Browsing by Type "journal article pre-print"
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Item An Approximate Fisher Scoring Algorithm for Finite Mixtures of MultinomialsRaim, Andrew M.; Liu, Minglei; Neerchal, Nagaraj K.; Morel, Jorge G.Finite mixture distributions arise naturally in many applications including clustering and classi cation. Since they usually do not yield closed forms for maximum likelihood estimates (MLEs), numerical methods using the well known Fisher Scoring or Expectation-Maximization algorithms are considered. In this work, an approximation to the Fisher Information Matrix of an arbitrary mixture of multinomial distributions is introduced. This leads to an Approximate Fisher Scoring algorithm (AFSA), which turns out to be closely related to Expectation-Maximization, and is more robust to the choice of initial value than Fisher Scoring iterations. A combination of AFSA and the classical Fisher Scoring iterations provides the best of both computational efficiency and stable convergence properties.Item Attribute Based Encryption for Secure Access to Cloud Based EHR Systems(IEEE, 2018-09-10) Joshi, Maithilee; Joshi, Karuna; Finin, TimMedical organizations find it challenging to adopt cloud-based electronic medical records services, due to the risk of data breaches and the resulting compromise of patient data. Existing authorization models follow a patient centric approach for EHR management where the responsibility of authorizing data access is handled at the patients' end. This however creates a significant overhead for the patient who has to authorize every access of their health record. This is not practical given the multiple personnel involved in providing care and that at times the patient may not be in a state to provide this authorization. Hence there is a need of developing a proper authorization delegation mechanism for safe, secure and easy cloud-based EHR management. We have developed a novel, centralized, attribute based authorization mechanism that uses Attribute Based Encryption (ABE) and allows for delegated secure access of patient records. This mechanism transfers the service management overhead from the patient to the medical organization and allows easy delegation of cloud-based EHR's access authority to the medical providers. In this paper, we describe this novel ABE approach as well as the prototype system that we have created to illustrate it.Item C-phase gates in SiMOS and Si/SiGe double quantum dotsGüngördü, Utkan; Kestner, J. P.We theoretically analyze the errors in one- and two-qubit gates in SiMOS and Si/SiGe spin qubit experiments, and present a pulse sequence which can suppress the errors in exchange coupling due to charge noise using ideal local rotations. In practice, the overall fidelity of the pulse sequence will be limited only by the quality of the single-qubit gates available: the C-phase infidelity comes out to be ≈2.5× the infidelity of the single-qubit operations. Based on experimental data, we model the errors and show that C-phase gate infidelities can be suppressed by two orders in magnitude. Our pulse sequence is simple and we expect an experimental implementation would be relatively straightforward. We also evaluate the performance of this gate against 1/f noise. Assuming a soft ultraviolet cutoff, we show that the pulse sequence designed for quasistatic noise still performs well when the cutoff occurs below ∼1 MHz given fast enough one-qubit Rabi frequencies, suppressing the infidelity by an order of magnitude compared to the existing direct adiabatic protocol. We also analyze the effects of nonadiabaticity during finite rise periods, and find that adiabaticity is not a limitation for the current values of exchange coupling.Item Computational predictions suggest that structural similarity in viral polymerases may lead to comparable allosteric binding sites.(Elsevier, 2016-06-01) Brown, J. A.; Espiritu, M. V.; Abraham, J.; Thorpe, I. F.The identification of ligand-binding sites is often the first step in drug targeting and design. To date there are numerous computational tools available to predict ligand binding sites. These tools can guide or mitigate the need for experimental methods to identify binding sites, which often require significant resources and time. Here, we evaluate four ligand-binding site predictor (LBSP) tools for their ability to predict allosteric sites within the Hepatitis C Virus (HCV) polymerase. Our results show that the LISE LBSP is able to identify all three target allosteric sites within the HCV polymerase as well as a known allosteric site in the Coxsackievirus polymerase. LISE was then employed to identify novel binding sites within the polymerases of the Dengue, West Nile, and Foot-and-mouth Disease viruses. Our results suggest that all three viral polymerases have putative sites that share structural or chemical similarities with allosteric pockets of the HCV polymerase. Thus, these binding locations may represent an evolutionarily conserved structural feature of several viral polymerases that could be exploited for the development of small molecule therapeutics.Item Efficient Simulation of a Reaction-Diffusion System with a Fast Reaction in the Asymptotic Limit(2012-09-25) Wang, Guan; Churchill, Aaron; Seidman, Thomas I.We study a reaction-diffusion system of three chemical species, where two chemicals react with a much faster reaction rate than the other reaction in the model. We