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Dense suspensions of pusher-type bacteria give rise to 'superfluids' in which the effective viscosity of the suspension is drastically reduced through collective motion, and in this study we investigate how a viscous environment affects this behavior.
Here, we present studies of Abrikosov vortex motion across the magnetically charged edges of long thin ferromagnetic stripes placed above or under a thin superconducting film. The magnetic charges at the stripe edges form attractive or repulsive potential wells for vortices. Using a relatively small in-plane magnetic field to polarize the stripe edges and normal-to-plane magnetic field to induce up or down polarized vortices, we tune the attractive or repulsive stripe-vortex interactions. Imaging of the vortex dynamics reveals that the repulsive magnetic potential U m + acts as a robust vortex pinning barrier, while the attractive U m - has practically no effect on the vortex motion irrespective of the position of the stripes located above or underneath the superconducting film. We analyze the observed asymmetry using equations of the overdamped vortex motion. The formal analytical solution yields an asymmetry, but the numerical modeling with and without noise terms does not confirm it. Instead, we find that the asymmetry is caused by the creation of spontaneous vortices at the maxima of U m , which depends on the edge polarity and suppress U m - . Furthermore, our experiment and time-dependent Ginzburg-Landau simulations demonstrate that magnetic pinning dominates over vortex pinning due to corrugations of the superconducting layer deposited on top of the ferromagnetic stripes.
With the rapid evolution of synchrotron x-ray sources, the demand for high-quality precision x-ray mirrors has greatly increased. Single nanometer shape accuracy is required to keep imaging capabilities at the diffraction limit. Ion beam figuring (IBF) has been used frequently for ultra-precision finishing of mirrors, but achieving the ultimate accuracy depends on three important points: careful alignment, accurate dwell time calculation and implementation, and accurate optical metrology. The Optical Metrology Group at National Synchrotron Light Source II has designed and built a position–velocity–time-modulated two-dimensional IBF system (PVT-IBF) with three novel characteristics: (1) a beam footprint on the mirror was used as a reference to align the coordinate systems between the metrology and the IBF hardware; (2) the robust iterative Fourier transform-based dwell time algorithm proposed by our group was applied to obtain an accurate dwell time map; and (3) the dwell time was then transformed to velocities and implemented with the PVT motion scheme. In this study, the technical aspects of the PVT-IBF systems are described in detail, followed by an experimental demonstration of the figuring results. In our first experiment, the 2D RMS in a 50mm×5mm clear aperture was reduced from 3.4 to 1.1 nm after one IBF run. In our second experiment, due to a 5 mm pinhole installed in front of the source, the 2D RMS in a 50mm×5mm clear aperture was reduced from 39.1 to 1.9 nm after three IBF runs, demonstrating that our PVT-IBF solution is an effective and deterministic figuring process.
ABSTRACT The Source Phenomenology Experiment (SPE-Arizona) included of a series of chemical explosions detonated within a copper mine in Arizona. This study focuses on ground motions from detonations in the copper mine, which are analyzed to assess the uniqueness of the resulting source representation when the source region propagation characteristics have a range of possible models. P-wave velocities are well constrained by refraction data with less constraint of the S-wave velocities. The effects of explosion source depth and VS are assessed with Green’s functions for a range of models in which VP is held constant. Propagation models with a Poisson’s value of 0.25 and a source depth 30–60 m most accurately replicate the data. The explosion was detonated at a centroid depth of 30 m, so trade-offs in depth are demonstrated. The compensated linear vector dipole and explosion components of the Green’s functions convolved with a Mueller–Murphy source function are compared. Both produce significant energy in the 2–12 Hz band, due to surface-wave contributions with no clear depth dependencies above 20 Hz. The range of propagation models is used with the observational data to invert for the frequency-domain moment tensor. Fits to the data from these inversions have cross-correlation values of 0.64, demonstrating effectiveness in replicating the observations with the assumed propagation path effects and resulting source function. Inversions produce horizontal dipoles (Mxx and Myy), roughly half the maximum amplitude of Mzz, consistent with a compensated linear vector dipole source, which is frequency dependent. Denny and Johnson, Mueller–Murphy, Walter and Ford, and the revised Mueller–Murphy source models, parameterized for granite, are compared to the moment tensors. Despite a nonisotropic moment tensor source, the revised Mueller–Murphy isotropic source model best replicates the long-period moments, overshoot, and corner frequency.
