Revisiting The First Galaxies: The effects of Population III stars on their host galaxies

We revisit the formation and evolution of the first galaxies using new hydrodynamic cosmological simulations with the ART code. Our simulations feature a recently developed model for H2 formation and dissociation, and a star formation recipe that is based on molecular rather than atomic gas. Here, we develop and implement a recipe for the formation of metal-free Population III stars in galaxy-scale simulations that resolve primordial clouds with sufficiently high density. We base our recipe on the results of prior zoom-in simulations that resolved the protostellar collapse in pre-galactic objects. We find the epoch during which Pop III stars dominated the energy and metal budget of the first galaxies to be short-lived. Galaxies which host Pop III stars do not retain dynamical signatures of their thermal and radiative feedback for more than 10^8 yr after the lives of the stars end in pair-instability supernovae, even when we consider the maximum reasonable efficiency of the feedback. Though metals ejected by the supernovae can travel well beyond the virial radius of the host galaxy, they typically begin to fall back quickly, and do not enrich a large fraction of the intergalactic medium. Galaxies with total mass in excess of 3 x 10^6 Msun re-accrete most of their baryons and transition to metal-enriched Pop II star formation.Comment: 13 pages, 9 figures, published in Ap

Revisiting The First Galaxies: The epoch of Population III stars

We investigate the transition from primordial Population III (Pop III) star formation to normal Pop II star formation in the first galaxies using new cosmological hydrodynamic simulations. We find that while the first stars seed their host galaxies with metals, they cannot sustain significant outflows to enrich the intergalactic medium, even assuming a top-heavy initial mass function. This means that Pop III star formation could potentially continue until z~6 in different unenriched regions of the universe, before being ultimately shut off by cosmic reionization. Within an individual galaxy, the metal production and stellar feedback from Pop II stars overtake Pop III stars in 20-200 Myr, depending on galaxy mass.Comment: 9 pages, 7 figures, published in Ap

The Origin and Evolution of the Galaxy Mass-Metallicity Relation

We use high-resolution cosmological zoom-in simulations from the Feedback in Realistic Environment (FIRE) project to study the galaxy mass-metallicity relations (MZR) from z=0-6. These simulations include explicit models of the multi-phase ISM, star formation, and stellar feedback. The simulations cover halo masses Mhalo=10^9-10^13 Msun and stellar mass Mstar=10^4-10^11 Msun at z=0 and have been shown to produce many observed galaxy properties from z=0-6. For the first time, our simulations agree reasonably well with the observed mass-metallicity relations at z=0-3 for a broad range of galaxy masses. We predict the evolution of the MZR from z=0-6 as log(Zgas/Zsun)=12+log(O/H)-9.0=0.35[log(Mstar/Msun)-10]+0.93 exp(-0.43 z)-1.05 and log(Zstar/Zsun)=[Fe/H]-0.2=0.40[log(Mstar/Msun)-10]+0.67 exp(-0.50 z)-1.04, for gas-phase and stellar metallicity, respectively. Our simulations suggest that the evolution of MZR is associated with the evolution of stellar/gas mass fractions at different redshifts, indicating the existence of a universal metallicity relation between stellar mass, gas mass, and metallicities. In our simulations, galaxies above Mstar=10^6 Msun are able to retain a large fraction of their metals inside the halo, because metal-rich winds fail to escape completely and are recycled into the galaxy. This resolves a long-standing discrepancy between "sub-grid" wind models (and semi-analytic models) and observations, where common sub-grid models cannot simultaneously reproduce the MZR and the stellar mass functions.Comment: 17 pages, 14 figures, re-submitted to MNRAS after revisions on referee comment

Gusty, gaseous flows of FIRE: galactic winds in cosmological simulations with explicit stellar feedback

