Publications

In this paper we analyze the dynamics of single-excitation states, which model the scattering of a single photon from multiple two level atoms. For short times and weak atom-field couplings we show that the atomic amplitudes are given by a sum of decaying exponentials, where the decay rates and Lamb shifts are given by the poles of a certain analytic function. This result is a refinement of the "pole approximation" appearing in the standard Wigner-Weisskopf analysis of spontaneous emission. On the other hand, at large times, the atomic field decays like O(1/t3) with a known constant expressed in terms of the coupling parameter and the resonant frequency of the atoms. Moreover, we show that for stronger coupling, the solutions also feature a collection of oscillatory exponentials which dominate the behavior at long times. Finally, we extend the analysis to the continuum limit in which atoms are distributed according to a given density.

DNA damage reshapes the cellular transcriptome by modulating RNA transcription and processing. In cancer cells, these changes can alter the expression of genes in the immune surveillance and cell death pathways. Here, we investigate how DNA damage impacts alternative polyadenylation (APA) using the PAPERCLIP technique. We find that APA shifts are a coordinated response for hundreds of genes to DNA damage, and we identify PCF11 as an important contributor of DNA damage-induced APA shifts. One of these APA shifts results in upregulation of the full-length MSL1 mRNA isoform, which protects cells from DNA damage-induced apoptosis and promotes cell survival from DNA-damaging agents. Importantly, blocking MSL1 upregulation enhances cytotoxicity of chemotherapeutic agents even in the absence of p53 and overcomes chemoresistance. Our study demonstrates that characterizing adaptive APA shifts to DNA damage has therapeutic implications and reveals a link between PCF11, the MSL complex, and DNA damage-induced apoptosis.

Abstract Several antimicrobial peptides, including magainin and the human cathelicidin LL-37, act by forming pores in bacterial membranes. Bacteria such as Staphylococcus aureus modify their membrane's cardiolipin composition to resist such types of perturbations that compromise their membrane stability. Here, we used molecular dynamics simulations to quantify the role of cardiolipin on the formation of pores in simple bacterial-like membrane models composed of phosphatidylglycerol and cardiolipin mixtures. Cardiolopin modified the structure and ordering of the lipid bilayer, making it less susceptible to mechanical changes. Accordingly, the free-energy barrier for the formation of a transmembrane pore and its kinetic instability augmented by increasing the cardiolipin concentration. This is attributed to the unfavorable positioning of cardiolipin near the formed pore, due to its small polar-head and bulky hydrophobic-body. Overall, our study demonstrates how cardiolipin prevents membrane-pore formation and this constitutes a plausible mechanism used by bacteria to act against stress perturbations and, thereby, gain resistance to antimicrobial agents.

We report on an all-sky search for continuous gravitational waves in the frequency band 20-2000\,Hz and with a frequency time derivative in the range of [−1.0,+0.1]×10−8\,Hz/s. Such a signal could be produced by a nearby, spinning and slightly non-axisymmetric isolated neutron star in our galaxy. This search uses the LIGO data from the first six months of Advanced LIGO's and Advanced Virgo's third observational run, O3. No periodic gravitational wave signals are observed, and 95\%\ confidence-level (CL) frequentist upper limits are placed on their strengths. The lowest upper limits on worst-case (linearly polarized) strain amplitude h0 are 1.7×10−25 near 200\,Hz. For a circularly polarized source (most favorable orientation), the lowest upper limits are ∼6.3×10−26. These strict frequentist upper limits refer to all sky locations and the entire range of frequency derivative values. For a population-averaged ensemble of sky locations and stellar orientations, the lowest 95\%\ CL upper limits on the strain amplitude are ∼1.×10−25. These upper limits improve upon our previously published all-sky results, with the greatest improvement (factor of ∼2) seen at higher frequencies, in part because quantum squeezing has dramatically improved the detector noise level relative to the second observational run, O2. These limits are the most constraining to date over most of the parameter space searched.

The characteristics of the stellar populations in the Galactic bulge inform and constrain the Milky Way’s formation and evolution. The metal-poor population is particularly important in light of cosmological simulations, which predict that some of the oldest stars in the Galaxy now reside in its centre. The metal-poor bulge appears to consist of multiple stellar populations that require dynamical analyses to disentangle. In this work, we undertake a detailed chemodynamical study of the metal-poor stars in the inner Galaxy. Using R ∼ 20 000 VLT/GIRAFFE spectra of 319 metal-poor (−2.55 dex ≤ [Fe/H] ≤ 0.83 dex, with [Fe/H] = −0.84 dex) stars, we perform stellar parameter analysis and report 12 elemental abundances (C, Na, Mg, Al, Si, Ca, Sc, Ti, Cr, Mn, Zn, Ba, and Ce) with precisions of ≈0.10 dex. Based on kinematic and spatial properties, we categorize the stars into four groups, associated with the following Galactic structures: the inner bulge, the outer bulge, the halo, and the disc. We find evidence that the inner and outer bulge population is more chemically complex (i.e. higher chemical dimensionality and less correlated abundances) than the halo population. This result suggests that the older bulge population was enriched by a larger diversity of nucleosynthetic events. We also find one inner bulge star with a [Ca/Mg] ratio consistent with theoretical pair-instability supernova yields and two stars that have chemistry consistent with globular cluster stars.

