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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Neutron spin echo shows pHLIP is capable of retarding membrane thickness fluctuations

In this study, cell membranes are responsible for a range of biological processes that require interactions between lipids and proteins. While the effects of lipids on proteins are becoming better understood, our knowledge of how protein conformational changes influence membrane dynamics remains rudimentary. Here, we performed experiments and computer simulations to study the dynamic response of a lipid membrane to changes in the conformational state of pH-low insertion peptide (pHLIP), which transitions from a surface-associated (SA) state at neutral or basic pH to a transmembrane (TM) α-helix under acidic conditions. Our results show that TM-pHLIP significantly slows down membrane thickness fluctuations due to an increase in effective membrane viscosity. Our findings suggest a possible membrane regulatory mechanism, where the TM helix affects lipid chain conformations, and subsequently alters membrane fluctuations and viscosity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Smoothed boundary method for simulating incompressible flow in complex geometries

Simulating flow through porous media with explicit considerations of complex microstructures is very challenging using conventional sharp-interface methods because of the difficulties in generating meshes conformal to complex geometries. In this work, a diffuse interface embedded boundary method known as the Smoothed Boundary Method (SBM) is utilized to facilitate simulations of fluid dynamics involving complex geometries. In diffuse-interface methods, the geometry is described by a domain parameter. The SBM allows the straightforward reformulation of the time-dependent Navier-Stokes equations in terms of this domain parameter, using only algebraic identities. Thus, enforcing the appropriate boundary conditions at the irregular embedded boundary is greatly simplified. Adaptive mesh refinement is used to increase the accuracy of the diffuse interface method by allowing thinner interfacial thickness to be used in the domain parameter. Here, the SBM-formulated Navier-Stokes equations are solved with the Finite Difference Method on refined mesh systems. Sharp-interface Finite Element Method simulations using the commercial software COMSOL on body-conforming meshes are also provided for comparison. Favorable agreement between the two methods is observed. Since it is no longer necessary for the mesh to conform to the complex geometry, the grid system for the SBM simulations can be generated rapidly and without additional manual interventions, making the entire simulation process more expedient.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Systematically derived thermodynamic properties for alkane oxidation

Key combustion properties, such as ignition delay time, show strong sensitivity to the thermochemistry of the main species in the standard radical oxidation pathway at low temperatures (600-1000K). Significant uncertainties persist in current estimates of thermodynamic properties, particularly for the larger species of relevance to common practical fuels. In this article, we use advanced computational schemes to evaluate thermodynamic properties for the fuel, fuel radical, peroxy, hydroperoxy-alkyl radical, and hydroperoxide species for a set of 17 fuels containing up to 9 carbon atoms, and with various degrees of branching in the alkane backbone. The procedure, termed STAR-1D, combines conformer sampling to find the minimum geometry, B2PLYP-D3/cc-pVTZ harmonic frequency evaluations, and omega B97X-D/cc-pVTZ one-dimensional torsional mapping. It includes two physically-based scaling routines: a frequency-dependent scaling to B2PLYP-D3/cc-pVTZ anharmonic frequencies and a scaling of one-dimensional omega B97X-D/ccpVTZ torsional profiles to reproduce the product of the B2PLYP-D3/cc-pVTZ frequencies in the harmonic limit. Substantive comparisons with existing experimental databases, together with careful examinations of key theoretical assumptions, are used to explore the accuracy of the predictions. These computationally intensive explorations of 195 species were facilitated by automated thermochemistry software. Further, high accuracy 0 K heats of formation from a separate study are used with the STAR-1D computations to generate NASA polynomial representations. In addition to their intrinsic value, the present results also provide a reliable database for the optimization of group additivity or machine learning schemes for scaling to larger combustion systems. Towards this end a complementary extensive conformational analysis is carried out for the medium sized species and the thermodynamic properties of the lowest energy hydrogen-bonded and non-hydrogen bonded conformers are contrasted for larger hydroperoxy-alkyl radical species.

