Publications

A single flexible filament can be actuated to escape from the scallop theorem and generate net propulsion at low Reynolds number. In this work, we study the dynamics of a simple boundary-driven multi-filament swimmer, a two-arm clamshell actuated at the hinged point, using a nonlocal slender body approximation with full hydrodynamic interactions. We first consider an elastic clamshell consisted of flexible filaments with intrinsic curvature, and then build segmental models consisted of rigid segments connected by different mechanical joints with different forms of response torques. The simplicity of the system allows us to fully explore the effect of various parameters on the swimming performance. Optimal included angles and elastoviscous numbers are identified. The segmental models capture the characteristic dynamics of the elastic clamshell. We further demonstrate how the swimming performance can be significantly enhanced by the asymmetric beating patterns induced by biased torques.

It has long been known that FGF signaling contributes to mesoderm formation, a germ layer found in triploblasts that is composed of highly migratory cells that give rise to muscles and to the skeletal structures of vertebrates. FGF signaling activates several pathways in the developing mesoderm, including transient activation of the Erk pathway, which triggers mesodermal fate specification through the induction of the gene brachyury and activates morphogenetic programs that allow mesodermal cells to position themselves in the embryo. In this review, we discuss what is known about the generation and interpretation of transient Erk signaling in mesodermal tissues across species. We focus specifically on mechanisms that translate the level and duration of Erk signaling into cell fate and cell movement instructions and discuss strategies for further interrogating the role that Erk signaling dynamics play in mesodermal gastrulation and morphogenesis.

Cytoskeletal networks are the main actuators of cellular mechanics, and a foundational example for active matter physics. In cytoskeletal networks, motion is generated on small scales by filaments that push and pull on each other via molecular-scale motors. These local actuations give rise to large-scale stresses and motion. To understand how microscopic processes can give rise to self-organized behavior on larger scales it is important to consider what mechanisms mediate long-ranged mechanical interactions in the systems. Two scenarios have been considered in the recent literature. The first scenario is systems that are relatively sparse, in which most of the large-scale momentum transfer is mediated by the solvent in which cytoskeletal filaments are suspended. The second scenario is systems in which filaments are coupled via cross-link molecules throughout. Here, we review the differences and commonalities between the physics of these two regimes. We also survey the literature for the numbers that allow us to place a material within either of these two classes.

In this note, we analyze the classical magneto-static approach to the theory of type I superconductors, and a Debye source representation that can be used numerically to solve the resultant equations. We also prove that one of the fields, J−, found within the superconductor via the London equations, is the physical current in that the outgoing part of the magnetic field is given as the Biot-Savart integral of J−. Finally, we compute the static currents for moderate values of London penetration depth, λL, for a sphere, a stellarator-like geometry and a two-holed torus.

Neurons in primate visual cortex (area V1) are tuned for spatial frequency, in a manner that depends on their position in the visual field. Several studies have examined this dependency using fMRI, reporting preferred spatial frequencies (tuning curve peaks) of V1 voxels as a function of eccentricity, but their results differ by as much as two octaves, presumably due to differences in stimuli, measurements, and analysis methodology. Here, we characterize spatial frequency tuning at a millimeter resolution within human primary visual cortex, across stimulus orientation and visual field locations. We measured fMRI responses to a novel set of stimuli, constructed as sinusoidal gratings in log-polar coordinates, which include circular, radial, and spiral geometries. For each individual stimulus, the local spatial frequency varies inversely with eccentricity, and for any given location in the visual field, the full set of stimuli span a broad range of spatial frequencies and orientations. Over the measured range of eccentricities, the preferred spatial frequency is well-fit by a function that varies as the inverse of the eccentricity plus a small constant. We also find small but systematic effects of local stimulus orientation, defined in both absolute coordinates and relative to visual field location. Specifically, peak spatial frequency is higher for pinwheel than annular stimuli and for horizontal than vertical stimuli.

Subsurface convection zones are ubiquitous in early-type stars. Driven by narrow opacity peaks, these thin convective regions transport little heat but play an important role in setting the magnetic properties and surface variability of stars. Here we demonstrate that these convection zones are \emph{not} present in as wide a range of stars as previously believed. In particular, there are regions which 1D stellar evolution models report to be convectively unstable but which fall below the critical Rayleigh number for onset of convection. For sub-solar metallicity this opens up a \emph{stability window} in which there are no subsurface convection zones. For LMC metallicity this surface stability region extends roughly between 8M⊙ and 16M⊙, increasing to 8M⊙ -- 35M⊙ for SMC metallicity. Such windows are then an excellent target for probing the relative influence of subsurface convection and other sources of photometric variability in massive stars.

