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- ItemAccounting for variability in a teacher’s epistemology: Resources and framing(2018-05-31) Lau, Matty; Elby, Andrew
- ItemAdenylyl cyclase mRNA localizes to the posterior of polarized DICTYOSTELIUM cells during chemotaxis(Springer Nature, 2017-05-25) Das, Satarupa; Parker, Joshua M.; Guven, Can; Wang, Weiye; Kriebel, Paul W.; Losert, Wolfgang; Larson, Daniel R.; Parent, Carole A.In Dictyostelium discoideum, vesicular transport of the adenylyl cyclase A (ACA) to the posterior of polarized cells is essential to relay exogenous 3′,5′-cyclic adenosine monophosphate (cAMP) signals during chemotaxis and for the collective migration of cells in head-to-tail arrangements called streams. Using fluorescence in situ hybridization (FISH), we discovered that the ACA mRNA is asymmetrically distributed at the posterior of polarized cells. Using both standard estimators and Monte Carlo simulation methods, we found that the ACA mRNA enrichment depends on the position of the cell within a stream, with the posterior localization of ACA mRNA being strongest for cells at the end of a stream. By monitoring the recovery of ACA-YFP after cycloheximide (CHX) treatment, we observed that ACA mRNA and newly synthesized ACA-YFP first emerge as fluorescent punctae that later accumulate to the posterior of cells. We also found that the ACA mRNA localization requires 3′ ACA cis-acting elements. Together, our findings suggest that the asymmetric distribution of ACA mRNA allows the local translation and accumulation of ACA protein at the posterior of cells. These data represent a novel functional role for localized translation in the relay of chemotactic signal during chemotaxis.
- ItemArguing about argument and evidence: Disagreements and ambiguities in science education research and practice(2022) Tang, Xiaowei; Levin, Daniel; Chumbley, Alexander; Elby, AndrewScience education researchers agree about the importance of evidence in science practices such as argumentation. Yet, disagreements and ambiguities about what counts as “evidence” in science classrooms pervade the literature. We argue that these ambiguities and disagreements can be viewed as falling along three fault lines: (i) the source of evidence, specifically, whether it must be first-hand; (ii) whether “evidence” must always be empirical; and (iii) the extent to which evidence is inferred, and what degree of inference transforms “evidence” into something else. In this paper, after showing how these three fault lines manifest in the literature, we argue that these three dimensions of disagreements and ambiguities are not confined to research and research-based curricula; they are also salient in teachers’ classroom practice, as illustrated by a dramatic, multi-day debate between a mentor teacher and her teacher intern. After establishing the salience of the three fault lines in both research and practice, we explore whether NGSS can provide a resolution to the teachers’ debate and to the disagreements/ambiguities in the literature. Our analysis reveals that NGSS reproduces rather than resolves those three fault lines—but in doing so, it invites a resolution of a different type. Instead of providing a single, precise, context-independent definition of “evidence,” NGSS implicitly reflects a defensible view that what counts as “evidence” depends on the epistemic aims of the practices in which the students are engaged. This implied context-dependency of what counts as good evidence use, we argue, could be made explicit in an addendum document clarifying aspects of NGSS. Doing so would provide valuable guidance to teachers, teacher educators, and researchers.
- ItemBeyond triplet: Unconventional superconductivity in a spin-3/2 topological semimetal(American Association for the Advancement of Science, 2018-04-06) Kim, Hyunsoo; Wang, Kefeng; Nakajima, Yasuyuki; Hu, Rongwei; Ziemak, Steven; Syers, Paul; Wang, Limin; Hodovanets, Halyna; Denlinger, Jonathan D.; Brydon, Philip M. R.; Agterberg, Daniel F.; Tanatar, Makariy A.; Prozorov, Ruslan; Paglione, JohnpierreIn all known fermionic superfluids, Cooper pairs are composed of spin-1/2 quasi-particles that pair to form either spin-singlet or spin-triplet bound states. The “spin” of a Bloch electron, however, is fixed by the symmetries of the crystal and the atomic orbitals from which it is derived and, in some cases, can behave as if it were a spin-3/2 particle. The superconducting state of such a system allows pairing beyond spin-triplet, with higher spin quasi-particles combining to form quintet or septet pairs. We report evidence of unconventional superconductivity emerging from a spin-3/2 quasi-particle electronic structure in the half-Heusler semimetal YPtBi, a low-carrier density noncentrosymmetric cubic material with a high symmetry that preserves the p-like j = 3/2 manifold in the Bi-based Γ8 band in the presence of strong spin-orbit coupling. With a striking linear temperature dependence of the London penetration depth, the existence of line nodes in the superconducting order parameter Δ is directly explained by a mixed-parity Cooper pairing model with high total angular momentum, consistent with a high-spin fermionic superfluid state. We propose a k ⋅ p model of the j = 3/2 fermions to explain how a dominant J = 3 septet pairing state is the simplest solution that naturally produces nodes in the mixed even-odd parity gap. Together with the underlying topologically nontrivial band structure, the unconventional pairing in this system represents a truly novel form of superfluidity that has strong potential for leading the development of a new series of topological superconductors.
