Matching Items (33)
Description
A general continuum model for simulating the flow of ions in the salt baths that surround and fill excitable neurons is developed and presented. The ion densities and electric potential are computed using the drift-diffusion equations. In addition, a detailed model is given for handling the electrical dynamics on interior membrane boundaries, including a model for ion channels in the membranes that facilitate the transfer of ions in and out of cells. The model is applied to the triad synapse found in the outer plexiform layer of the retina in most species. Experimental evidence suggests the existence of a negative feedback pathway between horizontal cells and cone photoreceptors that modulates the flow of calcium ions into the synaptic terminals of cones. However, the underlying mechanism for this feedback is controversial and there are currently three competing hypotheses: the ephaptic hypothesis, the pH hypothesis and the GABA hypothesis. The goal of this work is to test some features of the ephaptic hypothesis using detailed simulations that employ rigorous numerical methods. The model is first applied in a simple rectangular geometry to demonstrate the effects of feedback for different extracellular gap widths. The model is then applied to a more complex and realistic geometry to demonstrate the existence of strictly electrical feedback, as predicted by the ephaptic hypothesis. Lastly, the effects of electrical feedback in regards to the behavior of the bipolar cell membrane potential is explored. Figures for the ion densities and electric potential are presented to verify key features of the model. The computed steady state IV curves for several cases are presented, which can be compared to experimental data. The results provide convincing evidence in favor of the ephaptic hypothesis since the existence of feedback that is strictly electrical in nature is shown, without any dependence on pH effects or chemical transmitters.
ContributorsJones, Jeremiah (Author) / Gardner, Carl (Committee member) / Baer, Steven (Committee member) / Crook, Sharon (Committee member) / Kostelich, Eric (Committee member) / Ringhofer, Christian (Committee member) / Arizona State University (Publisher)
Created2013
Description
Numerical simulations are very helpful in understanding the physics of the formation of structure and galaxies. However, it is sometimes difficult to interpret model data with respect to observations, partly due to the difficulties and background noise inherent to observation. The goal, here, is to attempt to bridge this gap between simulation and observation by rendering the model output in image format which is then processed by tools commonly used in observational astronomy. Images are synthesized in various filters by folding the output of cosmological simulations of gasdynamics with star-formation and dark matter with the Bruzual- Charlot stellar population synthesis models. A variation of the Virgo-Gadget numerical simulation code is used with the hybrid gas and stellar formation models of Springel and Hernquist (2003). Outputs taken at various redshifts are stacked to create a synthetic view of the simulated star clusters. Source Extractor (SExtractor) is used to find groupings of stellar populations which are considered as galaxies or galaxy building blocks and photometry used to estimate the rest frame luminosities and distribution functions. With further refinements, this is expected to provide support for missions such as JWST, as well as to probe what additional physics are needed to model the data. The results show good agreement in many respects with observed properties of the galaxy luminosity function (LF) over a wide range of high redshifts. In particular, the slope (alpha) when fitted to the standard Schechter function shows excellent agreement both in value and evolution with redshift, when compared with observation. Discrepancies of other properties with observation are seen to be a result of limitations of the simulation and additional feedback mechanisms which are needed.
ContributorsMorgan, Robert (Author) / Windhorst, Rogier A (Thesis advisor) / Scannapieco, Evan (Committee member) / Rhoads, James (Committee member) / Gardner, Carl (Committee member) / Belitsky, Andrei (Committee member) / Arizona State University (Publisher)
Created2012
Description
This project discusses simulation results of star formation by Active Galactic Nuclei (AGN) jets using the WENO method. A typical AGN jet with velocity uj=0.3c, density ρj=10^(-2) H/cm3, and temperature Tj=10^(7) K was injected into a 425 light years square region. The jet passes through a stationary inhomogeneous ambient background of temperature Ta=5x10^4 K and density ρa= 2 H/cm^3 to test if AGN jets, by creating bow shocks propagating through the interstellar medium and molecular clouds, can form stars in the densest regions. According to the star formation criteria for gravitational collapse of Cen and Ostriker, the resulting simulations indicate the presence of star formation via AGN jets (1992). The parameters are tuned to match Centaurs A to identify star formation in this galaxy. The simulations will also be run in three dimensions in the future and for longer time intervals to gain a better understanding of the star formation process via AGN jets.
