Physics Department Theses and Dissertations

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https://hdl.handle.net/1805/2072

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Dynamics of Time-Delay Coupled Opto-Electronic Oscillators
(2025-09) Glover, Brenden Rodney; Vemuri, Gautam; Joglekar, Yogesh; Petrache, Horia; Suelzer, Joseph; Cheng, Rui
This thesis describes the theory, design, and testing of solitary and coupled optoelectronic oscillators (OEO). It includes the work of four papers: two on solitary OEOs, one on coupled OEOs, and one on noise characterizations of general OEO systems. The goal is to derive analytic characterizations then experimentally leverage predictions for amplification and sensing applications in radio frequency (RF) integrated photonic platforms. For the single OEO case we experimentally characterize and numerically model the amplification of RF signals injected into a sub-threshold optoelectronic oscillator. Further, we characterize the transient temporal characteristics when subject to a pulse square wave and derive a recursion relationship between the steps of the transient response. In injected single OEO experiments, a radio frequency gain of 27.5 dB is demonstrated at an optical power of 0.989 times the threshold optical power. The transient behavior shows signatures of both the intrinsic time-delay of the optoelectronic oscillator and the finite bandwidth of the electronic radio frequency filter. Approximating higher-order group delay contributions of the experimental band-pass filter as an external time-delay allows the system to be modeled with a well-known optoelectronic oscillator rate equation model. The solitary rate equation model is generalized to numerically model coupled OEOs. Linearization, stability analysis, and a modified slowly varying envelope technique are utilized to derive novel analytic predictions. A second attractor is identified above the critical point that overlaps the threshold with an exceptional point. Experiments show that the coupled OEO’s second attractor may be triggered from the off state with a relative » 78 dB RF injected signal.
Mechanical Quantification in Lipid Membrane and Live Cells using Fluorescence-based Molecular Sensors
(2025) Park, Kichul; Vemuri, Gautam; Liu, Jing; Wassall, Stephen; Petrache, Horia; Gavrin, Andrew
Fluorescence is a well-studied physical phenomenon and has been the basis for many research tools. Yet the recent advancements in ultrafast lasers and fluorescent molecules have opened the door to new ways to study the dynamical forces acting inside living cells. Fluorescence lifetime imaging microscopy, or FLIM, can move the fluorescence microscopy beyond being a tool of simple tracking and identification of cellular features and enables live monitoring of cellular activities and dynamics. New fluorophores and their arrangements have helped to take advantage of FRET, fluorescence resonance energy transfer process which enables measurement of qualities previously difficult to measure. The thesis focuses on demonstration of these newly developed tools and their applications as molecular sensors in biomedical research. Flipper-TR, a recently arrived molecular probe, shows how it can report via FLIM on lipid packing orders in different lipid membranes and how they change with the varying cholesterol contents. The measurements from FLIM-Flipper-TR are compared to those by deuterium NMR, a well-established method to study the structures and phase transitions within lipid membranes, to test an implicit hypothetical relationship between the intermolecular spacing reported by the fluorescence probe and order parameters derived from NMR spectra. The result yields a strong linear correlation between the two techniques and measurements obtained from them; additional experiment reveals a still incomplete picture but a definite potential of interchangeability for the two methods. Additionally, the work lists demonstrations of diverse molecular sensors based on FRET and how their utilization can aid in characterization of tumor cells and development of novel cancer treatments, not to mention study of general cellular dynamics. In summary, the thesis work offers a glimpse into the world of new fluorescence-based molecular sensors and their promising applications in biomedical research.
Theoretical Investigation of Optoelectronic Oscillators Near Higher Order Bifurcations for Radio-Frequency Sensing
(2025-08) Peigh, Vincent; Vemuri, Gautam; Sensale, Sebastian; Petrache, Horia
The optoelectronic oscillator (OEO) is a time delayed system that exhibits a period doubling route to chaos. The period doubling nature of the OEO introduces bifurcation points where the system transitions from simple periodic behavior to chaotic dynamics. Near these bifurcation points, the OEO can amplify and mix weak injected radio-frequency signals. We introduce a simple model that effectively captures the dynamics of OEOs. Analytic expressions are derived and shown to agree with numerical simulations.