- ItemCharged pion form factor between Q2=0.60 and 2.45 GeV2. II. Determination of, and results for, the pion form factor(2008-10) Huber, G.M.; Blok, H.P.; Horn, T.; Beise, E.J.; Gaskell, D.; Mack, D.J.; Tadevosyan, V.; Volmer, J.; Abbott, D.; Aniol, K.; Anklin, H.; Armstrong, C.; Arrington, J.; Assamagan, K.; Avery, S.; Baker, O.K.; Barrett, B.; Bochna, C.; Boeglin, W.; Brash, E.J.; Breuer, H.; Chang, C.C.; Chant, N.; Christy, M.E.; Dunne, J.; Eden, T.; Ent, R.; Fenker, H.; Gibson, E.F.; Gilman, R.; Gustafsson, K.; Hinton, W.; Holt, J.; Jackson, H.; Jin, S.; Jones, M.K.; Keppel, C.E.; Kim, P.H.; Kim, W.; King, P.M.; Klein, A.; Koltenuk, D.; Kovaltchouk, V.; Liang, M.; Liu, J.; Lolos, G.J.; Lung, A.; Margaziotis, D.J.; Markowitz, P.; Matsumura, A.; McKee, D.; Meekins, D.; Mitchell, J.; Miyoshi, T.; Mkrtchyan, H.; Mueller, B.; Niculescu, G.; Niculescu, I.; Okayasu, Y.; Pentchev, L.; Perdrisat, C.; Pitz, D.; Potterveld, D.; Punjabi, V.; Qin, L.M.; Reimer, P.E.; Reinhold, J.; Roche, J.; Roos, P.G.; Sarty, A.; Shin, I.K.; Smith, G.R.; Stepanyan, S.; Tang, L.G.; Tvaskis, V.; van der Meer, R.L.J.; Vansyoc, K.; VanWestrum, D.; Vidakovic, S.; Vulcan, W.; Warren, G.; Wood, S.A.; Xu, C.; Yan, C.; Zhao, W.-X.; Zheng, X.; Zihlmann, B.; The Jefferson Lab Fπ CollaborationThe charged pion form factor, Fπ(Q2), is an important quantity that can be used to advance our knowledge of hadronic structure. However, the extraction of Fπ from data requires a model of the 1H(e,e'π+)n reaction and thus is inherently model dependent. Therefore, a detailed description of the extraction of the charged pion form factor from electroproduction data obtained recently at Jefferson Lab is presented, with particular focus given to the dominant uncertainties in this procedure. Results for Fπ are presented for Q2=0.60-2.45 GeV2. Above Q2=1.5 GeV2, the Fπ values are systematically below the monopole parametrization that describes the low Q2 data used to determine the pion charge radius. The pion form factor can be calculated in a wide variety of theoretical approaches, and the experimental results are compared to a number of calculations. This comparison is helpful in understanding the role of soft versus hard contributions to hadronic structure in the intermediate Q2 regime.
