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Item Data from: Supercooling of the A phase of 3HeTian, Yefan; Lotnyk, Dmytro; Eyal, Anna; Zhang, Kuang; Zhelev, Nikolay; Abhilash, T.S.; Chavez, Aldo; Smith, Eric N.; Hindermarsh, Mark; Saunders, John; Mueller, Erich; Parpia, Jeevak M. (2022-12-08)These files contain data along with associated output from instrumentation supporting all results reported in Tien, et al, 2022, Supercooling of the A phase of 3He. In Tien, et al, 2022 we found: Because of the extreme purity, lack of disorder, and complex order parameter, the first-order superfluid 3He A-B transition is the leading model system for first order transitions in the early universe. Here we report on the path dependence of the supercooling of the A phase over a wide range of pressures below 29.3 bar at nearly zero magnetic field. The A phase can be cooled significantly below the thermodynamic A-B transition temperature. While the extent of supercooling is highly reproducible, it depends strongly upon the cooling trajectory: The metastability of the A phase is enhanced by transiting through regions where the A phase is more stable. We provide evidence that some of the additional supercooling is due to the elimination of B phase nucleation precursors formed upon passage through the superfluid transition. A greater understanding of the physics is essential before 3He can be exploited to model transitions in the early universe.Item Data from: STRAINS: A Big Data Method for Classifying Cellular Response to Stimuli at the Tissue ScaleZheng, Jingyang; Jackson, Thomas Wyse; Fortier, Lisa; Bonassar, Lawrence; Delco, Michelle; Cohen, Itai (2022)These files contain data supporting all results reported in Zheng et. al., STRAINS: A Big Data Method for Classifying Cellular Response to Stimuli at the Tissue Scale. Cellular response to stimulation governs tissue scale processes ranging from growth and development to maintaining tissue health and initiating disease. To determine how cells coordinate their response to such stimuli, it is necessary to simultaneously track and measure the spatiotemporal distribution of their behaviors throughout the tissue. Here, we report on a novel SpatioTemporal Response Analysis IN Situ (STRAINS) tool that uses fluorescent micrographs, cell tracking, and machine learning to measure such behavioral distributions. STRAINS is broadly applicable to any tissue where fluorescence can be used to indicate changes in cell behavior. For illustration, we use STRAINS to simultaneously analyze the mechanotransduction response of 5000 chondrocytes---over 20 million data points---in cartilage during the 50 ms to 4 hours after the tissue was subjected to local mechanical injury, known to initiate osteoarthritis. We find that chondrocytes exhibit a range of mechanobiological responses indicating activation of distinct biochemical pathways with clear spatial patterns related to the induced local strains during impact. These results illustrate the power of this approach.Item Code from: STRAINS: A Big Data Method for Classifying Cellular Response to Stimuli at the Tissue ScaleZheng, Jingyang; Wyse Jackson, Thomas; Fortier, Lisa; Bonassar, Lawrence; Delco, Michelle; Cohen, Itai (2022-08-06)These files contain data supporting all results reported in Zheng et. al., STRAINS: A Big Data Method for Classifying Cellular Response to Stimuli at the Tissue Scale. Cellular response to stimulation governs tissue scale processes ranging from growth and development to maintaining tissue health and initiating disease. To determine how cells coordinate their response to such stimuli, it is necessary to simultaneously track and measure the spatiotemporal distribution of their behaviors throughout the tissue. Here, we report on a novel SpatioTemporal Response Analysis IN Situ (STRAINS) tool that uses fluorescent micrographs, cell tracking, and machine learning to measure such behavioral distributions. STRAINS is broadly applicable to any tissue where fluorescence can be used to indicate changes in cell behavior. For illustration, we use STRAINS to simultaneously analyze the mechanotransduction response of 5000 chondrocytes---over 20 million data points---in cartilage during the 50 ms to 4 hours after the tissue was subjected to local mechanical injury, known to initiate osteoarthritis. We find that chondrocytes exhibit a range of mechanobiological responses indicating activation of distinct biochemical pathways with clear spatial patterns related to the induced local strains during impact. These results illustrate the power of this approach.Item Data for: Neuromuscular embodiment of feedback control elements in Drosophila flightWhitehead, Samuel