Optics Commons^™

Information-Rich 6d Single-Molecule Imaging Design Using Optimization, Tingting Wu

McKelvey School of Engineering Graduate Student Theses & Dissertations

When studying biochemical processes, localizing the targets alone will not paint a complete picture. We also need techniques to probe how biomolecules interact with one another, including how molecules are organized into larger structures, how they are oriented with respect to surrounding molecules, and how local chemical parameters, like pH and hydrophobicity, vary spatially and temporally. My dissertation focuses on single-molecule orientation localization microscopy (SMOLM, Chapter 1). The objective is to develop imaging techniques for measuring how molecules are oriented with respect to their surrounding molecules, namely, 3D orientation. Achieving optimal imaging performance requires careful design of both the forward …

Shock-Wave Tolerant Phase Reconstruction Algorithm For Shack–Hartmann Wavefront Sensor Data, Thomas E. Defoor, Matthew Kalensky, Matthew R. Kemnetz, Timothy J. Bukowski, Mark F. Spencer

Faculty Publications

We develop a phase reconstruction algorithm for the Shack–Hartmann wavefront sensor (SHWFS) that is tolerant to phase discontinuities, such as the ones imposed by shock waves. In practice, this algorithm identifies SHWFS locations where the resultant tilt information is affected by the shock and improves the tilt information in these locations using the local SHWFS observation-plane irradiance patterns. The algorithm was shown to work well over the range of conditions tested with both simulated and experimental data. In turn, the reconstruction algorithm will enable robust wavefront sensing in transonic, supersonic, and hypersonic environments.

Volumetric Imaging Using The Pupil-Matched Remote Focusing Technique In Light-Sheet Microscopy, Sayed Hassan Dibaji Foroushani

Optical Science and Engineering ETDs

ABSTRACT

The dissertation explores innovative techniques in light sheet microscopy, a pivotal tool in biomedical imaging, to enhance its speed, resolution, and efficiency in capturing dynamic biological processes. Light sheet microscopy allows for quick 3D imaging of biological specimens ranging from cells to organs with high spatiotemporal resolution, large field-of-view, and minimal damage, making it vital for in vivo imaging.

The first project introduces a novel optical concept designed to optimize Axially Swept Light Sheet Microscopy (ASLM). This technique is crucial for imaging specimens ranging from live cells to chemically cleared organs due to its versatility across different immersion media. …

Development Of An Optical Test Bed For The Fabrication And Characterisation Of An Analog Holographic Wavefront Sensor, Emma Branigan, Andreas Zepp, Suzanne Martin, Matthew Sheehan, Szymon Gladysz, Kevin Murphy

Conference Papers

A new holographic recording setup has been developed for the fabrication of single- and multi-mode photopolymer-based analog holographic wavefront sensors. A second setup has been built and used to characterise the sensor at several wavelengths.

Radiation Exposure Calibration Of The Al2o3:C With Radium-226 And Cesium-137 Using The Osl Method, Selma Tepeli Aydin

All Theses

Optically stimulated luminescence (OSL) dosimetry was utilized to calibrate Al₂O₃:C powder dosimeters, available commercially as the nanoDot® from Landauer Inc., and compare the dosimeter response to radium-226 (²²⁶Ra) and cesium-137 (¹³⁷Cs). The signal from the OSL was quantified using a microSTARii^® OSL reader also produced by Landauer Inc. Dose-response curves were developed for ²²⁶Ra and ¹³⁷Cs experiments (5 dosimeters each) at thirteen absorbed doses. Individual dosimeter response was tracked by serial number. Linear regression analysis was performed to determine if there were significant differences between the intercepts of the …

Femtosecond Laser Shock Peening And The Dynamics Of Femtosecond Laser-Induced Shock Waves, Yuxin Li

All Dissertations

Laser shock peening (LSP) is an important material surface strengthening technique that uses laserinduced shock waves to cause severe plastic deformation near material surfaces. It can significantly improve material properties like hardness, strength, fatigue life, and corrosion resistance and is widely used in industrial sectors such as automotive, aerospace, nuclear, and medical areas. The conventional nanosecond laser shock peening (ns-LSP) has demonstrated effectiveness but faces challenges such as complex setup, low throughput, high energy consumption, and inflexibility for complex geometries. Femtosecond laser shock peening (fs-LSP) offers a promising alternative to overcome these issues, thanks to its ultra-high laser intensity and …

