1403 Publications

On the stability of tidal streams in action space

A. Arora, R. Sanderson, N. Panithanpaisal, A. Wetzel, N. Garavito-Camargo, E. Cunningham

In the Gaia era it is increasingly apparent that traditional static, parameterized models are insufficient to describe the mass distribution of our complex, dynamically evolving Milky Way (MW). In this work, we compare different time-evolving and time-independent representations of the gravitational potentials of simulated MW-mass galaxies from the FIRE-2 suite of cosmological baryonic simulations. Using these potentials, we calculate actions for star particles in tidal streams around three galaxies with varying merger histories at each snapshot from 7 Gyr ago to the present day. We determine the action-space coherence preserved by each model using the Kullback-Leibler Divergence to gauge the degree of clustering in actions and the relative stability of the clusters over time. We find that all models produce a clustered action space for simulations with no significant mergers. However, a massive (mass ratio prior to infall more similar than 1:8) interacting galaxy not present in the model will result in mischaracterized orbits for stars most affected by the interaction. The locations of the action space clusters (i.e. the orbits of the stream stars) are only preserved by the time-evolving model, while the time-independent models can lose significant amounts of information as soon as 0.5--1 Gyr ago, even if the system does not undergo a significant merger. Our results imply that reverse-integration of stream orbits in the MW using a fixed potential is likely to give incorrect results if integrated longer than 0.5 Gyr into the past.

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July 27, 2022

Tuning a coiled-coil hydrogel via computational design of supramolecular fiber assembly

D. Britton, M. Meleties, D. Renfrew, et al.

The previously reported Q is a thermoresponsive coiled-coil protein capable of higher-order supramolecular assembly into fibers and hydrogels with upper critical solution temperature (UCST) behavior. Here, we introduce a new coiled-coil protein that is redesigned to disfavor lateral growth of its fibers and thus achieve a higher crosslinking density within the formed hydrogel. We also introduce a favorable hydrophobic mutation to the pore of the coiled-coil domain for increased thermostability of the protein. We note that an increase in storage modulus of the hydrogel and crosslinking density is coupled with a decrease in fiber diameter. We further fully characterize our α-helical coiled-coil (Q2) hydrogel for its structure, nano-assembly, and rheology relative to our previous single domain protein, Q, over the time of its gelation demonstrating the nature of our hydrogel self-assembly system. In this vein, we also characterize the ability of Q2 to encapsulate the small hydrophobic small molecule, curcumin, and its impact on the mechanical properties of Q2. The design parameters here not only show the importance of electrostatic potential in self-assembly but also provide a step towards predictable design of electrostatic protein interactions.

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Multiple phase spirals suggest multiple origins in Gaia DR3

J. Hunt, A. Price-Whelan, K. Johnston, E. Darragh-Ford

Gaia Data Release 2 revealed that the Milky Way contains significant indications of departures from equilibrium in the form of asymmetric features in the phase space density of stars in the Solar neighbourhood. One such feature is the z–vz phase spiral, interpreted as the response of the disc to the influence of a perturbation perpendicular to the disc plane, which could be external (e.g. a satellite) or internal (e.g. the bar or spiral arms). In this work, we use Gaia Data Release 3 to dissect the phase spiral by dividing the local data set into groups with similar azimuthal actions, Jϕ, and conjugate angles, θϕ, which selects stars on similar orbits and at similar orbital phases, thus having experienced similar perturbations in the past. These divisions allow us to explore areas of the Galactic disc larger than the surveyed region. The separation improves the clarity of the z–vz phase spiral and exposes changes to its morphology across the different action-angle groups. In particular, we discover a transition to two armed ‘breathing spirals’ in the inner Milky Way. We conclude that the local data contain signatures of not one, but multiple perturbations with the prospect to use their distinct properties to infer the properties of the interactions that caused them.

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Canary in the cardiac-valve coal mine: Flow velocity and inferred shear during prosthetic valve closure –predictors of blood damage and clotting

Lawrence N. Scotten, E. Kolahdouz

To demonstrate a clear link between predicted blood shear forces during valve closure and thrombogenicity that explains the thrombogenic difference between tissue and mechanical valves and provides a practical metric to develop and refine prosthetic valve designs for reduced thrombogenicity.

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Data-driven Derivation of Stellar Properties from Photometric Time Series Data Using Convolutional Neural Networks

K. Blancato, M. Ness, D. Huber, Y. (Lucy) Lu, R. Angus

Stellar variability is driven by a multitude of internal physical processes that depend on fundamental stellar properties. These properties are our bridge to reconciling stellar observations with stellar physics and to understand the distribution of stellar populations within the context of galaxy formation. Numerous ongoing and upcoming missions are charting brightness fluctuations of stars over time, which encode information about physical processes such as the rotation period, evolutionary state (such as effective temperature and surface gravity), and mass (via asteroseismic parameters). Here, we explore how well we can predict these stellar properties, across different evolutionary states, using only photometric time-series data. To do this, we implement a convolutional neural network, and with data-driven modeling we predict stellar properties from light curves of various baselines and cadences. Based on a single quarter of Kepler data, we recover the stellar properties, including the surface gravity for red giant stars (with an uncertainty of ≲0.06 dex) and rotation period for main-sequence stars (with an uncertainty of ≲5.2 days, and unbiased from ≈5 to 40 days). Shortening the Kepler data to a 27 days Transiting Exoplanet Survey Satellite–like baseline, we recover the stellar properties with a small decrease in precision, ∼0.07 for log g and ∼5.5 days for Prot, unbiased from ≈5 to 35 days. Our flexible data-driven approach leverages the full information content of the data, requires minimal or no feature engineering, and can be generalized to other surveys and data sets. This has the potential to provide stellar property estimates for many millions of stars in current and future surveys.