- ItemCoherent π0 photoproduction on the deuteron up to 4 GeV(1999-09) Meekins, D.G.; Abbott, D.J.; Ahmidouch, A.; Armstrong, C.S.; Arrington, J.; Assamagan, K.A.; Baker, O.K.; Barrow, S.P.; Beatty, D.P.; Beck, D.H.; Beedoe, S.Y.; Beise, E.J.; Belz, J.E.; Bochna, C.; Bosted, P.E.; Brash, E.J.; Breuer, H.; Cadman, R.V.; Cardman, L.; Carlini, R.D.; Cha, J.; Chant, N.S.; Collins, G.; Cothran, C.; Cummings, W.J.; Danagoulian, S.; Duncan, F.A.; Dunne, J.A.; Dutta, D.; Eden, T.; Ent, R.; Filippone, B.W.; Forest, T.A.; Fortune, H.T.; Frolov, V.V.; Gao, H.; Geesaman, D.F.; Gilman, R.; Gueye, P.L.J.; Gustafsson, K.K.; Hansen, J.-O.; Harvey, M.; Hinton, W.; Holt, R.J.; Jackson, H.E.; Keppel, C.E.; Khandaker, M.A.; Kinney, E.R.; Klein, A.; Koltenuk, D.M.; Kumbartzki, G.; Lung, A.F.; Mack, D.J.; Madey, R.; Markowitz, P.; McFarlane, K.W.; McKeown, R.D.; Meziani, Z.-E.; Miller, M.A.; Mitchell, J.H.; Mkrtchyan, H.G.; Mohring, R.M.; Napolitano, J.; Nathan, A.M.; Niculescu, G.; Niculescu, I.; O'Neill, T.G.; Owen, B.R.; Pate, S.F.; Potterveld, D.H.; Price, J.W.; Rakness, G.L.; Ransome, D.; Reinhold, J.; Rutt, P.M; Salgado, C.W.; Savage, G.; Segel, R.E.; Simicevic, N.; Stoler, P.; Suleiman, R.; Tang, L.; Terburg, B.P.; van Westrum, D.; Vulcan, W.F.; Williamson, S.E.; Witkowski, M.T.; Wood, S.A.; Yan, C.; Zeidman, B.The differential cross section for 2H(γ,d)π0 has been measured at deuteron center-of-mass angles of 90° and 136°. This work reports the first data for this reaction above a photon energy of 1 GeV, and permits a test of the apparent constituent counting rule and reduced nuclear amplitude behavior as observed in elastic ed scattering. Measurements were performed up to a photon energy of 4.0 GeV, and are in good agreement with previous lower energy measurements. Overall, the data are inconsistent with both constituent-counting rule and reduced nuclear amplitude predictions.
- ItemCollective phenomena in granular and atmospheric electrification(2015-07-29) Nordsiek, Freja; Lathrop, DanielThis repository contains data from the Granular Electrification Experiment in the University of Maryland Nonlinear Dynamics Lab. The experiment consists of a cylindrical cell with aluminum plates on the top and bottom. The cell is filled with granular particles and shaken vertically for several cycles. The vertical position of the cell and the electric potential between the top and bottom endplates of the cell are acquired. The data in this repository is from experiments in which the cylindrical cell is filled with only one type of particle. One exception uses two types of particles, pointed out below. A particle type is comprised of its material, form (spheres or powder), and size range. The acceleration timeseries of the shaking is approximately a square wave with amplitude a, meaning that the vertical position is approximately a sequence of parabolas of alternating concavity. The stroke-length of the oscillation is 10.0 cm. The shaking strength is quantified as a/g where g is the free fall acceleration due to gravity on Earth. The amount of particles is quantified by the dimensionless parameter lambda = 2 N_p d^2 / (3 D^2) where N_p is the number of particles, d is the particle diameter (or effective diameter), and D is the diameter of the cell.
- ItemConnecting self-efficacy and views about the nature of science in undergraduate research experiences(American Physical Society, 2016-11-21) Quan, Gina M.; Elby, AndrewUndergraduate research can support students’ more central participation in physics. We analyze markers of two coupled shifts in participation: changes in students’ views about the nature of science coupled to shifts in self-efficacy toward physics research. Students in the study worked with faculty and graduate student mentors on research projects while also participating in a seminar where they learned about research and reflected on their experiences. In classroom discussions and in clinical interviews, students described gaining more nuanced views about the nature of science, specifically related to who can participate in research and what participation in research looks like. This shift was coupled to gains in self-efficacy toward their ability to contribute to research; they felt like their contributions as novices mattered. We present two case studies of students who experienced coupled shifts in self-efficacy and views about nature-of-science shifts, and a case study of a student for whom we did not see either shift, to illustrate both the existence of the coupling and the different ways it can play out. After making the case that this coupling occurs, we discuss some potential underlying mechanisms. Finally, we use these results to argue for more nuanced interpretations of self-efficacy measurements.
