Advanced Computing Systems for Scientific Research

An advanced computing system was constructed at Bridgewater State University to provide students access to computing machines tailored to the purpose of computational scientific research. This paper provides an overview of the construction, design, capability, and future potential of the computing system. Project Reasoning During the course of projects utilizing a numerical weather prediction (NWP) model, it became evident that the desktop computing machines provided to students in computer labs were not capable of yielding results in a reasonable amount of time for non-standard applications. The standard configuration of computers in the Conant Science and Mathematics Center at Bridgewater State University is sufficient for the majority of student purposes; however, these standard computers become insufficient for more comprehensive applications. Because of this insufficiency, it became necessary to seek better performing computer systems to support research applications. Project Execution To increase the computational power of computing systems on campus, two distinct steps were taken. The first step was the upgrade of a standard desktop computer. This upgrade provided a single desktop machine with superior computing capability to the standard machines available to students. The second step was the construction of a Linux computer cluster from several networked previous generation machines

Bloch-Redfield equations for modeling light-harvesting complexes

We challenge the misconception that Bloch-Redfield equations are a less powerful tool than phenomenological Lindblad equations for modeling exciton transport in photosynthetic complexes. This view predominantly originates from an indiscriminate use of the secular approximation. We provide a detailed description of how to model both coherent oscillations and several types of noise, giving explicit examples. All issues with non-positivity are overcome by a consistent straightforward physical noise model. Herein also lies the strength of the Bloch-Redfield approach because it facilitates the analysis of noise-effects by linking them back to physical parameters of the noise environment. This includes temporal and spatial correlations and the strength and type of interaction between the noise and the system of interest. Finally we analyze a prototypical dimer system as well as a 7-site Fenna-Matthews-Olson (FMO) complex in regards to spatial correlation length of the noise, noise strength, temperature and their connection to the transfer time and transfer

Supersolid phases of light in extended Jaynes-Cummings-Hubbard systems

Jaynes-Cummings-Hubbard lattices provide unique properties for the study of correlated phases as they exhibit convenient state preparation and measurement, as well as "in situ" tuning of parameters. We show how to realize charge density and supersolid phases in Jaynes-Cummings-Hubbard lattices in the presence of long-range interactions. The long-range interactions are realized by the consideration of Rydberg states in coupled atom-cavity systems and the introduction of additional capacitive couplings in quantum-electrodynamics circuits. We demonstrate the emergence of supersolid and checkerboard solid phases, for calculations which take into account nearest neighbour couplings, through a mean-field decoupling.Comment: 9 pages with 6 figures, accepted for publication in Physical Review

Image quality and high contrast improvements on VLT/NACO

NACO is the famous and versatile diffraction limited NIR imager and spectrograph with which ESO celebrated 10 years of Adaptive Optics at the VLT. Since two years a substantial effort has been put in to understanding and fixing issues that directly affect the image quality and the high contrast performances of the instrument. Experiments to compensate the non-common-path aberrations and recover the highest possible Strehl ratios have been carried out successfully and a plan is hereafter described to perform such measurements regularly. The drift associated to pupil tracking since 2007 was fixed in October 2011. NACO is therefore even better suited for high contrast imaging and can be used with coronagraphic masks in the image plane. Some contrast measurements are shown and discussed. The work accomplished on NACO will serve as reference for the next generation instruments on the VLT, especially those working at the diffraction limit and making use of angular differential imaging (i.e. SPHERE, VISIR, possibly ERIS).Comment: 14 pages, 5 figures, SPIE 2012 Astronomical Instrumentation Proceedin

Tau Imaging in Alzheimer's Disease Diagnosis and Clinical Trials

In vivo imaging of the tau protein has the potential to aid in quantitative diagnosis of Alzheimer's disease, corroborate or dispute the amyloid hypothesis, and demonstrate biomarker engagement in clinical drug trials. A host of tau positron emission tomography agents have been designed, validated, and tested in humans. Several agents have characteristics approaching the ideal imaging tracer with some limitations, primarily regarding off-target binding. Dozens of clinical trials evaluating imaging techniques and several pharmaceutical trials have begun to integrate tau imaging into their protocols