This dataset contains solid-state 1H and 13C NMR relaxometry data, differential scanning calorimetry (DSC) data, and size exclusion chromatography (SEC/GPC) data supporting the study of sub-glass-transition (sub-Tg) molecular dynamics in a composition- and sequence-controlled series of diphenyl-substituted polysiloxanes (PDMS, 14Ph, 33Ph, 50Ph, 67Ph, and 100Ph; 0–100% diphenylsiloxane content by mole).All solid-state NMR data were acquired on a 200 MHz Bruker Avance III HD spectrometer using a static 7 mm HX probe or a 4 mm HX probe under 4 kHz magic-angle spinning. Raw Bruker TopSpin experiment folders are included for: (1) variable-temperature 1H lineshape measurements used to determine linewidth (FWHM) as a function of temperature across the glass transition; (2) 1H T1 (saturation recovery with solid-echo detection), probing nanosecond-scale dynamics near the 1H Larmor frequency; (3) 1H T1rho (direct spin-lock, 62.5 kHz), probing microsecond-scale segmental dynamics; (4) 13C-detected Lee–Goldburg cross-polarization 1H T1rho (LGCPH T1rho) for 33Ph and 50Ph, resolving aromatic and aliphatic proton environments; and (5) 13C T1 relaxation for 33Ph and 50Ph. Differential scanning calorimetry data (TA Instruments DSC 25, −150 to +120 °C, up to +300 °C for 100Ph, 10 °C/min) are included for all six compositions and support the glass-transition temperatures in Table 1 and Figure 1. Size exclusion chromatography data (Agilent 1200 Series, PL-Gel 300 mixed-C column, THF mobile phase, polystyrene calibration standards) are included for the three synthesized copolymers (33Ph, 50Ph, 67Ph) and support the number-average molecular weights in Table 1. Processed data include per-composition relaxation-time summaries (Excel), curve-fitting and Bloembergen-Purcell-Pound (BPP) model analysis notebooks (Jupyter/Python), and Igor Pro (.pxp) master files used to generate the manuscript's figures.
Ultrasonic spot welding using different welding conditions was applied to join dissimilar metals of galvanized DP590 steel and AZ31B magnesium sheets. In situ high-speed imaging, digital image correlation, and infrared thermography were utilized to quantitatively study the interfacial relative motion, surface indentation, and heat generation across the joint faying interface and the sheet/sonotrode interfaces under the welding condition of moderate welding power and short welding time. For welds made with high power and long welding time, lap shear tensile tests as well as fatigue tests were carried out. Different fracture modes were observed after the lap shear tensile tests and fatigue tests performed under different peak loads. Post-weld cross-sectional analysis with scanning electron microscopy coupled with energy dispersive X-Ray spectroscopy revealed the variation of morphology and chemical composition at the joint interface for welds made with different welding conditions.