Imaging the Dynamics of Chromatin at Single-Nucleosome Resolution
(2024-12) Iqbal, Mohamed Fadil; Vemuri, Gautam; Liu, Jing; Petrache, Horia; Decca, Ricardo; Wassall, Stephen
DNA is organized into chromatin – a complex polymeric structure which stores information and controls gene expressions. Advancements in microscopy have enabled us to see chromatin in motion – which was previously thought to be static, and these motions contribute to various cellular functions. In my thesis I will demonstrate the molecular tools and biophysical approaches our lab has developed to uncover the mysteries of chromatin dynamics and structures at the single nucleosome resolution; I will also discuss how these new discoveries in chromatin enable us to explore its role in cell functions. This dissertation will first describe the technology advancement of live-cell image analysis; particularly, I will discuss the utilization of AI to improve the spatial and temporal resolution of chromatin imaging. Then I will show complex nature of chromatin where depending on the temporal scale of observation we see a different behavior and how computer simulations can see these differences. Following that, I will introduce our investigation on the role of chromatin motion in DNA damage and repair. Afterwards, I will discuss how the cell regulates its chromatin dynamics in response to the metabolism indicators AMPK (AMP-activated protein kinase). I will also show how chromatin motion and structure behave without the presence of key proteins such as RAD51 that aid in DNA damage. Finally I will go over future directions and improvements we can do to our current techniques to improve our understanding of chromatin’s role is various biological functions. We expect that the exploration of the spatiotemporal dynamics in live cells will facilitate the diagnosis, treatment, and prevention of cancers.
Advancing super-resolution microscopy for quantitative in-vivo imaging of chromatin nanodomains
(2024-12) Seitz, Clayton; Liu, Jing; Vemuri, Gautam; Cheng, Ruihua; Wassall, Stephen; Petrache, Horia
Single molecule localization microscopy (SMLM) techniques, such as direct stochastic optical reconstruction microscopy (dSTORM), can be used to produce a pointillist representation of fluorescently-labeled biological structures at diffraction-unlimited precision. This class of techniques permits localization of fluorescent molecules in the cell with nanometer precision and thus is commonly referred to as nanoscopy. Conventional nanoscopy utilizes the deactivation of standard fluorescent tags, followed by spontaneous or photoinduced reactivation, to resolve fluorophores at distances below the diffraction limit. While powerful, this approach has limited throughput and requires localization in sparse scenes. This dissertation introduces fluorescence nanoscopy and covers its innovation and application as discussed in the following papers: Quantum enhanced localization microscopy with a single photon avalanche diode array [ 1 ] leverages recent advancements in single photon avalanche diode array technology to count fluorescent emitters using a widefield microscope. Uncertainty-aware localization microscopy by variational diffusion [ 2 ] describes a novel algorithm that applies a diffusion model in order to model a posterior distribution on high resolution localization microscopy images, given low resolution inputs. role of the BRD4 phosphoswitch in the maintenance of chromatin nanodomains via super resolution microscopy and molecular dynamics simulation. We demonstrate that BRD4 phosphorylation regulates chromatin packing and mobility in mammalian nuclei.
