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Results for “Rigidity function”

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 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

TRPV4-Rho GTPase complex structures reveal mechanisms of gating and disease

Crosstalk between ion channels and small GTPases is critical during homeostasis and disease, but little is known about the structural underpinnings of these interactions. TRPV4 is a polymodal, calcium-permeable cation channel that has emerged as a potential therapeutic target in multiple conditions. Gain-of-function mutations also cause hereditary neuromuscular disease. Here, we present cryo-EM structures of human TRPV4 in complex with RhoA in the ligand-free, antagonist-bound closed, and agonist-bound open states. These structures reveal the mechanism of ligand-dependent TRPV4 gating. Channel activation is associated with rigid-body rotation of the intracellular ankyrin repeat domain, but state-dependent interaction with membrane-anchored RhoA constrains this movement. Notably, many residues at the TRPV4-RhoA interface are mutated in disease and perturbing this interface by introducing mutations into either TRPV4 or RhoA increases TRPV4 channel activity. Together, these results suggest that RhoA serves as an auxiliary subunit for TRPV4, regulating TRPV4-mediated calcium homeostasis and disruption of TRPV4-RhoA interactions can lead to TRPV4-related neuromuscular disease. These insights will help facilitate TRPV4 therapeutics development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Low-frequency Raman signature of Ag-intercalated few-layer MoS 2

Density functional theory based calculations and experimental analysis on a limited number of real samples are performed to study how the presence of silver intercalated in the van der Waals gap of few-layer MoS 2 affects the low-frequency Raman active modes of this material. Silver is found to predominantly affect the breathing-like and shear-like vibrational modes of MoS 2 . These modes correspond to quasi-rigid movements of each individual layer with a restoring force (and, in turn, frequency) that is determined by modulations in the weak interlayer interactions. Noticeable red-shifts with increasing Ag concentration are found for all low-frequency modes. This finding indicates the potential for low-frequency vibrations as useful gauges for practical determination of silver concentration using low-frequency Raman spectroscopy. Finally, this work also describes a semi-classical linear chain model that allows to extrapolate results to a large number of layers. Further, first-principles calculations show how Raman spectroscopy can be used to characterize the quality of the two-dimensional interface between MoS 2 and a silver substrate.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Cooperative Self‐Assembly of Pyridine‐2,6‐Diimine‐Linked Macrocycles into Mechanically Robust Nanotubes

Abstract Nanotubes assembled from macrocyclic precursors offer a unique combination of low dimensionality, structural rigidity, and distinct interior and exterior microenvironments. Usually the weak stacking energies of macrocycles limit the length and mechanical strength of the resultant nanotubes. Imine‐linked macrocycles were recently found to assemble into high‐aspect ratio (>10 3 ), lyotropic nanotubes in the presence of excess acid. Yet these harsh conditions are incompatible with many functional groups and processing methods, and lower acid loadings instead catalyze macrocycle degradation. Here we report pyridine‐2,6‐diimine‐linked macrocycles that assemble into high‐aspect ratio nanotubes in the presence of less than 1 equiv of CF 3 CO 2 H per macrocycle. Analysis by gel permeation chromatography and fluorescence spectroscopy revealed a cooperative self‐assembly mechanism. The low acid concentrations needed to induce assembly enabled nanofibers to be obtained by touch‐spinning, which exhibit higher Young's moduli (1.33 GPa) than many synthetic polymers and biological filaments. These findings represent a breakthrough in the design of inverse chromonic liquid crystals, as assembly under such mild conditions will enable the design of structurally diverse and mechanically robust nanotubes from synthetically accessible macrocycles.

Strauss, Michael J.↗
DOE OSTI2019

Investigation of Solar Proton Access Into the Inner Magnetosphere on 11 September 2017

Here, access of solar energetic protons to the inner magnetosphere on 11 September 2017 is investigated by computing the reverse particle trajectories with the Dartmouth geomagnetic cutoff code (Kress et al., 2010). The maximum and minimum cutoff rigidity at each point along the orbit of Van Allen Probe A is numerically computed by extending the code to calculate cutoff rigidity for particles coming from arbitrary direction. Pulse height analyzed (PHA) data have the advantage of providing individual particle energies and effectively excluding background high-energy proton contamination. This technique is adopted to study the cutoff locations for solar protons with different energy. The results demonstrate that cutoff latitude is lower for solar protons with higher energy, consistent with low-altitude vertical cutoffs. Both the observations and numerical results show that proton access into the inner magnetosphere depends strongly on angle between particle arrival direction and magnetic west. Finally, the numerical result is approximately consistent with the observation that the energy of almost all solar protons stays above the minimum cutoff rigidity.