are interested in the asymptotic limit as the fast reaction rate becomes infinite. This forces the reaction interface to have an asymptotically small width with asymptotically large height. This interface is moving in time and causes interior layers that are progressively more challenging and costly for numerical simulations of the three species model, as the singularity becomes sharper with larger reaction rates. But in the asymptotic limit, an equivalent two component model can be defined that is significantly cheaper computationally and allows for effective studies for the model. The equivalence is demonstrated by the analytical definition of the two component model and by comparing numerical results to ones for the three species model with progressively larger reaction rates, which also demonstrate the computational efficiency. The state-of-the-art finite element package COMSOL Multiphysics is used for the simulations, thus also showing a practical way how to handle and visualize moving interior layers in reaction-diffusion systems. COMSOL is popular in many areas of engineering and the sciences and thus the mathematical example here can provide guidance to a wide range of users with models consisting of partial differential equations.Item Elastic capsule deformation in general irrotational linear flows(IOP Publishing Ltd, 2012-07-05) Szatmary, Alex C.; Eggleton, Charles D.Knowledge of the response of elastic capsules to an imposed fluid flow is necessary for predicting the deformation and motion of biological cells and synthetic capsules in microfluidic devices and in microcirculation. Capsules have been studied in shear, planar extensional and axisymmetric extensional flows. Here, the flow gradient matrix of a general irrotational linear flow is characterized by two parameters, its strain rate, defined as the maximum of the principal strain rates, and a new term, q, the difference of the two lesser principal strain rates, scaled by the maximum principal strain rate; this characterization is valid for ellipsoids in irrotational linear flow, and gives good results for spheres in general linear flows at low capillary numbers. We demonstrate that deformable non-spherical particles align with the principal axes of an imposed irrotational flow. Thus, it is most practical to model deformation of non-spherical particles already aligned with the flow, rather than considering each arbitrary orientation. Capsule deformation was modeled for a sphere, a prolate spheroid and an oblate spheroid, subjected to combinations of uniaxial, biaxial and planar extensional flows; modeling was performed using the immersed boundary method. The time response of each capsule to each flow was found, as were the steady-state deformation factor, mean strain energy and surface area. For a given capillary number, planar flows led to more deformation than uniaxial or biaxial extensional flows. Capsule behavior in all cases was bounded by the response of capsules to uniaxial, biaxial and planar extensional flows.Item Energized Rigid Body Fracture(Association for Computing Machinery (ACM), 2018-07) Li, Xiaokai; Jones, Ben; Andrews, Sheldon; Bargteil, AdamCompelling animation of fracture is a vital challenge for computer graphics. Methods based on continuum mechanics are physically accurate, but computationally expensive since they require computing elastic deformation. In many applications, this elastic deformation is imperceptible, so simulation methods based on rigid body dynamic with breakable constraints are popular in practice. Simply deleting constraints when thresholds on force or displacement are reached ignores the elastic energy that is stored just before fracture, which is captured by continuum mechanics based methods. Our approach computes the energy stored in these constraints when they are broken, and reintroduces it to the system as kinetic energy. As a result, our method is able to animate energetic fracture scenarios with results comparable to continuum mechanics approaches, but with the computational efficiency of rigid body simulation.Item Finite element approximation for time-dependent diffusion with measure-valued source(Springer-Verlag, 2012-06-20) Seidman, Thomas I.; Gobbert, Matthias K.; Trott, David W.; Kružík, MartinThe convergence of finite element methods for elliptic and parabolic partial differential equations is well-established if source terms are sufficiently smooth. Noting that finite element computation is easily implemented even when the source terms are measure-valued—for instance, modeling point sources by Dirac delta distributions—we prove new convergence order results in two and three dimensions both for elliptic and for parabolic equations with measures as source terms. These analytical results are confirmed by numerical tests using COMSOL Multiphysics.Item The Graph 500 Benchmark on a Medium-Size Distributed-Memory Cluster with High-Performance Interconnect(2012-12-17) Angel, Jordan B.; Flores, Amy M.; Heritage, Justine S.; Wardrip, Nathan C.; Raim, Andrew M.; Gobbert, Matthias K.; Murphy, Richard C.; Mountain, David J.While traditional performance benchmarks for high-performance computers measure the speed of arithmetic operations, memory access time is a more useful performance gauge for many large problems today. The Graph 500 benchmark has been developed to measure a computer’s performance in memory retrieval. The Graph 500 implementation considers large, randomly generated