On The Synthesis Of Heavy Rare Earth Solid Solutions And Their Hydrides, Joshua R. Van Cleave

UNLV Theses, Dissertations, Professional Papers, and Capstones

The theoretical predictions and results from the (La,Y)Hx ternary hydride solution provided evidence toward phase stability at comparatively lower pressures, as consequence the (Yb,Lu)H_x and (Tm,Lu)H_x ternary hydrides are studied here with pressures up to 25 GPa in the diamond anvil cell. The onset of an unknown feature in the XRD pattern coincides with crystallographic plane distortions in the tetragonal lattice of ytterbium hydride at their laser-heated interface, possibly driven by a solid solution of Lu-Yb. Findings in collected Raman spectra and X-ray diffraction patterns in an Ar environment suggest potential stability of the FCC and high-temperature HCP …

Aspects Of Stochastic Geometric Mechanics In Molecular Biophysics, David Frost

All Dissertations

In confocal single-molecule FRET experiments, the joint distribution of FRET efficiency and donor lifetime distribution can reveal underlying molecular conformational dynamics via deviation from their theoretical Forster relationship. This shift is referred to as a dynamic shift. In this study, we investigate the influence of the free energy landscape in protein conformational dynamics on the dynamic shift by simulation of the associated continuum reaction coordinate Langevin dynamics, yielding a deeper understanding of the dynamic and structural information in the joint FRET efficiency and donor lifetime distribution. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based …

Robust Zero Modes In Non-Hermitian Systems Without Global Symmetries, Jose D. H. Rivero, Courtney Fleming, Bingkun Qi, Liang Feng, Li Ge

Publications and Research

We present an approach to achieve zero modes in lattice models that do not rely on any symmetry or topology of the bulk, which are robust against disorder in the bulk of any type and strength. Such symmetry-free zero modes (SFZMs) are formed by attaching a single site or small cluster with zero mode(s) to the bulk, which serves as the “nucleus” that expands to the entire lattice. We identify the requirements on the couplings between this boundary and the bulk, which reveals that this approach is intrinsically non-Hermitian. We then provide several examples with either an arbitrary or structured …

Acoustically Levitated Whispering-Gallery Mode Microlasers, H. M. Reynoso-De La Cruz, E. D. Hernández-Campos, E. Ortiz-Ricardo, A. Martínez-Borquez, I. Rosas-Román, V. Contreras, G. Ramos-Ortiz, B. Mendoza-Santoyo, Cecilia Zurita-Lopez, R. Castro-Beltrán

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Acoustic levitation has become a crucial technique for contactless manipulation in several fields, particularly in biological applications. However, its application in the photonics field remains largely unexplored. In this study, we implement an affordable and innovative phased-array levitator that enables stable trapping in the air of micrometer dye-doped droplets, thereby enabling the creation of microlasers. For the first time, this paper presents a detailed performance of the levitated microlaser cavity, supported by theoretical analysis concerning the hybrid technology based on the combination of whispering-gallery modes and acoustic fields. The pressure field distribution inside the acoustic cavity is numerically solved and …

System-Level Noise Performance Of Coherent Imaging Systems, Derek J. Burrell, Joshua H. Follansbee, Mark F. Spencer, Ronald G. Driggers

Faculty Publications

We provide an in-depth analysis of noise considerations in coherent imaging, accounting for speckle and scintillation in addition to “conventional” image noise. Specifically, we formulate closed-form expressions for total effective noise in the presence of speckle only, scintillation only, and speckle combined with scintillation. We find analytically that photon shot noise is uncorrelated with both speckle and weak-to-moderate scintillation, despite their shared dependence on the mean signal. Furthermore, unmitigated speckle and scintillation noise tends to dominate coherent-imaging performance due to a squared mean-signal dependence. Strong coupling occurs between speckle and scintillation when both are present, and we characterize this behavior …

Quantitative, Photocurrent Multidimensional Coherent Spectroscopy, Adam Halaoui

Electronic Theses and Dissertations

Multidimensional coherent spectroscopy (MDCS) is a quickly growing field that has a lot of advantages over more conventional forms of spectroscopy. These advantages all come from the fact that MDCS allows us to get time resolved correlated emission and absorption spectra using very precisely chosen interactions between the density matrix and the excitation laser. MDCS spectra gives the researcher a lot of information that can be extracted purely through qualitative analysis. This is possible because state couplings are entirely separated on the spectra, and once we know how to read the data, we can see how carriers transport in the …

