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At least 523 records · Page 29

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DOE OSTI2021

Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP

YiiP is a secondary transporter that couples Zn 2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn 2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn 2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn 2+ . To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn 2+ and validated its performance with known Zn 2+ -binding proteins. Using these tools, we find that, in the presence of Zn 2+ , YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn 2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn 2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn 2+ binding sites and their role in the conformational dynamics that govern the transport cycle.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Modeling of Sagging for 3D Printed Layers During the Curing Process

Here, a printed layer of silica-enforced poly(dimethylsiloxane)-co-(diphenylsiloxane) is modeled as a two-phase system consisting of air and polymer with an interface set up during the printing process. The structural geometry changes mostly due to the action of surface tension, while all material properties are strongly temperature dependent. Polymer flow is described using equations of the extended Herschel–Bulkley model, with parameters strongly dependent on temperature and degree of curing. Parameters of the model are determined using flow sweep measurements and separate experiments with vertical structure sagging at different temperatures. The curing process is modeled using dependencies between the curing rate, degree of curing, and temperature obtained in studies by differential scanning calorimetry. The developed model is used for simulations of printed structure deformations with different initial and boundary conditions.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Deflection predictions of involute-shaped fuel plates using a fully-coupled numerical approach

This paper describes the modeling and simulation of fluid structure interactions (FSI) of involute-shaped fuel plates used in nuclear research reactors. We believe this to be the first time that this type of application is described in the literature using a fully-coupled, and monolithic, finite element approach. The simulations are validated against plate deflection data for the conceptual design of the Advanced Neutron Source Reactor (ANSR), which was envisioned to be the world’s most powerful nuclear research reactor for neutron scattering and other applications, but was ultimately never completed. The high performance of the ANSR creates a bounding envelope for involute-shaped research reactors such as that used in the High Flux Isotope Reactor (HFIR) at the Oak Ridge National Laboratory (ORNL) which is undergoing research for the conversion from highly-enriched uranium (HEU) to low-enriched uranium (LEU) fuel. As such, the findings from the present FSI analyses carried out herein for the ANSR plates provide good guidelines and inform designers what should be expected for the next generation of plates in the HFIR. Furthermore it is shown herein that the current approach can accurately capture the leading-edge deflections of the involute-shaped plates and simulations can predict the ‘S-shaped’ deflection of the first mode instilling confidence in the methodology.

42 ENGINEERING↗

DOE OSTI2022

Hybrid particle-in-cell simulations of electromagnetic coupling and waves from streaming burst debris

Various systems can be modeled as a point-like explosion of ionized debris into a magnetized, collisionless background plasma-including astrophysical examples, active experiments in space, and laser-driven laboratory experiments. Debris streaming from the explosion parallel to the magnetic field may drive multiple resonant and non-resonant ion-ion beam instabilities, some of which can efficiently couple the debris energy to the background and may even support the formation of shocks. We present a large-scale hybrid (kinetic ions + fluid electrons) particle-in-cell simulation, extending hundreds of ion inertial lengths from a 3D explosion, that resolves these instabilities. We show that the character of these instabilities differs notably from the 1D equivalent by the presence of unique transverse structure. Additional 2D simulations explore how the debris beam length, width, density, and speed affect debris-background coupling, with implications for the generation of quasi-parallel shocks.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Correlated Anion Disorder in Heteroanionic Cubic TiOF 2

Resolving anion configurations in heteroanionic materials is crucial for understanding and controlling their properties. For anion-disordered oxyfluorides, conventional Bragg diffraction cannot fully resolve the anionic structure, necessitating alternative structure determination methods. We have investigated the anionic structure of anion-disordered cubic (ReO 3 -type) TiOF 2 using X-ray pair distribution function (PDF), 19 F MAS NMR analysis, density functional theory (DFT), cluster expansion modeling, and genetic-algorithm structure prediction. Our computational data predict short-range anion ordering in TiOF 2 , characterized by predominant cis-[O 2 F 4 ] titanium coordination, resulting in correlated anion disorder at longer ranges. To validate our predictions, we generated partially disordered supercells using genetic-algorithm structure prediction and computed simulated X-ray PDF data and 19 F MAS NMR spectra, which we compared directly to experimental data. To construct our simulated 19 F NMR spectra, we derived new transformation functions for mapping calculated magnetic shieldings to predicted magnetic chemical shifts in titanium (oxy)fluorides, obtained by fitting DFT-calculated magnetic shieldings to previously published experimental chemical shift data for TiF 4 . We find good agreement between our simulated and experimental data, which supports our computationally predicted structural model and demonstrates the effectiveness of complementary experimental and computational techniques in resolving anionic structure in anion-disordered oxyfluorides. From additional DFT calculations, we predict that increasing anion disorder makes lithium intercalation more favorable by, on average, up to 2 eV, highlighting the significant effect of variations in short-range order on the intercalation properties of anion-disordered materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Small-molecule modulation of β-arrestins