58 GEOSCIENCES↗
DOE OSTI2025

Correlated solvent coordinates accelerate multi-donor proton-coupled electron transfer

The rate of charge transfer within a discrete donor–acceptor (D/A) pair is well-described by semi-classical electron transfer theory, but the effects of multiple equivalent redox sites remain less understood. We report a series of ground-state intramolecular proton-coupled electron transfer (PCET) complexes designed to isolate the effects of donor number, N, while holding geometry, coupling, and driving forces constant. The [Ru(L) 3−N (OH) N ] 2+ complexes incorporate one, two, or three identical phenolic electron donors linked to Ru through rigid phenanthroline bridges (OH = 2,4-di-tert-butyl-6-(1-methyl-1H-imidazo[4,5-f][1,10]phenanthrolin-2-yl)phenol). Upon flash photolysis and oxidative quenching with methyl viologen (MV 2+ ), the transient Ru(III) oxidizes an appended phenol by PCET with the hydrogen-bonded imidazole nitrogen atom functioning as the base. The rate increased by 3.4-fold and 5.7-fold (1.7-fold and 1.9-fold after statistical correction) for two- and three-donor complexes compared to the single-donor system. The supra-statistical acceleration is attributed to a reduced effective outer sphere reorganization energy (λ m ) modeled by a partially shared solvent reaction coordinate, in which a subset of solvent dipoles is already oriented to stabilize charge from any donor. The final phenoxyl radical state is localized due to the transfer of a proton, and the recombination reaction with the viologen radical is not accelerated. These results demonstrate the effects of solvent dynamics on intramolecular PCET rates, offering a new strategy for the design of synthetic charge transfer systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Communication: Programmable self-assembly of thin-shell mesostructures

For this article, we study numerically the possibility of programmable self-assembly of various thin-shell architectures. They include clusters isomorphic to fullerenes C 20 and C 60 , finite and infinite sheets, tube-shaped and toroidal mesostructures. Our approach is based on the recently introduced directionally functionalized nanoparticle platform, for which we employ a hybrid technique of Brownian dynamics with stochastic bond formation. By combining a number of strategies, we were able to achieve a near-perfect yield of the desired structures with a reduced “alphabet” of building blocks. Among those strategies are the following: the use of bending rigidity of the interparticle bond as a control parameter, programming the morphology with a seed architecture, use of chirality-preserving symmetries for reduction of the particle alphabet, and the hierarchic approach.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Annihilation-limited long-range exciton transport in high-mobility conjugated copolymer films

A combination of ultrafast, long-range, and low-loss excitation energy transfer from the photoreceptor location to a functionally active site is essential for cost-effective polymeric semiconductors. Delocalized electronic wavefunctions along π-conjugated polymer (CP) backbone can enable efficient intrachain transport, while interchain transport is generally thought slow and lossy due to weak chain–chain interactions. In contrast to the conventional strategy of mitigating structural disorder, amorphous layers of rigid CPs, exemplified by highly planar poly(indacenodithiophene-co-benzothiadiazole) (IDT-BT) donor-accepter copolymer, exhibit trap-free transistor performance and charge-carrier mobilities similar to amorphous silicon. Here, we report long-range exciton transport in HJ -aggregated IDTBT thin-film, in which the competing exciton transport and exciton–exciton annihilation (EEA) dynamics are spectroscopically separated using a phase-cycling-based scheme and shown to depart from the classical diffusion-limited and strong-coupling regime. In the thin film, we find an annihilation-limited mechanism with ≪100% per-encounter annihilation probability, facilitating the minimization of EEA-induced excitation losses. In contrast, excitons on isolated IDTBT chains diffuse over 350 nm with 0.56 cm 2 s −1 diffusivity, before eventually annihilating with unit probability on first contact. We complement the pump–probe studies with temperature-dependent photocurrent and EEA measurements from 295 K to 77 K and find a remarkable correspondence of annihilation rate and photocurrent activation energies in the 140 K to 295 K temperature range.

Shi, Yuping (ORCID:0000000318289415)↗
DOE OSTI2020

Bichromatic Wave Selection for Validation of the Difference-Frequency Transfer Function for the OC6 Validation Campaign: Preprint

The focus of the Offshore Code Comparison Collaboration, Continuation, with Correlation and unCertainity (OC6) project, which operates under the International Energy Agency (IEA) Wind Task 30, is to refine the accuracy of engineering tools used to design offshore wind turbines. In support of this work, a new validation campaign is being developed that seeks to better understand the nonlinear wave loading that excites floating wind systems at their low-frequency, rigid-body modes in surge and pitch. The validation data will be used in a three-way validation between simplified engineering tools and higher-fidelity tools, such as computational fluid dynamics (CFD). Irregular wave spectrums, which are traditionally used to examine the nonlinear wave interaction with offshore structures, are too computationally expensive to be simulated in CFD tools, and so bichromatic wave cases will be used instead. This paper reviews the process used to choose the bichromatic wave pairs to be used in the campaign to validate the second-order difference-frequency quadratic and potential loads at the surge and pitch natural frequencies of a floating semisubmersible.

