# Browsing by Subject "simulation"

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Item Open Access A modular simulation system for the bidomain equationsPormann, JCardiac 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.Item Open Access Charged Particle Optics Simulations and Optimizations for Miniature Mass and Energy Spectrometers(2021) DiDona, ShaneComputer simulation and modeling is a powerful tool for the analysis of physical systems; in this work we consider the use of computer modeling and optimization in improving the focusing properties of a variety of charged particle optics systems. The combined use of several software packages and custom computer code allows for modeling electrostatic and magnetostatic fields and the trajectory of particles through them. Several applications of this functionality are shown. The pieces of code which are shown are the starting point of an integrated charged particle simulation and optimization tool with focus on optimization. The applications shown are mass spectrographs and electron energy spectrographs. Simulation allowed additional information about the systems in question to be determined.In this work, coded apertures are shown to be compatible with sector instruments, though architectural challenges exist. Next, simulation allowed for the discovery of a new class of mass spectrograph which addresses these challenges and is compatible with computational sensing, allowing for both high resolution and high sensitivity, with a 1.8x improvement in spot size. Finally, a portion of this new spectrograph was adapted for use as an electron energy spectrograph, with a resolution 9.1x and energy bandwidth 2.1x that of traditional instruments.

Item Open Access 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, ShoLiquids 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.Item Open Access 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.Item Open Access 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, AThe 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.Item Open Access Epidemic potential by sexual activity distributions.(Netw Sci (Camb Univ Press), 2017-12) Moody, James; Adams, Jimi; Morris, MartinaFor 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.Item Open Access Exploration of Alkyne-bridged Multi[(Porphinato)metal] Oligomers for Charge Transport Applications and Spin-Spin Exchange Coupling Properties Using Synthetic, Spectroscopic, Potentiometric, and Magnetic Resonance Methods(2017) Wang, RuobingAs silicon-based microelectronics approaches its fundamental physical limit, molecular electronics is emerging as a promising candidate for future ultra-dense electronic devices with individual molecules as active device components. The emerging of molecular spintronics, which exploits the spin-dependent charge transport through organic materials, further demonstrate the promising future of molecular electronics. This dissertation describes the charge transport and spin-spin electronic coupling properties of an extraordinary class of molecular wires, alkyne-bridged porphyrin arrays. Chapter one provides a general background of molecular electronics and molecular wires, as well as the basics of electron paramagnetic resonance (EPR). Chapter two describes utilizing highly conjugated (porphinato)metal-based oligomers (PMn structures) as molecular wire components of nanotransfer printed (nTP) molecular junctions; electrical characterization of these “bulk” nTP devices highlights device resistances that depend on PMn wire length. This study demonstrates the ability to fabricate “bulk” and scalable electronic devices in which function derives from the electronic properties of discrete single molecules, and underscores how a critical device function—wire resistance—may be straightforwardly engineered by PMn molecular composition. Chapter three describe the electronic exchange coupling between two unpaired spin on Cu(II) ions in meso-meso alkyne-bridged multi[copper(II) porphyrin] (mmPCu2). Spin and conformational dynamics in symmetric mmPCu2 have been studied in toluene solution at variable temperature using EPR spectroscopy. Comparison of the dimer EPR spectra to those of Cu porphyrin monomers shows clear evidence of an isotropic exchange interaction (Javg) in these biradicaloid structures, manifested by a significant line broadening in the dimer spectra. Comparison of ethyne and butadiyne alkyne bridges reveals a remarkable sensitivity to orbital interactions between the spacer and the metal, which is reflected in measurements of Javg as a function of temperature. The results suggest that orbital symmetry relationships may be more important than previously recognized in the design of optimized molecular spintronic devices. Chapter four reports a study of β-β linked bis[(porphinato)copper(II)] complexes (ββPCu2), which exhibit very different electronic structures compared to their mm linked analogs. By using electron paramagnetic resonance (EPR) spectroscopy, this study exhibits that a wide range (3 orders of magnitude) of the average electronic spin-spin exchange coupling can be achieved by varying the length of bridges and points of connections between the porphyrin rings. The pathways for mmPCu2 and ββPCu2 complexes were also investigated, with the ββPCu2 complexes exhibiting a dominant σ-type pathway and the mmPCu2 complexes showing a dominant π-type pathway.