A Computational Framework for Investigating mRNA Localization Patterns in Pancreatic Beta-Cells During Type 1 Diabetes Progression
(2024-12) Chang, Hok Wai; Petrache, Horia; Liu, Jing; Wassall, Stephen; Vemuri, Gautam; Syed, Farooq
Spatial transcriptomics improves transcriptomic studies by incorporating RNA localization information, which provides a more profound insight into cellular functions, interactions between cells, and their reactions to external stimuli. Single-molecule fluorescent in situ hybridization (smFISH) is a commonly utilized technique in spatial transcriptomics that allows for the accurate visualization of mRNA distribution in cells. This method aids in the quantitative evaluation of mRNA localization patterns by utilizing various physical properties, thereby illuminating processes such as transcription, nuclear export, and localized translation. Nevertheless, existing computational approaches for analyzing smFISH images often have constraints, concentrating primarily on cellular expression or specific biological contexts while overlooking broader physical analysis. In my PhD research, I created STProfiler, a comprehensive tool aimed at an unbiased physical examination of mRNA distribution. STProfiler includes an image analysis workflow that processes raw biological images to effectively detect mRNA and nuclei. It also employs machine learning techniques to biologically interpret mRNA spatial characteristics and categorize cells based on these features. My dissertation illustrates the use of STProfiler in multiple studies investigating the transcriptomic profiles of β-cells during the progression of type 1 diabetes (T1D), uncovering spatial transcriptomic diversity in β-cells. These investigations involve analyzing mRNA clusters and stress granules in pancreatic β-cells, measuring the physical characteristics of mRNAs linked to cellular stress and inflammation in mice developing T1D, evaluating the rise in HLA-DMB mRNA spliced variant in T1D, and exploring miRNA as a potential biomarker for T1D. Furthermore, STProfiler has also proven beneficial in tissue-wide spatial transcriptomics by creating masks for nuclei and cells from biological images and assigning mRNA transcripts to develop subcellular expression profiles. This capability allows for more thorough bioinformatic evaluations. In summary, STProfiler serves as a robust tool for both cell- and tissue-level spatial transcriptomics, offering an unbiased platform for researchers to investigate complex transcriptomic variations within cells.
Novel Materials for Spintronic Devices
(2024-12) Dale, Ashley; Cheng, Ruihua; Petrache, Horia I.; Gavrin, Andrew D.; Amin, Vivek Pravin; Dowben, Peter A.
Spintronic devices are devices which use the spin properties of atoms to store information. Such devices are predicted to be lower power. In this work, two Fe- II spin crossover molecules are analyzed as candidate novel materials for spintronic devices through computational and experimental work. The molecular activation energy for spin crossover molecule [Fe{H2B(pz)2}2(bipy)] in thin film on a ferroelectric substrate is estimated using Monte Carlo simulations of an Ising-like Model to be 88 meV when the substrate is polarized towards the thin film surface and 198 meV when the substrate is polarized away from the thin film surface. Additional Monte Carlo simulations suggests that beyond-nearest neighbor interactions are required for observed spin-state domain formation. The magnetic anisotropy and spectroscopic g factor for [Fe{H2B(pz) 2}2 (bipy)] molecules are characterized using X-ray magnetic circular dichroism measurements; thin films were dominated by magnetocrystalline anisotropy and the spin-orbit coupling energy was found to be 1.47 kJ m-3. Spin and orbital moment anisotropy estimations from the XMCD measurement were 30.9 and 5.04 meV molecule-1, respectively, and the zero-field g factor was estimated to be gz = 2.26. The optical energy gap for [Fe{HB(tz)3}2] is estimated to be 1.93±0.15 eV using UV-Vis spectroscopic measurements and a newly derived Tauc method for large molecules in solvent. Finally, the [Fe{HB(tz)3}2] molecule in thin film form is confirmed to have increased resistance in the high-spin state, with an on-off ratio of 103. These measurements contribute to the development of novel spintronic devices.
