Optics Commons^™

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 …

Diffractive Imaging Of Laser Induced Molecular Reactions With Kiloelectron-Volt Ultrafast Electron Diffraction, Yanwei Xiong

Department of Physics and Astronomy: Dissertations, Theses, and Student Research

Capturing the structural changes during a molecular reaction with ultrafast electron diffraction (UED) requires a high spatiotemporal resolution and sufficiently high signal-to-noise to record the signals with high fidelity. In this dissertation, I have focused on the development of a tabletop gas phase keV-UED setup with a femtosecond temporal resolution. A DC electron gun was employed to generate electron pulses with a high repetition rate of 5 kHz. The space charge effect in the electron pulse was ameliorated by compressing the 90 keV electron pulse longitudinally with a time varying electric field in an RF cavity. The velocity mismatch between …

Color-Changing Reflection Hologram For Quality Assurance Of Therapeutic Ultrasound Systems, Tatsiana Mikulchyk, John Walsh, Jacinta Browne, Izabela Naydenova, Dervil Cody

Articles

The acoustic output of clinical therapeutic ultrasound equipment requires regular quality assurance (QA) testing to ensure the safety and efficacy of the treatment and that any potentially harmful deviations from the expected output power density are detected as soon as possible. A hologram, consisting of a reflection grating fabricated in an acrylate photopolymer film, has been developed to produce an immediate, visible, and permanent change in the color of the reconstructed hologram from red to green in response to incident ultrasound energy. The influence of the therapeutic ultrasound insonation parameters (exposure time, ultrasound power density, and proximity to the point …

Molecular Insights Into The Redox Of Atmospheric Mercury Through Laser Spectroscopy, Rongrong Wu Cohen

Theses and Dissertations

The widespread pollution of mercury motivates research into its atmospheric chemistry and transport. Gaseous elemental mercury (Hg(0)) dominates mercury emission to the atmosphere, but the rate of its oxidation to mercury compound (Hg(II)) plays a significant role in controlling where and when mercury deposits to ecosystems. Atomic bromine is regarded as the main oxidant for Hg(0) oxidation, known to initiate the oxidation via a two-step process in the atmosphere – formation of BrHg (R1) and subsequent reactions of BrHg with abundant free radicals Y, i.e., NO2, HOO, etc. (R2), where the reaction of BrHg +Y could also lead to the …

Monitoring Bacteria Cultures Using Near Infrared (Nir) Binary Spectronephelometry (Bsn), Raman Spectra And Principal Component Analysis (Pca), Steven Ortiz

Dissertations - ALL

Current noninvasive methods cannot continuously and simultaneously monitor the concentrations of cells and media components that define the state of native bacterial cultures, because of changing turbidity. A new technique, binary spectronephelometry (BSN) has the same or better sensitivity and precision for population monitoring as optical density at 600nm (OD600), while simultaneously measuring metabolic processes. The BSN algorithm uses laser induced emission to probe mildly turbid media i.e., propagation of light occurs in the single scattering regime. A BSN "training set" associates a grid of elastic emission measurements, comprising Rayleigh and Mie scattering, and inelastic emission measurements, comprising fluorescence and …

Limits Of Detection Of Mycotoxins By Laminar Flow Strips: A Review, Xinyi Zhao, Hugh Byrne, Christine M. O’Connor, James Curtin, Furong Tian

Articles

Mycotoxins are secondary metabolic products of fungi. They are poisonous, carcinogenic, and mutagenic in nature and pose a serious health threat to both humans and animals, causing severe illnesses and even death. Rapid, simple and low-cost methods of detection of mycotoxins are of immense importance and in great demand in the food and beverage industry, as well as in agriculture and environmental monitoring, and, for this purpose, lateral flow immunochromatographic strips (ICSTs) have been widely used in food safety and environmental monitoring. The literature to date describing the development of ICSTs for the detection of different types of mycotoxins using …

Resolving The Three-Dimensional Rotational And Translational Dynamics Of Single Molecules Using Radially And Azimuthally Polarized Fluorescence, Oumeng Zhang, Weiyan Zhou, Jin Lu, Tingting Wu, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