- ItemCorrelation between scale-invariant normal-state resistivity and superconductivity in an electron-doped cuprate(AAAS, 2019-05-17) Sarkar, Tarapada; Mandal, P. R.; Poniatowski, N. R.; Chan, M. K.; Greene, Richard L.An understanding of the normal state in the high-temperature superconducting cuprates is crucial to the ultimate understanding of the long-standing problem of the origin of the superconductivity itself. This so-called “strange metal” state is thought to be associated with a quantum critical point (QCP) hidden beneath the superconductivity. In electron-doped cuprates—in contrast to hole-doped cuprates—it is possible to access the normal state at very low temperatures and low magnetic fields to study this putative QCP and to probe the T ➔ 0 K state of these materials. We report measurements of the low-temperature normal-state magnetoresistance (MR) of the n-type cuprate system La2−xCexCuO4 and find that it is characterized by a linear-in-field behavior, which follows a scaling relation with applied field and temperature, for doping (x) above the putative QCP (x = 0.14). The magnitude of the unconventional linear MR decreases as Tc decreases and goes to zero at the end of the superconducting dome (x ~ 0.175) above which a conventional quadratic MR is found. These results show that there is a strong correlation between the quantum critical excitations of the strange metal state and the high-Tc superconductivity.
- ItemCrenshaw transcripts 2023(0023-08-24) Crenshaw, Kenyatta; Elby, Andrew
- ItemCross section measurements of charged pion photoproduction in hydrogen and deuterium from 1.1 to 5.5 GeV(2005-04) Zhu, L.Y.; Arrington, J.; Averett, T.; Beise, E.; Calarco, J.; Chang, T.; Chen, J.P.; Chudakov, E.; Coman, M.; Clasie, B.; Crawford, C.; Dieterich, S.; Dohrmann, F.; Dutta, D.; Fissum, K.; Frullani, S.; Gao, H.; Gilman, R.; Glashausser, C.; Gomez, J.; Hafidi, K.; Hansen, O.; Higinbotham, D.W.; Holt, R.J.; de Jager, C.W.; Jiang, X.; Kinney, E.; Kramer, K.; Kumbartzki, G.; LeRose, J.; Liyanage, N.; Mack, D.; Markowitz, P.; McCormick, K.; Meekins, D.; Meziani, Z.-E.; Michaels, R.; Mitchell, J.; Nanda, S.; Potterveld, D.; Ransome, R.; Reimer, P.E.; Reitz, B.; Saha, A.; Schulte, E.C.; Seely, J.; Sirca, S.; Strauch, S.; Sulkosky, V.; Vlahovic, B.; Weinstein, L.B.; Wijesooriya, K.; Williamson, C.; Wojtsekhowski, B.; Xiang, H.; Xiong, F.; Xu, W.; Zeng, J.; Zheng, X.; Jefferson Lab Hall A Collaboration; Jefferson Lab E94-104 CollaborationThe differential cross sections for the γn→π-p and the γp→π+n processes were measured at Jefferson Lab. The photon energies ranged from 1.1 to 5.5 GeV, corresponding to center-of-mass energies from 1.7 to 3.4 GeV. The pion center-of-mass angles varied from 50° to 110°. The π- and π+ photoproduction data both exhibit a global scaling behavior at high energies and high transverse momenta, consistent with the constituent counting rule prediction and the existing π+ data. The data suggest possible substructure of the scaling behavior, which might be oscillations around the scaling value. The data show an enhancement in the scaled cross section at center-of-mass energy near 2.2 GeV. The differential cross section ratios [dσ/dt(γn→π-p)/dσ/dt(γp→π+n)] at high energies and high transverse momenta can be described by calculations based on one-hard-gluon-exchange diagrams.