graphs, which may be spread across many nodes on a distributed memory cluster. The benchmark conducts breadth-first searches on these graphs, and measures performance in billions of traversed edges per second (GTEPS). We present our experience implementing and running the Graph 500 benchmark on the medium-size distributed-memory cluster tara in the UMBC High Performance Computing Facility (www.umbc.edu/hpcf). The cluster tara has 82 compute nodes, each with two quad-core Intel Nehalem X5550 CPUs and 24 GB of memory, connected by a high-performance quad-data rate InfiniBand interconnect. Results are explained in detail in terms of the machine architecture, which demonstrates that the Graph 500 benchmark indeed provides a measure of memory access as the chief bottleneck for many applications. Our best run to date was of scale 31 using 64 nodes and achieved a GTEPS rate that placed tara at rank 98 on the November 2012 Graph 500 list.Item A Hölder type inequality and an interpolation theorem in Euclidean Jordan algebras(2018-09-14) Gowda, Muddappa SeetharamaIn a Euclidean Jordan algebra V of rank n which carries the trace inner product, to each element x we associate the eigenvalue vector λ(x) whose components are the eigenvalues of x written in the decreasing order. For any p ∈ [1,∞], we define the spectral p-norm of x to be the p-norm of λ(x) in Rⁿ. In this paper, we show that ||x ◦ y||1 ≤ ||x|| ||y||q, where x ◦ y denotes the Jordan product of two elements x and y in V and q is the conjugate of p. For a linear transformation on V, we state and prove an interpolation theorem relative to these spectral norms. In addition, we compute/estimate the norms of Lyapunov transformations, quadratic representations, and positive transformations on V.Item Joint transformation based detection of false data injection attacks in smart grid(IEEE, 2017-06-28) Singh, Sandeep Kumar; Khanna, Kush; Bose, Ranjan; Joshi, AnupamFor reliable operation and control of smart grid, estimating the correct states is of utmost importance to the system operator. With recent incorporation of information technology and advanced metering infrastructure, the futuristic grid is more prone to cyber-threats. The false data injection (FDI) attack is one of the most thoroughly researched cyber-attacks. Intelligently crafted, it can cause false estimation of states, which further seriously affects the entire power system operation. In this paper, we propose joint-transformation-based scheme to detect FDI attacks in real time. The proposed method is built on the dynamics of measurement variations. Kullback-Leibler distance is used to find out the difference between probability distributions obtained from measurement variations. The proposed method is tested using IEEE 14 bus system considering attack on different state variables. The results shows that the proposed scheme detects FDI attacks with high detection probabilityItem Maximum-likelihood estimation of the random-clumped multinomial model as a prototype problem for large-scale statistical computing(Taylor and Francis Online, 2012-05-08) Raim, Andrew M.; Gobbert, Matthias K.; Neerchal, Nagaraj K.; Morel, Jorge G.Numerical methods are needed to obtain maximum-likelihood estimates (MLEs) in many problems. Computation time can be an issue for some likelihoods even with modern computing power. We consider one such problem where the assumed model is a random-clumped multinomial distribution. We compute MLEs for this model in parallel using the Toolkit for Advanced Optimization software library. The computations are performed on a distributed-memory cluster with low latency interconnect. We demonstrate that for larger problems, scaling the number of processes improves wall clock time significantly. An illustrative example shows how parallel MLE computation can be useful in a large data analysis. Our experience with a direct numerical approach indicates that more substantial gains may be obtained by making use of the specific structure of the random-clumped modelItem Numerical and Experimental Investigation for a Resonant Optothermoacoustic Sensor(IEEE, 2010-07-01) Petra, N.; Kosterev, A. A.; Zweck, J.; Minkoff, S. E.; Doty, J. H.A theoretical study of a resonant optothermoacoustic sensor employing a laser source and a quartz tuning fork receiver validates experimental results showing that the source should be positioned near the base of the receiver.Item The Optimal Relaxation Parameter for the SOR Method Applied to the Poisson Equation in Any Space Dimensions(Elsevier Ltd, 2009-03-24) Yang, Shiming; Gobbert, Matthias K.The finite difference discretization of the Poisson equation with Dirichlet boundary conditions leads to a large, sparse system of linear equations for the solution values at the interior mesh points. This problem is a popular and useful model problem for performance comparisons of iterative methods for the solution of linear systems. To use the successive overrelaxation (SOR) method in these comparisons, a formula for the optimal value of its relaxation parameter is needed. In standard texts, this value is only available for the case of two space dimensions, even though the model problem is also instructive in higher dimensions. This note extends the derivation of the optimal relaxation parameter to any space dimension and confirms its validity by means of test calculations in three dimensions.Item Parallelizing Computation of Expected Values in Recombinant