We report a radially and azimuthally polarized (raPol) microscope for high detection and estimation performance in single-molecule orientation-localization microscopy (SMOLM). With 5000 photons detected from Nile red (NR) transiently bound within supported lipid bilayers (SLBs), raPol SMOLM achieves 2.9 nm localization precision, 1.5° orientation precision, and 0.17 sr precision in estimating rotational wobble. Within DPPC SLBs, SMOLM imaging reveals the existence of randomly oriented binding pockets that prevent NR from freely exploring all orientations. Treating the SLBs with cholesterol-loaded methyl-β-cyclodextrin (MβCD-chol) causes NR’s orientational diffusion to be dramatically reduced, but curiously NR’s median lateral displacements drastically increase from 20.8 to …

Photophysics Of Metalloporphyrins Strongly Coupled To Cavity Photons, Aleksandr Avramenko

Wayne State University Dissertations

This dissertation will discuss the photophysics of metalloporphyrins, mainly CuTPP, ZnTPP, and H2TPP under strong light-matter coupling conditions. Strong light-matter coupling was achieved by embedding the previously mentioned chromophores into a spun coated PMMA polymer coating which is then incorporated as a spacer layer in a FabryPérot nano-cavity. The cavity thickness is chosen so that the cavity photon is of similar energy as the B, or Soret transition (2nd excited state) of the porphyrin molecule. The exchange of energy between the cavity photon and the molecular mode leads to the formation of polariton states.

Increasing the concentration of the molecules …

Single-Molecule Localization Microscopy Of 3d Orientation And Anisotropic Wobble Using A Polarized Vortex Point Spread Function, Tianben Ding, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Within condensed matter, single fluorophores are sensitive probes of their chemical environments, but it is difficult to use their limited photon budget to image precisely their positions, 3D orientations, and rotational diffusion simultaneously. We demonstrate the polarized vortex point spread function (PSF) for measuring these parameters, including characterizing the anisotropy of a molecule’s wobble, simultaneously from a single image. Even when imaging dim emitters (∼500 photons detected), the polarized vortex PSF can obtain 12 nm localization precision, 4°–8° orientation precision, and 26° wobble precision. We use the vortex PSF to measure the emission anisotropy of fluorescent beads, the wobble dynamics …

Computational Modelling Enables Robust Multidimensional Nanoscopy, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

The following sections are included:

• Present State of Computational Modelling in Fluorescence Nanoscopy

• Recent Contributions to Computational Modelling in Fluorescence Nanoscopy

• Outlook on Computational Modelling in Fluorescence Nanoscopy

• Acknowledgments

• References

Interactions Of Organic Fluorophores With Plasmonic Surface Lattice Resonances, Robert J. Collison

Dissertations, Theses, and Capstone Projects

It is common knowledge that metals, alloys and pure elements alike, are lustrous and reflective, the more so when a metal surface is flat, polished, and free from oxidation and surface fouling. However, some metals reflect visible light, in the 380 nm to 740 nm range of wavelengths, much more strongly than others. In particular, some metals reflect wavelengths in certain portions of the ultraviolet (UV), visible, and near-infrared (NIR) regime, let us say 200 nm to 2000 nm, while absorbing light strongly in other segments of this range. There are several factors that account for this difference between various …

Fabrication Of Metal-Silicon Nanostructures By Reactive Laser Ablation In Liquid, Eric J. Broadhead

Theses and Dissertations

Metal-silicon nanostructures are a growing area of research due to their applications in multiple fields such as biosensing and catalysis. In addition, silicon can provide strong support effects to metal nanoparticles while being more cost effective than traditionally used supports, like titania. Traditional wet-chemical methods are capable of synthesizing metal-silicon nanostructures with a variety of composition and nanoparticle shapes, but they often require high temperatures, toxic solvents, strong reducing agents, or need capping agents added to stabilize the nanoparticles. Laser processing is an emerging technique capable of synthesizing metal-silicon composite surfaces that offers a faster, simpler, and greener synthesis route …

The Aging And Impacts Of Atmospheric Soot: Closing The Gap Between Experiments And Models, Ogochukwu Yvonne Enekwizu

Dissertations

The main goal of this dissertation is to generate data and parameterizations to accurately represent soot aerosols in atmospheric models. Soot from incomplete combustion of fossil fuels and biomass burning is a major air pollutant and a significant contributor to climate warming. The environmental impacts of soot are strongly dependent on the particle morphology and mixing state, which evolve continuously during atmospheric transport via a process known as aging. To make predictions of soot impacts on the environment, most atmospheric models adopt simplifications of particle structure and mixing state, which lead to substantial uncertainties. Using an experimentally constrained modeling approach, …

