Optics Commons^™

6d Single-Fluorogen Orientation-Localization Microscopy For Elucidating The Architecture Of Beta-Sheet Assemblies And Biomolecular Condensates, Tingting Wu, Weiyan Zhou, Jai S. Rudra, Rohit V. Pappu, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

We develop six-dimensional single-molecule orientation-localization microscopy (SMOLM) to measure the 3D positions and 3D orientations simultaneously of single fluorophores. We show how careful optimization of phase and polarization modulation components can encode phase, polarization, and angular spectrum information from each fluorescence photon into a microscope’s dipole-spread function. We used the transient binding and blinking of Nile red (NR) to characterize the helical structure of fibrils formed by designed amphipathic peptides, KFE8^L and KFE8^D, and the pathological amyloid-beta peptide Aβ42. We also deployed merocyanine 540 to uncover the interfacial architectures of biomolecular condensates.

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 …

Characterization Of Boreal-Arctic Vegetation Growth Phases And Active Soil Layer Dynamics In The High-Latitudes Of North America: A Study Combining Multi-Year In Situ And Satellite-Based Observations, Michael G. Brown

Dissertations, Theses, and Capstone Projects

This dissertation examined the seasonal freeze/thaw activity in boreal-Arctic soils and vegetation physiology in Alaska, USA and Alberta, Canada, using in situ environmental measurements and passive microwave satellite observations. The boreal-Arctic high-latitudes have been experiencing ecosystem changes more rapidly in comparison to the rest of Earth due to the presently warming climatic conditions having a magnified effect over Polar Regions. Currently, the boreal-Arctic is a carbon sink; however, recent studies indicate a shift over the next century to become a carbon source. High-latitude vegetation and cold soil dynamics are influenced by climatic shifts and are largely responsible for the regions …

Novel As-S-Se Compositions Of Solution-Processed Chalcogenide Thin Films For Infrared Optics, Annabella Orsini

Physics and Astronomy Honors Papers

Chalcogenide glasses (ChGs) have a wide range of interdisciplinary applications. In industry, ChGs are used to vastly improve infrared sight abilities. There are, however, improvements that can be made to the films’ stability, cost, and flexibility. Our project seeks to produce thin films that have these improvements, with capabilities comparable or better than what is widely used in the field. Thin films created through solution-based processes have proven to be much more flexible in comparison to bulk glass versions. Other elements in Group 16, such as Sulfur and Selenium have shown across literature to be a cost-effective alternative to Tellurium …

Review-Electrode Kinetics And Electrolyte Stability In Vanadium Flow Batteries, Andrea Bourke, Daniela Oboroceanu, Nathan Quill, Catherine Lenihan, Maria Alhajji Safi Maria Alhajji Safi, Mallory A. Miller, Robert F. Savinell, Jesse S. Wainright, Varsha Sasikumarsp, Maria Rybalchenko, Pupak Amini, Niall Dalton, Robert P. Lynch, D. Noel Buckley

Articles

Two aspects of vanadium flow batteries are reviewed: electrochemical kinetics on carbon electrodes and positive electrolyte stability. There is poor agreement between reported values of kinetic parameters; however, most authors report that kinetic rates are faster for VIV/VV than for VII/VIII. Cycling the electrode potential increases the rates of both reactions initially due to roughening but when no further roughening is observed, the VII/VIII and VIV/VV reactions are affected oppositely by the pretreatment potential. Anodic pretreatment activates the electrode for the VII/VIII reaction, and deactivates it for VIV/VV. Three states of the carbon surface are suggested: reduced and oxidized states …

Optical Tweezers: Exerting Force With Light, Gabriella Seifert

Scripps Senior Theses

Photons carry momentum. When a tightly-focused beam of photons hit a particle, they transfer some of their momentum to the particle, exerting a force. Optical tweezers take advantage of this phenomenon to trap (or “tweeze”) a spherical bead just after the focus of a diverging laser beam, creating a potential well that pulls in beads. In this thesis, I predict the force exerted on trapped beads and measure the actual force using an optical tweezers setup that I built. To predict the force, I follow the path of all possible rays from a diverging beam incident on a spherical bead …