C.; Leone, Sofia; Lindsay, Theodore; Meiselman, Matthew R.; Cowan, Noah; Dickinson, Michael; Yapici, Nilay; Stern, David L.; Shirangi, Troy; Cohen, Itai (2022)These files contain data and code supporting all results reported in "Neuromuscular embodiment of feedback control elements in Drosophila flight" by Whitehead, et al. The abstract for that article is as follows: While insects like Drosophila are flying, aerodynamic instabilities require that they make millisecond-timescale adjustments to their wing motion to stay aloft and on course. These stabilization reflexes can be modeled as a proportional-integral (PI) controller; however, it is unclear how such control might be instantiated in insects at the level of muscles and neurons. Here, we show that the b1 and b2 motor units—prominent components of the fly’s steering muscles system—modulate specific elements of the PI controller: the angular displacement (integral, I) and angular velocity (proportional, P), respectively. Moreover, these effects are observed only during the stabilization of pitch. Our results provide evidence for an organizational principle in which each muscle contributes to a specific functional role in flight control, a finding that highlights the power of using top-down behavioral modeling to guide bottom-up cellular manipulation studies.Item Data from: Structural Origins of Cartilage Shear MechanicsWyse Jackson, Thomas; Michel, Jonathan; Lwin, Pancy; Fortier, Lisa A.; Das, Moumita; Bonassar, Lawrence J.; Cohen, Itai (2022-02-22)These files contain data supporting all results reported in Wyse Jackson et. al. . In Wyse Jackson et al., we found: Articular cartilage is a remarkable material able to sustain millions of loading cycles over decades of use outperforming any synthetic substitute. Crucially, how extracellular matrix constituents alter mechanical performance, particularly in shear, remains poorly understood. Here, we present experiments and theory in support of a rigidity percolation framework that quantitatively describes the structural origins of cartilage’s shear properties and how they arise from the mechanical interdependence of the collagen and aggrecan networks making up its extracellular matrix. This framework explains that near the cartilage surface, where the collagen network is sparse and close to the rigidity threshold, slight changes in either collagen or aggrecan concentrations, common in early stages of cartilage disease, create a marked weakening in modulus that can lead to tissue collapse. More broadly, this framework provides a map for understanding how changes in composition throughout the tissue alter its shear properties and ultimate in vivo function.Item Nanoscale Magnetization and Current Imaging Using Time-Resolved Scanning-Probe Magnetothermal MicroscopyZhang, Chi; Bartell, Jason M.; Karsch, Jonathan C.; Gray, Isaiah; Fuchs, Gregory D. (Nano Letters, 2021-06-08)Magnetic microscopy that combines nanoscale spatial resolution with picosecond scale temporal resolution uniquely enables direct observation of the spatiotemporal magnetic phenomena that are relevant to future high-speed, high-density magnetic storage and logic technologies. Magnetic microscopes that combine these metrics has been limited to facility-level instruments. To address this gap in lab-accessible spatiotemporal imaging, we develop a time-resolved near-field magnetic microscope based on magnetothermal interactions. We demonstrate both magnetization and current density imaging modalities, each with spatial resolution that far surpasses the optical diffraction limit. In addition, we study the near-field and time-resolved characteristics of our signal and find that our instrument possesses a spatial resolution on the scale of 100 nm and a temporal resolution below 100 ps. Our results demonstrate an accessible and comparatively low-cost approach to nanoscale spatiotemporal magnetic microscopy in a table-top form to aid the science and technology of dynamic magnetic devices with complex spin textures.Item Data from: Thermal transport of helium-3 in a strongly confining channelLotnyk, Dmytro; Eyal, Anna; Zhelev, Nikolay; Sebastian, Abhilash; Smith, Eric; Terilli, Michael; Wilson, John; Mueller, Erich; Einzel, Dietrich; Saunders, John; Parpia, Jeevak (2020-09-24)The investigation of transport properties in normal liquid helium-3 and its topological superfluid phases provides insights into related phenomena in electron fluids, topological materials, and putative topological superconductors. It relies on the measurement of mass, heat, and spin currents, due to system neutrality. Of particular interest is transport in strongly confining channels of height approaching the superfluid