Using Second Harmonic Generation To Study Gram-Positive Bacterial Membranes, Lindsey N. Miller

Doctoral Dissertations

Understanding how small-molecules, such as drugs, interact with bacterial membranes can quickly unravel into much more perplexing questions. No two bacterial species are alike, especially when comparing their membrane compositions which can even be altered by incorporating fatty acids from their surrounding environment into their lipid-membrane composition. To further complicate the comparison, discrete alterations in small-molecule structures can result in vastly different membrane-interaction outcomes, giving rise to the need for more "label-free" studies when analyzing drug mechanisms. The work presented in this dissertation highlights the benefits to using nonlinear spectroscopy and microscopy techniques for probing small-molecule interactions in living bacteria. …

3-D Fabry–Pérot Cavities Sculpted On Fiber Tips Using A Multiphoton Polymerization Process, Jonathan W. Smith, Jeremiah C. Williams, Joseph S. Suelzer, Nicholas G. Usechak, Hengky Chandrahalim

Faculty Publications

This paper presents 3-D Fabry–Pérot (FP) cavities fabricated directly onto cleaved ends of low-loss optical fibers by a two-photon polymerization (2PP) process. This fabrication technique is quick, simple, and inexpensive compared to planar microfabrication processes, which enables rapid prototyping and the ability to adapt to new requirements. These devices also utilize true 3-D design freedom, facilitating the realization of microscale optical elements with challenging geometries. Three different device types were fabricated and evaluated: an unreleased single-cavity device, a released dual-cavity device, and a released hemispherical mirror dual-cavity device. Each iteration improved the quality of the FP cavity's reflection spectrum. The …

Single‐Molecule 3d Orientation Imaging Reveals Nanoscale Compositional Heterogeneity In Lipid Membranes, Jin Lu, Hesam Mazidi, Tianben Ding, Oumeng Zhang, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

In soft matter, thermal energy causes molecules to continuously translate and rotate, even in crowded environments, thereby impacting the spatial organization and function of most molecular assemblies, such as lipid membranes. Directly measuring the orientation and spatial organization of large collections (>3000 molecules μm⁻²) of single molecules with nanoscale resolution remains elusive. In this paper, we utilize SMOLM, single‐molecule orientation localization microscopy, to directly measure the orientation spectra (3D orientation plus “wobble”) of lipophilic probes transiently bound to lipid membranes, revealing that Nile red's (NR) orientation spectra are extremely sensitive to membrane chemical composition. SMOLM images resolve …

Structural Organization And Chemical Activity Revealed By New Developments In Single-Molecule Fluorescence And Orientation Imaging, Tianben Ding

McKelvey School of Engineering Theses & Dissertations

Single-molecule (SM) fluorescence and its localization are important and versatile tools for understanding and quantifying dynamical nanoscale behavior of nanoparticles and biological systems. By actively controlling the concentration of fluorescent molecules and precisely localizing individual single molecules, it is possible to overcome the classical diffraction limit and achieve 'super-resolution' with image resolution on the order of 10 nanometers.

Single molecules also can be considered as nanoscale sensors since their fluorescence changes in response to their local nanoenvironment. This dissertation discusses extending this SM approach to resolve heterogeneity and dynamics of nanoscale materials and biophysical structures by using positions and orientations …

Designing A Reactor Chamber For Hot Electron Chemistry On Bimetallic Plasmonic Nanoparticles, Bryn Merrill, Bingjie Zhang, Jerry Larue

SURF Posters and Papers

Catalysis provides pathways for efficient and selective chemical reactions by lowering the energy barriers for desired products. Gold nanoparticles (AuNPs) show excellent promise as plasmonic catalysts. Plasmonic materials have localized surface plasmon resonances, oscillations of the electron bath at the surface of a nanoparticle, that generate energetically intense electric fields which rapidly decay into energetically excited electrons. The excited electrons have the potential to destabilize atoms strongly bound to the catalysts through occupation of antibonding orbitals. Tuning the antibonding orbitals to make them accessible for occupancy by electrons is achieved by coating the AuNP in a thin layer of another …

Monitoring And Identifying The Rhodamine 6g-Hydroxide Ion Reaction Using In-Situ, Surface-Enhanced Raman Spectroscopy, Ryan Lamb