Autism is a highly heritable neurodevelopmental disorder characterized by heterogeneous cognitive, behavioral and communication impairments. Disruption of the gut-brain axis (GBA) has been implicated in autism, with dozens of cross-sectional microbiome and other omic studies revealing autism-specific profiles along the GBA albeit with little agreement in composition or magnitude. To explore the functional architecture of autism, we developed an age and sex-matched Bayesian differential ranking algorithm that identified autism-specific profiles across 10 cross-sectional microbiome datasets and 15 other omic datasets, including dietary patterns, metabolomics, cytokine profiles, and human brain expression profiles. The analysis uncovered a highly significant, functional architecture along the GBA that encapsulated the overall heterogeneity of autism phenotypes. This architecture was determined by autism-specific amino acid, carbohydrate and lipid metabolism profiles predominantly encoded by microbial species in the genera Prevotella, Enterococcus, Bifidobacterium, and Desulfovibrio, and was mirrored in brain-associated gene expression profiles and restrictive dietary patterns in individuals with autism. Pro-inflammatory cytokine profiling and virome association analysis further supported the existence of an autism-specific architecture associated with particular microbial genera. Re-analysis of a longitudinal intervention study in autism recapitulated the cross-sectional profiles, and showed a strong association between temporal changes in microbiome composition and autism symptoms. Further elucidation of the functional architecture of autism, including of the role the microbiome plays in it, will require deep, multi-omic longitudinal intervention studies on well-defined stratified cohorts to support causal and mechanistic inference.

Autism is a highly heritable neurodevelopmental disorder characterized by heterogeneous cognitive, behavioral and communication impairments. Disruption of the gut-brain axis (GBA) has been implicated in autism, with dozens of cross-sectional microbiome and other omic studies revealing autism-specific profiles along the GBA albeit with little agreement in composition or magnitude. To explore the functional architecture of autism, we developed an age and sex-matched Bayesian differential ranking algorithm that identified autism-specific profiles across 10 cross-sectional microbiome datasets and 15 other omic datasets, including dietary patterns, metabolomics, cytokine profiles, and human brain expression profiles. The analysis uncovered a highly significant, functional architecture along the GBA that encapsulated the overall heterogeneity of autism phenotypes. This architecture was determined by autism-specific amino acid, carbohydrate and lipid metabolism profiles predominantly encoded by microbial species in the genera Prevotella, Enterococcus, Bifidobacterium, and Desulfovibrio, and was mirrored in brain-associated gene expression profiles and restrictive dietary patterns in individuals with autism. Pro-inflammatory cytokine profiling and virome association analysis further supported the existence of an autism-specific architecture associated with particular microbial genera. Re-analysis of a longitudinal intervention study in autism recapitulated the cross-sectional profiles, and showed a strong association between temporal changes in microbiome composition and autism symptoms. Further elucidation of the functional architecture of autism, including of the role the microbiome plays in it, will require deep, multi-omic longitudinal intervention studies on well-defined stratified cohorts to support causal and mechanistic inference.

Identification of chemically similar stars using elemental abundances is core to many pursuits within Galactic archeology. However, measuring the chemical likeness of stars using abundances directly is limited by systematic imprints of imperfect synthetic spectra in abundance derivation. We present a novel data-driven model that is capable of identifying chemically similar stars from spectra alone. We call this relevant scaled component analysis (RSCA). RSCA finds a mapping from stellar spectra to a representation that optimizes recovery of known open clusters. By design, RSCA amplifies factors of chemical abundance variation and minimizes those of nonchemical parameters, such as instrument systematics. The resultant representation of stellar spectra can therefore be used for precise measurements of chemical similarity between stars. We validate RSCA using 185 cluster stars in 22 open clusters in the Apache Point Observatory Galactic Evolution Experiment survey. We quantify our performance in measuring chemical similarity using a reference set of 151,145 field stars. We find that our representation identifies known stellar siblings more effectively than stellar-abundance measurements. Using RSCA, 1.8% of pairs of field stars are as similar as birth siblings, compared to 2.3% when using stellar-abundance labels. We find that almost all of the information within spectra leveraged by RSCA fits into a two-dimensional basis, which we link to [Fe/H] and α-element abundances. We conclude that chemical tagging of stars to their birth clusters remains prohibitive. However, using the spectra has noticeable gain, and our approach is poised to benefit from larger data sets and improved algorithm designs.

Tuning the step size of stochastic gradient descent is tedious and error prone. This has motivated the development of methods that automatically adapt the step size using readily available information. In this paper, we consider the family of SPS (Stochastic gradient with a Polyak Stepsize) adaptive methods. These are methods that make use of gradient and loss value at the sampled points to adaptively adjust the step size. We first show that SPS and its recent variants can all be seen as extensions of the Passive-Aggressive methods applied to nonlinear problems. We use this insight to develop new variants of the SPS method that are better suited to nonlinear models. Our new variants are based on introducing a slack variable into the interpolation equations. This single slack variable tracks the loss function across iterations and is used in setting a stable step size. We provide extensive numerical results supporting our new methods and a convergence theory.