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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.
Highly efficient parallel grand canonical simulations of interstitial-driven diffusion-deformation processes
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Verification methods for drift–diffusion reaction models for plasma simulations
Abstract Compared to other computational physics areas such as codes for general computational fluid dynamics, the documentation of verification methods for plasma fluid codes remains under developed. Current analytical solutions for plasma are often highly limited in terms of testing highly coupled physics, due to the harsh assumptions needed to derive even simple plasma equations. This work highlights these limitations, suggesting the method of manufactured solutions (MMSs) as a potential option for future verification efforts. To demonstrate the flexibility of MMS in verifying these highly coupled systems, the Multiphysics Object-Oriented Simulation Environment (MOOSE) framework was utilized. Thanks to the MOOSE framework’s robustness and modularity, as well as to its physics module capabilities and ecosystem applications (i.e. Zapdos and the chemical reaction network) developed for plasma physics modeling and simulation, this report lays the groundwork for a structured method of conducting plasma fluid code verification.
Parameter inference and uncertainty quantification with diffusion models: extending CDI to 2D spatial conditioning
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Diffusive and ballistic transport in thin InSb nanowire devices using a few-layer-graphene-AlO x gate
Abstract Quantum devices based on InSb nanowires (NWs) are a prime candidate system for realizing and exploring topologically-protected quantum states and for electrically-controlled spin-based qubits. The influence of disorder on achieving reliable quantum transport regimes has been studied theoretically, highlighting the importance of optimizing both growth and nanofabrication. In this work, we consider both aspects. We developed InSb NW with thin diameters, as well as a novel gating approach, involving few-layer graphene and atomic layer deposition-grown AlO x . Low-temperature electronic transport measurements of these devices reveal conductance plateaus and Fabry–Pérot interference, evidencing phase-coherent transport in the regime of few quantum modes. The approaches developed in this work could help mitigate the role of material and fabrication-induced disorder in semiconductor-based quantum devices.
Laser Wavelength Dependence on Perovskite Interface Elemental Diffusion During Atom Probe Experiments
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Nature of the diffuse emission sources in the H i supershell in the galaxy IC 1613
ABSTRACT We present a study of the nearby low-metallicity dwarf galaxy IC 1613, focusing on the search for massive stars and related feedback processes, as well as for faint supernova remnants (SNR) in late stages of evolution. We obtained the deepest images of IC 1613 in the narrow-band H α, He ii and [S ii] emission lines and new long-slit spectroscopy observations using several facilities (6-m BTA, 2.5m SAI MSU, and 150RTT telescopes), in combination with the multiwavelength archival data from MUSE/VLT, VLA, XMM–Newton, and Swift/XRT. Our deep narrow-band photometry identifies several faint shells in the galaxy, and we further investigate their physical characteristics with the new long-slit spectroscopy observations and the archival multiwavelength data. Based on energy balance calculations and assumptions about their possible nature, we propose that one of the shells is a possible remnant of a supernova explosion. We study five out of eight Wolf–Rayet (WR) star candidates previously published for this galaxy using the He ii emission line mapping, MUSE/VLT archival spectra, and new long-slit spectra. Our analysis discards the considered WR candidates and finds no new ones. We found P Cyg profiles in H α line in two stars, which we classify as Luminous Blue Variable (LBV) star candidates. Overall, the galaxy IC 1613 may have a lower rate of WR star formation than previously suggested.
Radial oscillations of viscous neutron stars: Zero diffusion case
In this article, the spectrum of radial oscillations of neutron stars is systematically studied within two frameworks of viscous relativistic hydrodynamics: the relativistic Navier-Stokes and Israel-Stewart theories. A correspondence is established between the discrete stellar eigenmodes and the continuous dispersion relation of perturbations around a homogeneous fluid, providing a basis for interpreting our numerical results. We analyze the Newtonian limit and assess the impact of relativistic corrections, such as the gravitational redshifting of microscopic relaxation timescales. We show that bulk viscosity can significantly affect the behavior of both hydrodynamic and nonhydrodynamic fundamental modes, and that, depending on the magnitude of the viscous effects, it is the nonhydrodynamic mode that becomes unstable beyond the turning point in a sequence of equilibrium configurations. These results provide a useful step toward systematic studies of neutron star quasinormal modes in the presence of viscosity.
Diffusivity-Free Turbulence in Liquid Metal Rotating Rayleigh-Bénard Convection Experiments
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Field, frequency, and temperature dependencies of the surface resistance of nitrogen diffused niobium superconducting radio frequency cavities
We investigate the rf performance of several single-cell superconducting radio-frequency cavities subjected to low temperature heat treatment in nitrogen environment. The cavities were treated at temperature 120 – 165 ° C for an extended period of time (24–48 h) either in high vacuum or in a low partial pressure of ultrapure nitrogen. The improvement in Q 0 with a Q rise was observed when nitrogen gas was injected at ∼ 300 ° C during the cavity cooldown from 800 ° C and held at 165 ° C , without any degradation in accelerating gradient over the baseline performance. The treatment was applied to several elliptical cavities with frequency ranging from 0.75 to 3.0 GHz, showing an improved quality factor as a result of low temperature nitrogen treatments. The Q rise feature is similar to that achieved by nitrogen alloying Nb cavities at higher temperature, followed by material removal by electropolishing. The surface modification was confirmed by the change in electronic mean free path and tuned with the temperature and duration of heat treatment. The decrease of the temperature-dependent surface resistance with increasing rf field, resulting in a Q rise, becomes stronger with increasing frequency and decreasing temperature. The data suggest a crossover frequency of ∼ 0.95 GHz above that the Q rise phenomenon occurs at 2 K. Some of these results can be explained qualitatively with an existing model of intrinsic field-dependence of the surface resistance with both equilibrium and nonequilibrium quasiparticle distribution functions. The change in the Q slope below 0.95 GHz may result from masking contribution of trapped magnetic flux to the residual surface resistance. Published by the American Physical Society 2024
Electron diffusion in microbunched electron cooling
Coherent electron cooling is a novel method to cool dense hadron beams on timescales of a few hours. This method uses a copropagating beam of electrons to pick up the density fluctuations within the hadron beam in one straight section and then provides corrective energy kicks to the hadrons in a downstream straight, cooling the beam. Microbunched electron cooling is an extension of this idea, which induces a microbunching instability in the electron beam as it travels between the two straights, amplifying the signal. However, initial noise in the electron bunch will also be amplified, providing random kicks to the hadrons downstream which tend to increase their emittance. In this paper, we develop an analytic estimate of the effect of the electron noise and benchmark it against simulations. We also discuss how this effect has impacted the cooler design. Published by the American Physical Society 2024
Theory of magnon diffuse scattering in scanning transmission electron microscopy
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Frustration-induced diffusive scattering anomaly and dimension change in FeGe 2
Magnetic frustration, arising from the competition of exchange interactions, has received great attention because of its relevance to exotic quantum phenomena in materials. In the current work, we report an unusual checkerboard-shaped scattering anomaly in FeGe 2 , far from the known incommensurate magnetic satellite peaks, by inelastic neutron scattering. More surprisingly, such phenomenon appears as spin dynamics at low temperature, but it becomes prominent above Néel transition as elastic scattering. Here, a model Hamiltonian that includes an intraplane next-nearest neighbor was proposed and such anomaly is attributed to the near-perfect magnetic frustration and the emergence of unexpected two-dimensional magnetic order in the quasi-one-dimensional FeGe 2 .
Unveiling the impact of temperature on magnon diffuse scattering detection in the transmission electron microscope
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Energy diffusion in weakly interacting chains with fermionic dissipation assisted operator evolution
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