Masters Theses & Specialist Projects

An effective method for monitoring chemical reactions is necessary to better understand their mechanisms and kinetics. Effective reaction monitoring requires a spectroscopy technique with fast data acquisition, high sensitivity, structure-to-spectrum correlation, and low solvent interference. Surface-enhanced Raman spectroscopy (SERS) provides these features, which makes it a valuable tool for monitoring reactions. To obtain the Raman enhancement, metallic nanostructures typically made of silver or gold are aggregated using a salt. The nanoparticles aggregates must then be stabilized using a surfactant to use this method in situ due to eventual nanoparticle precipitation. In this study, gold nanoparticles stabilized with sodium dodecyl sulfate …

Nanoscale Colocalization Of Fluorogenic Probes Reveals The Role Of Oxygen Vacancies In The Photocatalytic Activity Of Tungsten Oxide Nanowires, Meikun Shen, Tianben Ding, Steven T. Hartman, Fudong Wang, Christina Krucylak, Zheyu Wang, Che Tan, Bo Yin, Rohan Mishra, Matthew D. Lew, Bryce Sadtler

Electrical & Systems Engineering Publications and Presentations

Defect engineering is a strategy that has been widely used to design active semiconductor photocatalysts. However, understanding the role of defects, such as oxygen vacancies, in controlling photocatalytic activity remains a challenge. Here, we report the use of chemically triggered fluorogenic probes to study the spatial distribution of active regions in individual tungsten oxide nanowires using super-resolution fluorescence microscopy. The nanowires show significant heterogeneity along their lengths for the photocatalytic generation of hydroxyl radicals. Through quantitative, coordinate-based colocalization of multiple probe molecules activated by the same nanowires, we demonstrate that the nanoscale regions most active for the photocatalytic generation of …

Gravity-Drawing Flexible Silicone Filaments As Fiber Optics And Model Foldamers, Katherine Snell

CMC Senior Theses

Here, we present a method of gravity-drawing polydimethylsiloxane (PDMS) silicone fibers with application as fiber optics and as model foldamers. Beginning as a viscous liquid, PDMS is cured using heat until its measured viscosity reaches 4000 mPa•s. The semi-cured elastomer is then extruded through a tube furnace to produce thin (diameters on the order of hundred micrometers) filaments with scalable lengths. PDMS is biocompatible, gas-permeable, flexible, and hydrophobic. Additionally, the PDMS surface hydrophobicity can be modified via UV exposure, O2 plasma, and corona discharge. We demonstrate the patternibility (i.e patterns of hydrophobicity) of PDMS fibers, adding complexity to potential foldamer …

Studying Near-Critical And Super-Critical Fluids In Reduced Gravity, Christian Hawkins, Ana Oprisan, Carole Lecoutre-Chabot, Yves Garrabos, Daniel Beysens

Journal of the South Carolina Academy of Science

Critical and supercritical fluids have a variety of applications, from use as machine lubricants in high pressure or high temperature environments to the manufacturing of materials such as aerogel. The optical properties of fluids undergo rapid changes near the critical point resulting in a rapid increase in turbidity known as critical opalescence. These optical changes can be used to probe the universality of critical behavior. As a fluid approaches the critical point, the compressibility rapidly increases. In a gravitational field, this increase in compressibility leads to near-critical fluids stratifying by phase and density, making it difficult to observe the optical …

Erratum: "Imaging The Three‐Dimensional Orientation And Rotational Mobility Of Fluorescent Emitters Using The Tri‐Spot Point Spread Function", Oumeng Zhang, Jin Lu, Tianben Ding, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

In the original paper, a calibration error exists in the image-formation model used to analyze experimental images taken by our microscope, causing a bias in the orientation measurements in Figs. 2 and 3. The updated measurements are shown in Fig. E1. We have also updated the supplementary material for the original article to discuss the revised PSF model and estimation algorithms (supplementary material 2) and show the revised model and measurements (Figs. S1, S3, S7, S8, and S10–S13).

