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At least 1,621 records · Page 90

In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121

The P450 enzyme CYP121 from Mycobacterium tuberculosis catalyzes a carbon–carbon (C–C) bond coupling cyclization of the dityrosine substrate containing a diketopiperazine ring, cyclo(l-tyrosine-l-tyrosine) (cYY). An unusual high-spin (S = 5/2) ferric intermediate maximizes its population in less than 5 ms in the rapid freeze-quenching study of CYP121 during the shunt reaction with peracetic acid or hydrogen peroxide in acetic acid solution. Here, we show that this intermediate can also be observed in the crystalline state by EPR spectroscopy. By developing an on-demand-rapid-mixing method for time-resolved serial femtosecond crystallography with X-ray free-electron laser (tr-SFX-XFEL) technology covering the millisecond time domain and without freezing, we structurally monitored the reaction in situ at room temperature. After a 200 ms peracetic acid reaction with the cocrystallized enzyme–substrate microcrystal slurry, a ferric-hydroperoxo intermediate is observed, and its structure is determined at 1.85 Å resolution. The structure shows a hydroperoxyl ligand between the heme and the native substrate, cYY. The oxygen atoms of the hydroperoxo are 2.5 and 3.2 Å from the iron ion. The end-on binding ligand adopts a near-side-on geometry and is weakly associated with the iron ion, causing the unusual high-spin state. This compound 0 intermediate, spectroscopically and structurally observed during the catalytic shunt pathway, reveals a unique binding mode that deviates from the end-on compound 0 intermediates in other heme enzymes. The hydroperoxyl ligand is only 2.9 Å from the bound cYY, suggesting an active oxidant role of the intermediate for direct substrate oxidation in the nonhydroxylation C–C bond coupling chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Reorganization Energies for Interfacial Proton-Coupled Electron Transfer to a Water Oxidation Catalyst

The reorganization energy (λ) for interfacial electron transfer (ET) and proton-coupled electron transfer (PCET) from a conductive metal oxide (In 2 O 3 :Sn, ITO) to a surface-bound water oxidation catalyst were extracted from kinetic data measured as a function of the thermodynamic driving force. Visible light excitation resulted in rapid excited-state injection (k inj > 10 8 s -1 ) to the ITO, which photo-initiated the two interfacial reactions of interest. The rate constants for both reactions increased with the driving force, −ΔG°, to a saturating limit, k max , with rate constants consistently larger for ET than for PCET. Marcus-Gerischer analysis of the kinetic data provided the reorganization energy for interfacial PCET (0.90 ± 0.02 eV) and ET (0.40 ± 0.02 eV), respectively. The magnitude of k max for PCET was found to decrease with pH, behavior that was absent for ET. Both the decrease in k max and the larger reorganization energy for an unwanted competing PCET reaction from the ITO to the oxidized catalyst showcases a significant kinetic advantage for driving solar water oxidation at high pH. Computational analysis revealed a larger inner-sphere reorganization energy contribution for PCET than for ET arising from a more significant change in the Ru–O bond length for PCET. Extending Marcus-Gerischer theory to PCET by including the excited electron-proton vibronic states and the proton donor-acceptor motion provided an apparent reorganization energy of 1.01 eV. Furthermore, this study demonstrates that the Marcus-Gerischer theory initially developed for ET can be reliably extended to PCET for quantifying and interpreting reorganization energies observed experimentally.

Catalysts Kinetic parameters↗

Spectral analysis of product formulas for quantum simulation

We consider the time-independent Hamiltonian simulation using the first order Lie–Trotter–Suzuki product formula under the assumption that the initial state is supported on a low-dimension subspace. By comparing the spectral decomposition of the original Hamiltonian and the effective Hamiltonian, we obtain better upper bounds for various conditions. Especially, we show that the Trotter step size needed to estimate an energy eigenvalue within precision ϵ using quantum phase estimation can be improved in scaling from ϵ to ϵ 1/2 for a large class of systems. Our results also depend on the gap condition of the simulated Hamiltonian.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Theory of overparametrization in quantum neural networks