Observational limits on type 1 active galactic nucleus rate in COSMOS

We present black hole masses and accretion rates for 182 Type 1 active galactic nuclei (AGNs) in COSMOS. We estimate masses using the scaling relations for the broad H β, Mg ii, and C iv emission lines in the redshift ranges 0.16 < z < 0.88, 1 < z < 2.4, and 2.7 < z < 4.9. We estimate the accretion rate using an Eddington ratio LI/L_(Edd) estimated from optical and X-ray data.We find that very few Type 1 AGNs accrete below LI/L_(Edd) ∼ 0.01, despite simulations of synthetic spectra which show that the survey is sensitive to such Type 1 AGNs. At lower accretion rates the broad-line region may become obscured, diluted, or nonexistent. We find evidence that Type 1 AGNs at higher accretion rates have higher optical luminosities, as more of their emission comes from the cool (optical) accretion disk with respect to shorter wavelengths. We measure a larger range in accretion rate than previous works, suggesting that COSMOS is more efficient at finding low accretion rate Type 1 AGNs. However, the measured range in accretion rate is still comparable to the intrinsic scatter from the scaling relations, suggesting that Type 1 AGNs accrete at a narrow range of Eddington ratio, with LI/L_(Edd) ∼ 0.1

The Effects of Resistance and Plyometric Training on Vertical Jump

Several training protocols are available when it comes to increase the height of vertical jump. The purpose of the study was to test two different training protocols to see if they would generate a higher vertical jump at the end of a four week training period. This study tested to see if there was a correlation between two different types of training, resistance training and plyometric training, and the vertical jump. Both produce force and both have been used when training jump height, but which is best: resistance training or plyometric training? Six college-aged subjects who attend the University of Texas at Tyler (five male and one female) were divided into a resistance training group and a plyometric training group. Both groups then participated in four weeks of their designated training regimen. Each subject was tested at the end of each week using a Vertex and Ground Reaction Force plate to measure vertical height and force produced from each jump. We then normalized our data into percentages and inputted those values into an Excel program to create a Regression Line. The results showed that over a four-week period, plyometric training and resistance training saw an increase in vertical jump height, overall. However, the plyometric group increased their jump significantly over the four-week period and increased their force production. The resistance group, while they did increase their vertical, did not increase at the rate that the plyometric group did. Their force production generally speaking, decreased over the four-week period. However, with the data obtained, we can then use this to plan a program for coaches and their athletes. If coaches and trainers only have a short period of time, one month for example, then plyometric training is the best way to train for an increase in vertical jump height. More tests would have to be done to see if resistance training would be more effective than plyometric training over an extended period of time

Clustering, host halos and environment of z∼\sim2 galaxies as a function of their physical properties

Using a sample of 25683 star-forming and 2821 passive galaxies at $z\sim2$, selected in the COSMOS field following the BzK color criterion, we study the hosting halo mass and environment of galaxies as a function of their physical properties. Spitzer and Herschel provide accurate SFR estimates for starburst galaxies. We measure the auto- and cross-correlation functions of various galaxy sub-samples and infer the properties of their hosting halos using both an HOD model and the linear bias at large scale. We find that passive and star-forming galaxies obey a similarly rising relation between the halo and stellar mass. The mean host halo mass of star forming galaxies increases with the star formation rate between 30 and 200 M$_\odot$.yr$^{-1}$, but flattens for higher values, except if we select only main-sequence galaxies. This reflects the expected transition from a regime of secular co-evolution of the halos and the galaxies to a regime of episodic starburst. We find similar large scale biases for main-sequence, passive, and starburst galaxies at equal stellar mass, suggesting that these populations live in halos of the same mass. We detect an excess of clustering on small scales for passive galaxies and showed, by measuring the large-scale bias of close pairs, that this excess is caused by a small fraction ($\sim16$) of passive galaxies being hosted by massive halos ($\sim 3 \times 10^{13}$ M$_\odot$) as satellites. Finally, extrapolating the growth of halos hosting the z$\sim$2 population, we show that M$_\star \sim 10^{10}$ M$_\odot$ galaxies at z$\sim$2 will evolve, on average, into massive (M$_\star \sim 10^{11}$ M$_\odot$), field galaxies in the local Universe and M$_\star \sim 10^{11}$ M$_\odot$ galaxies at z=2 into local, massive, group galaxies. The most massive main-sequence galaxies and close pairs of massive, passive galaxies end up in today's clusters.Comment: 18 pages, 16 figures, Accepted by A&