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

An extrapolation method to remove spurious stress concentration in micromechanical analyses of composites using pixel-based meshes

It is easier to generate a finite element mesh of complicated geometries with voxel-based meshes compared to conformal meshes. However, the local stresses in voxel-based meshes are higher owing to artificial stress concentration caused due to jagged lines that approximate a curve. Here, we propose a method that accounts for this anomaly which would lead to accurate prediction of maximum von Mises stress in voxel-based meshes. The method is based on the variation of reciprocal of stresses and associated numerical gradient. The prediction of the proposed method is compared against the results of a conformal mesh by considering four two-dimensional example problems. The accuracy of the proposed method is verified using different mesh densities, material properties, and integration schemes. The proposed method was also implemented on a conformal mesh to verify that it filters out just the spurious stress concentration and not the realistic stress concentration.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Synthesis and spectroscopic characterization of actinyl(VI) tetrahalide coordination compounds containing 2, 2'-bipyridine

A series of three new actinide tetrahalide coordination compounds containing 2,2'-bipyridinium (H 2 bpy) have been synthesized by room temperature evaporation and characterized via single crystal X-ray diffraction, Raman spectroscopy, and infrared spectroscopy. The solid-state compounds (Np1, U1, and U2) contain the AnO 2 2+ cation coordinated to four halide (chloride or bromide) atoms to form the anionic tetrahalide molecular unit [AnO 2 X 4 ] 2– (X = Cl, Br) and are charge balanced by the 2,2'-bipyridinium cations that engage in electrostatic interactions with the actinyl complex. Np1 (N 2 C 10 H 10 )[NpO 2 Cl 4 ] contains 2,2'-bipyridine in the cis conformation where both the nitrogen atoms are directed towards the [NpO 2 Cl 4 ] 2– monomer. Within U1 (N 2 C 10 H 9 )[UO 2 Cl 4 ], the 2,2'-bipyridine is in a trans conformation, and found in the same orientation in the isomorphous structure U2 (N 2 C 10 H 9 )[UO 2 Br 4 ]. The compounds were further characterized by vibrational spectroscopy with specific interest in the actinyl cation. Raman spectroscopy provided information on the actinyl symmetric stretch (ν 1 ) whereas IR spectroscopy is used to determine the location of the asymmetric stretch (ν 3 ). Here, spectral similarities are observed between the two isomorphous structures, but slight variations across the series of structures are found to be associated with bipyridine bands in the various conformations. Additional analysis of these vibrational features in U1 and U2 provided information on the actinyl force constants, allowing insight into the relative uranyl bond strength that was compared to similar tetrahalide compounds.

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

Synthesis of multicomponent oxygen evolution reaction coatings via block copolymer templating with vapor- and solution-phase precursors

Porous mixed transition metal oxide heterostructures are promising electrocatalysts due to their high surface area. However, achieving conformal multicomponent oxide coatings with controlled nanoscale architectures remains challenging. Here, we report a synthesis strategy that integrates solution-based swelling infiltration (SBI) with gas-phase sequential infiltration synthesis (SIS) in a block copolymer template to fabricate porous, high-surface-area, conformal mixed-oxide electrocatalytic coatings. In this approach, a PS75-P4VP25 block copolymer (BCP) film is first infiltrated with transition metal acetylacetonate precursors via SBI, followed by exposure to gas phase precursors of ZnO via SIS process. Thermal annealing of the infiltrated BCP films converts them into all-inorganic Fe–ZnO, Fe–Co–ZnO, and Fe–Ni–ZnO coatings. Electrochemical testing on 70 nm thick conformal coatings demonstrates promising oxygen evolution reaction (OER) activity in alkaline media, with mass-specific current densities up to 1.0 × 10 5 mA/g at an overpotential of 330 mV (vs. RHE) at ultralow loading (~0.005 g/cm 2 ). Among the compositions, Fe–Co–ZnO and amorphous Fe–Ni–ZnO show the best OER performance, delivering current densities of 2.00 and 3.04 mA/cm 2 , respectively, compared to 1.52 mA/cm 2 for Fe–ZnO.. This work establishes SBI–SIS as a versatile route for fabricating nm-thin, high-performance multicomponent oxide heterostructures on cost-efficient supports, enabling efficient catalyst utilization in electrochemical energy conversion application.