Item Open Access Investigations into the Feasibility of Optical-CT 3D Dosimetry with Minimal Use of Refractively Matched Fluids(2014) Chisholm, KelseyPurpose: Optical-CT imaging with radiochromic dosimeters is a powerful method of evaluating 3D dose distributions at high resolution and sensitivity. Current optical-CT systems require large quantities of refractively matched fluid surrounding the dosimeter in order to minimize refraction artifacts. The use of a refractively matched solid polyurethane solid-tank, in place of a fluid bath, has the potential to greatly increase practical convenience, reduce cost, and improve the efficacy of flood corrections. This thesis aims to investigate the feasibility of solid-tank optical-CT imaging for 3D dosimetry, and to use computer simulation to investigate optimal design and scanning parameters.

Methods: A Matlab based ray-tracing simulation platform, ScanSim, was used to model a parallel-source imaging system through a cubic polyurethane solid-tank containing a central cylindrical hollow into which cylindrical PRESAGE® radiochromic dosimeters can be placed. A small amount of fluid surrounds the dosimeter in the tank. ScanSim's capabilities were expanded from previous work to include the geometry and physics of dry scanning. Two imaging methods were investigated, representing a telecentric detector and an ideal detector: in the latter, all light rays are collected and used in reconstruction. In order to characterize the efficacy of these systems, and dependence on refractive index (RI) mismatches between dosimeter, solid-tank, and fluid, simulations were run for a variety of dosimeter (RI = 1.5-1.47), and fluid (RI = 1.55-1.0) combinations. Additional simulations examined the effect of increasing gap size (1-5mm) between the dosimeter and solid-tank well. For the telecentric setup, the effects of changing the lens tolerance (0.5-5.0 degrees) were also investigated. The metric for evaluation of efficacy is the usable radius, which is defined as the distance from the dosimeter center where the measured and true (known) dose differs by less than 2%.

Results: As the refractive index mismatch between the dosimeter and tank increases from 0-0.02, the telecentric system showed a significant decrease in the usable radius from 97.6% to 50.2% compared to a decrease from 97.6% to 96.4% for the ideal system. When the three media are perfectly matched, the telecentric system and ideal system perform identically. For mismatched dosimeter and solid-tank in a telecentric system, the optimal fluid match has a refractive index lower than either the tank or dosimeter, decreasing non-linearly from 1.5-1.34 as the dosimeter-tank refractive mismatch increases from 0 to 0.02. Media mismatches between the dosimeter and solid-tank also exacerbate the effects of changing the gap size, with no apparent quantifiable relationship. Generally, the optimal fluid match is closer to the dosimeter RI when the gap size is large (>3mm). Increasing the telecentric lens tolerance improves the usable radius for all refractive media combinations, and approaches the behavior of the ideal system for tolerances >5.0°.

Item Open Access Nitrogenase Electron Tunneling Pathways Analysis: From the 4Fe-4S Cluster to the P-cluster(2018) Zhai, YujiaThe biological reduction of N2 to NH3 catalyzed by molybdenum nitrogenase requires eight steps to finish a completed catalysis cycle. This reaction cycle is associated with ATP-driven electron transfer (ET) from the Fe protein to the MoFe protein, and part of ET is experimentally confirmed to be ‘conformationally gated’. Although the overall sequence of ET in nitrogenase has been studied for decades, the nature of coupling between ET pathways and nucleotides binding/protein-protein docking is still unclear, especially from theoretical aspects. Here, we have utilized submicrosecond classical molecular dynamics simulations to allow the ADP-bound and ATP-bound nitrogenases to simulate their conformations in real biological systems. Then the Pathways plugin implemented by Balabin et al was employed to calculate the ET coupling and visualize the ET pathways between the F-cluster and the P-cluster in nitrogenase. The comparison of the ET couplings (the F-cluster to the P-cluster) we calculated and the edge-to-edge distance between the ET donor and acceptor suggests that the coupling pathways grow in strength more that that would be expected from simple distance changes. This result additionally indicates the electron of Fe protein is protected prior to the ATP binding and the protein-protein docking, using pathway switching effects.

