Poster for the May 10, 2014 "Music From a Mastermind" concert, presented by the Salisbury Symphony Orchestra. Featured guest Gloria Chien.
Poster of the March 8, 2014 performance of cellist Douw Fonda presented by the Salisbury Symphony Orchestra.
2014-2015 season brochure for the Salisbury Symphony Orchestra.
Poster for the May 14, 2016 performance "American Celebration." Featuring Capitol Quartet.
Poster for the annual holiday concert of the Salisbury Symphony Orchestra, December 6, 2014. Featured guest Igor Kalnin.
Poster for the October 11, 2014 concert "Music from an Elegant Era." Featured guest Nelson Padgett.
Motivation: Data from metagenomics projects remain largely untapped for the analysis of transcriptional regulatory networks. Here, we provide proof-of-concept that metagenomic data can be effectively leveraged to analyze regulatory networks by characterizing the SOS meta-regulon in the human gut microbiome. Results: We combine well-established in silico and in vitro techniques to mine the human gut microbiome data and determine the relative composition of the SOS network in a natural setting. Our analysis highlights the importance...
Calculation of the expected output spectrum for a mid-infrared supercontinuum source based on As₂S₃ chalcogenide photonic crystal fibers.R. J. Weiblen, A. Docherty, C. R. Menyuk, L. B. Shaw, J. S. Sanghera & I. D. Aggarwal
We computationally investigate supercontinuum generation in an As₂S₃ solid core photonic crystal fiber (PCF) with a hexagonal cladding of air holes. With a goal of obtaining a supercontinuum output spectrum that can predict what might be seen in an experiment, we investigate the spectral and statistical behavior of a mid-infrared supercontinuum source using a large ensemble average of 10⁶ realizations, in which the input pulse duration and energy vary. The output spectrum is sensitive to...
'What is,' 'What Was' and 'What Might Be': Reactionary metamorphosis of postwar acknowledgement in romanticismKelli D. Wilhelm
This graduate thesis explores the implications of reactions to the French Revolution and Napoleonic Wars upon perceived self and gender roles in the Romantic period as seen in William Wordsworth's The Prelude, Lord's Byron's Canto III of Childe Harold's Pilgrimage, Charlotte Smith's The Old Manor House and Jane Austen's Persuasion. Reactions to wartime manifest in nostalgic visions of past and present in which the male poets' dwell and which the female novelists' criticize. Interaction between...
Inhibitors for the hepatitis C virus RNA polymerase explored by SAR with advanced machine learning methodsIwona E. Weidlich, Igor V. Filippov, Jodian Brown, Neerja Kaushik Basu, Ramalingam Krishnan, Marc C. Nicklaus & Ian F. Thorpe
DOI:10.1016/j.bmc.2013.03.032 ; Author's post-print must be released with a Creative Commons Attribution Non-Commercial No Derivatives License
Indenone and cyclopentadienone energetics via mass spectrometry and computations: Are these species antiaromatic or “merely” nonaromatic?Alireza Fattahi, Joel F. Liebman, Margarida S. Miranda, Victor M.F. Morais, M. Agostinha R. Matos, Lev Lis & Steven R. Kass
The heat of hydrogenation of indenone was measured via two partially independent thermodynamic cycles by carrying out energetic measurements (i.e., electron affinities, proton affinities and ionization potentials) on both negative and positive ions (ΔH°(H2) = 17.8 ± 5.5 and 17.5 ± 5.7 kcal mol⁻¹, respectively). High level G3 computations were also carried out to provide the heats of formation of indenone (16.8 kcal mol⁻¹) and cyclopentadienone (14.0 kcal mol⁻¹). These 4n π electron systems are...
Transcription factors (TFs) regulate transcription by binding to specific sites in promoter regions. Information theory provides a useful mathematical framework to analyze the binding motifs associated with TFs but imposes several assumptions that limit their applicability to specific regulatory scenarios. Explicit simulations of the co-evolution of TFs and their binding motifs allow the study of the evolution of regulatory networks with a high degree of realism. In this work we analyze the impact of differential...
A Memory-Efficient Finite Volume Method for Advection-Diffusion-Reaction Systems with Non-Smooth SourcesJonas Schafer, Xuan Huang, Stefan Kopecz, Philipp Birken, Matthias K. Gobbert & Andreas Meister
Jonas Schafer, Xuan Huang, Stefan Kopecz, Philipp Birken, Matthias K. Gobbert, Andreas Meister, A memory‐efficient finite volume method for advection‐diffusion‐reaction systems with nonsmooth sources, Numerical Methods fro Partial Differential Equations, Volume 31, Issue1, January 2015, Pages 143-167, https://doi.org/10.1002/num.21897, https://onlinelibrary.wiley.com/doi/abs/10.1002/num.21897
Many physical phenomena can be described by partial differential equations which can be discretized to form systems of linear equations. We apply the finite difference method to the Poisson equation with homogeneous Dirichlet boundary conditions, which yields a system of linear equations with a large sparse system matrix. We implement pMatlab code which utilizes the conjugate gradient method to solve this system. We do not recommend the use of pMatlab at this time as we...