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

Recombinant FimH Adhesin Demonstrates How the Allosteric Catch Bond Mechanism Can Support Fast and Strong Bacterial Attachment in the Absence of Shear

The FimH protein of Escherichia coli is a model two-domain adhesin that is able to mediate an allosteric catch bond mechanism of bacterial cell attachment, where the mannose-binding lectin domain switches from an ‘inactive’ conformation with fast binding to mannose to an ‘active’ conformation with slow detachment from mannose. Because mechanical tensile force favors separation of the domains and, thus, FimH activation, it has been thought that the catch bonds can only be manifested in a fluidic shear-dependent mode of adhesion. Here, we used recombinant FimH variants with a weakened inter-domain interaction and show that a fast and sustained allosteric activation of FimH can also occur under static, non-shear conditions. Moreover, it appears that lectin domain conformational activation happens intrinsically at a constant rate, independently from its ability to interact with the pilin domain or mannose. However, the latter two factors control the rate of FimH deactivation. Thus, the allosteric catch bond mechanism can be a much broader phenomenon involved in both fast and strong cell-pathogen attachments under a broad range of hydrodynamic conditions. In conclusion, this concept that allostery can enable more effective receptor-ligand interactions is fundamentally different from the conventional wisdom that allostery provides a mechanism to turn binding off under specific conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Domain crossover in the reductase subunit of NADPH-dependent assimilatory sulfite reductase

NADPH-dependent assimilatory sulfite reductase (SiR) from Escherichia coli performs a six-electron reduction of sulfite to the bioavailable sulfide. SiR is composed of a flavoprotein (SiRFP) reductase subunit and a hemoprotein (SiRHP) oxidase subunit. There is no known high-resolution structure of SiR or SiRFP, thus we do not yet fully understand how the subunits interact to perform their chemistry. Here, we used small-angle neutron scattering to understand the impact of conformationally restricting the highly mobile SiRFP octamer into an electron accepting (closed) or electron donating (open) conformation, showing that SiR remains active, flexible, and asymmetric even with these conformational restrictions. From these scattering data, we then model the first solution structure of SiRFP. Further, computational modeling of the N-terminal 52 amino acids that are responsible for SiRFP oligomerization suggests an eight-helical bundle tethers together the SiRFP subunits to form the SiR core. Finally, mass spectrometry analysis of the closed SiRFP variant show that SiRFP is capable of inter-molecular domain crossover, in which the electron donating domain from one polypeptide is able to interact directly with the electron accepting domain of another polypeptide. This structural characterization suggests that SiR performs its high-volume electron transfer through both inter- and intramolecular pathways between SiRFP domains and, thus, cis or trans transfer from reductase to oxidase subunits. Such highly redundant potential for electron transfer makes this system a potential target for designing synthetic enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Weyl-ambient geometries

Weyl geometry is a natural extension of conformal geometry with Weyl covariance mediated by a Weyl connection. We generalize the Fefferman-Graham (FG) ambient construction for conformal manifolds to a corresponding construction for Weyl manifolds. We first introduce the Weyl-ambient metric motivated by the Weyl-Fefferman-Graham (WFG) gauge. From a top-down perspective, we show that the Weyl-ambient space as a pseudo-Riemannian geometry induces a codimension-2 Weyl geometry. Then, from a bottom-up perspective, we start from promoting a conformal manifold into a Weyl manifold by assigning a Weyl connection to the principal R+-bundle realizing a Weyl structure. We show that the Weyl structure admits a well-defined initial value problem, which determines the Weyl-ambient metric. Through the Weyl-ambient construction, we also investigate Weyl-covariant tensors on the Weyl manifold and define extended Weyl-obstruction tensors explicitly.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Quantum fisher information reveals UV-IR mixing in the strange metal

The density-density response in optimally doped Bi 2 Sr 2 CaCu 2 O 8+$x$ has recently been shown to exhibit conformal symmetry. Using, the experimentally inferred conformal dynamic susceptibility, we compute the resultant quantum Fisher information (QFI), a witness to multi-partite entanglement. For a Fermi liquid, we find that the QFI grows quadratically as the temperature increases, consistent then with the phase space available for scattering in the standard theory of metals. By contrast, the QFI in a strange metal increases as a power law at as the temperature decreases, but ultimately extrapolates to a constant at T=0. The constant is of the form, ω$^{2Δ}_g$, where Δ is the conformal dimension and ω g is the UV cutoff which is on the order of the pseudogap. As this constant depends on both UV and IR properties, it illustrates that multipartite entanglement in a strange metal exhibits UV-IR mixing, a benchmark feature of doped Mott insulators as exemplified by dynamical spectral weight transfer. We conclude with a discussion of the implication of our results for low-energy reductions of the Hubbard model.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Frameshifting Stimulatory Sequence Induces Large Structural Change of Ribosomal Proteins When Bound to E. coli Ribosomes