- ItemCross-Section Measurement of Charged-Pion Photoproduction from Hydrogen and Deuterium(American Physical Society, 2003-06-11) Zhu, L.Y.; Arrington, J.; Averett, T.; Beise, E.; Calarco, J.; Chang, T.; Chen, J.P.; Chudakov, E.; Coman, M.; Clasie, B.; Crawford, C.; Dieterich, S.; Dohrmann, F.; Dutta, D.; Fissum, K.; Frullani, S.; Gao, H.; Gilman, R.; Glashausser, C.; Gomez, J.; Hafidi, K.; Hansen, J.-O.; Higinbotham, D.W.; Holt, R.J.; de Jager, C.W.; Jiang, X.; Kinney, E.; Kramer, K.; Kumbartzki, G.; LeRose, J.; Liyanage, N.; Mack, D.; Markowitz, P.; McCormick, K.; Meekins, D.; Meziani, Z.-E.; Michaels, R.; Mitchell, J.; Nanda, S.; Potterveld, D.; Ransome, R.; Reimer, P.E.; Reitz, B.; Saha, A.; Schulte, E.C.; Seely, J.; Sirca, S.; Strauch, S.; Sulkosky, V.; Vlahovic, B.; Weinstein, L.B.; Wijesooriya, K.; Williamson, C.F.; Wojtsekhowski, B.; Xiang, H.; Xiong, F.; Xu, W.; Zeng, J.; Zheng, X.; Jefferson Lab Hall A ColloborationWe have measured the differential cross section for the γn→π-p and γp→π+n reactions at θc.m.=90° in the photon energy range from 1.1 to 5.5 GeV at Jefferson Lab (JLab). The data at Eγ≳3.3 GeV exhibit a global scaling behavior for both π- and π+ photoproduction, consistent with the constituent counting rule and the existing π+ photoproduction data. Possible oscillations around the scaling value are suggested by these new data. The data show enhancement in the scaled cross section at a center-of-mass energy near 2.2 GeV. The cross section ratio of exclusive π- to π+ photoproduction at high energy is consistent with the prediction based on one-hard-gluon-exchange diagrams.
- ItemData for "A tug of war between filament treadmilling and myosin induced contractility generates actin ring"(2022-06-23) Ni, Qin; Wagh, Kaustubh; Pathni, Aashli; Ni, Haoran; Vashisht, Vishavdeep; Upadhyaya, Arpita; Papoian, Garegin A.; Upadhyaya, Arpita; Papoian, Garegin A.In most eukaryotic cells, actin filaments assemble into a shell-like actin cortex under the plasma membrane, controlling cellular morphology, mechanics, and signaling. The actin cortex is highly polymorphic, adopting diverse forms such as the ring-like structures found in podosomes, axonal rings, and immune synapses. The biophysical principles that underlie the formation of actin rings and cortices remain unknown. Using a molecular simulation platform, called MEDYAN, we discovered that varying the filament treadmilling rate and myosin concentration induces a finite size phase transition in actomyosin network structures. We found that actomyosin networks condense into clusters at low treadmilling rates or high myosin concentration but form ring-like or cortex-like structures at high treadmilling rates and low myosin concentration. This mechanism is supported by our corroborating experiments on live T cells, which exhibit ring-like actin networks upon activation by stimulatory antibody. Upon disruption of filament treadmilling or enhancement of myosin activity, the pre-existing actin rings are disrupted into actin clusters or collapse towards the network center respectively. Our analyses suggest that the ring-like actin structure is a preferred state of low mechanical energy, which is, importantly, only reachable at sufficiently high treadmilling rates.
- ItemData for "Membrane-MEDYAN: Simulating Deformable Vesicles Containing Complex Cytoskeletal Networks"(2021) Ni, Haoran; Papoian, Garegin A.; Papoian, Garegin A.The plasma membrane defines the shape of the cell and plays an indispensable role in bridging intra- and extra-cellular environments. Mechanochemical interactions between plasma membrane and cytoskeleton are vital for cell biomechanics and mechanosensing. A computational model that comprehensively captures the complex, cell-scale cytoskeleton-membrane dynamics is still lacking. In this work, we introduce a triangulated membrane model that accounts for membrane's elastic properties, as well as for membrane-filament steric interactions. The corresponding force-field was incorporated into the active biological matter simulation platform, MEDYAN ("Mechanochemical Dynamics of Active Networks"). Simulations using the new model shed light on how actin filament bundling affects generation of tubular membrane protrusions. In particular, we used membrane-MEDYAN simulations to investigate protrusion initiation and dynamics while varying geometries of filament bundles, membrane rigidities and local G-Actin concentrations. We found that bundles' protrusion propensities sensitively depend on the synergy between bundle thickness and inclination angle at which the bundle approaches the membrane. The new model paves the way for simulations of biological systems involving intricate membrane-cytoskeleton interactions, such as occurring at the leading edge and the cortex, eventually helping to uncover the fundamental principles underlying the active matter organization in the vicinity of the membrane.
