Simulating Reionization: Character and Observability

In recent years there has been considerable progress in our understanding of the nature and properties of the reionization process. In particular, the numerical simulations of this epoch have made a qualitative leap forward, reaching sufficiently large scales to derive the characteristic scales of the reionization process and thus allowing for realistic observational predictions. Our group has recently performed the first such large-scale radiative transfer simulations of reionization, run on top of state-of-the-art simulations of early structure formation. This allowed us to make the first realistic observational predictions about the Epoch of Reionization based on detailed radiative transfer and structure formation simulations. We discuss the basic features of reionization derived from our simulations and some recent results on the observational implications for the high-redshift Ly-alpha sources.Comment: 3 pages, to appear in the Proceedings of First Stars III, Santa Fe, July 2007, AIP Conference Serie

Unconventional machine learning of genome-wide human cancer data

Recent advances in high-throughput genomic technologies coupled with exponential increases in computer processing and memory have allowed us to interrogate the complex aberrant molecular underpinnings of human disease from a genome-wide perspective. While the deluge of genomic information is expected to increase, a bottleneck in conventional high-performance computing is rapidly approaching. Inspired in part by recent advances in physical quantum processors, we evaluated several unconventional machine learning (ML) strategies on actual human tumor data. Here we show for the first time the efficacy of multiple annealing-based ML algorithms for classification of high-dimensional, multi-omics human cancer data from the Cancer Genome Atlas. To assess algorithm performance, we compared these classifiers to a variety of standard ML methods. Our results indicate the feasibility of using annealing-based ML to provide competitive classification of human cancer types and associated molecular subtypes and superior performance with smaller training datasets, thus providing compelling empirical evidence for the potential future application of unconventional computing architectures in the biomedical sciences

Nicotine promotes Streptococcus mutans extracellular polysaccharide synthesis, cell aggregation and overall lactate dehydrogenase activity

Several epidemiology studies have reported a positive relationship between smoking and dental caries. Nicotine, an alkaloid component of tobacco, has been demonstrated to stimulate biofilm formation and metabolic activity of Streptococcus mutans, one of the most important pathogens of dental caries. The first aim of the present study was to explore the possible mechanisms leading to increased biofilm by nicotine treatment from three aspects, extracellular polysaccharides (EPS) synthesis, glucosyltransferase (Gtf) synthesis and glucan-binding protein (Gbp) synthesis at the mRNA and protein levels. The second aim was to investigate how nicotine affects S. mutans virulence, particular in lactate dehydrogenase (LDH) activity. Confocal laser scanning microscopy results demonstrated that both biofilm bacterial cell numbers and EPS were increased by nicotine. Gtf and GbpA protein expression of S. mutans planktonic cells were upregulated while GbpB protein expression of biofilm cells were downregulated by nicotine. The mRNA expression trends of those genes were mostly consistent with results on protein level but not statistically significant, and gtfD and gbpD of biofilm cells were inhibited. Nicotine was not directly involved in S. mutans LDH activity. However, since it increases the total number of bacterial cells in biofilm, the overall LDH activity of S. mutans biofilm is increased. In conclusion, nicotine stimulates S. mutans planktonic cell Gtf and Gbp expression. This leads to more planktonic cells attaching to the dental biofilm. Increased cell numbers within biofilm results in higher overall LDH activity. This contributes to caries development in smokers

The Kinetic Sunyaev-Zel'dovich Effect from Radiative Transfer Simulations of Patchy Reionization

We present the first calculation of the kinetic Sunyaev-Zel'dovich (kSZ) effect due to the inhomogeneous reionization of the universe based on detailed large-scale radiative transfer simulations of reionization. The resulting sky power spectra peak at l=2000-8000 with maximum values of l^2C_l~1\times10^{-12}. The peak scale is determined by the typical size of the ionized regions and roughly corresponds to the ionized bubble sizes observed in our simulations, ~5-20 Mpc. The kSZ anisotropy signal from reionization dominates the primary CMB signal above l=3000. This predicted kSZ signal at arcminute scales is sufficiently strong to be detectable by upcoming experiments, like the Atacama Cosmology Telescope and South Pole Telescope which are expected to have ~1' resolution and ~muK sensitivity. The extended and patchy nature of the reionization process results in a boost of the peak signal in power by approximately one order of magnitude compared to a uniform reionization scenario, while roughly tripling the signal compared with that based upon the assumption of gradual but spatially uniform reionization. At large scales the patchy kSZ signal depends largely on the ionizing source efficiencies and the large-scale velocity fields: sources which produce photons more efficiently yield correspondingly higher signals. The introduction of sub-grid gas clumping in the radiative transfer simulations produces significantly more power at small scales, and more non-Gaussian features, but has little effect at large scales. The patchy nature of the reionization process roughly doubles the total observed kSZ signal for l~3000-10^4 compared to non-patchy scenarios with the same total electron-scattering optical depth.Comment: 14 pages, 13 figures (some in color), submitted to Ap

Chemistry and radiative shielding in star forming galactic disks

To understand the conditions under which dense, molecular gas is able to form within a galaxy, we post-process a series of three-dimensional galactic-disk-scale simulations with ray-tracing based radiative transfer and chemical network integration to compute the equilibrium chemical and thermal state of the gas. In performing these simulations we vary a number of parameters, such as the ISRF strength, vertical scale height of stellar sources, cosmic ray flux, to gauge the sensitivity of our results to these variations. Self-shielding permits significant molecular hydrogen (H2) abundances in dense filaments around the disk midplane, accounting for approximately ~10-15% of the total gas mass. Significant CO fractions only form in the densest, n>~10^3 cm^-3, gas where a combination of dust, H2, and self-shielding attenuate the FUV background. We additionally compare these ray-tracing based solutions to photochemistry with complementary models where photo-shielding is accounted for with locally computed prescriptions. With some exceptions, these local models for the radiative shielding length perform reasonably well at reproducing the distribution and amount of molecular gas as compared with a detailed, global ray tracing calculation. Specifically, an approach based on the Jeans Length with a T=40K temperature cap performs the best in regards to a number of different quantitative measures based on the H2 and CO abundances.Comment: 21 Pages, 15 figures. Submitted to MNRAS. Comments welcom

Multi-Choice Minority Game

The generalization of the problem of adaptive competition, known as the minority game, to the case of $K$ possible choices for each player is addressed, and applied to a system of interacting perceptrons with input and output units of the type of $K$-states Potts-spins. An optimal solution of this minority game as well as the dynamic evolution of the adaptive strategies of the players are solved analytically for a general $K$ and compared with numerical simulations.Comment: 5 pages, 2 figures, reorganized and clarifie