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At least 793 records · Page 44

Modeling bacterial microcompartment architectures for enhanced cyanobacterial carbon fixation

The carboxysome is a bacterial microcompartment (BMC) which plays a central role in the cyanobacterial CO 2 -concentrating mechanism. These proteinaceous structures consist of an outer protein shell that partitions Rubisco and carbonic anhydrase from the rest of the cytosol, thereby providing a favorable microenvironment that enhances carbon fixation. The modular nature of carboxysomal architectures makes them attractive for a variety of biotechnological applications such as carbon capture and utilization. In silico approaches, such as molecular dynamics (MD) simulations, can support future carboxysome redesign efforts by providing new spatio-temporal insights on their structure and function beyond in vivo experimental limitations. However, specific computational studies on carboxysomes are limited. Fortunately, all BMC (including the carboxysome) are highly structurally conserved which allows for practical inferences to be made between classes. Here, we review simulations on BMC architectures which shed light on (1) permeation events through the shell and (2) assembly pathways. These models predict the biophysical properties surrounding the central pore in BMC-H shell subunits, which in turn dictate the efficiency of substrate diffusion. Meanwhile, simulations on BMC assembly demonstrate that assembly pathway is largely dictated kinetically by cargo interactions while final morphology is dependent on shell factors. Overall, these findings are contextualized within the wider experimental BMC literature and framed within the opportunities for carboxysome redesign for biomanufacturing and enhanced carbon fixation.

59 BASIC BIOLOGICAL SCIENCES↗

CO 2 electro-reduction on Cu 3 P: Role of Cu(I) oxidation state and surface facet structure in C 1 -formate production and H 2 selectivity

We report the catalytic activity and mechanism of copper(I) phosphide, Cu 3 P, with predominant [00Ι] facet exposure for the electrochemical reduction of CO 2 (CO 2 RR) to formic acid. Crystalline nanosheets of this compound that show a preferential [00Ι] facet orientation exhibit undiminished CO 2 RR activity after 16 hours with full retention of crystal structure and surface chemical speciation and no detectable corrosion. In contrast to the range of products formed on Cu metal, CuO, and Cu 2 O, the CO 2 RR on Cu 3 P [00Ι] produces mainly hydrogen and formate as the sole carbon product in KHCO 3 electrolyte. Analysis of the Cu 3 P [00Ι] facet by HAADF-STEM was used to determine the surface lattice structure, while both XPS and Auger spectroscopies were used to determine the surface chemical speciation from the kinetic energies of ionized electrons. The presented analysis identifies isolated trigonal CuP 3 sites on the Cu 3 P[00Ι]-Cu 3 P 3 terminated surface and the Cu(I) oxidation state as precursor to the active catalyst. The CO 2 RR selectivity to formate and the higher turnover rate for H 2 production on the [00Ι] facet allows a structure-activity analysis and chemical mechanism to be proposed. Formation of a surface hydride at isolated *H-CuP 3 sites is proposed as the catalytic site in forming both H 2 and formate, while the long Cu—Cu separation retards forming C-C coupling products. In conclusion, these results disprove previously published claims of Cu(I) oxidation state as a sufficient criterion to promote CO 2 RR to C 2+ products, show that stronger bonded hydrides, *H-CuP 3 on Cu 3 P, favor production of the C1 product formate over all other carbon products, and predict that stronger formate binding (bidentate) is needed for CO 2 RR currents to compete with H 2 production.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ultrafast conformational dynamics of Rydberg-excited N -methyl piperidine

We have observed the ultrafast conformational dynamics of electronically excited N-methyl piperidine (NMP) using time-resolved Rydberg fingerprint spectroscopy. Optical excitation at various wavelengths ranging from 212 nm to 229 nm leads to the 3s or 3p Rydberg states and induces coherent oscillatory motions with periods of about 700 fs. Furthermore, these coherent motions survive the internal conversion from 3p to 3s but then dephase on a time scale of a few oscillations. Intramolecular vibrational energy redistribution on a picosecond time scale leads to an equilibrium between two conformeric structures that are separated in binding energy by 0.09 eV. Model calculations using the DFT-SIC method are in excellent agreement with the experiments and identify the conformers as the chair and twist structures of NMP. The analysis of the equilibrium parameters at long time delays as a function of excitation wavelength allows for the extraction of thermodynamic parameters for the conformeric transformation. We derive an enthalpy of the chair to twist reaction in the 3s excited state of 62 meV with an entropy of 19.70 J mol –1 K –1 . An activation energy of 276 meV is also obtained with a kinetic model.