Optimization Of Modular, Long-Range, Ultra-Fast Optical Tweezers With Fluorescence Capabilities For Single-Molecule And Single-Cell Based Biophysical Measurements, Subash C. Godar

All Dissertations

An Optical tweezer is a tightly focused laser beam that applies and senses precise and localized optical force to a dielectric microsphere and offers a unique and effective tool for manipulating the single cell or cell components, including nucleotides and dynein motor proteins. Here, I used highly stabilized optomechanical components and ultra-sensitive detection modules to significantly improve the measurement capabilities over a wide range of temporal and spatial scales. I combined the optical tweezer-based force spectroscopy technique with fluorescence microscopy to develop an integrated high-resolution force-fluorescence system capable of measuring displacements at sub-nanometer, forces at sub-piconewton over a temporal range …

Quantitative Raman Analysis Of Carotenoid Protein Complexes In Aqueous Solution, Joy Udensi, Ekaterina Loskutova, James Loughman, Hugh Byrne

Datasets

Carotenoids are naturally abundant fat-soluble pigmented compounds, with dietary, antioxidant and vision protection advantages. The dietary carotenoids, Beta Carotene, Lutein and Zeaxanthin, complexed with in bovine serum albumin (BSA) in aqueous solution, were explored using Raman spectroscopy to differentiate and quantify their spectral signatures. UV visible absorption spectroscopy was employed to confirm the linearity of responses over the concentration range employed (0.05-1mg/ml) and, of the 4 source wavelengths, 785nm, 660nm, 532nm, 473nm, 532nm was chosen to provide the optimal response. After preprocessing to remove water and BSA contributions, and correct for self-absorption, a partial least squares model with R^{2 …}

Abhd5 Induced Morphological Changes On Model Membrane Systems, Nasser S. Junedi

Honors College Theses

Proper regulation of neutral lipid storage (lipogenesis) and release (lipolysis) are critical molecular processes localized to an organelle called the Lipid Droplet (LD). The LD consists of a core with neutral lipids such as triacylglycerols (TAGs) and sterol esters surrounded by a phospholipid monolayer. Dysregulation of the processes localized to the LD are involved in the pathology of various diseases such as Neutral Lipid Storage Disease, diabetes, stroke and cancer. The non-enzymatic protein ABHD5 (α-β Hydrolase Domain-Containing Protein 5), is thought to play a key role in the process of lipolysis by forming homo-oligomers on the surface of the LD …

Live Cell Super-Resolution Microscopy Quanitifies An Interaction Between Influenza Hemagglutinin And Phosphatidylinositol 4,5-Bisphosphate, Jaqulin N. Wallace

Electronic Theses and Dissertations

Influenza virus, colloquially known as the flu, is an acute respiratory disease that infects several millions of individuals each year in the U.S. and kills tens of thousands of those infected. Yearly viral vaccines are widely available, however, due to the virus’s high mutation rate, their efficacy varies greatly. Due to the variability in vaccine efficiency against seasonal influenza, and the potential for even more pathogenic versions of influenza to emerge at any time, there is a high demand for a universal treatment option.