Most human body proteins' activity and functionality are related to configurational changes of entire subdomains within the protein crystal structure. The crystal structures build the basis for any calculation that describes the structure or dynamics of a protein, most of the time with strong geometrical restrictions. However, these restrictions from the crystal structure are not present in the solution. The structure of the proteins in the solution may differ from the crystal due to rearrangements of loops or subdomains on the pico to nanosecond time scale (i.e., the internal protein dynamics time regime). This study describes how slow motions on timescales of several tens of nanoseconds can be accessed using neutron scattering. In particular, the dynamical characterization of two major human proteins, an intrinsically disordered protein that lacks a well-defined secondary structure and a classical antibody protein, is addressed by neutron spin echo spectroscopy (NSE) combined with a wide range of laboratory characterization methods. Further insights into protein domain dynamics were achieved using mathematical modeling to describe the experimental neutron data and determine the crossover between combined diffusive and internal protein motions. The extraction of the internal dynamic contribution to the intermediate scattering function obtained from NSE, including the timescale of the various movements, allows further vision into the mechanical properties of single proteins and the softness of proteins in their nearly natural environment in the crowded protein solution.
Here, three-dimensional (3-D) nonlinear site response analyses are conducted using finite element models of actual soil profiles from ten nuclear power plant (NPP) sites in the United States to investigate the effects of soil properties and input motions on site amplification. The modeling approach developed in this study combines several novel elements, such as 3-D analysis (including vertical motions), nonlinear inelastic behavior of soil (strain-dependent shear modulus reduction and hysteretic damping), formulation of nonreflecting boundary conditions at the base, and generation of realistic outcrop ground motions for specific sites. All these elements of the modeling approach are first validated using actual data from five earthquakes at three downhole array stations recorded in the Kiban-Kyoshin network (KiK-net), Japan. The same approach is then used to develop site models of ten NPP sites in the United States and corresponding ground motions that are spectrally matched to the site hazard spectra. Eight sets of three-component input motions are used in the study and are categorized on the basis of presence or absence of a near-field pulse in the seed ground motions used for spectral matching. It is found that all sites retain a definite site amplification function regardless of the input motion, provided that the seed motion is spectrally matched to the site hazard spectra. The magnitude of site amplification and frequencies at which they occur depend upon soil properties, particularly the shear wave velocity profile and the constitutive relationship (strain-dependent shear modulus reduction and hysteretic damping) of soil. Amplification of spectral acceleration in the vertical direction (up-down motion) is found to be just as much as, if not more than, the amplification in the horizontal direction. Peak shear strain is found to be about 20% larger for near-field motions compared to far-field motions whereas maximum horizontal site amplification for far-field motions is found to be consistently larger than that of near-field motions, even though the differences between the two remain within the scatter resulting from individual ground motions.
Abstract Biomolecules undergo continuous conformational motions, a subset of which are functionally relevant. Understanding, and ultimately controlling biomolecular function are predicated on the ability to map continuous conformational motions, and identify the functionally relevant conformational trajectories. For equilibrium and near-equilibrium processes, function proceeds along minimum-energy pathways on one or more energy landscapes, because higher-energy conformations are only weakly occupied. With the growing interest in identifying functional trajectories, the need for reliable mapping of energy landscapes has become paramount. In response, various data-analytical tools for determining structural variability are emerging. A key question concerns the veracity with which each data-analytical tool can extract functionally relevant conformational trajectories from a collection of single-particle cryo-EM snapshots. Using synthetic data as an independently known ground truth, we benchmark the ability of four leading algorithms to determine biomolecular energy landscapes and identify the functionally relevant conformational paths on these landscapes. Such benchmarking is essential for systematic progress toward atomic-level movies of continuous biomolecular function.
Oceanic eddies accompanied by a significant vertical velocity ( w ) are known to be of great importance for the vertical transport of various climatically, biologically or biogeochemically relevant properties. Using quasi-geostrophic w -thinking to extend the classic “ β -spiral” w -theory for gyre circulations to isolated and nearly symmetric oceanic mesoscale eddies, we propose that their w motion will be dominated by a strong east-west dipole pattern with deep ocean penetrations. Contrasting numerical simulations of idealized isolated eddies together with w -equation diagnostics confirm that the w -dipole is indeed dominated by the “eddy β -spiral” mechanism in the β -plane simulation, whereas this w -dipole expectedly disappears in the f -plane simulation. Analyses of relatively isolated warm and cold eddy examples show good agreement with the proposed mechanism. Our studies further clarify eddy vertical motions, have implications for ocean mixing and vertical transport, and inspire further studies.
