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Electromagnetic precursor flares from the late inspiral of neutron star binaries
No full textThe coalescence of two neutron stars is accompanied by the emission of gravitational waves, and can also feature electromagnetic counterparts powered by mass ejecta and the formation of a relativistic jet after the merger. Since neutron stars can feature strong magnetic fields, the non-trivial interaction of the neutron star magnetospheres might fuel potentially powerful electromagnetic transients prior to merger. A key process powering those precursor transients is relativistic reconnection in strong current sheets formed between the two stars. In this work, we provide a detailed analysis of how the twisting of the common magnetosphere of the binary leads to an emission of electromagnetic flares, akin to those produced in the solar corona. By means of relativistic force-free electrodynamics simulations, we clarify the role of different magnetic field topologies in the process. We conclude that flaring will always occur for suitable magnetic field alignments, unless one of the neutron stars has a magnetic field significantly weaker than the other
Projecting the likely importance of weak-interaction-driven bulk viscosity in neutron star mergers
No full textIn this work, we estimate how much bulk viscosity driven by Urca processes is likely to affect the gravitational wave signal of a neutron star coalescence. In the late inspiral, we show that bulk viscosity affects the binding energy at fourth post-Newtonian order. Even though this effect is enhanced by the square of the gravitational compactness, the coefficient of bulk viscosity is likely too small to lead to observable effects in the waveform during the late inspiral, when only considering the orbital motion itself. In the post-merger, however, the characteristic time-scales and spatial scales are different, potentially leading to the opposite conclusion. We post-process data from a state-of-the-art equal-mass binary neutron star merger simulation to estimate the effects of bulk viscosity (which was not included in the simulation itself). In that scenario, we find that bulk viscosity can reach high values in regions of the merger. We compute several estimates of how much it might directly affect the global dynamics of the considered merger scenario, and find that it could become significant. Even larger effects could arise in different merger scenarios or in simulations that include non-linear effects. This assessment is reinforced by a quantitative comparison with relativistic heavy-ion collisions where such effects have been explored extensively
Alteration history of Séítah formation rocks inferred by PIXL x-ray fluorescence, x-ray diffraction, and multispectral imaging on Mars
No full textCollocated crystal sizes and mineral identities are critical for interpreting textural relationships in rocks and testing geological hypotheses, but it has been previously impossible to unambiguously constrain these properties using in situ instruments on Mars rovers. Here, we demonstrate that diffracted and fluoresced x-rays detected by the PIXL instrument (an x-ray fluorescence microscope on the Perseverance rover) provide information about the presence or absence of coherent crystalline domains in various minerals. X-ray analysis and multispectral imaging of rocks from the Séítah formation on the floor of Jezero crater shows that they were emplaced as coarsely crystalline igneous phases. Olivine grains were then partially dissolved and filled by finely crystalline or amorphous secondary silicate, carbonate, sulfate, and chloride/oxychlorine minerals. These results support the hypothesis that Séítah formation rocks represent olivine cumulates altered by fluids far from chemical equilibrium at low water-rock ratios
Resonance fluorescence of a chiral artificial atom
No full textWe demonstrate a superconducting artificial atom with strong unidirectional coupling to a microwave photonic waveguide. Our artificial atom is realized by coupling a transmon qubit to the waveguide at two spatially separated points with time-modulated interactions. Direction-sensitive interference arising from the parametric couplings in our scheme results in a non-reciprocal response, where we measure a forward/backward ratio of spontaneous emission exceeding 100. We verify the quantum nonlinear behavior of this artificial chiral atom by measuring the resonance fluorescence spectrum under a strong resonant drive and observing well-resolved Mollow triplets. Further, we demonstrate chirality for the second transition energy of the artificial atom and control it with a pulse sequence to realize a qubit-state-dependent non-reciprocal phase on itinerant photons. Our demonstration puts forth a superconducting hardware platform for the scalable realization of several key functionalities pursued within the paradigm of chiral quantum optics, including quantum networks with all-to-all connectivity, driven-dissipative stabilization of many-body entanglement, and the generation of complex non-classical states of light
Algebraic Perspectives on Signomial Optimization
No full textSignomials are obtained by generalizing polynomials to allow for arbitrary real exponents. This generalization offers great expressive power but has historically sacrificed the organizing principle of “degree” that is central to polynomial optimization theory. We reclaim that principle here through the concept of signomial rings, which we use to derive complete convex relaxation hierarchies of upper and lower bounds for signomial optimization via sums of arithmetic-geometric exponentials (SAGE) nonnegativity certificates. The Positivstellensatz underlying the lower bounds relies on the concept of conditional SAGE and removes regularity conditions required by earlier works, such as convexity of the feasible set or Archimedeanity of its representing signomial inequalities. Through worked examples we illustrate the practicality of this hierarchy in areas such as chemical reaction network theory and chemical engineering. These examples include comparisons to direct global solvers (e.g., BARON and ANTIGONE) and the Lasserre hierarchy (where appropriate). The completeness of our hierarchy of upper bounds follows from a generic construction whereby a Positivstellensatz for signomial nonnegativity over a compact set provides for arbitrarily strong outer approximations of the corresponding cone of nonnegative signomials. While working toward that result, we prove basic facts on the existence and uniqueness of solutions to signomial moment problems
Which graphs can be counted in C₄-free graphs?