74 ATOMIC AND MOLECULAR PHYSICS↗

Local analysis of fast magnetic reconnection

Fast magnetic reconnection is defined by the topology of the magnetic field lines changing on a timescale that is approximately an order of magnitude longer than the topology-conserving ideal-evolution timescale. Fast reconnection is an intrinsic property of Faraday's law when the evolving magnetic field depends non-trivially on all three spatial coordinates and is commonly observed—even when the effects that allow topology breaking are arbitrarily small. The associated current density need only be enhanced by a factor of approximately ten and flows in thin but broad ribbons along the magnetic field. These results follow from the variation in the separation of neighboring pairs of magnetic field lines, which in an ideal evolution typically increases exponentially with time, and the existence of a spatial scale below which magnetic field lines freely change their identities due to non-ideal effects, such as resistivity. Traditional reconnection theory ignores exponentially large variations and relies on the current density reaching a magnitude that is exponentially larger than is actually required. Here, an analysis of the behavior of magnetic field lines in the neighborhood of an arbitrarily chosen line is used to obtain more precise and rigorous results on intrinsic reconnection. The maximum parallel kinetic energy of collisionless charged particles is shown to have an exponential increase in time during a generic magnetic evolution.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Investigation of Delayed Neutron Sensitivities for Several ICSBEP Benchmarks using MCNP

The effective delayed neutron (β$_{eff}$) is a very important parameter for reactor and criticality applications. This parameter is equal to the difference in reactivity between delayed critical ($k_{eff}$ = 1, which requires both prompt and delayed neutrons to achieve criticality) and prompt critical ($k_p$ = 1, which requires only prompt neutrons to achieve criticality). This is often referred to as the delayed critical "window" (the region of criticality between delayed and prompt critical). β$_{eff}$ is a reactor kinetics parameters and depends on the nuclides in the system that undergo fission as well as the spectral characteristics of the system. Measurements of β$_{eff}$ have been performed for many criticality experiments. The EUCLID (Experiments Underpinned by Computational Learning for Improvements in nuclear Data) project at Los Alamos National Laboratory (LANL) aims to constrain nuclear data by using a suite of measurement types beyond $k_{eff}$. Our team has recently investigated the use of pulsed spheres for nuclear data validation. Several other measurement methods are also of interest, including β$_{eff}$ (investigated here) and reactivity coefficients (investigated in a separate work at this same meeting). One focus of our work is to determine if other methods are complimentary to the critical experiments already utilized for nuclear data validation. This is important because if a method has similar sensitivities then it will not be particularly useful for nuclear data validation as it will provide the same information as the critical experiments already being used. Here "similar" could refer to several characteristics, one being the shape of a sensitivity profile over energy. In the future, these methods will be utilized (with both existing and new experiments) in machine learning algorithms for nuclear validation, similar to what is currently done for criticality experiments. In order to use a measurement type for nuclear validation, it is necessary to obtain cross-section sensitivities for that parameter. This work looks at one approach to estimate β$_{eff}$ sensitivities by utilizing $k_{eff}$ sensitivities within Monte Carlo N-Particle ® Code Version 6.2. This is applied to several criticality benchmarks. Results are compared and the benefits and limitations of this approach are discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Electrochemical Studies of Redox Systems for Energy Storage