- ItemData for "Quantifying Dissipation in Actomyosin Networks"(2019) Floyd, Carlos; Papoian, Garegin; Jarzynski, Christopher; Papoian, Garegin; Jaryzynski, ChristopherQuantifying entropy production in various active matter phases would open new avenues for probing self-organization principles in these far-from-equilibrium systems. It has been hypothesized that the dissipation of free energy by active matter systems may be optimized to produce highly dissipative dynamical states, hence, leading to spontaneous emergence of more ordered states. This interesting idea has not been widely tested. In particular, it is not clear whether emergent states of actomyosin networks, which represent one of the most salient examples of biological active matter, self-organize following the principle of dissipa- tion optimization. In order to start addressing this question using detailed computational modeling, we rely on the MEDYAN simulation platform, which allows simulating active matter networks from fundamental molecular principles. We have extended the capabilities of MEDYAN to allow quantification of the rates of dissipation resulting from chemical re- actions and relaxation of mechanical stresses during simulation trajectories. This is done by computing precise changes in Gibbs free energy accompanying chemical reactions using a novel formula, and through detailed calculations of instantaneous values of the system’s mechanical energy. We validate our approach with a mean-field model that estimates the rates of dissipation from filament treadmilling. Applying this methodology to the self- organization of small disordered actomyosin networks, we find that compact and highly cross-linked networks tend to allow more efficient transduction of chemical free energy into mechanical energy. In these simple systems, we do not observe that spontaneous network reorganizations lead to increases in the total dissipation rate as predicted by the dissipation- driven adaptation hypothesis mentioned above. However, whether such a principle operates in more general, more complex cytoskeletal networks remains to be investigated.
- ItemData for "Signaling through polymerization and degradation: Analysis and simulations of T cell activation mediated by Bcl10"(2021) Campanello, Leonard; Traver, Maria; Shroff, Hari; Schaefer, Brian; Losert, WolfgangThe adaptive immune system serves as a potent and highly specific defense mechanism against pathogen infection. One component of this system, the effector T cell, facilitates pathogen clearance upon detection of specific antigens by the T cell receptor (TCR). A critical process in effector T cell activation is transmission of signals from the TCR to a key transcriptional regulator, NF-κB. The transmission of this signal involves a highly dynamic process in which helical filaments of Bcl10, a key protein constituent of the TCR signaling cascade, undergo competing processes of polymeric assembly and macroautophagy-dependent degradation. Through computational analysis of three-dimensional, super-resolution optical micrographs, we quantitatively characterize TCR-stimulated Bcl10 filament assembly and length dynamics, and demonstrate that filaments become shorter over time. Additionally, we develop an image-based, bootstrap-like resampling method that demonstrates the preferred association between autophagosomes and both Bcl10-filament ends and punctate-Bcl10 structures, implying that autophagosome-driven macroautophagy is directly responsible for Bcl10 filament shortening. We probe Bcl10 polymerization-depolymerization dynamics with a stochastic Monte-Carlo simulation of nucleation-limited filament assembly and degradation, and we show that high probabilities of filament nucleation in response to TCR engagement could provide the observed robust, homogeneous, and tunable response dynamic. Furthermore, we demonstrate that the speed of filament disassembly preferentially at filament ends provides effective regulatory control. Taken together, these data suggest that Bcl10 filament growth and degradation act as an excitable system that provides a digital response mechanism and the reliable timing critical for T cell activation and regulatory processes.