No full textFor which graphs F is there a sparse F-counting lemma in C₄-free graphs? We are interested in identifying graphs F with the property that, roughly speaking, if G is an n-vertex C₄-free graph with on the order of n^(3/2) edges, then the density of F in G, after a suitable normalization, is approximately at least the density of F in an ε-regular approximation of G. In recent work, motivated by applications in extremal and additive combinatorics, we showed that C₅ has this property. Here we construct a family of graphs with the property
Accurate quantification of single-nucleus and single-cell RNA-seq transcripts
No full textThe presence of both nascent and mature mRNA molecules in single-cell RNA-seq data leads to ambiguity in the notion of a “count matrix”. Underlying this ambiguity, is the challenging problem of separately quantifying nascent and mature mRNAs. We address this problem by relating k-mer assignment to read assignment in the context of different classes of molecules, and describe a unified approach to quantifying both single-cell and single-nucleus RNA-seq
Preservation of Conditioned Behavior Based on UV Light Sensitivity in Dissected Tail Halves of Planarians- a Proof by DNN
No full textPlanarians are aquatic worms with powerful regenerative and memory retention abilities. This paper examines whether a dissected tail half of a Planarian (Dugesia Dorotocephala) can retain and exhibit a previously-conditioned response, possibly before the regeneration of the head and the ganglia. We conditioned intact Planarians in a Pavlovian procedure with an electric shock (ES) as the unconditioned stimulus and weak ultraviolet (UV) light as the conditioned stimulus. Then, we dissected their bodies into halves, keeping the dissected tail halves. Starting from the 2nd day after dissection, we presented the same UV light 3 times daily while video-recording the responses. The recorded responses were then classified by a DNN: a VGG16 model was pre-trained by ImageNet for extracting features from images and additionally trained with 211 responses to ES and 118 to UV light before conditioning/dissection to categorize planarians’ reactions into “UV-induced” or “ES-induced” reactions. The cross-validated accuracy in categorization was 83.6%. We then let the DNN analyze 99 recorded responses to UV from 20 individual conditioned tail halves. 96.8 % of their reactions were classified as “ES-induced” (against 22.0% wrongly classified as “ES-induced” for unconditioned samples under UV), indicating they have shown the “Conditioned Response” (p<3.06E-30). This provides evidence that planarians can conserve and reveal a learned response even without the head/ganglia, as it takes approximately 7 days for the head/ganglia to regenerate versus the given 2-3 days. Although similar findings have been reported repeatedly in the literature, this is the first positive evidence with automated procedures and DNN classification. The result implies the presence of a decentralized nervous structure outside of its head/ganglia that allows a tail half to retain memory and execute motion accordingly, despite their cephalization
MicroED structure of a protoglobin reactive carbene intermediate
No full textMicrocrystal electron diffraction (MicroED) is an emerging technique which has shown great potential for describing new chemical and biological molecular structures. [1] Several important structures of small molecules, natural products and peptides have been determined usingab initiomethods. [2] However, only a couple of novel protein structures have thus far been derived by MicroED. [3, 4] Taking advantage of recent technological advances including higher acceleration voltage and using a low-noise detector in counting mode, we have determined the first structure of anAeropyrum pernixprotoglobin (ApePgb) variant by MicroED using an AlphaFold2 model for phasing. The structure revealed that mutations introduced during directed evolution enhance carbene transfer activity by reorienting an alphahelix ofApePgb into a dynamic loop making the catalytic active site more readily accessible. After exposing the tiny crystals to substrate, we also trapped the reactive iron-carbenoid intermediate involved in this engineeredApePgb’s new-to-nature activity, a challenging carbene transfer from a diazirine via a putative metallo-carbene. The bound structure discloses how an enlarged active site pocket stabilizes the carbene bound to the heme iron and, presumably, the transition state for formation of this key intermediate. This work demonstrates that improved MicroED technology and the advancement in protein structure prediction now enables investigation of structures that were previously beyond reach
Characterization of Integrase and Excisionase Activity in Cell-free Protein Expression System Using a Modeling and Analysis Pipeline
No full textWe present a full-stack modeling, analysis, and parameter identification pipeline to guide the modeling and design of biological systems starting from specifications to circuit implementations and parameterizations. We demonstrate this pipeline by characterizing the integrase and excisionase activity in cell-free protein expression system. We build on existing Python tools — BioCRNpyler, AutoReduce, and Bioscrape — to create this pipeline. For enzyme-mediated DNA recombination in cell-free system, we create detailed chemical reaction network models from simple high-level descriptions of the biological circuits and their context using BioCRNpyler. We use Bioscrape to show that the output of the detailed model is sensitive to many parameters. However, parameter identification is infeasible for this high-dimensional model, hence, we use AutoReduce to automatically obtain reduced models that have fewer parameters. This results in a hierarchy of reduced models under different assumptions to finally arrive at a minimal ODE model for each circuit. Then, we run sensitivity analysis-guided Bayesian inference using Bioscrape for each circuit to identify the model parameters. This process allows us to quantify integrase and excisionase activity in cell extracts enabling complex-circuit designs that depend on accurate control over protein expression levels through DNA recombination. The automated pipeline presented in this paper opens up a new approach to complex circuit design, modeling, reduction, and parameterization