coherence length, to enhance the relative contribution of surface excitations, and suppress hydrodynamic counter-flow. Here we report on the thermal conduction of helium-3 in a 1.1 um high channel. The experiment was carried out by locally heating one chamber and by measuring the flow of energy out of that chamber. Figure 2) In the normal state (Figures 3, 4 and Supplemental Figures 6, 7) we observe a diffusive thermal conductivity that is approximately temperature independent, consistent with interference of bulk and boundary scattering. In the superfluid, the thermal conductivity is only weakly temperature dependent (Figure 5), requiring detailed theoretical analysis. An anomalous thermal response is detected in the superfluid (Figures 6, 7 and Supplemental Figures 2, 3, 4) which we propose arises from the emission of a flux of surface excitations from the channel. Supplemental Figure 1 summarizes calculations that show that the anomalous heat transport cannot arise from normal-superfluid counterflow. In this package we provide the data set was used to plot the figures so that digitization is not needed and the data may be used for comparison in future works.Item The A-B transition in superfluid 3He under confinement in a thin slab geometryZhelev, Nikolay; Abhilash, Thanniyil Sebastian; Smith, Eric; Bennett, Robert; Rojas, Xavier; Levitin, Lev; Saunders, John; Parpia, Jeevak (2017)The influence of confinement on the topological phases of superfluid 3He is studied using the torsional pendulum method. We focus on the phase transition between the chiral A-phase and the time-reversal-invariant B-phase, motivated by the prediction of a spatially-modulated (stripe) phase at the A-B phase boundary. We confine superfluid 3He to a single 1.08 μm thick nanofluidic cavity incorporated into a high-precision torsion pendulum, and study the pressure dependence of the phase diagram between 0.1 and 5.6 bar. We observe only small supercooling of the A-phase, in comparison to bulk or when confined in aerogel. This has a non-monotonic pressure dependence, suggesting that a new intrinsic B-phase nucleation mechanism operates under confinement, mediated by the putative stripe phase. Both the pressure dependence of the phase diagram and the relative superfluid fraction of the A and B phases, show that strong coupling is present at all pressures, with implications for the stability of the stripe phase.Item Temperature Dependence of Wavelength Selectable Zero-Phonon Emission from Single Defects in Hexagonal Boron NitrideJungwirth, Nicholas R.; Calderon, Brian; Ji, Yanxin; Spencer, Michael G.; Flatté, Michael E.; Fuchs, Gregory D. (Nano Letters, 2016-08-31)We investigate the distribution and temperature-dependent optical properties of sharp, zero-phonon emission from defect-based single photon sources in multilayer hexagonal boron nitride (h-BN) flakes. We observe sharp emission lines from optically active defects distributed across an energy range that exceeds 500 meV. Spectrally-resolved photon-correlation measurements verify single photon emission, even when multiple emission lines are simultaneously excited within the same h-BN flake. We also present a detailed study of the temperature-dependent linewidth, spectral energy shift, and intensity for two different zero-phonon lines centered at 575 nm and 682 nm, which reveals a nearly identical temperature dependence despite a large difference in transition energy. Our temperature-dependent results are well described by a lattice vibration model that considers piezoelectric coupling to in-plane phonons. Finally, polarization spectroscopy measurements suggest that whereas the 575 nm emission line is directly excited by 532 nm excitation, the 682 nm line is excited indirectly.Item The A-B transition in superfluid 3He under confinement in a thin slab geometryZhelev, Nikolay; Sebastian, Abhilash; Smith, Eric; Bennett, Robert; Rojas, Xavier; Levitin, Lev; Saunders, John; Parpia, Jeevak (2016)The influence of confinement on the topological phases of superfluid 3He is studied using the torsional pendulum method. We focus on the phase transition between the chiral A-phase and the time-reversal-invariant B-phase, motivated by the prediction of a spatially-modulated (stripe) phase at the A-B phase boundary. We confine superfluid 3He to a single 1.08 μm thick nanofluidic cavity incorporated into a high-precision torsion pendulum, and study the pressure dependence of the phase diagram between 0.1 and 5.6 bar. We observe only small supercooling of the A-phase, in comparison to bulk or when confined in aerogel. This has a non-monotonic pressure dependence, suggesting that a new intrinsic B-phase nucleation mechanism operates