Influenza virus hijacks a variety of host cell components in order to replicate. The glycoprotein hemagglutinin …

Improved Antimicrobial Properties Of Silver Nanoparticles With Methylene Blue, Ermek Belekov

Masters Theses & Specialist Projects

Photosensitizing agents are the cornerstone of photodynamic therapy (PDT) that play essential role in deactivation process of multidrug resistant pathogens and tumor treatments. In this work we studied a photosensitizing agent made from mixture of silver nanoparticles (Ag NPs) and methylene blue (MB) which possess improved important characteristics like high photostability and high singlet oxygen yield. Ag NPs were synthesized by pulsed laser ablation technique in different aqueous solutions like Polyvinylpyrrolidone (PVP), citrate and Deionized (DI) water. The synthesized Ag NPs were characterized in depth using with transmission electron microscopy (TEM), UVVisible (UV-Vis), and photoluminescence (PL) spectra. Ag NPs were …

Quantification Of Interactions Between Influenza Hemagglutinin And Host Cell Phosphoinositides By Super-Resolution Microscopy, Matthew T. Parent

Electronic Theses and Dissertations

The influenza viral membrane protein hemagglutinin (HA) forms dense nanoscale clusters on host cell plasma membranes (PM), but the mechanisms that direct HA clustering are not well understood. Previous studies have observed HA associated with actin rich regions of the PM, but there are no known direct interactions between HA and actin. Phosphatidylinositol 4,5-biphosphate (PIP2) is a signaling lipid in the PM which can regulate the actin cytoskeleton, and actin comets initiated by PIP2 are known to be exploited by HA to reach the PM of infected cells. PIP2 is also used by other viruses, such as HIV and Ebola, …

Characterization Of The Anomalous Ph Of Aqueous Nanoemulsions, Kieran P. Ramos

Doctoral Dissertations

Aqueous water-in-oil nanoemulsions have emerged as a versatile tool for use in microfluidics, drug delivery, single-molecule measurements, and other research. Nanoemulsions are often prepared with perfluorocarbons which are remarkably biocompatbile due to their stability, low surface tension, lipophobicity, and hydrophobicity. Therefore it is often assumed that droplet contents are unperturbed by the perfluorinated surface. However, in microemulsions, which are similar to nanoemulsions, it is known that either the pH of the aqueous phase or the ionization constants of encapsulated molecules are different from bulk solution. There is also recent evidence of low pH in perfluorinated aqueous nanoemulsions. The current underlying …

Topics In Three-Dimensional Imaging, Source Localization And Super-Resolution, Zhixian Yu

Physics & Astronomy ETDs

The realization that twisted light beams with helical phasefronts could carry orbital angular momentum (OAM) that is in excess of the photon's spin angular momentum (SAM) has spawned various important applications. One example is the design of novel imaging systems that achieve three-dimensional (3D) imaging in a single snapshot via the rotation of point spread function (PSF).

Based on a scalar-field analysis, a particular simple version of rotating PSF imagery, which was proposed by my advisor Dr. Prasad, furnishes a practical approach to perform 3D source localization using a spiral phase mask that generates a combination of Bessel vortex beams. …

Optical Enhancement In Periodic Plasmonic Gratings For Sers And Metal-Semiconductor-Metal Photodetectors (Msm-Pds) Applications, Ahmad Aziz Darweesh

Graduate Theses and Dissertations

This dissertation is aimed to numerically study the effect of plasmonic grating electrodes on the efficiency of metal-semiconductor-metal photodetectors (MSM PDs) and the sensitivity of Surface Enhanced Raman Spectroscopy (SERS). This research can benefit many areas of nanoscience and optics, including plasmonic applications, such as, super lenses, nano-scale optical circuits, optical filters, surface plasmon enhanced photo-detectors solar cells, imaging sensors, charge-coupled devices (CCD), and optical-fiber communication systems. Several parameters, wire widths and thickness, gap space, taper angle, and the incident wavelength and angle, were investigated. The goal of this research is to utilize the plasmonic phenomenon by using plasmonic gratings …

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.

