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DTSTART;TZID=America/Los_Angeles:20260817T100000
DTEND;TZID=America/Los_Angeles:20260817T120000
DTSTAMP:20260810T162940Z
CREATED:20260810T162940Z
LAST-MODIFIED:20260810T162940Z
UID:10015328-1786960800-1786968000@live-events-ucsc.pantheonsite.io
SUMMARY:Nikolakakis\, M. (ECE) - Learned Gridless Representations of Cone Beam Computed Tomography Scans
DESCRIPTION:Medical image representation has long been dominated by voxel-grid matrices. While\ntheir inherent structure and order work efficiently for various linear transformations and\nprovide a seamless visualization method on monitors\, they fail to preserve the topology\nof the scan and to encode sparse information in a memory-efficient way.   The recent emergence of machine learning-based continuous coordinate-based\nscene representations such as neural radiance fields and Gaussian splatting has provided alternative representation techniques. These approaches overfit the weights of\na model by iterative differentiable rendering and have been shown to be more compact than grid representations. They are then able to perform novel view\nsynthesis from any given camera pose.\nOff-grid representations translate directly to Cone Beam Computed Tomography\nsparse-view acquisitions\, where streaking and quantum noise artifacts are dominant.\nUsing differentiable rendering\, a continuous representation is achieved\, with interpolation providing a path to recover some of the lost signal.\nIn this dissertation\, we apply a variety of methodologies\, including Gaussian splatting\, implicit occupancy fields\, and Neural Attenuation Fields regularized with an\nanatomic prior\, to Cone Beam Computed Tomography reconstruction\, and evaluate\ntheir performance across a range of anatomic datasets. Our models show that learned\ngridless representations achieve substantial memory reduction\, recover signal under\nextreme view sparsity\, and preserve scene topology. \nEvent Host: Manolis Nikolakakis\, Ph.D. Candidate\, Electrical and Computer Engineering  \nAdvisor: Razvan Marinescu \nZoom: https://ucsc.zoom.us/j/5964517596?pwd=c1AwRlJLNk5pVzFBUENibEw3by85Zz09
URL:https://live-events-ucsc.pantheonsite.io/event/nikolakakis-m-ece-learned-gridless-representations-of-cone-beam-computed-tomography-scans/
LOCATION:Engineering 2\, Engineering 2 1156 High Street\, Santa Cruz\, CA\, 95064
CATEGORIES:Ph.D. Presentations
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260817T130000
DTEND;TZID=America/Los_Angeles:20260817T150000
DTSTAMP:20260813T194341Z
CREATED:20260813T194341Z
LAST-MODIFIED:20260813T194341Z
UID:10015338-1786971600-1786978800@live-events-ucsc.pantheonsite.io
SUMMARY:Condon\, C. (BMEB) - Genomic conflict across scales
DESCRIPTION:Genomes are often viewed as cooperative systems in which genes work together to support organismal function. Yet genetic elements can also act in ways that favor their own transmission or persistence\, creating conflict within the genome. In this talk\, I examine the evolutionary and functional consequences of such genomic conflict across three systems. First\, I investigate segregation distortion in Arabidopsis hybrids and its potential role in the early evolution of reproductive isolation. Second\, I characterize the population dynamics and functional effects of introners\, mobile elements that generate new introns in the green alga Micromonas pusilla. Finally\, I explore widespread splicing dysfunction in algal mating-type chromosomes and its consequences for transcript diversity. Together\, these studies highlight how departures from genome cooperation can shape inheritance\, genome evolution\, and gene regulation. \nEvent Host: Chris Condon\, Ph.D. Candidate\, Biomolecular Engineering & Bioinformatics  \nAdvisor: Russell Corbett-Detig
URL:https://live-events-ucsc.pantheonsite.io/event/condon-c-bmeb-genomic-conflict-across-scales/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Ph.D. Presentations
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END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260818T100000
DTEND;TZID=America/Los_Angeles:20260818T110000
DTSTAMP:20260810T162245Z
CREATED:20260810T162245Z
LAST-MODIFIED:20260810T162245Z
UID:10015327-1787047200-1787050800@live-events-ucsc.pantheonsite.io
SUMMARY:Gutie\, J. (SciCAM) -  SORh: Hyperbolic Relaxation Methods For Elliptic Problems In Computational Fluid Dynamics