ContributorsFindley, Christina Marie (Author) / Gardner, Carl (Thesis director) / Scannapieco, Evan (Committee member) / Barrett, The Honors College (Contributor) / School of Earth and Space Exploration (Contributor) / School of Mathematical and Statistical Sciences (Contributor)
Created2015-05
Description
A comparison of the performance of CUDA versus OpenMP for Jacobi, Gauss-Seidel, and S.O.R. iterative methods for Laplace's Equation with Dirichlet boundary conditions is presented. Both the number of cores and the grid size were varied for the OpenMP program, while the grid size was varied for the CUDA program. CUDA outperforms the 8-core OpenMP program with the Jacobi and Gauss-Seidel schemes for all grid sizes, and is competitive with S.O.R for all grid sizes examined.
ContributorsProst, Spencer Arthur (Author) / Gardner, Carl (Thesis director) / Welfert, Bruno (Committee member) / Speyer, Gil (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2013-05
Description
In this research we consider stochastic models of Glioblastoma Multiforme brain tumors. We first look at a model by K. Swanson et al., which describes the dynamics as random diffusion plus deterministic logistic growth. We introduce a stochastic component in the logistic growth in the form of a random growth rate defined by a Poisson process. We show that this stochastic logistic growth model leads to a more accurate evaluation of the tumor growth compared its deterministic counterpart. We also discuss future plans to incorporate individual patient geometry, extend the model to three dimensions and to incorporate effects of different treatments into our model, in collaboration with a local hospital.
ContributorsManning, Michael Clare (Author) / Kostelich, Eric (Thesis director) / Kuang, Yang (Committee member) / Gardner, Carl (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / School of Letters and Sciences (Contributor) / School of Human Evolution and Social Change (Contributor)
Created2013-12
Description
This project attempts to create an accurate numerical simulation of the eastern limb of the HH 901 jet in the Mystic Mountain formation located in the Carina Nebula. Using a 3rd order accurate WENO numerical scheme in space, and a 3rd order accurate RK method in time, the temperature, density, radiative cooling, length, and average jet velocity of this astrophysical phenomenon were simulated based on observations made by Hubble Space Telescope and the work of Reiter and Smith (2013) and (2014). The results of this simulation are displayed in three figures, one each for temperature, radiative cooling, and density, which show a jet displaying morphology consistent with that of the HH 901 eastern limb without adjustment for stellar wind. Also discussed are the effects of different jet speeds, initial conditions, and pulse parameters on the shape and behavior of the simulated jets, as well as continuing work to be done on the simulation to enhance its accuracy and usefulness.
ContributorsKreitzer, Kyle (Author) / Gardner, Carl (Thesis director) / Jones, Jeremiah (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / Mechanical and Aerospace Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The purpose of this thesis is to accurately simulate the surface brightness in various spectral emission lines of the HH 901 jets in the Mystic Mountain Formation of the Carina Nebula. To accomplish this goal, we gathered relevant spectral emission line data for [Fe II] 12660 Å, Hα 6563 Å, and [S II] 6720 Å to compare with Hubble Space Telescope observations of the HH 901 jets presented in Reiter et al. (2016). We derived the emissivities for these lines from the spectral synthesis code Cloudy by Ferland et al. (2017). In addition, we used WENO simulations of density, temperature, and radiative cooling to model the jet. We found that the computed surface brightness values agreed with most of the observational surface brightness values. Thus, the 3D cylindrically symmetric simulations of surface brightness using the WENO code and Cloudy spectral emission models are accurate for jets like HH 901. After detailing these agreements, we discuss the next steps for the project, like adding an external ambient wind and performing the simulations in full 3D.