under confinement, mediated by the putative stripe phase. Both the pressure dependence of the phase diagram and the relative superfluid fraction of the A and B phases, show that strong coupling is present at all pressures, with implications for the stability of the stripe phase.Item Polarization Spectroscopy of Defect-Based Single Photon Sources in ZnOJungwirth, Nicholas R; Chang, Hung-Shen; Jiang, Mingde; Fuchs, Gregory D (ACS Nano, 2015-11-26)Point defects in wide bandgap semiconductors are promising candidates for future applications that necessitate quantum light sources. Recently, defect-based single photon sources have been observed in ZnO that are very bright and remain photoactive from 4.5 K to room temperature. Despite several investigations, the structure and electronic states of these emitters remain unknown. In this work, we establish a procedure to distinguish a Z dipole from an XY dipole when studying quantum emitters that are randomly oriented. Our cryogenic and room temperature polarization measurements collectively establish that these unidentified ZnO quantum emitters have a Z dipole. We show that the associated absorption and emission dipoles are parallel within experimental uncertainty for all 32 individuals studied. Additionally, we apply group theory and find that, assuming the defect symmetry belongs to a point group relevant to the ZnO wurtzite lattice, the ground and excited states are orbital singlets. These results are a significant step in identifying the structure and electronic states of defect-based single photon sources in ZnO.Item Observation of a new superfluid phase for ³He embedded in nematically ordered aerogelZhelev, Nikolay; Reichl, Matthew; Abhilash, Thanniyil Sebastian; Smith, Eric Nelson; Nguyen, Kayla X.-T.; Meuller, Erich J.; Parpia, Jeevak M. (2016)In bulk superfluid 3He at zero magnetic field, two phases emerge with the B phase stable everywhere except at high pressures and temperatures where the A phase is favored. Aerogels with nanostructure smaller than the superfluid coherence length are the only means to introduce disorder into the superfluid. Here we use a torsion pendulum to study 3He confined in an extremely anisotropic, nematically ordered aerogel consisting of roughly 10 nm thick alumina strands, spaced by about 100 nm, and aligned parallel to the pendulum axis. Kinks in the development of the superfluid fraction (at various pressures) as the temperature is varied correspond to phase transitions. Two such transitions are seen in the superfluid state, and we identify the superfluid phase closest to Tc at low pressure as the Polar state, a phase that is not seen in bulk 3He.Item Quantifying radiation damage in biomolecular small-angle X-ray scatteringHopkins, Jesse B; Thorne, Robert E (International Union of Crystallography, 2016-06)Small-angle X-ray scattering (SAXS) is an increasingly popular technique that provides low-resolution structural information about biological macromolecules in solution. Many of the practical limitations of the technique, such as minimum required sample volume, and of experimental design, such as sample flow cells, are necessary because the biological samples are sensitive to damage from the X-rays. Radiation damage typically manifests as aggregation of the sample, which makes the collected data unreliable. However, there has been little systematic investigation of the most effective methods to reduce damage rates, and results from previous damage studies are not easily compared with results from other beamlines. Here a methodology is provided for quantifying radiation damage in SAXS to provide consistent results between different experiments, experimenters and beamlines. These methods are demonstrated on radiation damage data collected from lysozyme, glucose isomerase and xylanase, and it is found that no single metric is sufficient to describe radiation damage in SAXS for all samples. The radius of gyration, molecular weight and integrated SAXS profile intensity constitute a minimal set of parameters that capture all types of observed behavior. Radiation sensitivities derived from these parameters show a large protein dependence, varying by up to six orders of magnitude between the different proteins tested. This work should enable consistent reporting of radiation damage effects, allowing more systematic studies of the most effective minimization strategies.Item Data from: Quantifying radiation damage in biomolecular small-angle X-ray scatteringHopkins, Jesse B; Thorne, Robert E (2016)Item Dissipation signatures of the normal and superfluid phases in torsion pendulum experiments with ³He in aerogelZhelev, Nikolay Z.; Bennett, Robert G.; Smith, Eric