Particular attention was paid to the Cr(II)/Cr(III) redox couple in aqueous solutions in the presence of Cl(-) ions. The aim of this research has been to unravel the electrode kinetics of this redox couple and the effect of Cl(1) and electrode substrate. Gold and silver were studied as electrodes and the results show distinctive differences; this is probably due to the role Cl(-) ion may play as a mediator in the reaction and the difference in state of electrical charge on these two metals (difference in the potential of zero charge, pzc). The competition of hydrogen evolution with CrCl3 reduction on these surfaces was studied by means of the rotating ring disk electrode (RRDE). The ring downstream measures the flux of chromous ions from the disk and therefore separation of both Cr(III) and H2 generation can be achieved by analyzing ring and disk currents. The conditions for the quantitative detection of Cr(2+) at the ring electrode were established. Underpotential deposition of Pb on Ag and its effect on the electrokinetics of Cr(II)/Cr(III) reaction was studied.

Wu, C. D.↗

Reaction of HO2 with O3 and the effect of water vapor on HO2 kinetics

The effects of temperature and water vapor concentration on the ratio of the rate constant of the reaction HO2 + O3 yields OH + 2(O2) to the square root of the rate constant for the reaction HO2 + HO2 yields H2O2 + O2 are determined. Photolysis of H2-O2-O3 mixtures at 253.7 nm was carried out with H2O pressures in the range 0 to 15 torr at a temperature range of -42.5 to 61 C along with 184.9 nm photolysis of H2O-O2-O3 mixtures. It is shown that the rate of O3 photolysis is suppressed by the addition of water vapor and it is suggested that this effect is realized in the HO2 + HO2 yields H2O2 + O2 reaction. The calculated expression for the temperature dependence of the rate constant ratio is found to be in good agreement with that calculated from separate rate constants. Rate constants determined for the reaction OH + HO2 yields H2O + O2 are found to be higher than those previously determined, presumably due to increased pressure, indicating that atmospheric models should take into account the possible pressure dependences of the reactions considered.

Demore, W. B.↗

Development of Transformational Solvents for CO2 Separations

The primary objective of this CRADA activity is to use a combined molecular modeling and experimental validation approach to refine and develop transformational solvents for carbon capture. PNNL’s role on this project is currently funded by the Department of Energy’s (DOE) Office of Fossil Energy (OFE). PNNL is developing advanced molecular modeling based on their CO2BOLs solvent platform as a demonstration solvent for the activity; the model was developed and compared against measured data for CO2BOL derivatives. Here, a CRADA with PNNL and GE will leverage their current molecular models and apply them to solvent classes that operate on carbamate chemistry, specifically GE’s aminosilicone solvent class. The molecular models will be used to predict physical and thermodynamic properties, such as viscosity, as a means to predict advanced formulations with reduced viscosity compared to current aminosilicone derivatives, enabling optimized thermodynamic and kinetic metrics for economical carbon capture for this class of materials. Together, PNNL and GE will develop a comprehensive means of linking molecular modeling parameters to intermediate physical properties as a means to improve solvent performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bipolar membrane polarization behavior with systematically varied interfacial areas in the junction region

The palette of applications for bipolar membranes (BPMs) has expanded recently beyond electrodialysis as they are now being considered for fuel cell and electrolysis applications. Their deployment in emerging electrochemical technologies arises from the need to have a membrane separator that provides disparate pH environments and to prevent species crossover. Most materials research for BPMs has focused on water dissociation catalysts and less emphasis has been given to the design of the polycation–polyanion interface for improving BPM performance. Here, soft lithography fabricated a series of micropatterned BPMs with precise control over the interfacial area in the bipolar junction. Polarization experiments showed that a 2.28× increase in interfacial area led to a 250 mV reduction in the onset potential. Additionally, the same increase in interfacial area yielded marginal improvements in current density due to the junction region being under kinetics-diffusion control. A simple physics model based on the electric field of the junction region rationalized the reduction in the overpotential for water dissociation as a function of interfacial area. Finally, the soft lithography approach was also conducive for fabricating BPMs with different chemistries ranging from perfluorinated polymer backbones to alkaline stable poly(arylene) hydrocarbon polymers. These polymer chemistries are better suited for fuel cell and electrolysis applications. The BPM featuring the alkaline stable poly(terphenyl) anion exchange membrane had an onset potential of 0.84 V, which was near the thermodynamic limit, and was about 150 mV lower than a commercially available variant.