- ItemData for the figures in the paper "Turbulence and Transport During Guide-Field Reconnection at the Magnetopause"(2019) Price, L; Swisdak, M; Drake, JF; Graham, DBWe analyze the development and influence of turbulence in three-dimensional particle-in-cell simulations of guide-field magnetic reconnection at the magnetopause with parameters based on observations of an electron diffusion region by the Magnetospheric Multiscale (MMS) mission. Along the separatrices the turbulence is a variant of the lower hybrid drift instability (LHDI) that produces electric field fluctuations with amplitudes much greater than the reconnection electric field. The turbulence controls the scale length of the density and current profiles while enabling significant transport across the magnetopause despite the electrons remaining frozen-in to the magnetic field. Near the X-line the electrons are not frozen-in and the turbulence, which differs from the LHDI, makes a significant net contribution to the generalized Ohm's law through an anomalous viscosity. The characteristics of the turbulence and associated particle transport are consistent with fluctuation amplitudes in the MMS observations. However, for this event the simulations suggest that the MMS spacecraft were not close enough to the core of the electron diffusion region to identify the region where anomalous viscosity is important.
- ItemData for: Understanding cytoskeletal avalanches using mechanical stability analysis(2021-08) Floyd, Carlos; Levine, Herbert; Jarzynski, Christopher; Papoian, Garegin A.Eukaryotic cells are mechanically supported by a polymer network called the cytoskeleton, which consumes chemical energy to dynamically remodel its structure. Recent experiments \textit{in vivo} have revealed that this remodeling occasionally happens through anomalously large displacements, reminiscent of earthquakes or avalanches. These cytoskeletal avalanches might indicate that the cytoskeleton's structural response to a changing cellular environment is highly sensitive, and they are therefore of significant biological interest. However, the physics underlying ``cytoquakes'' is poorly understood. Here, we use agent-based simulations of cytoskeletal self-organization to study fluctuations in the network's mechanical energy. We robustly observe non-Gaussian statistics and asymmetrically large rates of energy release compared to accumulation in a minimal cytoskeletal model. The large events of energy release are found to correlate with large, collective displacements of the cytoskeletal filaments. We also find that the changes in the localization of tension and the projections of the network motion onto the vibrational normal modes are asymmetrically distributed for energy release and accumulation. These results imply an avalanche-like process of slow energy storage punctuated by fast, large events of energy release involving a collective network rearrangement. We further show that mechanical instability precedes cytoquake occurrence through a machine learning model that dynamically forecasts cytoquakes using the vibrational spectrum as input. Our results provide the first connection between the cytoquake phenomenon and the network's mechanical energy and can help guide future investigations of the cytoskeleton's structural susceptibility.
- ItemData from: Inferring single cell behavior from large-scale epithelial sheet migration patterns(2017) Lee, Rachel M.; Yue, Haicen; Rappel, Wouter-Jan; Losert, WolfgangCell migration plays an important role in a wide variety of biological processes and can incorporate both individual cell motion and collective behavior. The emergent properties of collective migration are receiving increasing attention as collective motion’s role in diseases such as metastatic cancer becomes clear. Yet, how individual cell behavior influences large-scale, multi-cell collective motion remains unclear. In our study, we provided insight into the mechanisms behind collective migration by studying cell migration in a spreading monolayer of epithelial MCF10A cells. We quantify migration using particle image velocimetry and find that cell groups have features of motion that span multiple length scales. Comparing our experimental results to a model of collective cell migration, we find that cell migration within the monolayer can be affected in qualitatively different ways by cell motion at the boundary, yet it is not necessary to introduce leader cells at the boundary or specify other large-scale features to recapitulate this large-scale phenotype in simulations. Instead, in our model, collective motion can be enhanced by increasing the overall activity of the cells or by giving the cells a stronger coupling between their motion and polarity. This suggests that investigating the activity and polarity persistence of individual cells will add insight into the collective migration phenotypes observed during development and disease. This dataset provides microscopy images and analysis to support the article in the Journal of the Royal Society Interface (doi 10.1098/rsif.2017.0147) describing these migration behaviors.
- ItemDataset for work presented in "Perfect Absorption in Complex Scattering Systems with or without Hidden Symmetries"(2020) Chen, Lei; Anlage, StevenDataset supports: Chen, L. et al (2020). "Perfect Absorption in Complex Scattering Systems with or without Hidden Symmetries,” Nature Communications.