Biological macromolecular machines occupy a continuum of structural conformations to perform cellular tasks. Mapping this conformational space provides an insight into its functionality. While the cryo-electron microscopy resolution revolution has expanded our ability to characterize the conformational continuums, there are obstacles in structurally characterizing regions of high flexibility. These technical barriers have impeded characterization of flexible ribosomal proteins when the ribosome is interacting with mRNA stem-loop structures such as a frameshifting stimulatory sequence (FSS). Small-angle neutron/X-ray scattering and electron microscopy were used to study ribosomal samples and compared structural differences between a ribosome that is bound to an FSS stem-loop compared to a ribosome bound to linear mRNA. This comparison shows that a large protein stalk elongates by 22% when the 70S interacts with an mRNA stem-loop. Finally, our results suggest that ribosomal proteins have extensive flexibility and may influence important ribosomal mechanisms, such as those that involve FSS.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Effect of Solvent on the Interaction of Lignin with a Zeolite Nanosheet in the Condensed Phase

Lignin is the essential building block of lignocellulosic biomass, an excellent renewable source of different aromatic monomers for the polymer and biofuel industry. The depolymerization of lignin into value-added chemicals and fuels through the catalytic process poses a significant challenge due to the complex structure of lignin. Understanding lignin’s conformational diversity and dynamics in the liquid phase is crucial to designing an effective depolymerization process. Here, we conducted all-atom molecular dynamics simulations to understand the conformation and dynamics of softwood lignin on the all-silica zeolite nanosheet based on the MFI topology in a binary mixture of water–methanol at three different molar compositions (0%, 50%, and 100% methanol). We observed that the methanol–surface interaction is stronger than the water–surface interaction, and methanol readily diffused into the MFI core. Lignin surface contacts decrease with increasing methanol composition due to higher solubility and dynamics. Lignin dynamics on the surface in neat water is an order of magnitude smaller than methanol. Here, we also found that lignin adopts a slightly extended conformation when it stays on the surface than in the bulk solution phase for the pure water case, whereas for pure methanol and the binary solution structures are statistically similar.

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

How Rigid Are Anthranilamide Molecular Electrets?

As important as molecular electrets are for electronic materials and devices, conformational fluctuations strongly impact their macrodipoles and intrinsic properties. Herein, we employ molecular dynamics (MD) simulations with the polarizable charge equilibrium (PQEq) method to investigate the persistence length (L P ) of molecular electrets composed of anthranilamide (Aa) residues. The PQEq-MD dissipates the accepted static notions about Aa macromolecules, and L P represents the shortest Aa rigid segments. The classical model with a single L P value does not describe these oligomers. Introducing multiple L P values for the same macromolecule follows the observed trends and discerns the enhanced rigidity in their middle sections from the reduced stiffness at their terminal regions. Furthermore, L P distinctly depends on solvent polarity. The Aa oligomers maintain extended conformations in nonpolar solvents with L P exceeding 4 nm, while in polar media, increased conformational fluctuations reduce L P to about 2 nm. These characteristics set key guidelines about the utility of Aa conjugates for charge-transfer systems within organic electronics and energy engineering.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

A Metal-on-Metal Growth Approach to Metal–Metal Oxide Core–Shell Nanostructures with Plasmonic Properties

Hybrid core–shell nanoparticles integrate the material properties from individual components; however, the synthesis of core–shell nanoparticles with dissimilar materials remains challenging. Herein, we applied a metal-on-metal thin film growth approach to control the conformal deposition of non-precious metal shells on the Cu-based metal cores to form core–shell structures of metal–metal oxide hybrids (M–M'O x , where M = AuCu 3 or Cu, M' = Fe, Mn, and Ni). The deposition kinetics were controlled by a temperature-regulated thermal decomposition of zerovalent transition metal complexes. It is predicted that the conformal deposition can be promoted by keeping the initial deposition temperature close to the thermal decomposition temperature of the zerovalent precursors. The mechanisms of strain reduction and interdiffusion facilitate conformal deposition over island growth in the synthesis with slow reaction kinetics. This study provides insightful guidance to metal-on-metal growth in solution at the nanoscale and thus the seed-mediated approach to hybrid core–shell structures. The optical properties of these metal–metal oxide hybrids were investigated experimentally and interpreted by theoretical simulations. Despite damping effects, the plasmonic properties of these Cu-based core-metal oxide shell structures may have the potential to enable plasmon-enhanced applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Investigation of the Self-Assembly Behavior of Statistical Bottlebrush Copolymers via Self-Consistent Field Theory Simulations

