Publications

Macronovae (kilonovae) that arise in binary neutron star mergers are powered by radioactive beta decay of hundreds of r-process nuclides. We derive, using Fermi's theory of beta decay, an analytic estimate of the nuclear heating rate. We show that the heating rate evolves as a power law ranging between t−6/5 and t−4/3. The overall magnitude of the heating rate is determined by the mean values of nuclear quantities, e.g. the nuclear matrix elements of beta decay. These values are specified by using nuclear experimental data. We discuss the role of higher order beta transitions and the robustness of the power law. The robust and simple form of the heating rate suggests that observations of the late-time bolometric light curve ∝ t−4/3 would be direct evidence of a r-process driven macronova. Such observations could also enable us to estimate the total amount of r-process nuclei produced in the merger.

Macronovae (kilonovae) that arise in binary neutron star mergers are powered by radioactive beta decay of hundreds of r-process nuclides. We derive, using Fermi's theory of beta decay, an analytic estimate of the nuclear heating rate. We show that the heating rate evolves as a power law ranging between t−6/5 to t−4/3. The overall magnitude of the heating rate is determined by the mean values of nuclear quantities, e.g., the nuclear matrix elements of beta decay. These values are specified by using nuclear experimental data. We discuss the role of higher order beta transitions and the robustness of the power law. The robust and simple form of the heating rate suggests that observations of the late-time bolometric light curve ∝t−43 would be a direct evidence of a r-process driven macronova. Such observations could also enable us to estimate the total amount of r-process nuclei produced in the merger.

We quantify the error in the results of mixed baryon--dark-matter hydrodynamic simulations, stemming from outdated approximations for the generation of initial conditions. The error at redshift 0 in contemporary large simulations, is of the order of few to ten percent in the power spectra of baryons and dark matter, and their combined total-matter power spectrum. After describing how to properly assign initial displacements and peculiar velocities to multiple species, we review several approximations: (1) {using the total-matter power spectrum to compute displacements and peculiar velocities of both fluids}, (2) scaling the linear redshift-zero power spectrum back to the initial power spectrum using the Newtonian growth factor ignoring homogeneous radiation, (3) using longitudinal-gauge velocities with synchronous-gauge densities, and (4) ignoring the phase-difference in the Fourier modes for the offset baryon grid, relative to the dark-matter grid. Three of these approximations do not take into account that dark matter and baryons experience a scale-dependent growth after photon decoupling, which results in directions of velocity which are not the same as their direction of displacement. We compare the outcome of hydrodynamic simulations with these four approximations to our reference simulation, all setup with the same random seed and simulated using Gadget-III.

The inversion of the Laplace-Beltrami operator and the computation of the Hodge decomposition of a tangential vector field on smooth surfaces arise as computational tasks in many areas of science, from computer graphics to machine learning to com- putational physics. Here, we present a high-order accurate pseudo-spectral approach, applicable to closed surfaces of genus one in three dimensional space, with a view toward applications in plasma physics and fluid dynamics.

Membrane proteins are underrepresented in structural databases, which has led to a lack of computational tools and the corresponding inappropriate use of tools designed for soluble proteins. For membrane proteins, lipid accessibility is an essential property. Although programs are available for sequence-based prediction of lipid accessibility and structure-based identification of solvent-accessible surface area, the latter does not distinguish between water accessible and lipid accessible residues in membrane proteins.

Type 1 regulatory T cells (Tr1 cells) are induced by interleukin-27 (IL-27) and have critical roles in the control of autoimmunity and resolution of inflammation. We found that the transcription factors IRF1 and BATF were induced early on after treatment with IL-27 and were required for the differentiation and function of Tr1 cells in vitro and in vivo. Epigenetic and transcriptional analyses revealed that both transcription factors influenced chromatin accessibility and expression of the genes required for Tr1 cell function. IRF1 and BATF deficiencies uniquely altered the chromatin landscape, suggesting that these factors serve a pioneering function during Tr1 cell differentiation.

We explore to which extent stars within Galactic disk open clusters resemble each other in the high-dimensional space of their photospheric element abundances, and contrast this with pairs of field stars. Our analysis is based on abundances for 20 elements, homogeneously derived from APOGEE spectra (with carefully quantified uncertainties, with a median value of ∼0.03 dex). We consider 90 red giant stars in seven open clusters and find that most stars within a cluster have abundances in most elements that are indistinguishable (in a χ2-sense) from those of the other members, as expected for stellar birth siblings. An analogous analysis among pairs of >1000 field stars shows that highly significant abundance differences in the 20-dimensional space can be established for the vast majority of these pairs, and that the APOGEE-based abundance measurements have high discriminating power. However, pairs of field stars whose abundances are indistinguishable even at 0.03~dex precision exist: ∼0.3 percent of all field star pairs, and ∼1.0 percent of field star pairs at the same (solar) metallicity [Fe/H] = 0±0.02. Most of these pairs are presumably not birth siblings from the same cluster, but rather doppelganger. Our analysis implies that 'chemical tagging' in the strict sense, identifying birth siblings for typical disk stars through their abundance similarity alone, will not work with such data. However, our approach shows that abundances have extremely valuable information for probabilistic chemo-orbital modeling and combined with velocities, we have identified new cluster members from the field.