Active-Illumination Extension To The Priest And Meier Pbrdf, Mark F. Spencer, Milo W. Hyde Iv, Santasri R. Bose-Pillai, Michael A. Marciniak

Faculty Publications

This paper develops a 3D vector solution for the scattering of partially coherent laser-beam illumination from statistically rough surfaces. Such a solution enables a rigorous comparison to the well-known Priest and Meier polarimetric bidirectional reflectance distribution function (pBRDF) [Opt Eng 41(5),988 (2002).]. Overall, the comparison shows excellent agreement for the normalized spectral density and the degree of polarization. Based on this agreement, the 3D vector solution also enables an extension to the Priest and Meier pBRDF that accounts for the effects of active illumination. In particular, the 3D vector solution enables the development of a closed-form expression for the spectral …

Optics Studies For Multipass Energy Recovery At Cebaf: Er@Cebaf, Isurumali Neththikumara

Physics Theses & Dissertations

Energy recovery linacs (ERLs), focus on recycling the kinetic energy of electron beam for the purpose of accelerating a newly injected beam within the same accelerating structure. The rising developments in the super conducting radio frequency technology, ERL technology has achieved several noteworthy milestones over the past few decades. In year 2003, Jefferson Lab has successfully demonstrated a single pass energy recovery at the CEBAF accelerator. Furthermore, they conducted successful experiments with IR-FEL demo and upgrades, as well as the UV FEL driver. This multi-pass, multi-GeV range energy recovery demonstration proposed to be carried out at CEBAF accelerator at Jefferson …

Non-Hermitian Gauged Laser Arrays With Localized Excitations: Anomalous Threshold And Generalized Principle Of Selective Pumping, Li Ge, Zihe Gao, Liang Feng

Publications and Research

We investigate non-Hermitian skin modes in laser arrays with spatially localized excitation. Intriguingly, we observe an unusual threshold behavior when selectively pumping either the head or the tail of these modes: both cases exhibit the same lasing threshold and hence defy the conventional principle of selective pumping, which aims to maximize the overlap between the pump profile and the target lasing mode. To shed light on this enigma, we reveal a previously overlooked phenomenon, i.e., energy exchange at non-Hermitian coupling junctions with the photonic environment, which does not occur with uniform gain or loss. Utilizing a transfer matrix approach, we …

Tunneling Time And Faraday/Kerr Effects In Pt-Symmetric Systems, Peng Guo, Vladimir Gasparian, Antonio Antonio Perez-Garrido, Ester Jodar Ferrandez

Research & Publications

We review the generalization of tunneling time and anomalous behaviour of Fara- day and Kerr rotation angles in parity and time (PT )-symmetric systems. Similarities of two phenomena are discussed, both exhibit a phase transition-like anomalous behaviour in a certain range of model parameters. Anomalous behaviour of tunneling time and Faraday/Kerr angles in PT -symmetric systems is caused by the motion of poles of scattering amplitudes in the en- ergy/frequency complex plane.

Dynamics Of Spin And Charge Of Color Centers In Diamond Under Cryogenic Conditions, Richard G. Monge

Dissertations, Theses, and Capstone Projects

Individual quantum systems in semiconductors are currently the most sought-after platform for applications in quantum science. Most notably, the nitrogen-vacancy (NV) center in diamond features a defect deep within the electronic bandgap, making it amenable for precise manipulation to help pave the way to perform fundamental quantum physics experimentation. The NV center also offers long coherence times and versatile spin-dependent fluorescent properties, making it an ideal candidate for a nanoscale magnetometer. Furthermore, multi-color excitation offers deterministic charge state manipulation. While ambient operation has been key to their appeal, bringing NVs to cryogenic conditions opens new opportunities for alternate forms of …

Nonlinear Processes In Room Temperature Exciton-Polaritons, Prathmesh Deshmukh

Dissertations, Theses, and Capstone Projects

Strong light-matter coupling in solid state systems is an intriguing process that allows one to exploit the advantages of both light and matter. In this context, microcavities have become essential platforms for studying the strong coupling regime, where hybrid light-matter states known as exciton-polaritons form, leading to enhanced light matter interaction, modified material properties, and novel quantum phenomena. In this thesis, we explore the phenomenology of exciton-polaritons in strained TMD microcavities, 2D perovskites, fluorescent proteins and organic dyes encompassing thermalization, polariton lasing, and the observation of nonlinear effects.