Bottlebrush copolymers, a class of high-density side-chain-grafted copolymers with high molecular weights, have recently attracted extensive research attention due to the dramatic reduction of chain entanglement in these copolymers, unique self-assembly behaviors, and distinctive physical properties. In this study, we employ self-consistent field theory simulations to systemically investigate the phase behavior of statistical bottlebrush copolymers A-stat-B, an intriguing subclass of bottlebrush copolymers with random or alternating sequences of A and B side chains. We find that a broader variety of ordered mesophases can be stabilized in the melts of these copolymers relative to the more extensively studied bottlebrush block copolymers. In particular, we observe that these statistical copolymers can stabilize sphere phases over a larger range of species volume fractions than their diblock and tetrablock counterparts but require much higher segregation strength to achieve this. The sphere and hexagonally packed cylinder phases formed by conformationally symmetric statistical bottlebrush copolymers possess interesting discrete core–shell structures with the backbone and lower volume fraction side-chain species forming shells and cores, respectively. Moreover, we uncover a new strategy of stabilizing the Frank–Kasper phase A15 by introducing conformational asymmetry through different side-chain lengths and also observe deflection of order–order phase boundaries and significant mixing between the backbones and short side chains as conformational asymmetry is introduced.

36 MATERIALS SCIENCE↗
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 OSTI2026

Determinants of Stereoselectivity in Monoterpene Synthases

Monoterpene synthases (MTSs) catalyze the conversion of an achiral prenyl diphosphate precursor, most commonly geranyl diphosphate (GPP), into structurally and stereochemically diverse products. However, remains poorly understood. Here, we combine enzymatic assays with six MTSs and selected variants, along with extensive molecular dynamics simulations to the mechanistic basis of stereoselectivity. We demonstrate that the preferred helical binding conformation of GPP, determined from free-energy calculations and selected crystal structures of MTSs, correlates well with the experimentally determined stereoselectivity of MTSs, whereas only a poor correlation is observed between the binding of enantiomers of linalyl diphosphate (LPP), a chiral intermediate of MTS catalysis, and the stereochemical reaction outcomes. Free energy maps indicate that enzyme-bound GPP conformers preferentially occupy regions that enable a direct and stereochemically faithful transition from GPP to subsequent carbocations. In contrast, LPP frequently populates regions of the energy surface where conformational scrambling can occur, thus leading to a lack of correlation between LPP enantiomer binding and product stereochemistry. Overall, these findings establish that the configuration of GPP is the primary determining factor for stereochemical outcomes in MTSs, offering a new framework for designing stereoselective terpene synthases.

Srividya, Narayanan (ORCID:0000000179347987)↗
DOE OSTI2024

Hydrogen–Deuterium Exchange Mass Spectrometry Identifies Local and Long-Distance Interactions within the Multicomponent Radical SAM Enzyme, PqqE

Interactions among proteins and peptides are essential for many biological activities including the tailoring of peptide substrates to produce natural products. The first step in the production of the bacterial redox cofactor pyrroloquinoline quinone (PQQ) from its peptide precursor is catalyzed by a radical SAM (rSAM) enzyme, PqqE. We describe the use of hydrogen–deuterium exchange mass spectrometry (HDX-MS) to characterize the structure and conformational dynamics in the protein–protein and protein–peptide complexes necessary for PqqE function. HDX-MS-identified hotspots can be discerned in binary and ternary complex structures composed of the peptide PqqA, the peptide-binding chaperone PqqD, and PqqE. Structural conclusions are supported by size-exclusion chromatography coupled to small-angle X-ray scattering (SEC-SAXS). HDX-MS further identifies reciprocal changes upon the binding of substrate peptide and S-adenosylmethionine (SAM) to the PqqE/PqqD complex: long-range conformational alterations have been detected upon the formation of a quaternary complex composed of PqqA/PqqD/PqqE and SAM, spanning nearly 40 Å, from the PqqA binding site in PqqD to the PqqE active site Fe 4 S 4 . Interactions among the various regions are concluded to arise from both direct contact and distal communication. The described experimental approach can be readily applied to the investigation of protein conformational communication among a large family of peptide-modifying rSAM enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