xvii, 289 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / This thesis provides a design and development of a software architecture and programming framework that enables domain-oriented scientific investigations to be more easily developed and productively applied. The key research concept is the representation and automation of scientific studies by capturing common methods for experimentation, analysis and evaluation used in simulation science. Such methods include parameter studies, optimization, uncertainty analysis, and sensitivity analysis. While the framework provides a generic way to conduct investigation on an arbitrary simulation, its intended use is to be extended to develop a domain computational environment. The framework hides the access to distributed system resources and the multithreaded execution. A prototype of such a framework called ODESSI (Open Domain-oriented Environment for Simulation-based Scientific Investigation, pronounced odyssey) is developed and evaluated on realistic problems in human neuroscience and computational chemistry domains. ODESSI was inspired by our domain problems encountered in the computational modeling of human head electromagnetic for conductivity analysis and source localization. In this thesis we provide tools and methods to solve state of the art problems in head modeling. In particular, we developed an efficient and robust HPC solver for the forward problem and a generic robust HPC solver for bEIT (bounded Electrical Impedance Tomography) inverse problem to estimate the head tissue conductivities. Also we formulated a method to include skull inhomogeneity and other skull variation in the head model based on information obtained from experimental studies. ODESSI as a framework is used to demonstrate the research ideas in this neuroscience domain and the domain investigations results are discussed in this thesis. ODESSI supports both the processing of investigation activities as well as manage its evolving record of information, results, and provenance. / Committee in charge: Allen Malony, Chairperson, Computer & Information Science; John Conery, Member, Computer & Information Science; Dejing Dou, Member, Computer & Information Science; Don Tucker, Outside Member, Psychology

Magnetic Resonance Electrical Impedance Mammography (MREIM) is a new imaging technique under development by Wollin Ventures, Inc. in conjunction with the H. Lee Moffitt Cancer Center & Research Institute. MREIM addresses the problem of low specificity of magnetic resonance mammography and high false-positive rates, which lead to unnecessary biopsies. Because cancerous tissue has a higher electrical conductivity than benign tissue, it may serve as a biomarker for differentiation between malignant and benign lesions. The MREIM principle is based on measuring both magnetic resonance and electric properties of the breast by adding a quasi-steady-state electric field to the standard magnetic resonance breast image acquisition. This applied electric field produces a current density that creates an additional magnetic field that in turn alters the native magnetic resonance signal in areas of higher electrical conductivity, corresponding to cancerous tissue. This work comprises MREIM theory, computer simulations, and experimental developments. First, a general overview and background review of tissue modeling and electrical-impedance imaging techniques are presented. The experimental part of this work provides a description of the MREIM apparatus and the imaging results of a custom-made breast phantom. This phantom was designed and developed to mimic the magnetic resonance and electrical properties of the breast. The theoretical part of this work provides an extension to the initial MREIM theoretical developments to further understand the MREIM effects. MREIM computer simulations were developed for both idealized and realistic tumor models. A method of numerical calculation of electric potential and induced magnetic field distribution in objects with irregular boundaries and anisotropic conductivity was developed based on the Finite Difference Method. Experimental findings were replicated with simulations. MREIM effects were analyzed with contrast diagrams to show the theoretical perceptibility as a function of the acquisition parameters. An important goal was to reduce the applied current. A new protocol for an MREIM sequence is suggested. This protocol defines parameters for the applied current synchronized to a specific magnetic resonance imaging sequence. A simulation utilizing this protocol showed that the MREIM effect is detectable for a 3-mm-diameter tumor with a current density of 0.5 A/m², which is within acceptable limits.