The prospect of achieving quantum advantage with quantum neural networks (QNNs) is exciting. Understanding how QNN properties (for example, the number of parameters $M$) affect the loss landscape is crucial to designing scalable QNN architectures. Here we rigorously analyze the overparametrization phenomenon in QNNs, defining overparametrization as the regime where the QNN has more than a critical number of parameters $M_c$ allowing it to explore all relevant directions in state space. In this study, our main results show that the dimension of the Lie algebra obtained from the generators of the QNN is an upper bound for $M_c$, and for the maximal rank that the quantum Fisher information and Hessian matrices can reach. Underparametrized QNNs have spurious local minima in the loss landscape that start disappearing when $M$ ≥ $M_c$. Thus, the overparametrization onset corresponds to a computational phase transition where the QNN trainability is greatly improved. We then connect the notion of overparametrization to the QNN capacity, so that when a QNN is overparametrized, its capacity achieves its maximum possible value.

97 MATHEMATICS AND COMPUTING↗

dCache: from Resilience to Quality of Service

A major goal of future dCache development will be to allow users to define file Quality of Service (QoS) in a more flexible way than currently available. This will mean implementing what might be called a QoS rule engine responsible for registering and managing time-bound QoS transitions for files or storage units. In anticipation of this extension to existing dCache capabilities, the Resilience service, which maintains on-disk replica state, needs to undergo both structural modification and generalization. This paper describes ongoing work to transform Resilience into the new architecture which will eventually support a more broadly defined file QoS.

97 MATHEMATICS AND COMPUTING↗

Low-energy magnons in the chiral ferrimagnet Cu 2 OSeO 3 : A coarse-grained approach

We report a comprehensive neutron scattering study of low energy magnetic excitations in the breathing pyrochlore helimagnetic Cu2OSeO3. Fully documenting the four lowest energy magnetic modes that leave the ferrimagnetic configuration of the “strong tetrahedra” intact (| ℏ ω| < 13 meV), we find gapless quadratic dispersion at the Γ point for energies above 0.2 meV, two doublets separated by 1.6(2) meV at the R point, and a bounded continuum at the X point. Our constrained rigid spin cluster model relates these features to Dzyaloshinskii-Moriya (DM) interactions and the incommensurate helical ground state. Combining conventional spin wave theory with a spin cluster form factor accurately reproduces the measured equal time structure factor through multiple Brillouin zones. An effective spin Hamiltonian describing complex anisotropic intercluster interactions is obtained.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Superconducting Dome in Nd 1-x Sr x NiO 2 Infinite Layer Films

We show the phase diagram of Nd 1-x Sr x NiO 2 infinite layer thin films grown on SrTiO 3 . A superconducting dome spanning 0.125 < x < 0.25 is found, remarkably similar to cuprates, albeit over a narrower doping window. However, while cuprate superconductivity is bounded by an insulator for underdoping and a metal for overdoping, here we observe weakly insulating behavior on either side of the dome. Furthermore, the normal state Hall coefficient is always small and proximate to a continuous zero crossing in doping and in temperature, in contrast to the ~ 1/x dependence observed for cuprates. This suggests the presence of both electronlike and holelike bands, consistent with band structure calculations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The Coronal Line Spectrum of the Iron Nova V3666 Ophiuchi

Optical and infrared spectroscopy are presented for the classical nova V3666 Ophiuchi (Nova Ophiuchi 2018 No.3) from 11 months after its outburst. At that epoch, V3666 Oph displayed an [Fe x] λ0.6375 emission line stronger than Hα and nearly a factor of 3 larger, relative to Hα, than in any nova observed previously. The [Fe x] feature, with an equivalent width exceeding 1300 Å, was enormously strong relative to the continuum emission as well. V3666 Oph also reached a state of high excitation for an Fe ii type nova, displaying coronal lines of [Fe xi], [S ix], and [Ar x], and permitted features that can be identified with the C vi (8–7), (9–8), and (10–9) transitions. In addition to [Fe x] and [Fe xi], V3666 Oph also displayed bright lines of [Fe vii], indicating that the prominent iron features were not confined to a single or narrow range of ionization states. Modeling the emission line spectrum of V3666 Oph with the photoionization code Cloudy indicated that the bulk of the emission line gas was matter-bounded, severely reducing the amount of low ionization gas and resulting in coronal lines that were very strong in comparison to lines such as H i and He i, and the familiar low excitation forbidden lines of nitrogen and oxygen. Such matter-bounded regions are observationally rare in novae since they are both faint and short-lived, offering a plausible explanation for why [Fe x] λ0.6375 had not be seen at this strength previously.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Uncertainties in the effects of organic aerosol coatings on polycyclic aromatic hydrocarbon concentrations and their estimated health effects

