Bulletin of the American Physical Society
Joint Spring 2016 Meeting of the Texas Sections of APS, AAPT, and Zone 13 of the SPS
Volume 61, Number 3
Thursday–Saturday, March 31–April 2 2016; Beaumont, Texas
Session D1: APS Session - Computational Science |
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Chair: Martin Tchernookov, Lamar University Room: 206 |
Friday, April 1, 2016 4:00PM - 4:24PM |
D1.00001: Extrinsic and intrinsic correlations in molecular information transmission Invited Speaker: Martin Tchernookov Cells learn about their environment by measuring concentrations of external ligands. They do so by capturing ligand molecules with cell surface receptors. On one hand, the variation in the numbers of molecules captured by different receptors depends on the spatio-temporal structure of the extrinsic ligand fluctuations. On the other, this variation is affected by the intrinsic stochasticity of chemical processes because a single molecule randomly captured by a receptor cannot be captured by another. Such structure of receptor correlations is generally believed to lead to an increase in information about the external signal compared to the case of independent receptors. We analyse a model of two single-occupancy receptors and show that, contrary to the established intuition, the correlations have a small and negative effect on the information about the ligand concentration. Further, we show that measurements that average over multiple receptors are almost as informative as those that track the states of every individual one. [Preview Abstract] |
Friday, April 1, 2016 4:24PM - 4:36PM |
D1.00002: Correlation study of human daytime activity pattern and night time sleep quality. Sharmin Sultana, Dr. Gleb Tcheslavski Although day-time activities and night-time sleep may seem to be controlled by different physical mechanisms in human, several methods have been developed over the last years to estimate a correlation between them. The total counts of actigraphy data and self-rated evaluation of sleep quality have been used in most research. In this paper, a new correlation study of human daytime activity pattern and sleep quality based on completely objective and quantitative data is discussed. Many factors, such as light exposure, diet, daytime activity, have been identified as possibly affecting human sleep. In this method, the quality of sleep is evaluated using the delta power of non-rapid eye movement stage sleep in the electroencephalogram. The fluctuation of human actigraphy data follows a scale-invariant pattern that is quantified by the detrended fluctuation analysis. A positive correlation exists between the human day-time activity pattern and the sleep quality. The subjects, whose daytime activity pattern followed a robust scale-invariant pattern, are more likely to experience a better sleep characterized by a higher total delta power. The aim of this paper is to assess how human day-time activity pattern correlates with the night-time sleep quality. [Preview Abstract] |
Friday, April 1, 2016 4:36PM - 4:48PM |
D1.00003: Implementation Of An Efficient Parallel 3-D Finite Element Solver For The Equations of Viscous, Resistive Magnetohydrodynamics Using A Velocity-Current Formulation. Keith Brauss, Amnon Meir We describe the implementation of a parallel finite element method for the viscous, resistive magnetohydrodynamics (MHD) equations using a velocity-current formulation [proposed by A.J. Meir and Paul G. Schmidt]. The velocity-current formulation of the viscous, resistive MHD equations can be used for modeling phenomena occurring in plasma fusion reactors, liquid metal casting of aluminum, and the Czochralski crystal growth of silicon for the semiconductor industry. The velocity-current formulation is a system of nonlinear integro-differential equations whose solution is approximated through a Picard linearization, discretized using the finite element method, and solved iteratively with the Krylov subspace method GMRES. Effective preconditioning strategies are required to numerically solve the equations. A simple preconditioner is constructed and successfully tested with the Krylov method GMRES. ~The parallel solver for the equations utilizes open-source, freely-available, academic and government funded supercomputing software libraries. [Preview Abstract] |
Friday, April 1, 2016 4:48PM - 5:00PM |
D1.00004: Estimating the Abundance of Ambrosia Pollen using Machine Learning Xun Liu Plants of the genus Ambrosia (ragweed) are known to produce a variety of allergies.Early warning of likely pollen levels can be of use to people with asthma and COPD, etc. However, providing accurate early warnings is challenging. The traditional approach to measuring pollen is labor intensive, including counting the number of pollen particles under a microscope. The purpose of this research is to estimate pollen concentration, with a suite of environmental parameters from meteorology and remote sensing, using machine learning. Machine learning method are applied on the history pollen data and environmental data in Tulsa, to build a regression model describing the way that environmental data influencing pollen concentration. This model is then being used to predict pollen data with new environmental data. The prediction is then compared with new real observation. The result shows the ranking of most influencing environmental factors. As well as the effectiveness of such prediction. [Preview Abstract] |
Friday, April 1, 2016 5:00PM - 5:12PM |
D1.00005: openGR: An Infrastructure for Numerical Relativity Paul Walter, Andrea Nerozzi, Matt Anderson, Richard Matzner, Jon Allen, Greg McIvor, Matt Selover, Uli Sperhake We present the current state of the code {\it openGR}, which is a modular, open framework developed to carry out simulations of binary black hole mergers. While designed with the two-body problem in mind, {\it openGR} will evolve most general vacuum spacetimes. The code is based on the adaptive mesh refinement library \texttt{SAMRAI}. We describe the main features of the code and give the results of simulations of head-on binary black hole mergers. We will discuss the scaling properties of {\it openGR} and its overall status. The code will be made publicly available. [Preview Abstract] |
Friday, April 1, 2016 5:12PM - 5:24PM |
D1.00006: Many-Body Density Matrix Theory CJ Tymczak Accurate many-body formalisms for quantum chemical methods do exist, but these methods are computationally very expensive. Methods also exist that are much less computationally expensive such as Hatree-Fock, Density Functional and the Hybrid Functional theories, but at a reduced representation of the exact many-body ground state. This severely limits either the system size that can be addressed accurately, or the accuracy of the representation. What is needed is a method that represents the many-body ground states accurately, but with a low computational cost. Recently, a method for determining the response, to any order of the perturbation, within the density matrix formalism has been discovered. This method opens up the possibility of computing the variational many-body ground states to unprecedented accuracy within a simplified computational approach. We report on the theoretical development of this methodology, which we refer to as Many Body Density Matrix Theory. This theory has many significant advantages over existing methods. One, its computational cost is equivalent to Hartree-Fock or Density Functional theory. Two it is a variational upper bound to the exact many-body ground state energy. Three, like Hartree-Fock, it has no self-interaction. And four, it is size extensive. [Preview Abstract] |
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