We present an analysis of the galaxy-scale gaseous outflows from the Feedback in Realistic Environments (FIRE) simulations. This suite of hydrodynamic cosmological zoom simulations resolves formation of star-forming giant molecular clouds to z = 0, and features an explicit stellar feedback model on small scales. Our simulations reveal that high-redshift galaxies undergo bursts of star formation followed by powerful gusts of galactic outflows that eject much of the interstellar medium and temporarily suppress star formation. At low redshift, however, sufficiently massive galaxies corresponding to L* progenitors develop stable discs and switch into a continuous and quiescent mode of star formation that does not drive outflows far into the halo. Mass-loading factors for winds in L* progenitors are η ≈ 10 at high redshift, but decrease to η ≪ 1 at low redshift. Although lower values of η are expected as haloes grow in mass over time, we show that the strong suppression of outflows with decreasing redshift cannot be explained by mass evolution alone. Circumgalactic outflow velocities are variable and broadly distributed, but typically range between one and three times the circular velocity of the halo. Much of the ejected material builds a reservoir of enriched gas within the circumgalactic medium, some of which could be later recycled to fuel further star formation. However, a fraction of the gas that leaves the virial radius through galactic winds is never regained, causing most haloes with mass M_h ≤ 10^(12) M_⊙ to be deficient in baryons compared to the cosmic mean by z = 0

Mechanism of dynamic reorientation of cortical microtubules due to mechanical stress

Directional growth caused by gravitropism and corresponding bending of plant cells has been explored since 19th century, however, many aspects of mechanisms underlying the perception of gravity at the molecular level are still not well known. Perception of gravity in root and shoot gravitropisms is usually attributed to gravisensitive cells, called statocytes, which exploit sedimentation of macroscopic and heavy organelles, amyloplasts, to sense the direction of gravity. Gravity stimulus is then transduced into distal elongation zone, which is several mm far from statocytes, where it causes stretching. It is suggested that gravity stimulus is conveyed by gradients in auxin flux. We propose a theoretical model that may explain how concentration gradients and/or stretching may indirectly affect the global orientation of cortical microtubules, attached to the cell membrane and induce their dynamic reorientation perpendicular to the gradients. In turn, oriented microtubules arrays direct the growth and orientation of cellulose microfibrils, forming part of the cell external skeleton and determine the shape of the cell. Reorientation of microtubules is also observed in reaction to light in phototropism and mechanical bending, thus suggesting universality of the proposed mechanism.Comment: publishe

Data Set Modelability by QSAR

We introduce a simple MODelability Index (MODI) that estimates the feasibility of obtaining predictive QSAR models (Correct Classification Rate above 0.7) for a binary dataset of bioactive compounds. MODI is defined as an activity class-weighted ratio of the number of the nearest neighbor pairs of compounds with the same activity class versus the total number of pairs. The MODI values were calculated for more than 100 datasets and the threshold of 0.65 was found to separate non-modelable from the modelable datasets

Modelling of self-organizaton of microtubules in plant cells

Microtubules are ubiquitous elements of any eucaryotic cell, serving many functions at different stages of its life. In plant cells they form so-called plant cell cortex, where they are organized into parallel arrays. These arrays serve as a matrix of synthesis of a plant cell wall, defining the direction of growth. Microtubule arrays are sensible to tropic stimuli. However, the nature of such sensibility is still not well established. We provide a computational analysis of this phenomenon. Using both kinetic Monte-Carlo simulations and theoretical investigation, we show that compression due to mechanical stress may cause orientation of microtubules along major stress lines. We also show that anisotropic distribution of chemical agents interacting with microtubule-associated proteins may also cause orientation of microtubules. Such mechanisms are primarily connected with gravitropism but similar reorientations of microtubules in response to light may suggest that these mechanisms can also be relevant for other tropisms.Los microtúbulos son elementos ubicuos de cualquier célula eucariota, que poseen distintas funciones en diferentes etapas de su vida. En células de plantas ellos forman la estructura llamada corteza célula vegetal, donde se organizan en conjuntos paralelos. Estos conjuntos sirven como una matriz de síntesis de una pared celular vegetal, definiendo la dirección del crecimiento de la célula. Los conjuntos de microtúbulos son sensibles a estímulos trópicos. Sin embargo, la naturaleza de dicha sensibilidad todavía no está bien establecida. Les ofrecemos un análisis computacional de este fenómeno. Usando simulaciones cinéticas Monte-Carlo y la investigación teórica, nos mostramos que la compresión debida al estrés mecánico puede causar la orientación de los microtúbulos a lo largo de las principales líneas de tensión. También se muestra que la distribución anisotrópica de agentes químicos que interactúan con las proteínas asociadas a los microtúbulos también puede provocar orientación de los microtúbulos. Estos mecanismos están conectados principalmente con gravitropismo pero reorientaciones similares de microtúbulos en respuesta a la luz puede sugerir que estos mecanismos también pueden ser relevantes para otros tropismos

Cosmological Small-Scale Structure: The Formation of The First Stars, Galaxies, and Globular Clusters.