β-Arrestins are multifunctional regulators of G-protein-coupled receptor (GPCR) signalling and orchestrate diverse downstream signalling events and physiological responses across the GPCR superfamily. Although GPCR pharmacology has advanced to target orthosteric and allosteric sites, as well as G proteins and GPCR kinases, direct chemical tools to modulate β-arrestin activities have remained conspicuously absent. Here we report the identification of small-molecule inhibitors that selectively target β-arrestins and delineate their mechanism of action through integrated pharmacological, biochemical, biophysical and structural analyses. These inhibitors disrupt β-arrestin engagement with agonist-activated GPCRs, impairing desensitization, internalization and β-arrestin-dependent physiological functions while sparing G protein–receptor coupling. Cryo-electron microscopy, molecular dynamics simulations and structure-guided mutagenesis reveal that one modulator, Cmpd-5, engages a pocket within the central crest of β-arrestin1 formed by the middle, C and lariat loops, a critical receptor-binding interface, stabilizing a distinct conformation that is incompatible with full β-arrestin–receptor engagement. Together, these findings establish a mechanistic framework for β-arrestin modulation, reveal a novel allosteric site for structure-based drug design, and open new avenues for transducer-targeted, pathway-specific GPCR therapeutic agents.

Kahsai, Alem W. [Duke University, Durham, NC (Unit↗

DOE OSTI2021

Large Eddy Simulation of Lean Mixed-Mode Combustion Assisted by Partial Fuel Stratification in a Spark-Ignition Engine

Partial fuel stratification (PFS) is a promising fuel injection strategy to improve the stability of lean combustion by applying a small amount of pilot injection right before spark timing. Mixed-mode combustion, which makes use of end-gas autoignition following conventional deflagration-based combustion, can be further utilized to speed up the overall combustion. In this study, PFS-assisted mixed-mode combustion in a lean-burn direct injection spark-ignition (DISI) engine is numerically investigated using multi-cycle large eddy simulation (LES). A previously developed hybrid G-equation/well-stirred reactor combustion model for the well-mixed operation is extended to the PFS-assisted operation. The experimental spray morphology is employed to derive spray model parameters for the pilot injection. The LES-based model is validated against experimental data and is further compared with the Reynolds-averaged Navier–Stokes (RANS)-based model. Overall, both RANS and LES predict the mean pressure and heat release rate traces well, while LES outperforms RANS in capturing the cycle-to-cycle variation (CCV) and the combustion phasing in the mass burned space. Liquid and vapor penetrations obtained from the simulations agree reasonably well with the experiment. Detailed flame structures predicted from the simulations reveal the transition from a sooting diffusion flame to a lean premixed flame, which is consistent with experimental findings. LES captures more wrinkled and stretched flames than RANS. Finally, the LES model is employed to investigate the impacts of fuel properties, including heat of vaporization (HoV) and laminar burning speed (SL). Combustion phasing is found more sensitive to SL than to HoV, with a larger fuel property sensitivity of the heat release rate from autoignition than that from deflagration. Moreover, the combustion phasing in the PFS-assisted operation is shown to be less sensitive to SL compared with the well-mixed operation.

fuel property sensitivity↗

DOE OSTI2021

Simulation of enhanced light extraction from periodic, disordered, and quasi-periodic OLED structures

Here we have developed a rigorous scattering matrix theory of light emission from periodically structured media using a Green’s function approach. We computationally simulate the spectral power inside the structure, incorporating Purcell factor enhancements, and find internal waveguiding modes and plasmonic losses. We simulate the light-outcoupling factor η out and describe how corrugations and structured media can enhance η out . We have extended our framework to describe non-periodic disordered arrays as well as aperiodic quasi-crystalline arrays. Flat organic light-emitting diodes (OLEDs) have low outcoupling with η out ~20% since most of the light is trapped in waveguided modes in higher index layers or lost to plasmonic excitations at the metal cathode. Periodically corrugated OLEDs can achieve highly enhanced η out ~65%-70% for pitch values between 1000 and 2000 nm, representing an enhancement factor >3 over planar structures. Periodic corrugations strongly diffract trapped waveguided and plasmonic modes to the emissive air cone. Disordered templates also can cause significant enhanced outcoupling with η out ~50%-55% for smaller nearest-neighbor separations of 300–400 nm. Quasi-crystalline tilings can also lead to enhancements of η out ~50%-55%. This framework can be utilized to design novel structured media that can generate high light extraction.