Transition metal dichalcogenides (TMDs) have emerged as a remarkable class of two- …

Tunable Linear And Nonlinear Metasurfaces Based On Hybrid Gold-Graphene Plasmons, Matthew Feinstein

Dissertations, Theses, and Capstone Projects

Optical Metasurfaces are planar structures that are patterned with subwavelength structures and are very thin compared to the wavelength of light. Despite their thinness, these structured materials can strongly interact with incident light to effect the functionalities of conventional optical components, such as rotation of the polarization state, beam steering, lensing, spectral filtering, and holography, to name a few. Metasurfaces can also facilitate nonlinear optical effects, such as the mixing of beams at different frequencies to generate a beam at a new frequency.

The ability to alter the behavior of a metasurface during operation is highly desired for applications such …

Atmospheric Propagation Of Qubits: Laboratory Experiments To Field Demonstrations, Keith A. Wyman

Theses and Dissertations

Free-space quantum networks can enable global-scale quantum communication via satellite-based nodes and quantum ground transceivers. To enable building of robust global quantum networks, it is critical to learn how the state of the qubit is transformed while propagating through the atmosphere. With such an overarching goal, we built a laboratory based atmospheric turbulence simulator (ATS) to characterize the effects of atmospheric turbulence on an entangled pair of photons as a function of statistical quantities such as the Fried parameter or scintillation index for long-distance communication. Specifically, the changes in the statistical properties associated with a quantum source was investigated using …

Thermal Blooming With Laser-Induced Convection: Radial Basis Function Simulation, Benjamin F. Akers, Steven T. Fiorino, Jonah A. Reeger

Faculty Publications

The propagation of a high energy laser through a nearly stagnant absorbing medium is studied. The absorption values and time scale of the problem are such that the laser induces convective heat currents transverse to the beam. These currents couple to the laser via the refractive index, causing time dependent thermal blooming. A numerical method is developed and applied to the model in [ J. Electromagn. Waves Appl. 33, 96 (2019) ], using radial basis functions for spatial differencing, which allows for irregular point spacings and a wide class of geometries. Both the beam and laser-induced fluid dynamics are …

The Importance Of Contrast Sensitivity, Color Vision, And Electrophysiological Testing In Clinical And Occupational Settings, Frances Silva

Theses & Dissertations

Visual acuity (VA) is universally accepted as the gold standard metric for ocular vision and function. Contrast sensitivity (CS), color vision, and electrophysiological testing for clinical and occupational settings are warranted despite being deemed ancillary and minimally utilized by clinicians. These assessments provide essential information to subjectively and objectively quantify and obtain optimal functional vision. They are useful for baseline data and monitoring hereditary and progressive ocular conditions and cognitive function. The studies in this dissertation highlight the value of contrast sensitivity, color vision, and cone specific electrophysiological testing, as well as the novel metrics obtained with potential practical clinical …

Design Of A Resonant Optical Cavity For Imaging Magneto-Optically Active Thin Film Samples, Cody Robert Brelage

Graduate Theses - Physics and Optical Engineering

This document describes the design and fabrication of an optical resonator system to investigate magneto-optic properties of thin film samples. This system uses an open-air optical resonator to enable photons to make multiple passes through each thin film and thus increase the magnitude of the Faraday rotation that each sample imposes onto the light that exits the system. This system promises many future experiments to study the magneto-optic properties of thin film and nano-particle samples. Using an optical resonator to enhance Faraday rotation should enable an improved signal-to-noise ratio in taking measurements and images with a photodetector.

Hybridly Integrated Semiconductor Lasers And Amplifiers On Iii-V/Si3n4 Platform For Beam Combining And Other Advanced Applications, Siwei Zeng

All Dissertations

Photonic integrated circuits (PICs) are devices that integrate multiple photonic functions on a small chip and allow for accurate dimension control and massive production. Similar to electronic integrated circuits, PICs can significantly reduce the system cost, size, weight, and operation power (CSWaP). Recently, the PIC technology has transformed many optical technologies which traditionally rely on tabletop systems and bulky components, such as optical interconnects, nonlinear optics, and quantum photonics, into a chip-scale platform. This device and system miniaturization has successfully led to a wide range of practical applications in computing, sensing, spectroscopy, and communication. However, the traditional passive PIC platform …

Fem Simulations Of Plasmon Field Enhancement In Gold Nanoparticle Dimers And Gold Nanoparticle-Nanorod Dimers, Edward J. Lipchus