Study of the Valence Tautomer Complex [Co(sq)(cat)(3-tpp)2] for Applications in Molecular Spintronics
(2023-12) Phillips, Jared; Cheng, Ruihua; Gavrin, Andrew; Joglekar, Yogesh; Anasori, Babak; Kenning, Gregory
Molecular materials exhibiting bistability between two states are intriguing candidates for next generation electronic devices. Two similar classes of materials, known as spin crossover (SCO) and valence tautomers (VT) respectively, are of particular interest due to their multifunctional properties, which are controllable via several external parameters, such as temperature, light irradiation, pressure, magnetic field, and electric field. In recent years, considerable research has been dedicated to better understanding the underlying principles that govern the behavior of these materials, so that their implementation into nano-based devices might be achieved. In this report, a systematic study of the valence tautomer molecule [Co(sq)(cat)(3-tpp)2] is presented. In the first chapter, the phenomenon of valence tautomerism (VT) occurring in coordination compounds is introduced and described from the perspective of Crystal Field Theory (CFT). Further, the molecular structure and physical properties of the [Co(sq)(cat)(3-tpp)2] molecule are explored. The properties of the ferroelectric material Polyvinylidene fluoride- hexafluoropropylene (PVDF-HFP), and the 2-D Mxene Ti3C2 are also discussed. The next section details equipment development and experimental methods. Thin films of VT molecules were prepared from solution via a drop-casting approach. For thin film analysis, we have developed a custom made, fully automated Vibrating Sample Magnetometer (VSM) with a sensitivity on the order of 1 × 10-5 emu, as well as a fully automated, variable temperature, under vacuum electron transport stage, and a magneto-optic Kerr effect apparatus (MOKE). Additional experimental methods used to characterize the VT thin films include X-ray Absorption Spectroscopy (XAS), UV-visible Spectrometry (UV-Vis) and Differential Scanning Calorimetry. Experimental results obtained from these techniques are discussed and analyzed in the third section. PVDF-HFP polarization dependent isothermal spin state switching of [Co(sq)(cat)(3-tpp)2] is also discussed as well as the effects of doping [Co(sq)(cat)(3-tpp)2] with Ti3C2, followed by a conclusion and an outline of future work.
Short Range Probes to Extensions of the Standard Model
(2023-08) Bsaibes, Thomas; Decca, Ricardo; Petrache, Horia; Cheng, Ruihua; Joglekar, Yogesh; Gavrin, Andrew; Michael, Snow
As successful as the Standard Model has been in describing particle interactions, there are still many open questions it does not answer; the strong CP violation and the existence of dark matter among them. To address these issues many extensions to the Standard Model have been devised. Some of these extensions propose a new force mediating particle; a massive particle results in a potential described by a Yukawa-like interaction, while a massless exchange particle leads to power law type potentials. Limits on the strength of these interactions at the sub-micron range of separation between two particles are poorly characterized, but previous experiments conducted at IUPUI placed the best limits to date on the strength of a Yukawa-like interaction. Those experiments used a spherical test mass and a planar source mass. However, if a cylindrical test mass was used, the increased interaction volume of the cylinder would result in an increased sensitivity of about an order of magnitude over the spherical test mass experiment. Building such a system presents many challenges, namely the alignment of the cylinder with respect to the planar source mass. A capacitance based scheme to determine the alignment of a cylinder with respect to a plane will be discussed. The thesis concludes with an outline for a new type of measurement system. The new experiment attempts to induce a gravitational Π-pulse in a nanoshphere to probe extensions to the Standard Model.
Exceptional Points and their Consequences in Open, Minimal Quantum Systems
(2022-08) Muldoon, Jacob E.; Joglekar, Yogesh; Decca, Ricardo; Cheng, Rui; Vemuri, Gautam; Cincio, Lukasz
Open quantum systems have become a rapidly developing sector for research. Such systems present novel physical phenomena, such as topological chirality, enhanced sensitivity, and unidirectional invisibility resulting from both their non-equilibrium dynamics and the presence of exceptional points. We begin by introducing the core features of open systems governed by non-Hermitian Hamiltonians, providing the PT -dimer as an illustrative example. Proceeding, we introduce the Lindblad master equation which provides a working description of decoherence in quantum systems, and investigate its properties through the Decohering Dimer and periodic potentials. We then detail our preferred experimental apparatus governed by the Lindbladian. Finally, we introduce the Liouvillian, its relation to non-Hermitian Hamiltonians and Lindbladians, and through it investigate multiple properties of open quantum systems.

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