N.; Pollanen, Johannes; Halperin, William P.; Parpia, Jeevak M. (Physical Review B, 2014-03-13)We present data for the energy dissipation factor Q⁻¹ over a broad temperature range at various pressures of a torsion pendulum setup used to study ³He confined in a 98% open silica aerogel. Values for Q⁻¹ above Tc are temperature independent and have weak pressure dependence. Below Tc, a deliberate axial compression of the aerogel by 10% widens the range of metastability for a superfluid equal spin pairing (ESP) state; we observe this ESP phase on cooling and the B phase on warming over an extended temperature region. While the dissipation for the B phase tends to zero as T → 0, Q⁻¹ exhibits a peak value greater than that at Tc at intermediate temperatures. Values for Q⁻¹ in the ESP phase are consistently higher than in the B phase and are proportional to the superfluid fraction until the ESP to B phase transition is attained. We apply a viscoelastic collision-drag model, which couples the motion of the helium and the aerogel through a frictional relaxation time. We conclude that unless the frictional relaxation time is an order of magnitude larger than expected, an additional mechanism to dissipate energy not captured in the collision-drag model and related to the emergence of the superfluid order must exist. The extra dissipation below Tc is possibly associated with mutual friction between the superfluid phases and the clamped normal fluid. The pressure dependence of the measured dissipation in both superfluid phases is likely related to the pressure dependence of the gap structure of the "dirty" superfluid. The large dissipation in the ESP state is consistent with the phase being the A or the Polar with the order parameter nodes oriented in the plane of the cell and perpendicular to the aerogel anisotropy axis.Item A single-molecule approach to ZnO defect studies: Single photons and single defectsJungwirth, N. R.; Pai, Y. Y.; Chang, H. S.; MacQuarrie, E. R.; Nguyen, K. X.; Fuchs, G. D. (Figures published in: Journal of Applied Physics, 2014-08-26)Investigations that probe defects one at a time offer a unique opportunity to observe properties and dynamics that are washed out of ensemble measurements. Here we present confocal fluorescence measurements of individual defects in Al-doped ZnO nanoparticles and undoped ZnO sputtered films that are excited with sub-bandgap energy light. Photon correlation measurements yield both antibunching and bunching, indicative of single-photon emission from isolated defects that possess a metastable shelving state. The single-photon emission is in the range ~560 – 720 nm and typically exhibits two broad spectral peaks separated by ~150 meV. The excited state lifetimes range from 1 – 13 ns, consistent with the finite-size and surface effects of nanoparticles and small grains. We also observe discrete jumps in the fluorescence intensity between a bright state and a dark state. The dwell times in each state are exponentially distributed and the average dwell time in the bright (dark) state does (may) depend on the power of the exciting laser. Taken together, our measurements demonstrate the utility of a single-molecule approach to semiconductor defect studies and highlight ZnO as a potential host material for single-defect based applications.Item Data for "A microfabricated fixed path length silicon sample holder improves background subtraction for cryoSAXS"Hopkins, Jesse B.; Katz, Andrea M.; Meisburger, Steve P.; Warkentin, Matthew A.; Thorne, Robert E.; Pollack, Lois (Journal of Applied Crystallography, 2015-02)The application of small-angle X-ray scattering (SAXS) for high-throughput characterization of biological macromolecules in solution is limited by radiation damage. By cryocooling samples, radiation damage and required sample volumes can be reduced by orders of magnitude. However, the challenges of reproducibly creating the identically sized vitrified samples necessary for conventional background subtraction limit the widespread adoption of this method. Fixed path length silicon sample holders for cryoSAXS have been micro fabricated to address these challenges. They have low background scattering and X-ray absorption, require only 640 nl of sample, and allow reproducible sample cooling. Data collected in the sample holders from a nominal illuminated sample volume of 2.5 nl are reproducible down to q ’ 0.02 Å-1, agree with previous cryoSAXS work and are of sufficient quality for reconstructions that match measured crystal structures. These sample holders thus allow faster, more routine cryoSAXS data collection. Additional development is required to reduce sample fracturing and improve data quality at low q.