Problems with networks of coupled oscillators arise in multiple contexts, commonly leading to the question about the dependence of network dynamics on network structure. Previous work has addressed this question in Drosophila oogenesis, where stable cytoplasmic bridges connect the future oocyte to the supporting nurse cells that supply the oocyte with molecules and organelles needed for its development. To increase their biosynthetic capacity, nurse cells enter the endoreplication program, a special form of the cell cycle formed by the iterated repetition of growth and synthesis phases without mitosis. Recent studies have revealed that the oocyte orchestrates nurse cell endoreplication cycles, based on retrograde (oocyte to nurse cells) transport of a cell cycle inhibitor produced by the nurse cells and localized to the oocyte. Furthermore, the joint dynamics of endocycles has been proposed to depend on the intercellular connectivity within the oocyte-nurse cell cluster. We use a computational model to argue that this connectivity guides, but does not uniquely determine the collective dynamics and identify several oscillatory regimes, depending on the time scale of intercellular transport. Our results provide insights into collective dynamics of coupled cell cycles and motivate future quantitative studies of intercellular communication in the germline cell clusters.

The sensitivity of X-ray facilities and our ability to detect fainter active galactic nuclei (AGNs) will increase with the upcoming Athena mission and the AXIS and Lynx concept missions, thus improving our understanding of supermassive black holes (BHs) in a luminosity regime that can be dominated by X-ray binaries. We analyze the population of faint AGN (L_x (2-10 keV) 2, while XRBs dominate in some simulations at z<2. Whether the AGN or XRB emission dominates in star-forming and quenched galaxies depends on the simulations. These differences in simulations can be used to discriminate between galaxy formation models with future high-resolution X-ray observations. We compare the luminosity of simulated faint AGN host galaxies to observations of stacked galaxies from Chandra. Our comparison indicates that the simulations post-processed with our X-ray modeling tend to overestimate the AGN+XRB X-ray luminosity; luminosity that can be strongly affected by AGN obscuration. Some simulations reveal clear AGN trends as a function of stellar mass (e.g., galaxy luminosity drop in massive galaxies), which are not apparent in the observations.

We characterize mass, momentum, energy and metal outflow rates of multi-phase galactic winds in a suite of FIRE-2 cosmological "zoom-in" simulations from the Feedback in Realistic Environments (FIRE) project. We analyze simulations of low-mass dwarfs, intermediate-mass dwarfs, Milky Way-mass halos, and high-redshift massive halos. Consistent with previous work, we find that dwarfs eject about 100 times more gas from their interstellar medium (ISM) than they form in stars, while this mass "loading factor" drops below one in massive galaxies. Most of the mass is carried by the hot phase (>105 K) in massive halos and the warm phase (103−105 K) in dwarfs; cold outflows (<103 K) are negligible except in high-redshift dwarfs. Energy, momentum and metal loading factors from the ISM are of order unity in dwarfs and significantly lower in more massive halos. Hot outflows have 2−5× higher specific energy than needed to escape from the gravitational potential of dwarf halos; indeed, in dwarfs, the mass, momentum, and metal outflow rates increase with radius whereas energy is roughly conserved, indicating swept up halo gas. Burst-averaged mass loading factors tend to be larger during more powerful star formation episodes and when the inner halo is not virialized, but we see effectively no trend with the dense ISM gas fraction. We discuss how our results can guide future controlled numerical experiments that aim to elucidate the key parameters governing galactic winds and the resulting associated preventative feedback.

Despite over three hundred years of effort, no solutions exist for predicting when a general planetary configuration will become unstable. We introduce a deep learning architecture to push forward this problem for compact systems. While current machine learning algorithms in this area rely on scientist-derived instability metrics, our new technique learns its own metrics from scratch, enabled by a novel internal structure inspired from dynamics theory. Our Bayesian neural network model can accurately predict not only if, but also when a compact planetary system with three or more planets will go unstable. Our model, trained directly from short N-body time series of raw orbital elements, is more than two orders of magnitude more accurate at predicting instability times than analytical estimators, while also reducing the bias of existing machine learning algorithms by nearly a factor of three. Despite being trained on compact resonant and near-resonant three-planet configurations, the model demonstrates robust generalization to both non-resonant and higher multiplicity configurations, in the latter case outperforming models fit to that specific set of integrations. The model computes instability estimates up to five orders of magnitude faster than a numerical integrator, and unlike previous efforts provides confidence intervals on its predictions. Our inference model is publicly available in the SPOCK package, with training code open-sourced.

We examine the magneto-optical response of chiral multifold fermions. Specifically, we show that they are ideal candidates for observing the Helical Magnetic Effect (HME) previously predicted for simple Weyl fermions. Unlike Weyl fermions, the HME is present in multifold fermions even in the simplest case where the low-energy dispersion is linear and spherically symmetric. In this ideal case, we derive an analytical expression for the HME and find it is proportional to the circular photogalvanic effect; for realistic parameters and accounting for the geometry of the setup, the HME photocurrent could be roughly the same order of magnitude as the circular photogalvanic effect observed in multifold fermions. Additional non-linear and symmetry-breaking terms will ruin the quantization but not hurt the observation of the HME.