Development Of A Ground-Based Aerial-Tracking Instrument For Open-Path Spectroscopy To Monitor Atmospheric Constituents, Haden Hodges

Civil Engineering Undergraduate Honors Theses

A ground-based aerial-tracking instrument, known as the Ground Tracker, designed to provide spectral data to quantify greenhouse gases is under development. The Ground Tracker includes an Optical System including a high power rifle scope, video camera, and spectrometer used to locate an active light source from the Emitter, and collect spectral data by utilizing an actuating mirror. The implementation of this instrument could be made low cost by utilizing existing weather balloon infrastructure to allow the Emitter to be placed into the lower stratosphere. The recovery of the emitter will be possible by tracking the GPS coordinates. Weather balloon instrument …

The Development Of An Integrated Simulation Model On Understandings On The Interaction Between Electromagnetic Waves And Nanoparticles, Xiaojin Wang

Masters Theses & Specialist Projects

To investigate the interaction between nanoparticles and electromagnetic waves, a numerical simulation model based on FEM was built in this thesis. Numerical simulation is an important auxiliary research method besides experiments. The optical properties of nanoparticles consist of scattering, absorption, and extinction, and in the case of nanoparticle suspension, the transmission is also involved. This thesis addressed two typical applications based on the established model, one was regarding the nanofluids for solar energy harvesting, and the other was regarding the optical properties of atmospheric soot. In the case of the nanofluids solar energy harvesting, the established model provided a convenient …

An In-Situ Study Of The Aqueous Speciation Of Uranium (Vi) Under Hydrothermal Conditions, Diwash Dhakal

MSU Graduate Theses

Rigorous study of the speciation distribution of uranyl-chloride bearing solutions under hydrothermal conditions is important to understand the transport mechanism of uranium underground, which is of uttermost interest to parties studying the geological uranium deposits and those studying the possibilities of geological repositories for spent nuclear waste. I report an in-situ Raman spectroscopic study of the speciation distribution of aqueous uranyl-chloride complexes upto 500°C conducted using a HDAC as the high PT spectroscopic cell. The samples studied contained the species UO₂²⁺, UO₂Cl⁺, UO₂Cl₂⁰ and UO₂Cl₃^{- …}

Application Of X-Ray Grating Interferometry To Polymer/Flame Retardant Blends In Additive Manufacturing, Omoefe Joy Kio

LSU Doctoral Dissertations

X-ray grating interferometry is a nondestructive tool for visualizing the internal structures of samples. Image contrast can be generated from the absorption of X-rays, the change in phase of the beam and small-angle X-ray scattering (dark-field). The attenuation and differential phase data obtained complement each other to give the internal composition of a material and large-scale structural information. The dark-field signal reveals sub-pixel structural detail usually invisible to the attenuation and phase probe, with the potential to highlight size distribution detail in a fashion faster than conventional small-angle scattering techniques. This work applies X-ray grating interferometry to the study of …

Fundamental Limits Of Measuring Single-Molecule Rotational Mobility, Oumeng Zhang, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Various methods exist for measuring molecular orientation, thereby providing insight into biochemical activities at nanoscale. Since fluorescence intensity and not electric field is detected, these methods are limited to measuring even-order moments of molecular orientation. However, any measurement noise, for example photon shot noise, will result in nonzero measurements of any of these even-order moments, thereby causing rotationally-free molecules to appear to be partially constrained. Here, we build a model to quantify measurement errors in rotational mobility. Our theoretical framework enables scientists to choose the optimal single-molecule orientation measurement technique for any desired measurement accuracy and photon budget.

Energy Transfer Between Eu2+ And Mn2+ For Na(Sr,Ba)Po4 And Ba2mg(Bo3)2, Kevin Bertschinger

Dissertations, Master's Theses and Master's Reports

There is no debate of the affect that solid-state lighting has had on the world we live in. Throughout the centuries, lighting has continued to improve from kerosene lanterns to white light emitting diodes. Even though lighting today is sufficient there is still much room to improve color rendering index and efficiency. An active area of research to improve today's lighting technology is by doping inorganic phosphors with luminescent ion centers. There have been numerous reports of inorganic phosphors showing a variety of emission color and luminescence. In this thesis we discuss two new inorganic phosphors codoped with Eu^{2+ …}

A System For Conducting Laser-Induced Fluorescence Measurements On Gas Mixtures Exposed To Alpha Radiation, Patrick Ables

Master's Theses

This paper documents modifications to an existing vacuum system to allow laser-induced fluorescence spectroscopy measurements within simulated atmospheres under a variety of conditions. This added capability will expand the laboratory’s ability to experimentally validate a computational model that calculates the effects of radiation within the atmosphere. The computational model could reveal radiation-induced chemical products that can be used to develop an alternative detection method that can be implemented from a safe distance. The selection of molecules for experimental validation has been limited to those which can be detected utilizing cavity ringdown spectroscopy. The current model indicates nitric oxide and ozone …