Reducing Communication in the Solution of Linear Systems

There is a growing performance gap between computation and communication on modern computers, making it crucial to develop algorithms with lower latency and bandwidth requirements. Because systems of linear equations are important for numerous scientific and engineering applications, I have studied several approaches for reducing communication in those problems. First, I developed optimizations to dense LU with partial pivoting, which downstream applications can adopt with little to no effort. Second, I consider two techniques to completely replace pivoting in dense LU, which can provide significantly higher speedups, albeit without the same numerical guarantees as partial pivoting. One technique uses randomized preprocessing, while the other is a novel combination of block factorization and additive perturbation. Finally, I investigate using mixed precision in GMRES for solving sparse systems, which reduces the volume of data movement, and thus, the pressure on the memory bandwidth

Dominant gain-of-function mutations in Hsp104p reveal crucial roles for the middle region

Heat-shock protein 104 (Hsp104p) is a protein-remodeling factor that promotes survival after extreme stress by disassembling aggregated proteins and can either promote or prevent the propagation of prions (protein-based genetic elements). Hsp104p can be greatly overexpressed without slowing growth, suggesting tight control of its powerful protein-remodeling activities. We isolated point mutations in Hsp104p that interfere with this control and block cell growth. Each mutant contained alterations in the middle region (MR). Each of the three MR point mutations analyzed in detail had distinct phenotypes. In combination with nucleotide binding site mutations, Hsp104p(T499I) altered bud morphology and caused septin mislocalization, colocalizing with the misplaced septins. Point mutations in the septin Cdc12p suppressed this phenotype, suggesting that it is due to direct Hsp104p–septin interactions. Hsp104p(A503V) did not perturb morphology but stopped cell growth. Remarkably, when expressed transiently, the mutant protein promoted survival after extreme stress as effectively as did wild-type Hsp104p. Hsp104p(A509D) had no deleterious effects on growth or morphology but had a greatly reduced ability to promote thermotolerance. That mutations in an 11-amino acid stretch of the MR have such profound and diverse effects suggests the MR plays a central role in regulating Hsp104p function

PRESENCE AND PREVALENCE OF BD (BATRACHOCHYTRIUM DENDROBATIDIS) IN CENTRAL PENNSYLVANIAN WOODLAND VERNAL POOLS

Batrachochytrium dendrobatidis (Bd), a virulent chytrid fungus responsible for dramatic amphibian declines, has been detected in the northwestern and southeastern regions of Pennsylvania. However, little environmental Bd testing has been performed in central Pennsylvania, particularly in the unique and speciose habitats of woodland vernal pools. Our study included sampling in four vernal pools over a period of three months during amphibian breeding periods. Skin swabs were taken from three caudate and two anuran species, during the course of late winter and spring migrations (n = 143). Low Bd zoospore equivalent loads were detected in only a few individuals, in three of the five species but in all four vernal pools sampled. No significant trends were seen between zoospore loads and ambient temperature or migration timing across the species sampled

Measurement of temperature profiles in hot gases and flames

Computer program was written for calculation of molecular radiative transfer from hot gases. Shape of temperature profile was approximated in terms of simple geometric forms so profile could be characterized in terms of few parameters. Parameters were adjusted in calculations using appropriate radiative-transfer expression until best fit was obtained with observed spectra

Subunit interactions influence the biochemical and biological properties of Hsp104

Point mutations in either of the two nucleotide-binding domains (NBD) of Hsp104 (NBD1 and NBD2) eliminate its thermotolerance function in vivo. In vitro, NBD1 mutations virtually eliminate ATP hydrolysis with little effect on hexamerization; analogous NBD2 mutations reduce ATPase activity and severely impair hexamerization. We report that high protein concentrations overcome the assembly defects of NBD2 mutants and increase ATP hydrolysis severalfold, changing V(max) with little effect on K(m). In a complementary fashion, the detergent 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate inhibits hexamerization of wild-type (WT) Hsp104, lowering V(max) with little effect on K(m). ATP hydrolysis exhibits a Hill coefficient between 1.5 and 2, indicating that it is influenced by cooperative subunit interactions. To further analyze the effects of subunit interactions on Hsp104, we assessed the effects of mutant Hsp104 proteins on WT Hsp104 activities. An NBD1 mutant that hexamerizes but does not hydrolyze ATP reduces the ATPase activity of WT Hsp104 in vitro. In vivo, this mutant is not toxic but specifically inhibits the thermotolerance function of WT Hsp104. Thus, interactions between subunits influence the ATPase activity of Hsp104, play a vital role in its biological functions, and provide a mechanism for conditionally inactivating Hsp104 function in vivo

General Relativistic Radiative Transfer

We present a general method to calculate radiative transfer including scattering in the continuum as well as in lines in spherically symmetric systems that are influenced by the effects of general relativity (GR). We utilize a comoving wavelength ansatz that allows to resolve spectral lines throughout the atmosphere. The used numerical solution is an operator splitting (OS) technique that uses a characteristic formal solution. The bending of photon paths and the wavelength shifts due to the effects of GR are fully taken into account, as is the treatment of image generation in a curved spacetime. We describe the algorithm we use and demonstrate the effects of GR on the radiative transport of a two level atom line in a neutron star like atmosphere for various combinations of continuous and line scattering coefficients. In addition, we present grey continuum models and discuss the effects of different scattering albedos on the emergent spectra and the determination of effective temperatures and radii of neutron star atmospheres

IoTility:Architectural Requirements for Enabling Health IoT Ecosystems

The increasing ubiquity of the Internet of Things (IoT) has the potential to drastically alter the way healthcare systems are utilized at home or in a care environment. Smart things offer new ways to assist in general patient wellness, such as promoting an active and healthy lifestyle and simplifying treatment management. We believe smart health things bring new requirements not typically addressed in traditional IoT systems, and that an architecture targeting these devices must address such requirements to fully utilize their potential and safe usage. We believe such an architecture will help improve adoption and efficacy, closing gaps between the variety of emerging health IoT systems. In this paper, we present a number of requirements we consider integral to the continued expansion of the digital health IoT ecosystem (Health IoT). We consider the current landscape of IoT in relation to these requirements and present solutions that address two pressing requirements: 1) democratizing mobile health apps (giving users control and ownership over their app and data), and 2) making mobile apps act and behave like any other thing in an IoT. We present an implementation and evaluation of these Health IoT requirements to show how health-specific solutions can drive and influence the design of more generalized IoT architectures