ContributorsMohan, Arun (Author) / Gardner, Carl (Thesis director) / Jones, Jeremiah (Committee member) / Computer Science and Engineering Program (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
The goal of this thesis is to extend the astrophysical jet model created by Dr.
Gardner and Dr. Jones to model the surface brightness of astrophysical jets. We attempt to accomplish this goal by modeling the astrophysical jet HH30 in the spectral emission lines [SII] 6716Å, [OI] 6300Å, and [NII] 6583Å. In order to do so, we used the jet model to simulate the temperature and density of the jet to match observational data by Hartigan and Morse (2007). From these results, we derived the emissivities in these emission lines using Cloudy by Ferland et al. (2013). Then we used the emissivities to determine the surface brightness of the jet in these lines. We found that the simulated surface brightness agreed with the observational surface brightness and we conclude that the model could successfully be extended to model the surface brightness of a jet.
Gardner and Dr. Jones to model the surface brightness of astrophysical jets. We attempt to accomplish this goal by modeling the astrophysical jet HH30 in the spectral emission lines [SII] 6716Å, [OI] 6300Å, and [NII] 6583Å. In order to do so, we used the jet model to simulate the temperature and density of the jet to match observational data by Hartigan and Morse (2007). From these results, we derived the emissivities in these emission lines using Cloudy by Ferland et al. (2013). Then we used the emissivities to determine the surface brightness of the jet in these lines. We found that the simulated surface brightness agreed with the observational surface brightness and we conclude that the model could successfully be extended to model the surface brightness of a jet.
ContributorsVargas, Perry Bialek (Author) / Gardner, Carl (Thesis director) / Scannapieco, Evan (Committee member) / School of Mathematical and Statistical Sciences (Contributor) / School of Earth and Space Exploration (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
ContributorsPowell, Devon (Author) / Gardner, Carl (Thesis director) / Scannapieco, Evan (Committee member) / Windhorst, Rogier (Committee member) / Barrett, The Honors College (Contributor)
Created2012-05
Description
Electrical stimulation of the human peripheral nervous system can be a powerful tool to treat various medical conditions and provide insight into nervous system processes. A critical challenge for many applications is to selectively activate neurons that have the desired effect while avoiding the activation of neurons that produce side effects. To stimulate peripheral fibers, the longitudinal intrafascicular electrode (LIFE) targets small groups of fibers inside the fascicle using low-amplitude pulses and is well-suited for chronic use. This work aims to understand better the ability to use intrafascicular stimulation with LIFEs to activate small groups of neurons within a fascicle selectively.A hybrid workflow was developed to simulate: 1) the production/propagation of the electric field induced by the stimulation pulse and 2) the effect of the electric field on fiber activation (recruitment). To create efficient and robust strategies for the selective recruitment of axons, recognizing the effect of each parameter on their recruitment and activation pattern is essential. Thus, using this hybrid workflow, the effects of various factors such as fascicular anatomy, electrode parameters, and stimulation pulse parameters on recruitment have been characterized, and the sensitivity of the recruitment patterns to these parameters has been explored.
Results demonstrated the potential advantages of specific stimulation strategies and the sensitivity of recruitment patterns to electrode placement and tissue properties. For example, it is demonstrated: the significant effect of endoneurium conductivities on threshold levels; that a configuration with a LIFE as a local ground can be used to deselect its surrounding axons; the advantages of changing the delay between pulses in dual monopolar stimulation in targeting different axons clusters and increasing the activation frequency of some axons; how monopolar and bipolar configurations can be used to enhance spatial selectivity; the effect of longitudinal displacement of axons, electrode length and electrode movement on the recruitment and the activation pattern. In summary, this work forms the foundation for developing stimulation strategies to enhance the selectivity that can be achieved with intrafascicular stimulation.
ContributorsRouhani, Morteza (Author) / Abbas, James J (Thesis advisor) / Crook, Sharon M (Thesis advisor) / Baer, Steven M (Committee member) / Sadleir, Rosalind (Committee member) / Gardner, Carl (Committee member) / Arizona State University (Publisher)
Created2022