Graduate Masters Theses

Plasmon resonance refers to the collective oscillation of free electrons in a nanomaterial in response to an incident electromagnetic field. When two plasmonic nanoparticles are placed close together, their localized surface plasmon resonances can couple and interact. The resulting plasmonic coupling leads to the formation of new plasmonic modes in the dimer system, significantly enhancing the electromagnetic fields in the vicinity of the nanoparticles, with various interesting and potentially useful applications. This thesis investigates the optical field enhancement arising from gold nanoparticle dimers in an aqueous dielectric medium, using the Finite Element Method simulation software COMSOL Multiphysics. The simulations provide …

High-Power Laser Cooling And Temperature-Dependent Fluorescence Studies Of Ytterbium Doped Silica, Brian Topper

Optical Science and Engineering ETDs

Experimental observation of optical refrigeration using ytterbium doped silica glass in recent years has created a new solution for heat mitigation in high-power laser systems, nonlinear fiber experiments, integrated photonics, and precision metrology. Current efforts of different groups focus on compositional optimization, fiber fabrication, and investigating how much silica can be cooled with a laser. At the start of this work, the best effort in laser cooling ytterbium doped silica saw cooling by 6 K from room temperature. This dissertation follows the experimental efforts that culminated in the increase of this initial record by one order of magnitude. Comprehensive spectroscopic …

Super-Resolution Microscopy With Color Centers In Diamond, Forrest A. Hubert

Optical Science and Engineering ETDs

This dissertation explores the development and application of diamond color centers, specifically the silicon-vacancy (SiV) and nitrogen-vacancy (NV) centers, in super-resolution microscopy and magnetic imaging techniques. It demonstrates the potential of SiV centers as photostable fluorophores in stimulated emission depletion (STED) microscopy, with a resolution of approximately 90 nm. The research also presents a method for nanoscale magnetic microscopy using NV centers by combining charge state depletion (CSD) microscopy with optically detected magnetic resonance (ODMR) to image magnetic fields produced by 30 nm iron-oxide nanoparticles. The individual magnetic feature width reaches ~100 nm while resolving magnetic field patterns from nanoparticles …

Propagation Of Spatiotemporal Optical Vortex Beams In Linear, Second-Order Dispersive Media, Milo W. Hyde Iv, Miguel A. Porras

Faculty Publications

In this paper, we study the behaviors of spatiotemporal optical vortex (STOV) beams propagating in linear dispersive media. Starting with the Fresnel diffraction integral, we derive a closed-form expression for the STOV field at any propagation distance z in a general second-order dispersive medium. We compare our general result to special cases published in the literature and examine the characteristics of higher-order STOV beams propagating in dispersive materials by varying parameters of the medium and source-plane STOV field. We validate our analysis by comparing theoretical predictions to numerical computations of a higher-order STOV beam propagating through fused silica, where we …

Wave Optics Approach To Solar Cell Brdf Modeling With Experimental Results, Madilynn Compean, Todd V. Small, Milo W. Hyde Iv, Michael Marciniak

Faculty Publications

Light curve analysis is often used to discern information about satellites in geosynchronous orbits. Solar panels, comprising a large part of the satellite’s body, contribute significantly to these light curves. Historically, theoretical bidirectional reflectance distribution functions (BRDFs) have failed to capture key features in the scattered light from solar panels. In recently published work, a new solar cell BRDF was developed by combining specular microfacet and “two-slit” diffraction terms to capture specular and periodic/array scattering, respectively. This BRDF was experimentally motivated and predicted many features of the solar cell scattered irradiance. However, the experiments that informed the BRDF were limited …

Enhanced Acousto-Optic Properties Of Silicon Carbide Based Layered Structure, Namrata Dewan Soni

Al-Bahir

This study investigates the feasibility of using silicon carbide-based layered surface acoustic wave (SAW) devices in acousto-optic applications. The acousto-optic properties of the temperature-stable layered structure TeO3/SiC/128oY-X LiNbO3 are investigated through theoretical analysis. This analysis includes the evaluation of key parameters such as the overlap integral, figure of merit, and diffraction efficiency. The SAW propagation characteristics and field profiles required for these calculations are obtained using SAW software. Results show that the layered structure has high diffraction efficiency of nearly 96% and a promising value for the acousto-optic figure of merit, indicating potential use in low driving power acousto-optic devices. …