We used the CAM5 model to examine how different particle-bound polycyclic aromatic hydrocarbon (PAH) degradation approaches affect the spatial distribution of benzo(a)pyrene (BaP). Three approaches were evaluated: NOA (no effect of OA coatings state on BaP), shielded (viscous OA coatings shield BaP from oxidation under cool and dry conditions) and ROI-T (viscous OA coatings slow BaP oxidation in response to temperature and humidity). Results show that BaP concentrations vary seasonally, influenced by emissions, deposition, transport and degradation approach, all of which are influenced by meteorological conditions. All simulations predict higher population-weighted global average (PWGA) fresh BaP concentrations during December–January–February (DJF) compared to June–July–August (JJA), due to increased emissions from household activities and reduced removal processes during colder months. The shielded and ROI-T approaches, which account for OA coatings, result in 2–6 times higher BaP concentrations in DJF compared to NOA. The shielded simulation predicts the highest PWGA fresh BaP concentration (1.3 ng m −3 ), with 90 % of BaP protected from oxidation. In contrast, the ROI-T approach forecasts lower concentrations in middle to low latitudes, as it assumes less effective OA coatings under warmer, more humid conditions. Evaluations against observed BaP concentrations show the shielded approach performs best, with a normalized mean bias (NMB) within ± 20 %. The combined incremental lifetime cancer risk (ILCR) for both fresh and oxidized PAHs is similar across simulations, emphasizing the importance of considering both forms in health risk assessments. This study highlights the critical role of accurate degradation approaches in PAH modeling.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Forced shelf circulation by an alongshore wind band

The forced circulation over a continental shelf generated by the alongshore wind stress is studied within the frictional regime. The model alongshore wind stress has a finite extent in the alongshore direction and oscillates monochromatically, resembling a series of anticyclones traveling across the coastline. Both the shelf-wave response and the localized non-wavelike response exist within the wind band. The numerical results show that the interaction of shelf waves with locally wind-forced response generates a large increase in the phase speed within the wind band. Given an alongshore variation in the alongshore wind stress, a right-bounded phase propagation is possible even in the absence of continental shelf waves. Given a reasonable friction currently accepted for the east coast of the United States, the resonance mechanism at the cutoff frequency may not be important, and lower frequency wind events generate larger amplitude continental shelf circulation. By reducing the friction, energy at cutoff fequencies leaks out of the wind band in both directions effectively. It also is shown that non-wavelike response depends only on the local wind stress and is not affected significantly by friction.

Chao, S.-Y.↗

The ion cyclotron dispersion relation in a proton-alpha solar wind

Solutions to the WKB warm plasma dispersion relation are investigated for the case of a proton-alpha plasma, to determine when parallel ion cyclotron waves can propagate at the alpha particle gyrofrequency. Examples are given of the behavior of the dispersion curves in this resonant regime, for several types of plasma states that are appropriate to the fast solar wind. It is found that while ion cyclotron waves can propagate at the alpha particle gyrofrequency for a bounded set of plasma parameters, use of the correct dispersion relation will probably make resonant cyclotron acceleration of solar wind plasma particles less feasible as a mechanism for the generation of the observed preferential effects.

