation within a protein shell. Unlike other biological polyhedra, such as viral capsids and encapsulins, BMC shells can exhibit a highly advantageous structural and functional plasticity, conforming to a variety of anabolic (CO 2 fixation in carboxysomes) and catabolic (nutrient assimilation in metabolosomes) roles. Consequently, understanding the subunit properties and associated protein–protein interaction processes that guide shell assembly and function is a necessary step to fully harness BMCs as modular, biotechnological nanomachines. Here, we describe the recent insights into the dynamics of structural features of the key BMC domain (Pfam00936)-containing proteins, which serve as a structural template for BMC-H and BMC-T shell building blocks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structure–Function Relationships in Sequence-Controlled Copolymers for Rare Earth Element Chelation

The ability to tune material function through primary sequence is a defining feature of biological macromolecules, allowing precise control over structure and target interactions in complex aqueous environments. However, translating sequence–structure–function relationships to synthetic macromolecules is challenging due to their dispersity in sequence, conformation, and composition. Here, we report systematic studies of amphiphilic polymer chelators designed to probe how composition and patterning influence binding affinity and selectivity for rare earth elements (REEs), a series of technologically relevant metals with challenging separation profiles. A library of copolymers varying hydrophobic monomer composition and patterning was synthesized via reversible addition–fragmentation chain transfer (RAFT) polymerization, spanning statistical, gradient, and block architectures. REE binding was quantified using a high-throughput colorimetric assay, and reconstruction of polymer ensembles using kinetic stochastic simulations enabled quantitative comparisons of sequence heterogeneity, linking local monomer colocalization to emergent REE binding. Further, we investigated the role of different hydrophobic comonomers in tuning metal coordination, with binding trends linked to structural features that influence binding site desolvation. Complementary dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) measurements showed that both polymer and monomer architecture modulate metal-induced conformational changes, and that multichain assembly behavior emerges beyond critical hydrophobic thresholds. Sequence control also altered REE selectivity, with nonmonotonic differences observed across compositionally identical polymers with different sequence architectures. Together, these findings establish design principles that connect polymer sequence and structure to binding performance, guiding the design of macromolecular chelators with enhanced affinity and selectivity for applications in separations, sensing, and catalysis.

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

A Decentralized Market Mechanism for Energy Communities under Operating Envelopes

Here, we propose an operating envelopes (OEs) aware energy community market mechanism that dynamically charges/rewards its members based on two-part pricing. The OEs are imposed exogenously by a regulated distribution system operator (DSO) on the energy community's revenue meter and is subject to a generalized net energy metering (NEM) tariff design. By formulating the interaction of the community operator and its members as a Stackelberg game, we show that the proposed two-part pricing achieves a Nash equilibrium and maximizes the community's social welfare in a decentralized fashion while ensuring that the community's operation abides by the OEs. The market mechanism conforms with the cost-causation principle and guarantees community members a surplus level no less than their maximum surplus when they autonomously face the DSO. The dynamic and uniform community price is a monotonically decreasing function of the community's aggregate renewable generation. We also analyze the impact of exogenous parameters such as NEM rates and OEs on the value of joining the community. Lastly, through numerical studies, we showcase the community's welfare, and pricing, and compare its members' surplus to customers under the DSO's regime.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2026

Quantum simulation of massive Thirring and Gross--Neveu models for arbitrary number of flavors

The study of fermionic quantum field theories is an important problem for realizing the standard model of particle physics on a quantum computer. As a step towards this goal, we consider the massive Thirring and Gross--Neveu models with arbitrary number of fermion flavors, $N_f$, discretized on a spatial one-dimensional lattice of size $L$ in the Hamiltonian formulation. We compute the gate complexity using the higher-order product formula and using block-encoding/qubitization and quantum singular value transformations in the limit of large $N_f$ and $L$. We also prepare the ground states of both models with excellent fidelity for system sizes up to 20 qubits with $N_f = 1,2,3,4$ using the adaptive-variational quantum imaginary time algorithm. In addition, we also classify the dynamical Lie algebras of these relativistic fermionic models and show that they belong to the same isomorphism class. Our work is a concrete step towards the quantum simulation of real-time dynamics of large $N_f$ fermionic quantum field theories models relevant for chiral symmetry breaking, understanding dimensional transmutation, and exploring the conformal window of field theories on near-term and early fault-tolerant quantum computers.