Plasmonic Enhancement Of Photoluminescence And Photobrightening In Cdse Quantum Dots, David Alan French

Graduate Theses and Dissertations

Quantum dots are gaining recognition not just in the physics and chemistry community, but in the public eye as well. Quantum dot technologies are now being used in sensors, detectors, and even television displays. By exciting quantum dots with light or electricity, they can be made to emit light, and by altering the quantum dot characteristics the wavelength can be finely tuned. The light emitted can be also be made more intense by an increase in the excitation energy. The excitation light can be increased via plasmonic enhancement, leading to increased luminescence. Aside from the relatively steady-state response, quantum dots …

Combined High-Speed Single Particle Tracking Of Membrane Proteins And Super-Resolution Of Membrane-Associated Structures, Hanieh Mazloom Farsibaf, Keith A. Lidke

Shared Knowledge Conference

Many experiments have shown that the diffusive motion of lipids and membrane proteins are slower on the cell surface than those in artificial lipid bilayers or blebs. One hypothesis that may partially explain this mystery is the effect of the cytoskeleton structures on the protein dynamics. A model proposed by Kusumi [1] is the Fence-Picket Model which describes the cell membrane as a set of compartment regions, each ~ 10 to 200 nm in size, created by direct or indirect interaction of lipids and proteins with actin filaments just below the membrane. To test this hypothesis, we have assembled a …

Estimating And Correcting Interference Fringes In Infrared Spectra In Infrared Hyperspectral Imaging, Ghazal Azarfar, Ebrahim Aboualizadeh, Nicholas Walter,, Simona Ratti, Camilla Olivieri, Alessandra Alessandra, Michael Nasse, Achim Kohler, Mario Giordano, Carol Hirschmugl

Physics Faculty Articles

Short-term acclimation response of individual cells of Thalassiosira weissflogii was monitored by Synchrotron FTIR imaging over the span of 75 minutes. The cells, collected from batch cultures, were maintained in a constant flow of medium, at an irradiance of 120 μmol m−2 s−1 and at 20 °C. Multiple internal reflections due to the micro fluidic channel were modeled, and showed that fringes are additive sinusoids to the pure absorption of the other components of the system. Preprocessing of the hyperspectral cube (x, y, Abs(λ)) included removing spectral fringe using an EMSC approach. Principal component analysis of the time series of …

Photonic Tools For Advanced Sensing And Imaging At The Nanoscale., Jafar Hamed Ghithan

Electronic Theses and Dissertations

This dissertation reports a novel bio-sensing strategy based on single-mode, electro-active, integrated optical waveguide (SM-EA-IOW) platforms. It also reports the development of a super-resolved far-field optical imaging tool to enable optical, electronic, and spectroelectrochemical investigations at the nanoscale. SM-EA-IOW platforms with its outstanding sensitivity for spectroelectrochemical interrogation was combined with a sandwich bioassay for the development of a novel immunosensing based strategy for label-free detection of infectious pathogens. The strategy begins with the functionalization of the electroactive waveguide surface with a capturing antibody aimed at a specific target analyte. Once the target analyte is bound to the photonic interface, it …

Achieving A Stable Magneto-Optical Trap, Chasen S. Himeda

Honors Thesis

The utilization of the Magneto-Optical Trap (MOT) as a method for cooling and confining atoms is a recent development in the field of modern optical physics. Producing an effective MOT relies on a constant magnetic field throughout the trapping region and successful laser cooling, a technique used to achieve optical molasses by slowing particles using a three-dimensional intersection of laser beams. A successful MOT occurs when the trapped atoms slow down to approximately 30 cm/s at a temperature in the microkelvin range and is observable when a small bright orb of atoms is located in the center of the chamber. …

Basic Vision Research With Clinical Applications And Science Education Assessments, Andrew Wilson

Electronic Theses and Dissertations

Visual Acuity (VA) examinations are one of the most commonly conducted medical assessment throughout the world. Recent advances in computer technology allows for new forms of visual assessment to be conducted. In Part I of this thesis I demonstrate the capability of an automated computer program named VISION to assess human visual acuities. Different color combinations of an object against a background emitted from a computer screen are used to examine a variety of human color vision acuities. Results indicated a large difference in acuity scores between human subjects tested with these different color combinations. A single human subject exhibits …