We investigate high performance solutions to the global illumination problem in computer graphics. An existing CPU serial implementation using the radiosity method is given as the performance baseline where a scene and corresponding form-factor coefficients are provided. The initial computational radiosity solver uses the classical Jacobi method as an iterative approach to solving the radiosity linear system. We add the option of using the modern BiCG-STAB method with the aim of reduced runtime through a...
Parallelization of code, using multiple cores/threads, and heterogeneous computing, using the CPU with other devices, has come to the forefront of computing as methods to reduce the execution time of computationally demanding algorithms. For our project, we test various hardware setups on the maya cluster at UMBC, which include multiple nodes and GPUs, by solving the Poisson equation using the conjugate gradient method. To explore these different setups, we made use of both industry benchmarks...
Our goal is to create a computational model of an islet of Langerhans, consisting of 𝛼-, β -, and 𝛿-cells. We will focus on varying the geometries and proportions of the cells in this islet, and study the hormonal secretion and reception of each cell at any point in time. We are currently considering basic cubic and spherical models, among others. Besides changing the physical shape of our islet, we will change the sequential ordering...
This project creates software tools to streamline the computational procedures to generate high-resolution weather parameters from low resolution Global Climate Models (GCM) to be input into the Soil and Water Assessment Tool (SWAT) and to visualize GCM temperature and precipitation data as well as SWAT outputs of crop data. Data from GCMs have relatively low spatial resolution ( 100km x 100km), which needs to be downscaled to a higher resolution to match the resolution of...
The study of allostery, a regulatory process that occurs in complex macromolecules such as proteins, is of particular interest as it has a key role in determining the function of these macromolecules. Allostery produces motional correlations that can be analyzed using different statistical methods. We implement a program in the statistical programming language R that uses polynomial regression and leave-one-out cross-validation to model relationships in data obtained from different sites in the protein, using the...
A Comparison of Solving the Poisson Equation Using Several Numerical Methods in Matlab and Octave on the Cluster mayaSarah Swatski, Samuel Khuvis & Matthias K. Gobbert
Systems of linear equations resulting from partial differential equations arise frequently in many phenomena such as heat, sound, and fluid flow. We apply the finite difference method to the Poisson equation with homogeneous Dirichlet boundary conditions. This yields in a system of linear equations with a large sparse system matrix that is a classical test problem for comparing direct and iterative linear solvers. We compare the performance of Gaussian elimination, three classical iterative methods, and...
Numerical Methods to Solve 2-D and 3-D Elliptic Partial Differential Equations Using Matlab on the Cluster mayaDavid Stonko, Samuel Khuvis & Matthias K. Gobbert
Discretizing the elliptic Poisson equation with homogeneous Dirichlet boundary conditions by the finite difference method results in a system of linear equations with a large, sparse, highly structured system matrix. It is a classical test problem for comparing the performance of direct and iterative linear solvers. We compare in this report Gaussian elimination applied to a dense system matrix, Gaussian elimination applied to a sparse system matrix, the classical iterative methods of Jacobi, Gauss-Seidel, and...
High performance parallel computing depends on the interaction of a number of factors including the processors, the architecture of the compute nodes, their interconnect network, and the numerical method, and its implication. In this note, we present performance and scalability studies on the newest portion of the cluster maya, referred to as maya 2013, using an existing parallel code for a three-species application problem. This application problem requires long-time simulations on a fine mesh, thus...
We report parallel performance studies on the newest portion of the cluster maya in the UMBC High Performance Computing Facility (HPCF), referred to as maya 2013, for a parabolic test problem given by a time-dependent, scalar, linear reaction-diffusion equation in three dimensions. The results show very good performance up to 64 compute nodes and support several key conclusions: (i) The newer nodes are faster per core as well as per node, however, for most serial...
The UMBC High Performance Computing Facility (HPCF) is the community-based, interdisciplinary core facility for scientific computing and research on parallel algorithms at UMBC. Released in Summer 2014, the current machine in HPCF is the 240-node distributed-memory cluster maya. The cluster is comprised of three uniform portions, one consisting of 72 nodes based on 2.6 GHz Intel E5-2650v2 Ivy Bridge CPUs from 2013, another consisting of 84 nodes based on 2.8 GHz Intel Nehalem X5560 CPUs...
Quarterly newsletter for the alumni of the Ropers Victim Assistance Academy of Maryland.
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