42 ENGINEERING↗

DOE OSTI2019

Inter-subunit coupling enables fast CO 2 -fixation by reductive carboxylases

Enoyl-CoA carboxylases/reductases (ECRs) belong to the most efficient CO 2 -fixing enzymes described to date. However, the molecular mechanisms underlying ECR’s extraordinary catalytic activity on the level of the protein assembly remain elusive. Here we used a combination of ambient temperature X-ray Free Electron Laser (XFEL) and cryogenic synchrotron experiments to study the structural organization of the ECR from Kitasatospora setae. K. setae ECR is a homo-tetramer that differentiates into a dimer of dimers of open- and closed-form subunits in the catalytically active state. Using molecular dynamics simulations and structure-based mutagenesis, we show that catalysis is synchronized in K. setae ECR across the pair of two dimers. This conformational coupling of catalytic domains is conferred by individual amino acids to achieve high CO 2 -fixation rates. Our results provide unprecedented insights into the dynamic organization and synchronized inter- and intra-subunit communications of this remarkably efficient CO 2 -fixing enzyme during catalysis.

DeMirci, Hasan↗

DOE OSTI2020

A fluid-structure interaction solver for investigating torsional galloping in solar-tracking photovoltaic panel arrays

Solar-tracking photovoltaic arrays are susceptible to aeroelastic fluttering during high-wind events. This dynamic fluttering behavior can grow in amplitude until the panels enter an unstable mode known as torsional galloping which can lead to panel failure or total array destruction. To better understand the physics of the torsional galloping phenomenon and to inform the discussion around panel design and recommended panel stow positions during high wind events, a fluid-structure interaction solver composed of a simulated atmospheric boundary layer with simplified panel structural responses was designed. The simulation choices and features of this solver were informed by the geometry and physical properties of an experimental panel array known to exhibit torsional galloping behavior during hind-wind events. Furthermore, these simulations revealed that the torsional galloping instability is driven by a combination of cyclic vortex shedding from the sun-facing side of the panel and the elastic properties of the torque tube linking the panel assemblies. Testing different stow angles across a range of wind speeds indicates that panels are generally more stable when stowed at negative angles where the leading edge is closer to the ground, hypothesized to be due to ground-blocking effects. These results are supplemented by a discussion of stability trends noted during testing and possible implications when considering multi-row array interactions.

14 SOLAR ENERGY↗

DOE OSTI2020

A Fluid Solver for Studying Torsional Galloping in Solar-Tracking PV Panel Arrays

Solar-tracking photovoltaic arrays are susceptible to aeroelastic fluttering during high-wind events. This dynamic fluttering behavior can grow in amplitude until the panels enter an unstable mode known as torsional galloping which can lead to panel failure or total array destruction. To better understand the physics of the torsional galloping phenomenon, and to inform the discussion around panel design and recommended panel stow positions during high wind events, a fluid-structure interaction solver composed of a simulated atmospheric boundary layer with simplified panel structural responses was designed. The simulation choices and features of this solver were informed by the geometry and physical properties of an experimental panel array known to exhibit torsional galloping behavior during hind-wind events. These simulations revealed that the torsional galloping instability is driven by a combination of cyclic vortex shedding from the sun-facing side of the panel and the elastic properties of the torque tube linking the panel assemblies. Testing different stow angles across a range of wind speeds indicates that panels are generally more stable when stowed at negative angles where the leading edge is closer to the ground, hypothesized to be due to ground-blocking effects.

41 EE - Solar Energy Technologies Office (EE-4S)↗

DOE OSTI2021

How Do Ionic Liquids “Fold” Ionenes? Computational and Experimental Analysis of Imidazolium Polymers Based on Ether and Alkyl Chain Variations Dissolved in an Ionic Liquid

Molecular dynamics (MD) simulations and complementary experiments are used here to understand the inter- and intramolecular structure and conformational properties of ionenes (i.e., cationic polymers formed from condensation reactions) dissolved in an ionic liquid (IL), 1-ethyl-3-methylimidazolium bistriflimide [C 2 mim + ][Tf 2 N - ]. The simulated structural properties are benchmarked against experimental analyses of these same polymers, mainly using dynamic light scattering (DLS) experiments. Four different imidazolium ionenes are considered, corresponding to variations in the chemistry and structure of the repeat units including: (1) poly (decylimidazolium) (PD 10 ); (2) poly (tetraethyleneglycolimidazolium) (PE 10 ); (3) alternating copolymer (P(ED) 5 ); and (4) a block copolymer (PE 5 D 5 ). Detailed computational analyses of the polymer structure and conformational properties were performed, including the radius of gyration, end-to-end distance, torsional distributions, and site-site and spatial distribution functions. Overall, there is a competition between intramolecular associations between the imidazolium groups and the ether sites in the polymers versus the intermolecular interactions of the polymer imidazolium groups with the surrounding anion molecules. The polymer with only ether linkages (PE 10 ) results in the most intramolecular interactions, leading to significant coiling behavior and chain contraction. These strong interactions reduce chain flexibility, but they also result in much more linear chain configurations and alignment of the imidazolium groups. The polymer structure is strongly affected as the concentration of alkyl groups is increased, and we find that the polymer architecture (alternating versus block copolymer) also has an important influence. Furthermore, these detailed observations are important for understanding the connection between the molecular design of imidazolium polymers and their emergent structural properties, which could lead to unique opportunities for creating polymer composites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Explicit structure-preserving geometric particle-in-cell algorithm in curvilinear orthogonal coordinate systems and its applications to whole-device 6D kinetic simulations of tokamak physics