Binomial Trees(Taylor and Francis Online, 2017-11-24) Popuri, Sai K.; Raim, Andrew M.; Neerchal, Nagaraj K.; Gobbert, Matthias K.Recombinant binomial trees are binary trees where each non-leaf node has two child nodes, but adjacent parents share a common child node. Such trees arise in option pricing in finance. For example, an option can be valued by evaluating the expected payoffs with respect to random paths in the tree. The cost to exactly compute expected values over random paths grows exponentially in the depth of the tree, rendering a serial computation of one branch at a time impractical. We propose a parallelization method that transforms the calculation of the expected value into an embarrassingly parallel problem by mapping the branches of the binomial tree to the processes in a multiprocessor computing environment. We also discuss a parallel Monte Carlo method and verify the convergence and the variance reduction behavior by simulation study. Performance results from R and Julia implementations are compared on a distributed computing cluster.Item Resolving the X-ray obscuration in a low flux observation of the quasar PDS 456(2018-09-19) Reeves, James; Braito, Valentina; Nardini, Emanuele; Hamann, Fred; Chartas, George; Lobban, Andrew; O'Brien, Paul; Turner, JaneSimultaneous XMM-Newton, NuSTAR and HST observations, performed in March 2017, of the nearby (z=0.184 ) luminous quasar PDS 456 are presented. PDS 456 had a low X-ray flux compared to past observations, where the first of the two new XMM-Newton observations occurred during a pronounced dip in the X-ray lightcurve. The broad-band X-ray spectrum is highly absorbed, attenuated by a soft X-ray absorber of column density N H =6×10 ²² cm ⁻² . An increase in obscuration occurs during the dip, which may be due to an X-ray eclipse. In addition, the persistent, fast Fe K outflow is present, with velocity components of −0.25c and −0.4c . The soft absorber is less ionized (logξ=3 ) compared to the iron K outflow (logξ=5 ) and is outflowing with a velocity of approximately −0.2c . A soft X-ray excess is present below 1 keV against the highly absorbed continuum and can be attributed to the re-emission from a wide angle wind. The complex X-ray absorption present in PDS 456 suggests that the wind is inhomogeneous, whereby the soft X-ray absorber originates from denser clumps or filaments which may form further out along the outflow. In contrast to the X-ray observations, the simultaneous UV spectrum of PDS 456 is largely unabsorbed, where only a very weak broad absorption trough is present bluewards of Lyα , compared to a past observation in 2000 when the trough was significantly stronger. The relative weakness of the UV absorption may be due to the soft X-ray absorber being too highly ionized and almost transparent in the UV band.Item Storage stability of electrospun pure gelatin stabilized with EDC/Sulfo‐NHS(Wiley Periodicals, 2018-09-06) Ghassemi, Zahra; Slaughter, GymamaWith the rapid development of biomimetic polymers for cell‐based assays and tissue engineering, crosslinking electrospun nanofibrous biopolymer constructs is of great importance for achieving sustainable and efficient three‐dimensional scaffold constructs. Uncrosslinked electrospun gelatin nanofibrous constructs immediately and completely dissolved in aqueous solutions due to their aqueous solubility and poor storage stability. Here, a novel and versatile approach for the fabrication and crosslinking of electrospun gelatin construct with tunable porosity and high aspect ratio nanofibers is presented. Uncrosslinked electrospun gelatin/genipin nanofibrous and pure gelatin nanofibrous constructs exhibited smooth surfaces that were well‐defined, with a diameter in the range of 448 ± 364 nm and 257 ± 57 nm, respectively. Dehydrothermal, genipin‐EDC/Sulfo‐NHS, and EDC/Sulfo‐NHS crosslinking approaches were examined to achieve insoluble gelatin nanofibrous constructs that were suitable for cell‐based assays. Mechanical characterization demonstrated that the pure gelatin nanofibrous construct crosslinked via EDC/Sulfo‐NHS exhibited an increased mechanical strength and stiffness and showed no dissolution in aqueous solutions and retained its fiber morphology. An excellent 1 month storage stability was demonstrated at 22, 4, −20, and −80°C (dehydrated) and at 4°C (hydrated). The as‐crosslinked gelatin nanofibrous construct was highly biocompatible (90% cell viability), as demonstrated by the promoted proliferation of PC12 cells.Item A Theoretical Method to determine unstressed off-rate from multiple bond force spectroscopy(Elsevier B.V, 2012-06-15) Eggleton, C.D.; Gupta, V.K.Using dynamic force spectroscopy to measure the kinetic off-rates of intermolecular bonds currently requires the isolation of single molecules. This requirement arises in part because no tractable analytic method for determining kinetic off-rates from the rupture of a large number of bonds under dynamic forces is currently available. We introduce a novel method for determining the unstressed off-rate from dynamic force spectroscopy experiments involving a large number of bonds. Using both the Bell and Dembo models we show that the unstressed off-rate calculated using the proposed method is in good agreement with the prescribed unstressed off-rate used in Monte-Carlo simulations of multiple bond dynamic force spectroscopy experiments given initial number of bonds (50–500) and loading rate 10³ – 10⁶ pN/s.