In this study, we examine the effects of the radiation reaction force on electrons in a radial magnetically insulated transmission line (MITL) near a load with peak currents of 60+ MA. More specifically, we study the differences in electron motion and kinetic energy with or without radiation reaction physics using a novel guiding center drift approach that incorporates E $\times$ B and ∇B drifts. A key finding of this study is that an electron's magnetic moment, which would be conserved when radiation reaction physics is not incorporated, can be significantly reduced in magnetic fields on the order of 10,000's T when radiation reaction is included. The reduction of magnetic moment gives rise to a significant reduction in cycloidal kinetic energy as well as a reduction in the electron's ∇B drift.
In this study, a computational fluid dynamics (CFD) model was developed to model the motion of a solid cold cap in a waste glass melter. Forced convection bubblers at the base of the melter release air into the molten glass, which forms large bubbles that travel upwards to the cold cap and augment heat transfer from the glass to the cold cap. The CFD model employs the Navier- Stokes equations to solve for the fluctuating flowfield using a rigid body motion dynamic fluid body interaction module. This allows for movement of the floating body in response to the bubbling forces calculated at each time step. Further, the heat flux delivered to the cold cap by the convective bubbling is studied as a function of the bubbling rate. Results for the moving cold cap are compared with the computed heat flux trends for a stationary cold cap. The heat flux delivered to the cold cap from the glass is 25% higher for the case with the moving cold cap. The heat flux was found to be proportional to v0.6 as opposed to v0.9 (where v is the normalized bubbling rate) for the stationary cold cap.
Ultrafast motion of molecules, particularly the coherent motion, has been intensively investigated as a key factor guiding the reaction pathways. Recently, X-ray free-electron lasers (XFELs) have been utilized to elucidate the ultrafast motion of molecules. However, the studies on proteins using XFELs have been typically limited to the crystalline phase, and proteins in solution have rarely been investigated. Here we applied femtosecond time-resolved X-ray solution scattering (fs-TRXSS) and a structure refinement method to visualize the ultrafast motion of a protein. We succeeded in revealing detailed ultrafast structural changes of homodimeric hemoglobin involving the coherent motion. In addition to the motion of the protein itself, the time-dependent change of electron density of the hydration shell was tracked. Besides, the analysis on the fs-TRXSS data of myoglobin allows for observing the effect of the oligomeric state on the ultrafast coherent motion.
Here, we develop an approximate, analytical model for the velocity of defects in active nematics by combining recent results for the velocity of topological defects in nematic liquid crystals with the flow field generated from individual defects in active nematics. Importantly, our model takes into account the long-range interactions between defects that result from the flows they produce as well as the orientational coupling between defects inherent in nematics. Our work complements previous studies of active nematic defect motion by introducing a linear approximation that allows us to treat defect interactions as two-body interactions and incorporates the hydrodynamic screening length as a tuning parameter. We show that the model can analytically predict bound states between two +1/2 winding number defects, effective attraction between two –1/2 defects, and the scaling of a critical unbinding length between ±1/2 defects with activity. The model also gives predictions for the trajectories of defects, such as the scattering of +1/2 defects by –1/2 defects at a critical impact parameter that depends on activity. In the presence of circular confinement, the model predicts a braiding motion for three +1/2 defects that was recently seen in experiments, as well as stable and ergodic trajectories for four or more defects.