FOS: Physical sciences↗
DOE OSTI2025

Statistical evaluation of microscale stress conditions leading to void nucleation in the weak shock regime

Here, we investigate the heterogeneity of the stress state driven by anisotropic deformation response at the single crystal level through five statistical volume element (SVE) calculations of polycrystalline BCC tantalum. This work focuses on grain boundaries as a prominent material defect type prone to void nucleation based upon experimental observations of predominantly intergranular void nucleation in this material. The SVEs are constructed to be statistically representative of larger volumes of material and are meshed such that mean and standard deviation of grain size and orientation information is reconstructed. The computational meshes feature hexahedral (brick) elements and smooth conformal grain boundaries where significant stress concentration is known to occur, a tail effect of interest in the extreme events process of dynamic ductile damage. An existing micromechanical crystallographic plasticity model shown to capture the single crystal behavior of BCC tantalum well is used to perform the polycrystal calculations. The model includes representation of the non-Schmid effect of non-planar screw dislocation kinetics in tantalum. A three-dimensional stress state time profile predicted by damage modeling of a flyer plate impact experiment is applied as boundary conditions to each SVE. Resulting grain boundary stress state statistics are strongly non-Gaussian. Significant structural evolution is observed within the compressive hold before unloading into tension in the stress profile. Strong angular dependence of grain boundary traction magnitude with shock direction is observed. Non-Schmid effects continue to suggest their influence on propensity of microstructural defect types to nucleate voids. A general void nucleation criterion is proposed using probability theory. The general framework is specified to polycrystalline BCC tantalum in the weak shock regime to include the SVE calculations and literature molecular dynamics calculations of grain boundary void nucleation strength. Probability density functions (PDFs) are used to describe the interaction between the local stress state heterogeneity and the distributed grain boundary void nucleation strength state. A causation entropy maximization procedure removes the requirement for ad hoc selection of a PDF functional form and provides a rigorous procedure for data-based PDF determination. The resulting physically informed PDF describes the spatial appearance frequency of nucleated voids as a function of applied macroscale pressure. Lower length scale physics are thus packaged in a precise and computationally efficient way to provide computational plasticity insight to macroscale dynamic ductile damage models.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Light-Modulated Self-Assembly of Synthetic Nanotubes

Artificial biomolecular polymers with the capacity to respond to stimuli are emerging as a key component to the development of living materials and synthetic cells. Here, in this work, we demonstrate artificial DNA tubular nanostructures that form in response to light in a dose-dependent manner. These nanotubes assemble from programmable DNA tile motifs that are engineered to include a UV-responsive domain so that UV irradiation activates nanotube self-assembly. We demonstrate that the nanotube formation speed can be tuned by adjusting the UV dose. We then couple the light-dependent activation of tiles with RNA transcription, making it possible to control nanotube formation via concurrent physical and biochemical stimuli. Finally, we illustrate how UV activation effectively controls nanotube assembly in confinement as a rudimentary stimulus-responsive cytoskeletal system that can achieve various conformations in a minimal synthetic cell. This study contributes new tile designs that are immediately useful to building biomolecular scaffolds with controllable dynamics in response to multiple stimuli.

DNA nanotechnology↗
DOE OSTI2025

Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks

Cryogenic electron microscopy (CryoEM) produces structures of macromolecules at near-atomic resolution. However, building molecular models with good stereochemical geometry from those structures can be challenging and time-consuming, especially when many structures are obtained from datasets with conformational heterogeneity. Here we present a model refinement protocol that automatically generates series of molecular models from CryoEM datasets, which describe the dynamics of the macromolecular system and have near-perfect geometry scores. This method makes it easier to interpret the movement of the protein complex from heterogeneity analysis and to compare the structural dynamics observed from CryoEM data with results from other experimental and simulation techniques.

59 BASIC BIOLOGICAL SCIENCES↗