DESCRIPTION:This thesis explores iterative methods for solving elliptic partial differential equations (PDEs)\, which are used in computational fluid dynamics (CFD) to model a wide range of physical phenomena. The primary application of interest here is self-gravity\, modeled by Poisson’s equation. Although many numerical approaches exist\, including direct matrix inversion\, FFT-based methods\, and classical iterative methods such as Jacobi and Gauss-Seidel\, these approaches involve tradeoffs in computational cost\, scalability\, implementation complexity\, and adaptability to changing boundary conditions and problem configurations. \nTherefore\, we introduce SORh\, a simple and efficient relaxation method derived from a hyperbolic reformulation of Poisson’s equation. SORh generalizes classical successive over-relaxation (SOR) by providing independent control of residual relaxation and the directional propagation of Gauss–Seidel corrections. We present formulations of SORh in one and two spatial dimensions and investigate its stability\, accuracy\, and computational performance through analytical derivations and numerical comparisons with established relaxation methods. The results identify favorable SORh formulations\, clarify their relationships to classical relaxation methods\, and demonstrate improved convergence on selected test problems. Finally\, we demonstrate applications of SORh to astrophysical self-gravity simulations in the FLASH code and to magnetohydrodynamic (MHD) divergence cleaning. \nEvent Host: Jonathan Guite\, M.S. Candidate\, Scientific Computing & Applied Mathematics  \nAdvisor: Dongwook Lee \nZoom: https://ucsc.zoom.us/j/92153750104?pwd=ZdLiDZeLqOAlVNX9C4bCloKno9tAeB.1 \nPasscode: 769232
URL:https://live-events-ucsc.pantheonsite.io/event/gutie-j-scicam-sorh-hyperbolic-relaxation-methods-for-elliptic-problems-in-computational-fluid-dynamics/
CATEGORIES:Ph.D. Presentations
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LOCATION:
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260820T130000
DTEND;TZID=America/Los_Angeles:20260820T150000
DTSTAMP:20260814T163909Z
CREATED:20260814T163815Z
LAST-MODIFIED:20260814T163909Z
UID:10015340-1787230800-1787238000@live-events-ucsc.pantheonsite.io
SUMMARY:Penunuri\, G. (BMEB) - Genomic\, Proteomic\, and Computational Approaches to the Study of Host-Microbe Systems
DESCRIPTION:Host-microbe systems are core to some of biology’s most consequential interactions\, from the pathogens that drive infectious disease to symbionts affecting agricultural pest control and vector-borne disease transmission. Yet unlike the model organisms that have driven most of modern molecular biology\, the microbes at the center of these interactions are rarely genetically tractable: many cannot be cultured outside a host\, resist standard tools for genetic manipulation\, and are annotated largely by homology to distantly related free-living relatives. This dissertation develops genomic\, proteomic\, and computational methods to work around this lack of infrastructure and contribute techniques and tools to the study and further understanding of host-microbe systems. Using Wolbachia cultured in Drosophila melanogaster cell lines\, I demonstrate that chemical mutagenesis can be used to perturb intracellular genomes leaving a detectable mutational signal. I employ a low error rate sequencing technique to record and model the mutational landscape left by the mutagen ethyl methanesulfonate (EMS) demonstrating its use for mutagenesis screens of intracellular bacteria. I next utilize structural proteome datasets to screen host-microbe proteomes for strong candidates of molecular mimicry\, microbe proteins that have coevolved a eukaryotic like domain or structure and suggest use for host manipulation or microbe survival in the host environment. Building off of this screen for novel effectors through structural alignments I develop and test a distributed computing system for performing large scale systematic literature reviews. Altogether these projects represent generalizable approaches to the study of host-microbe systems reaching from classically studied and thoroughly understood to novel and non-model systems. \nEvent Host: Gabriel Penunuri\, Ph.D. Candidate\, Biomolecular Engineering & Bioinformatics  \nAdvisor: Russell Corbett-Detig \nZoom: https://ucsc.zoom.us/j/98216883331?pwd=uqmUSQba2X6GVNBhOhAGRwgCZyjAyj.1 \nPasscode: 730377
URL:https://live-events-ucsc.pantheonsite.io/event/penunuri-g-bmeb-genomic-proteomic-and-computational-approaches-to-the-study-of-host-microbe-systems/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Ph.D. Presentations
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