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Independently paced Ca2+ oscillations in progenitor and differentiated cells in an ex vivo epithelial organ

Ann A. Kim, Amanda Nguyen, X. Du, et al.

Cytosolic Ca2+ is a highly dynamic, tightly regulated and broadly conserved cellular signal. Ca2+ dynamics have been studied widely in cellular monocultures, yet organs in vivo comprise heterogeneous populations of stem and differentiated cells. Here, we examine Ca2+ dynamics in the adult Drosophila intestine, a self-renewing epithelial organ in which stem cells continuously produce daughters that differentiate into either enteroendocrine cells or enterocytes. Live imaging of whole organs ex vivo reveals that stem-cell daughters adopt strikingly distinct patterns of Ca2+ oscillations after differentiation: enteroendocrine cells exhibit single-cell Ca2+ oscillations, whereas enterocytes exhibit rhythmic, long-range Ca2+ waves. These multicellular waves do not propagate through immature progenitors (stem cells and enteroblasts), of which the oscillation frequency is approximately half that of enteroendocrine cells. Organ-scale inhibition of gap junctions eliminates Ca2+ oscillations in all cell types – even, intriguingly, in progenitor and enteroendocrine cells that are surrounded only by enterocytes. Our findings establish that cells adopt fate-specific modes of Ca2+ dynamics as they terminally differentiate and reveal that the oscillatory dynamics of different cell types in a single, coherent epithelium are paced independently.

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Electric Field Screening in Pair Discharges and Generation of Pulsar Radio Emission

E. Tolman, A. A. Philippov, A. N. Timokhin

Pulsar radio emission may be generated in pair discharges that fill the pulsar magnetosphere with plasma as an accelerating electric field is screened by freshly created pairs. In this Letter, we develop a simplified analytic theory for the screening of the electric field in these pair discharges and use it to estimate total radio luminosity and spectrum. The discharge has three stages. First, the electric field is screened for the first time and starts to oscillate. Next, a nonlinear phase occurs. In this phase, the amplitude of the electric field experiences strong damping because the field dramatically changes the momenta of newly created pairs. This strong damping ceases, and the system enters a final linear phase, when the electric field can no longer dramatically change pair momenta. Applied to pulsars, this theory may explain several aspects of radio emission, including the observed luminosity, Lrad ∼ 1028 erg s−1, and the observed spectrum, Sω ∼ ω−1.4±1.0.

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Active Microphase Separation in Mixtures of Microtubules and Tip-Accumulating Molecular Motors

Bezia Lemma , Noah P. Mitchell, D. Needleman, et al.

Mixtures of filaments and molecular motors form active materials with diverse dynamical behaviors that vary based on their constituents’ molecular properties. To develop a multiscale of these materials, we map the nonequilibrium phase diagram of microtubules and tip-accumulating kinesin-4 molecular motors. We find that kinesin-4 can drive either global contractions or turbulent like extensile dynamics, depending on the concentrations of both microtubules and a bundling agent. We also observe a range of spatially heterogeneous nonequilibrium phases, including finite-sized radial asters, 1D wormlike chains, extended 2D bilayers, and system-spanning 3D active foams. Finally, we describe intricate kinetic pathways that yield microphase-separated structures and arise from the inherent frustration between the orientational order of filamentous microtubules and the positional order of tip-accumulating molecular motors. Our work reveals a range of novel active states. It also shows that the form of active stresses is not solely dictated by the properties of individual motors and filaments, but is also contingent on the constituent concentrations and spatial arrangement of motors on the filaments.

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A sequence-based global map of regulatory activity for deciphering human genetics

Kathleen Chen, A. Wong, O. Troyanskaya, Jian Zhou

Epigenomic profiling has enabled large-scale identification of regulatory elements, yet we still lack a systematic mapping from any sequence or variant to regulatory activities. We address this challenge with Sei, a framework for integrating human genetics data with sequence information to discover the regulatory basis of traits and diseases. Sei learns a vocabulary of regulatory activities, called sequence classes, using a deep learning model that predicts 21,907 chromatin profiles across >1,300 cell lines and tissues. Sequence classes provide a global classification and quantification of sequence and variant effects based on diverse regulatory activities, such as cell type-specific enhancer functions. These predictions are supported by tissue-specific expression, expression quantitative trait loci and evolutionary constraint data. Furthermore, sequence classes enable characterization of the tissue-specific, regulatory architecture of complex traits and generate mechanistic hypotheses for individual regulatory pathogenic mutations. We provide Sei as a resource to elucidate the regulatory basis of human health and disease.

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Weakly nonlinear analysis of pattern formation in active suspensions

Laurel Ohm, M. Shelley

We consider the Saintillan--Shelley kinetic model of active rodlike particles in Stokes flow (Saintillan & Shelley 2008a,b), for which the uniform, isotropic suspension of pusher particles is known to be unstable in certain settings. Through weakly nonlinear analysis accompanied by numerical simulations, we determine exactly how the isotropic steady state loses stability in different parameter regimes. We study each of the various types of bifurcations admitted by the system, including both subcritical and supercritical Hopf and pitchfork bifurcations. Elucidating this system's behavior near these bifurcations provides a theoretical means of comparing this model with other physical systems which transition to turbulence, and makes predictions about the nature of bifurcations in active suspensions that can be explored experimentally.

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