17 WIND ENERGY↗
DOE OSTI2016

Predicting the Macroscopic Fracture Energy of Epoxy Resins from Atomistic Molecular Simulations

Predicting the macroscopic fracture energy of highly crosslinked glassy polymers from atomistic simulations is challenging due to the size of the process zone being large in these systems. Here, we present a scale-bridging approach that links atomistic molecular dynamics simulations to macroscopic fracture properties on the basis of a continuum fracture mechanics model for two different epoxy materials. Our approach reveals that the fracture energy of epoxy resins strongly depends on the functionality of epoxy resin and the component ratio between the curing agent (amine) and epoxide. The most intriguing part of our study is that we demonstrate that the fracture energy exhibits a maximum value within the range of conversion degrees considered (from 65% to 95%), which can be attributed to the combined effects of structural rigidity and post-yield deformability. Our study provides physical insight into the molecular mechanisms that govern the fracture characteristics of epoxy resins and demonstrates the success of utilizing atomistic molecular simulations towards predicting macroscopic material properties.

42 ENGINEERING↗
DOE OSTI2025

Cryogenic thermal modeling of microwave high density signaling

Superconducting quantum computers require microwave control lines running from room temperature to the mixing chamber of a dilution refrigerator. Adding more lines without preliminary thermal modeling to make predictions risks overwhelming the cooling power at each thermal stage. In this paper, we investigate the thermal load of SC-086/50-SCN-CN semi-rigid coaxial cable, which is commonly used for the control and readout lines of a superconducting quantum computer, as we increase the number of lines to a quantum processor. We investigate the makeup of the coaxial cables, verify the materials and dimensions, and experimentally measure the total thermal conductivity of a single cable as a function of the temperature from cryogenic to room temperature values. We also measure the cryogenic DC electrical resistance of the inner conductor as a function of temperature, allowing for the calculation of active thermal loads due to Ohmic heating. Fitting this data produces a numerical thermal conductivity function used to calculate the static heat loads due to thermal transfer within the wires resulting from a temperature gradient. The resistivity data is used to calculate active heat loads, and we use these fits in a cryogenic model of a superconducting quantum processor in a typical Bluefors XLD1000-SL dilution refrigerator, investigating how the thermal load increases with processor sizes ranging from 100 to 225 qubits. We conclude that the theoretical upper limit of the described architecture is approximately 200 qubits. However, including an engineering margin in the cooling power and the available space for microwave readout circuitry at the mixing chamber, the practical limit is approximately 140 qubits.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

A continuous symmetry breaking measure for finite clusters using Jensen-Shannon divergence

A quantitative measure of symmetry breaking is introduced that allows the quantification of which symmetries are most strongly broken due to the introduction of some kind of defect in a perfect structure. The method uses a statistical approach based on the Jensen-Shannon divergence. The measure is calculated by comparing the transformed atomic density function with its original. Software code is presented that carries the calculations out numerically using Monte Carlo methods. The behavior of this symmetry breaking measure is tested for various cases including finite size crystallites (where the surfaces break the crystallographic symmetry), atomic displacements from high symmetry positions, and collective motions of atoms due to rotations of rigid octahedra. Finally, the approach provides a powerful tool for assessing local symmetry breaking and offers new insights that can help researchers understand how different structural distortions affect different symmetry operations.

atomic & molecular structure↗
DOE OSTI2022

Freely jointed chain models with extensible links

We report analytical relations for the mechanical response of single polymer chains are valuable for modeling purposes, on both the molecular and the continuum scale. These relations can be obtained using statistical thermodynamics and an idealized single-chain model, such as the freely jointed chain model. To include bond stretching, the rigid links in the freely jointed chain model can be made extensible, but this almost always renders the model analytically intractable. Here, an asymptotically correct statistical thermodynamic theory is used to develop analytic approximations for the single-chain mechanical response of this model. The accuracy of these approximations is demonstrated using several link potential energy functions. This approach can be applied to other single-chain models, and to molecular stretching in general.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Thermochemical Data for Furan-based Monomer Candidates for Frontal Ring-Opening Metathesis Polymerization (FROMP)