Item Open Access PSTD Method for Thermoacoustic Tomography (TAT) and Related Experimental Investigation(2009) Ye, GangIn this work, the simulation (forward problem) and reconstruction (inverse problem) in Thermoacoustic Tomography (TAT) are studied using a pseudospectral time-domain (PSTD) method with 4th-order time integration.

The objective of the TAT simulation is to solve for the thermoacoustic pressure field in an inhomogeneous medium. Using the PSTD method, the spatial derivatives of pressure field and particle velocity can be obtained using fast fourier transform (FFT). Since the Fourier transforms used to represent the spatial derivatives of smooth functions are exact, only 2 points per wavelength are needed in the spatial discretization. The time integration is achieved by a 4th-order method to effectively reduce the computational time. The results of the algorithm are validated by analytical solutions. Perfectly Matched Layers (PMLs) are applied to absorb the outgoing waves and avoid ``wraparound'' effect. The maximum attenuation coefficient of the PMLs has an optimum value to minimize the reflections due to discretization and wraparound effect for 2D and 3D problems. Different PML profiles are also compared, quadratic profile is chosen because it can minimize the overall reflection. Spatial smoothing is needed for PSTD to avoid Gibbs' phenomenon in the modeling of a point source, and the effect of the smoothing function is studied.

In the TAT reconstruction problem, the PSTD method is used to reconstruct the thermoacoustic sources by solving the thermoacoustic wave equations in a reversed temporal order within the framework of time reversal imaging. The back-propagated pressure waves then refocus at the spatial locations of the original sources. Most other TAT reconstruction algorithms are based on the assumption that the tissue medium is acoustically homogeneous. In practice, however, even the mild tissue inhomogeneity will cause large phase errors and cause spatial misplacement and distortion of the sources. The proposed PSTD method utilizes a two-step process to solve this problem. In the first step, a homogeneous time reversal reconstruction is performed. Since an inhomogeneity itself is usually a source because of spatially dependent electrical conductivity (thus microwave absorption), the spatial location and the shape of the inhomogeneity can be estimated. In the second step, the updated acoustic property map is loaded followed by an inhomogeneous reconstruction. Numerical results show that this method greatly improves the reconstruction results. Images with improved quality are reconstructed from experimental data.

A 3D PSTD algorithm is developed and validated. Numerical results show that the PSTD algorithm with the 4th-order time integration is capable of simulating large 3D acoustic problems accurately and efficiently. A 3D breast phantom model is used to study the inhomogeneous reconstruction in 3D. Improved results over the homogeneous method are observed.

A preliminary study of the Thermoacoustic Tomography (TAT) using continuous-wave (CW) modulated microwaves is summarized. The theoretical background, system configuration, experiment setup, and measurement results are presented.

Item Open Access Rational Pessimism, Rational Exuberance, and Asset Pricing Models(1999) Bansal, R; Gallant, AR; Tauchen, Gestimates 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.Item Open Access Superconducting Radiofrequency Probes for Magnetic Resonance Microscopy, Simulation and Experiments(2009) Nouls, John ClaudeIn magnetic resonance microscopy, insufficient signal-to-noise ratio currently limits imaging performance. Superconducting probes can potentially increase the sensitivity of the magnetic resonance experiment. However, many superconducting probes failed to entirely deliver the expected increase in signal-to-noise ratio.

We present a method based on finite-element radiofrequency simulations. The radiofrequency model computes several figures of merit of a probe, namely: i) the resonant frequency, ii) the impedance, iii) the magnetic field homogeneity, iv) the filling factor, and v) the sensitivity. The probe is constituted by several components. The method calculates the electromagnetic losses induced by every component within the probe, and identifies the component limiting the sensitivity of the probe. Subsequently, the probe design can be improved iteratively.

We show that the sensitivity of an existing superconducting Helmholtz pair can be improved by increasing the filling factor of the probe and cooling the radiofrequency shield, which was implemented in the design of a new superconducting probe. The second probe exhibits a sensitivity three times as high, leading to improved imaging performance.

Item Open Access Three-dimensional computer generated breast phantom based on empirical data(MEDICAL IMAGING 2008: PHYSICS OF MEDICAL IMAGING, PTS 1-3, 2008) Li, CM; Segars, WP; Lo, JY; Veress, AI; Boone, JM; III, DJT