The Nature of the Warm/Hot Intergalactic Medium I. Numerical Methods, Convergence, and OVI Absorption

We perform a series of cosmological simulations using Enzo, an Eulerian adaptive-mesh refinement, N-body + hydrodynamical code, applied to study the warm/hot intergalactic medium. The WHIM may be an important component of the baryons missing observationally at low redshift. We investigate the dependence of the global star formation rate and mass fraction in various baryonic phases on spatial resolution and methods of incorporating stellar feedback. Although both resolution and feedback significantly affect the total mass in the WHIM, all of our simulations find that the WHIM fraction peaks at z ~ 0.5, declining to 35-40% at z = 0. We construct samples of synthetic OVI absorption lines from our highest-resolution simulations, using several models of oxygen ionization balance. Models that include both collisional ionization and photoionization provide excellent fits to the observed number density of absorbers per unit redshift over the full range of column densities (10^13 cm-2 <= N_OVI <= 10^15 cm^-2). Models that include only collisional ionization provide better fits for high column density absorbers (N_OVI > 10^14 cm^-2). The distribution of OVI in density and temperature exhibits two populations: one at T ~ 10^5.5 K (collisionally ionized, 55% of total OVI) and one at T ~ 10^4.5 K (photoionized, 37%) with the remainder located in dense gas near galaxies. While not a perfect tracer of hot gas, OVI provides an important tool for a WHIM baryon census.Comment: 22 pages, 21 figures, emulateapj, accepted for publication in Ap

Engineering Approaches for Neurobiology

Neurobiological systems span a wide dimensional range. We present a scale-driven methodological development for three biological systems to demonstrate the utility of applied engineering approaches in neurobiology and provide an avenue for future study. Concepts in computational modeling, microfluidic device platforms, and MRI phantoms are examined - starting from the level of a single synapse and concluding with long-distance cortical connectivity.Single synapse models were developed using a Monte Carlo simulation environment to study biophysically realistic mechanisms of spike timing dependent plasticity (STDP). A model of spatiotemporal intracellular Calcium detection was extended to include subunit-specific receptor kinetics and distributions. Using STDP-based activation protocols, global and local molecular time courses were then produced for NR2a and NR2b knockout models. To study network level oscillatory activity, a model of spatially-constrained networks was created based on cyclic geometry to look at the effects of circumference and track-width on spontaneous network activity. Transverse wave activity is demonstrated and characterized by velocity and origin. Microfluidic technology provides an experimental means to extend the study of network organization and activity in vitro. We have developed a microfluidic control platform that integrates multiple design strategies to address the intrinsic spatiotemporal resolution of neurons. Microfluidic devices were fabricated using multilayer soft-lithography with internal valves to guide multiple laminar streams. A control platform using dynamic pressure produces a targeted hydrodynamic stream from variable internal resistance control. Feedback containing video and pressure data provides online analysis of the microfluidic device. Devices were characterized with arbitrary profile generation, profile repeatability, flow rate measurement, and lid-driven flow production. Finally, a microfluidic phantom for diffusion-weighted magnetic resonance imaging was developed for validation studies of long-distance cortical white matter connections. The diffusion phantom provides a reliable physical structure with which high resolution fiber tractography methods can be tested against. The diffusion phantom was fabricated using conventional photolithographic techniques with an internal channel network that mimics white matter fiber tracts and crossings. We show mapped tracts to the features inside of the phantom via post-processing of diffusion-weighted images

A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large- scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform- specific implementations or dynamical models that are different from Brownian dynamics

Direct Detection of sub-GeV Dark Matter with Semiconductor Targets

Dark matter in the sub-GeV mass range is a theoretically motivated but largely unexplored paradigm. Such light masses are out of reach for conventional nuclear recoil direct detection experiments, but may be detected through the small ionization signals caused by dark matter-electron scattering. Semiconductors are well-studied and are particularly promising target materials because their ${\cal O}(1~\rm{eV})$ band gaps allow for ionization signals from dark matter as light as a few hundred keV. Current direct detection technologies are being adapted for dark matter-electron scattering. In this paper, we provide the theoretical calculations for dark matter-electron scattering rate in semiconductors, overcoming several complications that stem from the many-body nature of the problem. We use density functional theory to numerically calculate the rates for dark matter-electron scattering in silicon and germanium, and estimate the sensitivity for upcoming experiments such as DAMIC and SuperCDMS. We find that the reach for these upcoming experiments has the potential to be orders of magnitude beyond current direct detection constraints and that sub-GeV dark matter has a sizable modulation signal. We also give the first direct detection limits on sub-GeV dark matter from its scattering off electrons in a semiconductor target (silicon) based on published results from DAMIC. We make available publicly our code, QEdark, with which we calculate our results. Our results can be used by experimental collaborations to calculate their own sensitivities based on their specific setup. The searches we propose will probe vast new regions of unexplored dark matter model and parameter space.Comment: 30 pages + 22 pages appendices/references, 17 figures, website at http://ddldm.physics.sunysb.edu/, v2 added references, minor edits to text and Figs. 2 and 14, version to appear in JHE

Supernova feedback in numerical simulations of galaxy formation: separating physics from numerics

While feedback from massive stars exploding as supernovae (SNe) is thought to be one of the key ingredients regulating galaxy formation, theoretically it is still unclear how the available energy couples to the interstellar medium and how galactic scale outflows are launched. We present a novel implementation of six sub-grid SN feedback schemes in the moving-mesh code Arepo, including injections of thermal and/or kinetic energy, two parametrizations of delayed cooling feedback and a `mechanical' feedback scheme that injects the correct amount of momentum depending on the relevant scale of the SN remnant resolved. All schemes make use of individually time-resolved SN events. Adopting isolated disk galaxy setups at different resolutions, with the highest resolution runs reasonably resolving the Sedov-Taylor phase of the SN, we aim to find a physically motivated scheme with as few tunable parameters as possible. As expected, simple injections of energy overcool at all but the highest resolution. Our delayed cooling schemes result in overstrong feedback, destroying the disk. The mechanical feedback scheme is efficient at suppressing star formation, agrees well with the Kennicutt-Schmidt relation and leads to converged star formation rates and galaxy morphologies with increasing resolution without fine tuning any parameters. However, we find it difficult to produce outflows with high enough mass loading factors at all but the highest resolution, indicating either that we have oversimplified the evolution of unresolved SN remnants, require other stellar feedback processes to be included, require a better star formation prescription or most likely some combination of these issues