Browsing by Subject "simulation"

Now showing 1 - 6 of 6
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    A modular simulation system for the bidomain equations
    Pormann, J
    Cardiac arrhythmias and fibrillation are potentially life threatening diseases that can result from the improper conduction of electrical impulses in the heart. Experimental study of such cardiac abnormalities are dangerous at best, often requiring the subject to be placed in fibrillation for some time before attempting a large ``rescue'' shock. Thus, most all studies are done in animals and not humans. Furthermore, there is some indication that heart size may have considerable implications for fibrillation and other conduction abnormalities. Thus animal models for defibrillation studies must be chosen with great care. As an alternative, researchers are now using computer simulation to study the factors that generate and sustain arrhythmias, hoping to obtain at least preliminary data to guide fewer, more targeted experimental studies. Computer simulations of the Bidomain Equations have become very complex as they have been applied to many problems in cardiac electrophysiology. More complex membrane dynamics, irregular grids, and 3-D data sets are all being investigated. Software engineering principles will need to be applied to manage this continuing growth in complexity. We propose a modular framework for development of a Simulation System whereby a researcher may mix and match program elements to generate a simulator tailored to their particular problem. The modular approach will simplify the generation and maintenance of the different program elements and it will enable the end-researcher to determine the proper mix of complexity versus speed for their particular problem of interest. The contrary approach, one monolithic program which can run all simulations of all complexities, is simply unrealistic. It would impose too great a burden on maintenance and upgradability, and it would be difficult to provide good performance for a wide range of applications. The modular approach also allows for the incremental inclusion of various complexities in the bidomain model. From a simple 2-D homogeneous, isotropic regular grid, monodomain simulation, we can progress, step by step, to a bidomain simulation with a fully implicit time-integration scheme on irregular, 3-D grids with arbitrary anisotropy and inhomogeneity, with a non-trivial membrane model. Simulations with such a wealth of complexity have not been performed to date. As microprocessors have become cheaper and more powerful, parallel computing has become more widespread. Machines with hundreds of high-performance CPUs connected by fast networks are commonplace and are now capable of surpassing traditional vector-based supercomputers in terms of overall performance. The Simulation System presented here incorporates data-parallelism to allow large scale Bidomain problems to be run on these newest parallel supercomputers. The large amount of distributed memory in such machines can be harnessed to allow extremely large scale simulations to be run. The large number of CPUs provide a tremendous amount of computational power which can be used to run such simulations more quickly. Finally, the results presented here show that a modular Simulation System is feasible for a wide range of pplications, and that it can obtain very good performance over this range of applications. The parallel speed-up seen was very good, regularly achieving a factor of 13 speed-up on 16 processors. The results presented here also show that we can simulate bidomain problems using an implicit time-integrator with an irregular, anisotropic and inhomogeneous, grid and a non-trivial membrane model. We are able to run such simulations on parallel computers, thereby harnessing a tremendous amount of memory and computational resources. Such simulations have not been run to date.
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    Configurational entropy measurements in extremely supercooled liquids that break the glass ceiling.
    (Proceedings of the National Academy of Sciences of the United States of America, 2017-10-10) Berthier, Ludovic; Charbonneau, Patrick; Coslovich, Daniele; Ninarello, Andrea; Ozawa, Misaki; Yaida, Sho
    Liquids relax extremely slowly on approaching the glass state. One explanation is that an entropy crisis, because of the rarefaction of available states, makes it increasingly arduous to reach equilibrium in that regime. Validating this scenario is challenging, because experiments offer limited resolution, while numerical studies lag more than eight orders of magnitude behind experimentally relevant timescales. In this work, we not only close the colossal gap between experiments and simulations but manage to create in silico configurations that have no experimental analog yet. Deploying a range of computational tools, we obtain four estimates of their configurational entropy. These measurements consistently confirm that the steep entropy decrease observed in experiments is also found in simulations, even beyond the experimental glass transition. Our numerical results thus extend the observational window into the physics of glasses and reinforce the relevance of an entropy crisis for understanding their formation.
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    Development of a National Academic Boot Camp to Improve Fellowship Readiness.