Development of mice with hepatocyte knockout of lanosterol 14α-demethylase (HCyp51−/−) from cholesterol synthesis is characterized by the progressive onset of liver injury with ductular reaction and fibrosis. These changes begin during puberty and are generally more aggravated in the knockout females. However, a subgroup of (pre)pubertal knockout mice (runts) exhibits a pronounced male prevalent liver dysfunction characterized by downregulated amino acid metabolism and elevated Casp12. RORC transcriptional activity is diminished in livers of all runt mice, in correlation with the depletion of potential RORC ligands subsequent to CYP51 disruption. Further evidence for this comes from the global analysis that identified a crucial overlap between hepatic Cyp51−/− and Rorc−/− expression profiles. Additionally, the reduction in RORA and RORC transcriptional activity was greater in adult HCyp51−/− females than males, which correlates well with their downregulated amino and fatty acid metabolism. Overall, we identify a global and sex-dependent transcriptional de-regulation due to the block in cholesterol synthesis during development of the Cyp51 knockout mice and provide in vivo evidence that sterol intermediates downstream of lanosterol may regulate the hepatic RORC activity.

We study formation of stellar mass binary black holes (BBHs) originating from Population III (PopIII) stars, performing stellar evolution simulations for PopIII binaries with MESA. We find that a significant fraction of PopIII binaries form massive BBHs through stable mass transfer between two stars in a binary, without experiencing common envelope phases. We investigate necessary conditions required for PopIII binaries to form BBHs coalescing within the Hubble time with a semi-analytical model calibrated by the stellar evolution simulations. The formation efficiency of coalescing PopIII BBHs is estimated for two different initial conditions for PopIII binaries with large and small separations, respectively. Consequently, in both models, ∼10% of the total PopIII binaries form BBHs only through stable mass transfer and ∼10% of these BBHs merge due to gravitational wave emission within the Hubble time. Furthermore, the chirp mass of merging BBHs has a flat distribution over 15≲Mchirp/M⊙≲35. This formation pathway of PopIII BBHs is presumably robust because stable mass transfer is less uncertain than common envelope evolution, which is the main formation channel for Population II BBHs. We also test the hypothesis that the BBH mergers detected by LIGO originate from PopIII stars using our result and the total number of PopIII stars formed in the early universe as inferred from the optical depth measured by Planck. We conclude that the PopIII BBH formation scenario can explain the mass-weighted merger rate of the LIGO's O1 events with the maximal PopIII formation efficiency inferred from the Planck measurement, even without BBHs formed by unstable mass transfer or common envelope phases.

We present a novel platform for the large-scale simulation of three-dimensional fibrous structures immersed in a Stokesian fluid and evolving under confinement or in free-space in three dimensions. One of the main motivations for this work is to study the dynamics of fiber assemblies within biological cells. For this, we also incorporate the key biophysical elements that determine the dynamics of these assemblies, which include the polymerization and depolymerization kinetics of fibers, their interactions with molecular motors and other objects, their flexibility, and hydrodynamic coupling. This work, to our knowledge, is the first technique to include many-body hydrodynamic interactions (HIs), and the resulting fluid flows, in cellular assemblies of flexible fibers. We use non-local slender body theory to compute the fluid–structure interactions of the fibers and a second-kind boundary integral formulation for other rigid bodies and the confining boundary. A kernel-independent implementation of the fast multipole method is utilized for efficient evaluation of HIs. The deformation of the fibers is described by nonlinear Euler–Bernoulli beam theory and their polymerization is modeled by the reparametrization of the dynamic equations in the appropriate non-Lagrangian frame. We use a pseudo-spectral representation of fiber positions and implicit time-stepping to resolve large fiber deformations, and to allow time-steps not excessively constrained by temporal stiffness or fiber–fiber interactions. The entire computational scheme is parallelized, which enables simulating assemblies of thousands of fibers. We use our method to investigate two important questions in the mechanics of cell division: (i) the effect of confinement on the hydrodynamic mobility of microtubule asters; and (ii) the dynamics of the positioning of mitotic spindle in complex cell geometries. Finally to demonstrate the general applicability of the method, we simulate the sedimentation of a cloud of semi-flexible fibers.