Wildfire behavior is dictated by the complex interaction of numerous physical phenomena including dynamic ambient and fire-induced winds, heat transfer, aerodynamic drag on the wind by the fuel and combustion. These phenomena create complex feedback effects between the fire and its surroundings. In this study, we aim to study the mechanisms by which buoyant flame dynamics along with vortical motions and instabilities control wildfire propagation. Specifically, this study employs a suite of simulations conducted with the physics-based coupled fire-atmosphere behavior model (FIRETEC). The simulations are initialized with a fire line and the fires are allowed to propagate on a grass bed, where the fuel heights and wind conditions are varied systematically. Flow variables are extracted to identify the characteristics of the alternating counter-rotational vortices, called towers and troughs, that drive convective heat transfer and fire spread. These vortices have previously been observed in wildfires and laboratory fires, and have also been observed to arise spontaneously in FIRETEC due to the fundamental physics incorporated in the model. However, these past observations have been qualitative in nature and no quantitative studies can be found in the literature which connected these coherent structures fundamental to fire behavior with the constitutive flow variables. To that end, a variety of state variables are examined in the context of these coherent structures under various wind profile and grass height conditions. Identification of various correlated signatures and fire-atmosphere feedbacks in simulations provides a hypothesis that can be tested in future observational or experimental efforts, potentially assisting experimental design, and can aid in the interpretation of data from in situ detectors.
Excited state intramolecular proton transfer (ESIPT) is a fundamental chemical process with several applications. Ultrafast ESIPT involves coupled electronic and atomic motions and has been primarily studied using femtosecond optical spectroscopy. X-ray spectroscopy is particularly useful because it is element-specic and enables direct, individual probes of the proton donating and accepting atoms. Here, we report a computational study to resolve the ESIPT in 10-Hydroxybenzo[h]quinoline (HBQ), an intramolecularly hydrogen bonded compound, using time-dependent density functional theory combined with ab initio molecular dynamics (AIMD) and time-resolved X-ray absorption spectroscopy (XAS) computations to track the ultrafast excited-state dynamics. Overall, our results reveal clear X-ray spectral signatures of coupled electronic and atomic motions during and following ESIPT at the oxygen and nitrogen K-edge paving the way for future experiments at X-ray free electron lasers.
Earthquake-induced ground shaking near rupturing faults is highly sensitive to the rupture characteristics, seismic wave propagation patterns and site conditions, and field recordings of near-fault shaking are relatively sparse. These challenges complicate the assessment of the seismic performance of near-fault structures. A common approach to representing near-fault ground motion in engineering analysis is to explicitly consider and select records with strong directivity pulses (pulse records). We use three-dimensional high-resolution physics-based earthquake simulations to test this approach in the context of scenario-based ground motion record selection, and to study the important characteristics of near-fault ground shaking. We highlight the deficiencies associated with classifying near-fault simulated records as “pulse” or “non-pulse,” based on the presence of a single dominating pulse in the velocity time history. We show that this approach is inadequate for characterizing near-fault shaking on soft soils which can be dominated by both forward rupture directivity and basin amplification effects. We conduct ground motion selection experiments for the analysis of near-fault structures with and without explicit classification of the pulse features in the records, and evaluate the bias in the predicted structural demands. We find that the maximum interstory drift demands on building structures imposed by unscaled site-specific simulated ground motion records selected based on relevant spectral shape features are not sensitive to the classification of records as pulse/non-pulse. Therefore, with regard to predicting the maximum interstory drifts in near-fault buildings, we do not find justification for the binary pulse classification of near-fault records.
We study the many-body localization (MBL) transition for interacting fermions subject to quasiperiodic potentials by constructing the local integrals of motion (LIOMs) in the MBL phase as time-averaged local operators. Here, we study numerically how these time-averaged operators evolve across the MBL transition. We find that the norm of such time-averaged operators drops discontinuously to zero across the transition; as we discuss, this implies that LIOMs abruptly become unstable at some critical localization length of order unity. We analyze the LIOMs using hydrodynamic projections and isolating the part of the operator that is associated with interactions. Equipped with these data we perform a finite-size scaling analysis of the quasiperiodic MBL transition. Our results suggest that the quasiperiodic MBL transition occurs at considerably stronger quasiperiodic modulations and has a larger correlation-length critical exponent than previous studies had found.