    (ATS scholar, 2020-12-22) Drake, Matthew G; Shah, Nirav G; Lee, May; Brady, Anna; Connors, Geoffrey R; Clark, Brendan J; Kritek, Patricia A; McCallister, Jennifer W; Burkart, Kristin M; Pedraza, Isabel; Jamieson, Daniel; Ingram, Jennifer L; Lynch, Lauren; Makani, Samir S; Siegel-Gasiewski, Jennifer; Larsson, Eileen M; Zemanick, Edith T; Liptzin, Deborah R; Good, Ryan; Crotty Alexander, Laura E
    Background: Pulmonary and critical care medicine (PCCM) fellowship requires a high degree of medical knowledge and procedural competency. Gaps in fellowship readiness can result in significant trainee anxiety related to starting fellowship training.Objective: To improve fellowship readiness and alleviate anxiety for PCCM-bound trainees by improving confidence in procedural skills and cognitive domains.Methods: Medical educators within the American Thoracic Society developed a national resident boot camp (RBC) to provide an immersive, experiential training program for physicians entering PCCM fellowships. The RBC curriculum is a 2-day course designed to build procedural skills, medical knowledge, and clinical confidence through high-fidelity simulation and active learning methodology. Separate programs for adult and pediatric providers run concurrently to provide unique training objectives targeted to their learners' needs. Trainee assessments include multiple-choice pre- and post-RBC knowledge tests and confidence assessments, which are scored on a four-point Likert scale, for specific PCCM-related procedural and cognitive skills. Learners also evaluate course material and educator effectiveness, which guide modifications of future RBC programs and provide feedback for individual educators, respectively.Results: The American Thoracic Society RBC was implemented in 2014 and has grown annually to include 132 trainees and more than 100 faculty members. Mean knowledge test scores for participants in the 2019 RBC adult program increased from 55% (±14% SD) on the pretest to 72% (±11% SD; P < 0.001) after RBC completion. Similarly, mean pretest scores for pediatric course attendees increased from 54% (±13% SD) to 62% (±19% SD; P = 0.17). Specific content domains that improved by 10% or more between pre- and posttests included airway management, bronchoscopy, pulmonary function testing, and code management for adult course participants, and airway management, pulmonary function testing, and extracorporeal membrane oxygenation for pediatric course participants. Trainee confidence also significantly improved across all procedural and cognitive domains for adult trainees and in 10 of 11 domains for pediatric course attendees. Course content for the 2019 RBC was overwhelmingly rated as "on target" for the level of learner, with <4% of respondents indicating any specific session was "much too basic" or "much too advanced."Conclusion: RBC participation improved PCCM-bound trainee knowledge, procedural familiarity, and confidence. Refinement of the RBC curriculum over the past 7 years has been guided by educator and course evaluations, with the ongoing goal of meeting the evolving educational needs of rising PCCM trainees.
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    Dipole strength in La-139 below the neutron-separation energy
    (2010) Makinaga, A; Schwengner, R; Rusev, G; Dönau, F; Frauendorf, S; Bemmerer, D; Beyer, R; Crespo, P; Erhard, M; Junghans, AR; Klug, J; Kosev, K; Nair, C; Schilling, KD; Wagner, A
    The gamma-ray strength function is an important input quantity for the determination of the photoreaction rate and the neutron capture rate for astrophysics as well as for nuclear technologies. To test model predictions, the photoabsorption cross section of La-139 up to the neutron-separation energy was measured using bremsstrahlung produced at the electron accelerator ELBE of Forschungszentrum Dresden-Rossendorf with an electron beam of 11.5 MeV kinetic energy. The experimental data were analyzed by applying Monte Carlo simulations of gamma-ray cascades to obtain the intensities of the ground-state transitions and their branching ratios. We found a significant enhancement of electric dipole strength in the energy range from 6 to 10 MeV that may be related with a pygmy dipole resonance. The present data are combined with photoneutron cross sections for La-139 and compared with results of calculations on the basis of a quasiparticle-random-phase approximation using an instantaneous-shape sampling.
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    Epidemic potential by sexual activity distributions.
    (Netw Sci (Camb Univ Press), 2017-12) Moody, James; Adams, Jimi; Morris, Martina
    For sexually transmitted infections like HIV to propagate through a population, there must be a path linking susceptible cases to currently infectious cases. The existence of such paths depends in part on thedegree distribution.Here, we use simulation methods to examine how two features of the degree distribution affect network connectivity: Mean degree captures a volume dimension, while the skewness of the upper tail captures a shape dimension. We find a clear interaction between shape and volume: When mean degree is low, connectivity is greater for long-tailed distributions, but at higher mean degree, connectivity is greater in short-tailed distributions. The phase transition to a giant component and giant bicomponent emerges as a positive function of volume, but it rises more sharply and ultimately reaches more people in short-tail distributions than in long-tail distributions. These findings suggest that any interventions should be attuned to how practices affect both the volume and shape of the degree distribution, noting potential unanticipated effects. For example, policies that primarily affect high-volume nodes may not be effective if they simply redistribute volume among lower degree actors, which appears to exacerbate underlying network connectivity.
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    Rational Pessimism, Rational Exuberance, and Asset Pricing Models
    (1999) Bansal, R; Gallant, AR; Tauchen, G
    estimates and examines the empirical plausibility of asset pricing models that attempt to explain features of financial markets such as the size of the equity premium and the volatility of the stock market. In one model, the long-run risks (LRR) model of Bansal and Yaron, low-frequency movements, and time-varying uncertainty in aggregate consumption growth are the key channels for understanding asset prices. In another, as typified by Campbell and Cochrane, habit formation, which generates time-varying risk aversion and consequently time variation in risk premia, is the key channel. These models are fitted to data using simulation estimators. Both models are found to fit the data equally well at conventional significance levels, and they can track quite closely a new measure of realized annual volatility. Further, scrutiny using a rich array of diagnostics suggests that the LRR model is preferred.