This dataset includes 471 furan-based monomer candidates for frontal ring-opening metathesis polymerization (FROMP) and relevant thermochemistry as calculated with density functional theory (DFT). The monomer candidates were combinatorically enumerated using Diels-Alder reactions of furan derivatives as dienes and four types of dienophiles (alkenes, alkynes, allenes, and benzynes). Common substituents were enumerated for the dienophile classes, and methyl substitution on the diene was explored. We used the SMILES arbitrary target specification (SMARTS) language to produce monomers and ring-opened structures from diene and dienophile precursor SMILES, and we studied the ring-opening reaction using a homodesmotic equation with ethene. RDKit conformers were initially generated from SMILES, then optimized with GFN2-xTB. The two conformers lowest in energy were then optimized with DFT using the wb97x-D3 functional, def2-TZVP basis set, and def2/J auxiliary basis set. Gibbs free energy corrections were obtained through frequency calculations. Structures with imaginary frequencies below -50 cm^{-1} were excluded from this work, and smaller imaginary modes were flipped to be positive for free energy calculations. Modes below 50 cm^{-1} were treated with the modified rigid rotor approximation, and all thermochemical values were calculated at T=200C. The CSV file contains the monomer SMILES, the free energy of reaction for Diels-Alder addition (G_DA_200), and the enthalpy of the ring-opening reaction (H_RO_200). All energies are given in kcal/mol. An interactive HTML is also included to visualize the monomers in this dataset.

Chua, Lauren↗
DOE OSTI2023

Benchmark Data Set of Crystalline Organic Semiconductors

This work reports a Benchmark Data set of Crystalline Organic Semiconductors to test calculations of the structural and electronic properties of these materials in the solid state. The data set contains 67 crystals consisting of mostly rigid molecules with a single dominant conformer, covering the majority of known structural types. The experimental crystal structure is available for the entire data set, whereas zero-temperature unit cell volume can be reliably estimated for a subset of 28 crystals. Using this subset, we benchmark r 2 SCAN-D3 and PBE-D3 density functionals. Then, for the entire data set, we benchmark approximate density functional theory (DFT) methods, including GFN1-xTB and DFTB3(3ob-3-1), with various dispersion corrections against r 2 SCAN-D3. Our results show that r 2 SCAN-D3 geometries are accurate within a few percent, which is comparable to the statistical uncertainty of experimental data at a fixed temperature, but the unit cell volume is systematically underestimated by 2% on average. The several times faster PBE-D3 provides an unbiased estimate of the volume for all systems except for molecules with highly polar bonds, for which the volume is substantially overestimated in correlation with the underestimation of atomic charges. Considered approximate DFT methods are orders of magnitude faster and provide qualitatively correct but overcompressed crystal structures unless the dispersion corrections are fitted by unit cell volume.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Active microrheology of smectic membranes

Thin fluid membranes embedded in a bulk fluid of different viscosity are of fundamental interest as experimental realizations of quasi-two-dimensional fluids and as models of biological membranes. We have probed the hydrodynamics of thin fluid membranes by active microrheology using small tracer particles to observe the highly anisotropic flow fields generated around a rigid oscillating post inserted into a freely suspended smectic liquid crystal film that is surrounded by air. In general, at distances more than a few Saffman lengths from the meniscus around the post, the measured velocities are larger than the flow computed by modeling a moving disklike inclusion of finite extent by superposing Levine-MacKintosh response functions for pointlike inclusions in a viscous membrane. The observed discrepancy is attributed to additional coupling of the film with the air below the film that is displaced directly by the shaft of the moving post.

42 ENGINEERING↗
DOE OSTI2023

Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock

Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group or lattice symmetries. Current methods for docking and designing such assemblies are tailored to specific classes of symmetry and are difficult to modify for novel applications. Here we describe RPXDock, a fast, flexible, and modular software package for sequence-independent rigid-body protein docking across a wide range of symmetric architectures that is easily customizable for further development. RPXDock uses an efficient hierarchical search and a residue-pair transform ( RPX ) scoring method to rapidly search through multidimensional docking space. We describe the structure of the software, provide practical guidelines for its use, and describe the available functionalities including a variety of score functions and filtering tools that can be used to guide and refine docking results towards desired configurations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase

De novo macrocyclic peptides, derived using selection technologies such as phage and mRNA display, present unique and unexpected solutions to challenging biological problems. This is due in part to their unusual folds, which are able to present side chains in ways not available to canonical structures such as α-helices and β-sheets. Despite much recent interest in these molecules, their folding and binding behavior remains poorly characterized. In this work, we present cocrystallization, docking, and solution NMR structures of three de novo macrocyclic peptides that all bind as competitive inhibitors with single-digit nanomolar Ki to the active site of human pancreatic α-amylase. We show that a short stably folded motif in one of these is nucleated by internal hydrophobic interactions in an otherwise dynamic conformation in solution. Comparison of the solution structures with a target-bound structure from docking indicates that stabilization of the bound conformation is provided through interactions with the target protein after binding. These three structures also reveal a surprising functional convergence to present a motif of a single arginine sandwiched between two aromatic residues in the interactions of the peptide with the key catalytic residues of the enzyme, despite little to no other structural homology. Our results suggest that intramolecular hydrophobic interactions are important for priming binding of small macrocyclic peptides to their target and that high rigidity is not necessary for high affinity.

59 BASIC BIOLOGICAL SCIENCES↗