25 ENERGY STORAGE↗

Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases

Replication-initiating HUH endonucleases (Reps) are sequence-specific nucleases that cleave and rejoin single-stranded DNA (ssDNA) during rolling-circle replication. These functions are mediated by covalent linkage of the Rep to its substrate post cleavage. Here, we describe the structures of the endonuclease domain from the Muscovy duck circovirus Rep in complex with its cognate ssDNA 10-mer with and without manganese in the active site. Structural and functional analyses demonstrate that divalent cations play both catalytic and structural roles in Reps by polarizing and positioning their substrate. Further structural comparisons highlight the importance of an intramolecular substrate Watson-Crick (WC) base pairing between the -4 and +1 positions. Subsequent kinetic and functional analyses demonstrate a functional dependency on WC base pairing between these positions regardless of the pair’s identity (i.e., A·T, T·A, G·C, or C·G), highlighting a structural specificity for substrate interaction. Finally, considering how well WC swaps were tolerated in vitro, we sought to determine to what extent the canonical -4T·+1A pairing is conserved in circular Rep-encoding single-stranded DNA viruses and found evidence of noncanonical pairings in a minority of these genomes. Altogether, our data suggest that substrate intramolecular WC base pairing is a universal requirement for separation and reunion of ssDNA in Reps.

59 BASIC BIOLOGICAL SCIENCES↗

Verification of neoclassical toroidal viscosity induced by energetic particles

The thermal particles contributed neoclassical toroidal viscosity (NTV) have been successfully developed and explored by many impressive works such as the study by Shaing et al. [Phys. Plasmas 10, 1443 (2003)] and Zhu et al. [Phys. Rev. Lett. 96, 225002 (2006)]. In this work, the scope of the NTV study is extended to explore the contribution of energetic particles (EPs) through both theory and experiments. In theory, the existence of the NTV torque due to the precessional drift resonance of trapped EPs is identified based on the equivalence between the NTV torque and the perturbed drift kinetic energy [J. Park, Phys. Plasmas 18, 110702 (2011)]. Toroidal modeling with the Magneto Resistive Spectrum - drift Kinetic code [Y. Liu, Phys. Plasmas 15, 112503 (2008)], based on this equivalence, indicates that trapped EPs can contribute a significant amount of the NTV torque. Meanwhile, this work also focuses on developing the dedicated DIII-D experiments in the presence of the n = 2 external magnetic perturbation to verify the EP induced NTV (EP-NTV) by measuring the change of the NTV torque while varying the angle and the voltage of the neutral beam injection. However, the developed experiments have been unable to create conditions necessary to clearly demonstrate the presence of EP-NTV. The main challenge is separating the resonant and non-resonant momentum transport responses in the plasma. Finally, the experience, gained from this study, can help the further exploration of EP-NTV in the future experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Three-dimensional ocular kinematics during eccentric rotations: evidence for functional rather than mechanical constraints