Isenberg, P. A.↗

High Tc superconductors: The scaling of Tc with the number of bound holes associated with charge transfer neutralizing the multivalence cations

It is observed that for the known high-T(sub c) Cu-, Tl-, and Bi-based superconductors, T(sub c) scales consistently with the number of bound holes per unit cell which arise from charge transfer excitations of frequency approximately = 3 x 10(exp 13) that neutralized the multivalence cations into diamagnetic states. The resulting holes are established on the oxygens. Extrapolation of this empirical fit in the up-temperature direction suggests a T(sub c) of about 220-230 K at a value of 25 holes/unit cell (approximately the maximum that can be materials-engineered into a high-T(sub c) K2MnF4 or triple Perovskite structure). In the down-temperature direction, the extrapolation gives a T(sub c) in the vicinity of 235 K for the Y-Ba-Cu-O system as well as the known maximum temperature of 23 K for low-T(sub c) materials shown by Nb3Ge. The approach is also consistent with the experimental findings that only multivalence ions which are diamagnetic in their atomic state (Cu, Tl, Bi, Pb, and Sb) associate with high-T(sub c) compounds.

Vezzoli, G. C.↗

A Refined Zigzag Beam Theory for Composite and Sandwich Beams

A new refined theory for laminated composite and sandwich beams that contains the kinematics of the Timoshenko Beam Theory as a proper baseline subset is presented. This variationally consistent theory is derived from the virtual work principle and employs a novel piecewise linear zigzag function that provides a more realistic representation of the deformation states of transverse-shear flexible beams than other similar theories. This new zigzag function is unique in that it vanishes at the top and bottom bounding surfaces of a beam. The formulation does not enforce continuity of the transverse shear stress across the beam s cross-section, yet is robust. Two major shortcomings that are inherent in the previous zigzag theories, shear-force inconsistency and difficulties in simulating clamped boundary conditions, and that have greatly limited the utility of these previous theories are discussed in detail. An approach that has successfully resolved these shortcomings is presented herein. Exact solutions for simply supported and cantilevered beams subjected to static loads are derived and the improved modelling capability of the new zigzag beam theory is demonstrated. In particular, extensive results for thick beams with highly heterogeneous material lay-ups are discussed and compared with corresponding results obtained from elasticity solutions, two other zigzag theories, and high-fidelity finite element analyses. Comparisons with the baseline Timoshenko Beam Theory are also presented. The comparisons clearly show the improved accuracy of the new, refined zigzag theory presented herein over similar existing theories. This new theory can be readily extended to plate and shell structures, and should be useful for obtaining relatively low-cost, accurate estimates of structural response needed to design an important class of high-performance aerospace structures.

Tessler, Alexander↗

Hybrid suboptimal control of multi-rate multi-loop sampled-data systems

A hybrid state-space controller is developed for suboptimal digital control of multirate multiloop multivariable continuous-time systems. First, an LQR is designed for a continuous-time subsystem which has a large bandwidth and is connnected in the inner loop of the overall system. The designed LQR would optimally place the eigenvalues of a closed-loop subsystem in the common region of an open sector bounded by sector angles + or - pi/2k for k = 2 or 3 from the negative real axis and the left-hand side of a vertical line on the negative real axis in the s-plane. Then, the developed continuous-time state-feedback gain is converted into an equivalent fast-rate discrete-time state-feedback gain via a digital redesign technique (Tsai et al. 1989, Shieh et al. 1990) reviewed here. A real state reconstructor is redeveloped utilizing the fast-rate input-output data of the system of interest. The design procedure of multiloop multivariable systems using multirate samplers is shown, and a terminal homing missile system example is used to demonstrate the effectiveness of the proposed method.

Shieh, Leang S.↗

Measurements of electron detection efficiencies in solid state detectors.

Detailed laboratory measurement of the electron response of solid state detectors as a function of incident electron energy, detector depletion depth, and energy-loss discriminator threshold. These response functions were determined by exposing totally depleted silicon surface barrier detectors with depletion depths between 50 and 1000 microns to the beam from a magnetic beta-ray spectrometer. The data were extended to 5000 microns depletion depth using the results of previously published Monte Carlo electron calculations. When the electron counting efficiency of a given detector is plotted as a function of energy-loss threshold for various incident energies, the efficiency curves are bounded by a smooth envelope which represents the upper limit to the detection efficiency. These upper limit curves, which scale in a simple way, make it possible to easily estimate the electron sensitivity of solid-state detector systems.