Micro-Spectroscopy Of Bio-Assemblies At The Single Cell Level, Jeslin Kera

Honors Undergraduate Theses

In this thesis, we investigate biological molecules on a micron scale in the ultraviolet spectral region through the non-destructive confocal absorption microscopy. The setup involves a combination of confocal microscope with a UV light excitation beam to measure the optical absorption spectra with spatial resolution of 1.4 μm in the lateral and 3.6 μm in the axial direction. Confocal absorption microscopy has the benefits of requiring no labels and only low light intensity for excitation while providing a strong signal from the contrast generated by the attenuation of propagating light due to absorption. This enables spatially resolved measurements of single …

Quantitative Analysis And Process Of High Speed Live Cell Interferometry Measurements, Daniel Guest

Theses and Dissertations

The application of auto focus, using an optical beam deflection technique, to existing live cell interferometry measurements was developed and examined. The benefit to relevant experiments, currently being performed, is shown as well as its performance across various magnifications. Enough information is given so that the system can be reproduced to fit any end users needs.

Investigating High Speed Localization Microscopy Through Experimental Methods, Data Processing Methods, And Applications Of Localization Microscopy To Biological Questions, Andrew J. Nelson

Electronic Theses and Dissertations

Fluorescence Photoactivation Localization Microscopy(FPALM) and other super resolution localization microscopy techniques can resolve structures with nanoscale resolution. Unlike techniques of electron microscopy, they are also compatible with live cell and live animal studies, making FPALM and related techniques ideal for answering questions about the dynamic nature of molecular biology in living systems. Many processes in biology occur on rapid sub second time scales requiring the imaging technique to be capable of resolving these processes not just with a high enough spatial resolution, but with an appropriate temporal resolution. To that end, this Dissertation in part investigates high speed FPALM as …

Distributions Of Long-Lived Radioactive Nuclei Provided By Star-Forming Environments, Marco Fatuzzo, Fred Adams

Faculty Scholarship

Radioactive nuclei play an important role in planetary evolution by providing an internal heat source, which affects planetary structure and helps facilitate plate tectonics. A minimum level of nuclear activity is thought to be necessary—but not sufficient—for planets to be habitable. Extending previous work that focused on short-lived nuclei, this paper considers the delivery of long-lived radioactive nuclei to circumstellar disks in star forming regions. Although the long-lived nuclear species are always present, their abundances can be enhanced through multiple mechanisms. Most stars form in embedded cluster environments, so that disks can be enriched directly by intercepting ejecta from supernovae …

A Lego® Brewster Angle Microscope For Quantitative Monolayer Film Analysis, Nicholas Benz

Physics

In order to study single-molecule thick films and their phase behavior we built a Brewster Angle Microscope (BAM). BAM’s are inherently expensive due to their accuracy and precision. We built a fully functional BAM using Lego® Mindstorm® kits for the fraction of the price of a commercial BAM. And by utilizing the 10µm patented Lego® tolerance, comparable accuracy was attained. The BAM was mounted to a Langmuir-trough and will be used for laboratory experiments for optics and physical chemistry along with research on lung surfactant and on liquid crystals.

Sucralose Destabilization Of Protein Structure.Pdf, Nimesh Shukla

Nimesh Shukla

No abstract provided.

Charged Particle Dynamics In The Magnetic Field Of A Long Straight Current-Carrying Wire, M. Fatuzzo, A. Prentice, T. Toepker

Faculty Scholarship

The article discusses the concept behind motion of a charged particle in a non-uniform filed of a wire carrying current. Topics discussed include possible types of motion in a current carrying field, vector analysis of velocity and magnetic field of the particle and Coupled differential equations.

A Numerical Assessment Of Cosmic-Ray Energy Diffusion Through Turbulent Media, M. Fatuzzo, F. Melia

Faculty Scholarship

No abstract provided.