Previous studies have reported that the translational vestibuloocular reflex (TVOR) follows a three-dimensional (3D) kinematic behavior that is more similar to visually guided eye movements, like pursuit, rather than the rotational VOR (RVOR). Accordingly, TVOR rotation axes tilted with eye position toward an eye-fixed reference frame rather than staying relatively fixed in the head like in the RVOR. This difference arises because, contrary to the RVOR where peripheral image stability is functionally important, the TVOR like pursuit and saccades cares to stabilize images on the fovea. During most natural head and body movements, both VORs are simultaneously activated. In the present study, we have investigated in rhesus monkeys the 3D kinematics of the combined VOR during yaw rotation about eccentric axes. The experiments were motivated by and quantitatively compared with the predictions of two distinct hypotheses. According to the first (fixed-rule) hypothesis, an eye-position-dependent torsion is computed downstream of a site for RVOR/TVOR convergence, and the combined VOR axis would tilt through an angle that is proportional to gaze angle and independent of the relative RVOR/TVOR contributions to the total eye movement. This hypothesis would be consistent with the recently postulated mechanical constraints imposed by extraocular muscle pulleys. According to the second (image-stabilization) hypothesis, an eye-position-dependent torsion is computed separately for the RVOR and the TVOR components, implying a processing that takes place upstream of a site for RVOR/TVOR convergence. The latter hypothesis is based on the functional requirement that the 3D kinematics of the combined VOR should be governed by the need to keep images stable on the fovea with slip on the peripheral retina being dependent on the different functional goals of the two VORs. In contrast to the fixed-rule hypothesis, the data demonstrated a variable eye-position-dependent torsion for the combined VOR that was different for synergistic versus antagonistic RVOR/TVOR interactions. Furthermore, not only were the eye-velocity tilt slopes of the combined VOR as much as 10 times larger than what would be expected based on extraocular muscle pulley location, but also eye velocity during antagonistic RVOR/TVOR combinations often tilted opposite to gaze. These results are qualitatively and quantitatively consistent with the image-stabilization hypothesis, suggesting that the eye-position-dependent torsion is computed separately for the RVOR and the TVOR and that the 3D kinematics of the combined VOR are dependent on functional rather than mechanical constraints.

Non-NASA Center↗

Flowfield Comparisons from Three Navier-Stokes Solvers for an Axisymmetric Separate Flow Jet

To meet new noise reduction goals, many concepts to enhance mixing in the exhaust jets of turbofan engines are being studied. Accurate steady state flowfield predictions from state-of-the-art computational fluid dynamics (CFD) solvers are needed as input to the latest noise prediction codes. The main intent of this paper was to ascertain that similar Navier-Stokes solvers run at different sites would yield comparable results for an axisymmetric two-stream nozzle case. Predictions from the WIND and the NPARC codes are compared to previously reported experimental data and results from the CRAFT Navier-Stokes solver. Similar k-epsilon turbulence models were employed in each solver, and identical computational grids were used. Agreement between experimental data and predictions from each code was generally good for mean values. All three codes underpredict the maximum value of turbulent kinetic energy. The predicted locations of the maximum turbulent kinetic energy were farther downstream than seen in the data. A grid study was conducted using the WIND code, and comments about convergence criteria and grid requirements for CFD solutions to be used as input for noise prediction computations are given. Additionally, noise predictions from the MGBK code, using the CFD results from the CRAFT code, NPARC, and WIND as input are compared to data.

Koch, L. Danielle↗

Decoupling Complex Multi–Length–Scale Morphology in Non–Fullerene Photovoltaics with Nitrogen K–Edge Resonant Soft X–ray Scattering

Complex morphology in organic photovoltaics (OPVs) and other functional soft materials commonly dictates performance. Such complexity in OPVs originates from the mesoscale kinetically trapped non-equilibrium state, which governs device charge generation and transport. Resonant soft X-ray scattering (RSoXS) has been revolutionary in the exploration of OPV morphology in the past decade due to its chemical and orientation sensitivity. However, for non-fullerene OPVs, RSoXS analysis near the carbon K-edge is challenging, due to the chemical similarity of the materials used in active layers. Here, an innovative approach is provided by nitrogen K-edge RSoXS (NK-RSoXS), utilizing the spatial and orientational contrasts from the cyano groups in the acceptor materials, which allows for determination of phase separation. NK-RSoXS clearly visualizes the combined feature sizes in PM6:Y6 blends from crystallization and liquid-liquid demixing, while PM6:Y6:Y6-BO ternary blends with reduced phase-separation size and enhanced material crystallization can lead to current amplification in devices. Nitrogen is common in organic semiconductors and other soft materials, and the strong and directional N 1s → π* resonances make NK-RSoXS a powerful tool to uncover the mesoscale complexity and open opportunities to understand heterogeneous systems.