Lupton, J. E.↗

Energy dissipation efficiency in the CP43 assembly intermediate complex of photosystem II

Photosystem II in oxygenic organisms is a large membrane bound rapidly turning over pigment protein complex. During its biogenesis, multiple assembly intermediates are formed, including the CP43-preassembly complex (pCP43). Here, to understand the energy transfer dynamics in pCP43, we first engineered a His-tagged version of the CP43 in a CP47-less strain of the cyanobacterium Synechocystis 6803. Isolated pCP43 from this engineered strain was subjected to advanced spectroscopic analysis to evaluate its excitation energy dissipation characteristics. These included measurements of steady-state absorption and fluorescence emission spectra for which correlation was tested with Stepanov relation. Comparison of fluorescence excitation and absorptance spectra determined that efficiency of energy transfer from β-carotene to chlorophyll a is 39 %. Time-resolved fluorescence images of pCP43-bound Chl a were recorded on streak camera, and fluorescence decay dynamics were evaluated with global fitting. These demonstrated that the decay kinetics strongly depends on temperature and buffer used to disperse the protein sample and fluorescence decay lifetime was estimated in 3.2–5.7 ns time range, depending on conditions. The pCP43 complex was also investigated with femtosecond and nanosecond time-resolved absorption spectroscopy upon excitation of Chl a and β-carotene to reveal pathways of singlet excitation relaxation/decay, Chl a triplet dynamics and Chl a → β-carotene triplet state sensitization process. The latter demonstrated that Chl a triplet in the pCP43 complex is not efficiently quenched by carotenoids. Finally, detailed kinetic analysis of the rise of the population of β-carotene triplets determined that the time constant of the carotenoid triplet sensitization is 40 ns.

59 BASIC BIOLOGICAL SCIENCES↗

One-shot holography

Following the work of [J. High Energy Phys. 04, 062 (2021)], we define a generally covariant max-entanglement wedge of a boundary region B, which we conjecture to be the bulk region reconstructible from B. We similarly define a covariant min-entanglement wedge, which we conjecture to be the bulk region that can influence the state on B. We prove that the min- and max-entanglement wedges obey various properties necessary for this conjecture, such as nesting, inclusion of the causal wedge, and a reduction to the usual quantum extremal surface prescription in the appropriate special cases. These proofs rely on one-shot versions of the (restricted) quantum focusing conjecture (QFC) that we conjecture to hold. We argue that these QFCs imply a one-shot generalized second law (GSL) and quantum Bousso bound. Moreover, in a particular semiclassical limit we prove this one-shot GSL directly using algebraic techniques. Finally, in order to derive our results, we extend both the frameworks of one-shot quantum Shannon theory and state-specific reconstruction to finite-dimensional von Neumann algebras, allowing nontrivial centers.

Akers, Chris (ORCID:0000000227929827)↗

SZ3: A Modular Framework for Composing Prediction-Based Error-Bounded Lossy Compressors

Today's scientific simulations require a significant reduction of data volume because of extremely large amounts of data they produce and the limited I/O bandwidth and storage space. Here, error-bounded lossy compression has been considered one of the most effective solutions to the above problem. In practice, however, the best-fit compression method often needs to be customized or optimized in particular because of diverse characteristics in different datasets and various user requirements on the compression quality and performance. In this paper, we address this issue with a novel modular, composable compression framework named SZ3. Our contributions are four-folds. (1) We develop SZ3 which features an innovative modular abstraction for the prediction-based compression framework, such that compression modules can be plugged in easily to create new compressors based on characteristics of data and user requirements. (2) We create a new compression pipeline by SZ3 for GAMESS data, which significantly improves the compression ratios over state-of-the-art compressors. (3) We develop an adaptive compression pipeline by SZ3 for APS data with minimal efforts, which leads to the best rate-distortion among all existing error-bounded lossy compressors for any bit-rate. (4) We compare the sustainability of SZ3 with leading error-bounded prediction-based compressors, and then demonstrate the necessity of diverse pipelines by integrating and evaluating several compression pipelines on diverse scientific datasets from multiple disciplines. Experiments show that SZ3 incurs very limited overhead in compressor integration and our customized compression pipelines lead to up to 20% improvement in compression ratios under the same data distortion, when compared with the best existing approach.

97 MATHEMATICS AND COMPUTING↗