Though the majority of stars now live in large, massive galaxies, understanding the origins of all galaxies ab initio requires fully comprehensive modeling of cosmological small-scale structure. In this thesis, I present a theoretical study of galaxy formation that focuses on low-mass halos. These halos are the sites for the formation of the first stars and galaxies at high redshift, and they also they play a role in forming massive globular clusters in the outskirts of the Milky Way. I develop a physical model for Population III star formation and feedback, and implemented it into the Eulerian hydrodynamic Adaptive Refinement Tree (ART) code. With this code, I designed, performed, and analyzed a suite of cosmological simulations that resolve the formation of the first stars and galaxies. I quantify the extent of the dynamical signatures Population III stars can impart on their host galaxies, and derive a characteristic mass threshold, 3 million solar masses, above which Population III stellar feedback is no longer dynamically significant over significant cosmic timescales. I measure the duration of time for which Population III stars are the dominant drivers of feedback in the universe. Due to the inhomogeneous and patchy enrichment of the intergalactic medium, I find Population III stars can continue forming in some environments well after the end of the cosmic dark ages. However, in individual galaxies that are sufficiently massive, Population II star formation takes over soon after the efficient enrichment by a single pair-instability supernova. Globally, Population II is dominant at cosmic epochs later than redshift (z ~ 15). Finally, I construct a semi-analytical model for globular cluster formation in hierarchical cosmology, and use it to demonstrate a plausible scenario for the formation of the Milky Way’s globular cluster system. My model is successful in matching both the metallicity and mass distributions of galactic globular clusters. In particular, the bimodal nature of the metallicity distribution is for the first time explained by the single mechanism of the merging of protogalaxies.PHDAstronomy and AstrophysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/99887/1/muratov_1.pd

Predicting Adverse Drug Effects from Literature- and Database-Mined Assertions

IntroductionGiven that adverse drug effects (ADEs) have led to post-market patient harm and subsequent drug withdrawal, failure of candidate agents in the drug development process, and other negative outcomes, it is essential to attempt to forecast ADEs and other relevant drug-target-effect relationships as early as possible. Current pharmacologic data sources, providing multiple complementary perspectives on the drug-target-effect paradigm, can be integrated to facilitate the inference of relationships between these entities.ObjectiveThis study aims to identify both existing and unknown relationships between chemicals (C), protein targets (T), and ADEs (E) based on evidence in the literature.Materials and MethodsCheminformatics and data mining approaches were employed to integrate and analyze publicly available clinical pharmacology data and literature assertions interrelating drugs, targets, and ADEs. Based on these assertions, a C-T-E relationship knowledge base was developed. Known pairwise relationships between chemicals, targets, and ADEs were collected from several pharmacological and biomedical data sources. These relationships were curated and integrated according to Swanson's paradigm to form C-T-E triangles. Missing C-E edges were then inferred as C-E relationships.ResultsUnreported associations between drugs, targets, and ADEs were inferred, and inferences were prioritized as testable hypotheses. Several C-E inferences, including testosterone†’myocardial infarction, were identified using inferences based on the literature sources published prior to confirmatory case reports. Timestamping approaches confirmed the predictive ability of this inference strategy on a larger scale.ConclusionsThe presented workflow, based on free-access databases and an association-based inference scheme, provided novel C-E relationships that have been validated post hoc in case reports. With refinement of prioritization schemes for the generated C-E inferences, this workflow may provide an effective computational method for the early detection of potential drug candidate ADEs that can be followed by targeted experimental investigations