Explicit structure-preserving geometric particle-in-cell (PIC) algorithm in curvilinear orthogonal coordinate systems is developed. The work reported represents a further development of the structure-preserving geometric PIC algorithm achieving the goal of practical applications in magnetic fusion research. The algorithm is constructed by discretizing the field theory for the system of charged particles and electromagnetic field using Whitney forms, discrete exterior calculus, and explicit non-canonical symplectic integration. In addition to the truncated infinitely dimensional symplectic structure, the algorithm preserves exactly many important physical symmetries and conservation laws, such as local energy conservation, gauge symmetry and the corresponding local charge conservation. As a result, the algorithm possesses the long-term accuracy and fidelity required for first-principles-based simulations of the multiscale tokamak physics. The algorithm has been implemented in the SymPIC code, which is designed for high-efficiency massively-parallel PIC simulations in modern clusters. The code has been applied to carry out whole-device 6D kinetic simulation studies of tokamak physics. A self-consistent kinetic steady state for fusion plasma in the tokamak geometry is numerically found with a predominately diagonal and anisotropic pressure tensor. The state also admits a steady-state sub-sonic ion flow in the range of 10 km s -1 , agreeing with experimental observations and analytical calculations Kinetic ballooning instability in the self-consistent kinetic steady state is simulated. It is shown that high-n ballooning modes have larger growth rates than low-n global modes, and in the nonlinear phase the modes saturate approximately in 5 ion transit times at the 2% level by the E × B flow generated by the instability. These results are consistent with early and recent electromagnetic gyrokinetic simulations.

43 PARTICLE ACCELERATORS↗

DOE OSTI2020

High-Resolution Comonomer Sequencing of Blocky Brominated Syndiotactic Polystyrene Copolymers Using 13C NMR Spectroscopy and Computer Simulations

This work demonstrates the first high-resolution comonomer sequencing of Blocky brominated syndiotactic polystyrene (sPS-co-sPS-Br) copolymers based on pentad assign- ments of the quaternary carbon region of the nuclear magnetic resonance spectrum. Copolymers containing p-bromostyrene (Br-Sty) units were prepared in matched sets using postpolymerization bromination methods carried out in the heterogeneous gel state (Blocky) and homogeneous solution state (Random). Quantitative information from the quaternary carbon spectra, heteronuclear multiple bond correlation spectroscopy, electronic structure calculations, and simulated statistically random copolymers was correlated to confirm the carbon resonance assignments for all 20 possible pentad comonomer sequences. Using the experimental pentad sequence prevalences, a computer code was developed to simulate chains with microstructures typical of each sample as a means to visually represent the copolymer blockiness with quantitative precision. Based on the microstructure and distribution of run lengths in these chains, the simulations revealed that the Blocky copolymers contain a high degree of blockiness. By comparing the run lengths in the simulated chains to the average number of styrene units in a crystalline segment of sPS (found by small-angle X-ray scattering), copolymer crystallizability was predicted. For the simulated Blocky B-21% (21 mol % Br-Sty) chain, the probability of randomly selecting a styrene unit in a crystallizable block was 25.8%, while that in the simulated Random R-18% was zero, in excellent agreement with the experimental crystallization behavior measured by differential scanning calorimetry. Additionally, these predictions confirmed that the simulated chains accurately represent the ensemble of chains in their respective copolymer samples. Furthermore, each simulated Blocky chain contained one or more long sPS blocks that paralleled the measured 38-40 styrene units spanning a crystalline segment within the sPS/CCl4 gel. This finding affirmed that the long sPS segments originated from the precise lamellar structure within the heterogeneous gel morphology (i.e., block length is correlated with lamellar thickness). Overall, the ability to tailor the copolymer microstructure through control of the semicrystalline gel morphology opens the door to synthesizing ordered copolymers by postpolymerization functionalization processes with unprecedented levels of compositional control.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019