36 MATERIALS SCIENCE↗

Antiphase boundary migration as a diffusion mechanism in a P3 sodium layered oxide

The electrode materials of Na-ion batteries must exhibit fast ion transport, a property that is often negatively impacted when mobile cations order. Many layered Na (and K) intercalation compounds adopt the P3 crystal structure, which tends to stabilize cation-vacancy orderings over a wide range of Na concentrations. The ordered phases have been predicted to consist of domains that are periodically separated by antiphase boundaries (APBs) to accommodate variations in Na concentration. The mechanisms and rates with which Na diffuses within such ordered phases of P3 are not understood. We have conducted a first-principles study of Na diffusion in the P3 structure, using Na x CoO 2 as a model system. We find that most simple nearest-neighbor hops in Na-vacancy ordered phases in P3 result in unstable configurations and are therefore forbidden. We identify an alternative mechanism of Na transport that is mediated by APB migration via the formation and expansion of kinks along domain boundaries. The limiting kinetic barriers for this mechanism are quite low (0.03 to 0.30 eV). Vacancy defects are not required, and furthermore have formation energies that are higher than those of the APB kink defects. Furthermore, our results suggest that APB migration is a fundamental diffusion mechanism in the P3 structure.

36 MATERIALS SCIENCE↗

Rheology and dynamics of a solvent segregation driven gel (SeedGel)

Bicontinuous structures promise applications in a broad range of research fields, such as energy storage, membrane science, and biomaterials. Kinetically arrested spinodal decomposition is found responsible for stabilizing such structures in different types of materials. A recently developed solvent segregation driven gel (SeedGel) is demonstrated to realize bicontinuous channels thermoreversibly with tunable domain sizes by trapping nanoparticles in a particle domain. As the mechanical properties of SeedGel are very important for its future applications, a model system is characterized by temperature-dependent rheology. The storage modulus shows excellent thermo-reproducibility and interesting temperature dependence with the maximum storage modulus observed at an intermediate temperature range (around 28 °C). SANS measurements are conducted at different temperatures to identify the macroscopic solvent phase separation during the gelation transition, and solvent exchange between solvent and particle domains that is responsible for this behavior. Further, the long-time dynamics of the gel is further studied by X-ray Photon Correlation Spectroscopy (XPCS). The results indicate that particles in the particle domain are in a glassy state and their long-time dynamics are strongly correlated with the temperature dependence of the storage modulus.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Global Kinetic Modeling of the Intrabinary Shock in Spider Pulsars

Abstract Spider pulsars are compact binary systems composed of a millisecond pulsar and a low-mass companion. The relativistic magnetically dominated pulsar wind impacts onto the companion, ablating it and slowly consuming its atmosphere. The interaction forms an intrabinary shock, a proposed site of particle acceleration. We perform global fully kinetic particle-in-cell simulations of the intrabinary shock, assuming that the pulsar wind consists of plane-parallel stripes of alternating polarity and that the shock wraps around the companion. We find that particles are efficiently accelerated via shock-driven reconnection. We extract first-principles synchrotron spectra and light curves, which are in good agreement with X-ray observations: (1) the synchrotron spectrum is nearly flat, F ν ∝ const; (2) when the pulsar spin axis is nearly aligned with the orbital angular momentum, the light curve displays two peaks, just before and after the pulsar eclipse (pulsar superior conjunction), separated in phase by ∼0.8 rad; (3) the peak flux exceeds the one at the inferior conjunction by a factor of 10.

79 ASTRONOMY AND ASTROPHYSICS↗

Simulation Tool for Dielectric Barrier Discharge Plasma Actuators

Traditional approaches for active flow separation control using dielectric barrier discharge (DBD) plasma actuators are limited to relatively low speed flows and atmospheric conditions. This results in low feasibility of the DBDs for aerospace applications. For active flow control at turbine blades, fixed wings, and rotary wings and on hypersonic vehicles, DBD plasma actuators must perform at a wide range of conditions, including rarified flows and combustion mixtures. An efficient, comprehensive, physically based DBD simulation tool can optimize DBD plasma actuators for different operation conditions. Researchers are developing a DBD plasma actuator simulation tool for a wide range of ambient gas pressures. The tool will treat DBD using either kinetic, fluid, or hybrid models, depending on the DBD operational condition.

Likhanskii, Alexander↗