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 …

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 …

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 …

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

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 …

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 …

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 …

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).

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.

Super‐Resolution Imaging Of Amyloid Structures Over Extended Times By Using Transient Binding Of Single Thioflavin T Molecules, Kevin Spehar, Tianben Ding, Yuanzi Sun, Niraja Kedia, Jin Lu, George R. Nahass, Matthew D. Lew, Jan Bieschke

Electrical & Systems Engineering Publications and Presentations

Oligomeric amyloid structures are crucial therapeutic targets in Alzheimer's and other amyloid diseases. However, these oligomers are too small to be resolved by standard light microscopy. We have developed a simple and versatile tool to image amyloid structures by using thioflavin T without the need for covalent labeling or immunostaining. The dynamic binding of single dye molecules generates photon bursts that are used for fluorophore localization on a nanometer scale. Thus, photobleaching cannot degrade image quality, allowing for extended observation times. Super‐resolution transient amyloid binding microscopy promises to directly image native amyloid by using standard probes and record amyloid dynamics …

Raman Spectroscopy Of Oxygen Evolution Catalysts And Psii Manganese Model Compounds, Sergei Shmakov, Daniel A. Hartzler, Alireza Karbakhsh Ravari, Yulia Pushkar

The Summer Undergraduate Research Fellowship (SURF) Symposium

Photosynthesis is the basis of life on earth, and oxygen evolution catalysts are key components of this complicated, yet not fully understood process. Photosystem II, a large membrane bound pigment-protein complex, is the key system that facilitates oxygenic photosynthesis via the oxygen evolving complex (a natural oxygen evolving catalyst). It is a key component in oxygen producing catalysts, which can be used in fields such as energy production and biomimetic catalysts. The oxygen evolution cycle, or Kok cycle going within it is still not studied completely. In this project, we were studying the vibrational (and structural) state of a Manganese …

Nuclear Spin Alignment In Optically Pumped Semiconductors, Matthew M. Willmering

Arts & Sciences Electronic Theses and Dissertations

Nuclear magnetic resonance (NMR) has shown its ability to be a very informative analytical technique due to the ability to measure very small changes in the energy splittings due to the nuclei’s local environment. However, this ability is hindered by the low sensitivity of the experiment. Many methods have been postulated and implemented to enhance the sensitivity of NMR experiments; one of which is optically pumped NMR (OPNMR). In this dissertation, the usefulness and potential applications of OPNMR are presented. First, a doubly resonant OPNMR probe was fabricated in order to complete more advanced NMR techniques while optically pumping the …

Using Low-Coherence Interferometry To Monitor Cell Invasion In An In-Vitro Model System, Behnaz Davoudi Nasab

Honors Undergraduate Theses

In an optically random system, such as naturally occurring and man-made media, light undergoes pronounced multiple scattering. This phenomenon has shown a remarkable potential in characterizing complex materials. In this regime, scattering occurs from each individual center of the scattering and independent scattering events lead to multiple light scattering. This phenomenon is often described as a random walk of photons and can be modeled in terms of a diffusion equation based on the radiative transfer theory. In this thesis, we used optical path-length spectroscopy (OPS), which is an experimental method to obtain the path-length probability density of the propagating light …

Variable Pathlength Cavity Spectroscopy Development Of An Automated Prototype, Ryan Schmeling

Theses and Dissertations

ABSTRACT

VARIABLE PATHLENGTH CAVITY SPECTROSCOPY

DEVELOPMENT OF AN AUTOMATED PROTOTYPE

by

Ryan Andrew Schmeling

The University of Wisconsin-Milwaukee, 2016

Under the Supervision of Professor Joseph H. Aldstadt III

Spectroscopy is the study of the interaction of electromagnetic radiation (EMR) with matter to probe the chemical and physical properties of atoms and molecules. The primary types of analytical spectroscopy are absorption, emission, and scattering methods. Absorption spectroscopy can quantitatively determine the chemical concentration of a given species in a sample by the relationship described by Beer’s Law. Upon inspection of Beer’s Law, it becomes apparent that for a given analyte concentration, …

Two-Photon Excitation Based Photochemistry And Neural Imaging, Kevin Andrew Hatch

Open Access Theses & Dissertations

Two-photon microscopy is a fluorescence imaging technique which provides distinct advantages in three-dimensional cellular and molecular imaging. The benefits of this technology may extend beyond imaging capabilities through exploitation of the quantum processes responsible for fluorescent events. This study utilized a two-photon microscope to investigate a synthetic photoreactive collagen peptidomimetic, which may serve as a potential material for tissue engineering using the techniques of two-photon photolysis and two-photon polymerization. The combination of these techniques could potentially be used to produce a scaffold for the vascularization of engineered three-dimensional tissues in vitro to address the current limitations of tissue engineering. Additionally, …

The Dawn Of New Quantum Dots: Synthesis And Characterization Of Ge1-Xsnx Nanocrystals For Tunable Bandgaps., Richard J. Esteves

Theses and Dissertations

Ge_1-xSn_x alloys are among a small class of benign semiconductors with composition tunable bandgaps in the near-infrared spectrum. As the amount of Sn is increased the band energy decreases and a transition from indirect to direct band structure occurs. Hence, they are prime candidates for fabrication of Si-compatible electronic and photonic devices, field effect transistors, and novel charge storage device applications. Success has been achieved with the growth of Ge_1-xSn_x thin film alloys with Sn compositions up to 34%. However, the synthesis of nanocrystalline alloys has proven difficult due to larger discrepancies (~14%) in …

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.

Optical And Scanning Probe Studies Of Isolated Poly (3-Hexylthiophene) Nanofibers, Mina Baghgarbostanabad

Doctoral Dissertations

Plastic electronics have an essential role in the future technologies owing to their compelling characteristics such as light weight, biocompatibity, low cost fabrication, and tunable optoelectronic properties. However, the performance of polymer-based devices strongly depends on the efficiency of exciton formation and dynamics that are themselves strongly sensitive to polymer molecular packing and structural order. Therefore, the current challenge in achieving high efficiency is establishing a correlation between molecular packing and exciton coupling. P3HT nanofibers represent an attractive platform for studying optical and electronic properties of exciton coupling because their nominal (highly crystalline) internal chain packing structure is known. A …

Absorption Cross-Section Measurements Of Methane, Ethane, Ethylene And Methanol At High Temperatures, Majed Alrefae, Et-Touhami Es-Sebbar, Aamir Farooq

Dr. Et-touhami Es-sebbar

Mid-IR absorption cross-sections are measured for methane, ethane, ethylene and methanol over 2800–3400 cm−1 (2.9–3.6 μm) spectral region. Measurements are carried out using a Fourier-Transform-Infrared (FTIR) spectrometer with temperatures ranging 296–1100 K and pressures near atmospheric. As temperature increases, the peak cross-sections decrease but the wings of the bands increase as higher rotational lines appear. Integrated band intensity is also calculated over the measured spectral region and is found to be a very weak function of temperature. The absorption cross-sections of the relatively small fuels studied here show dependence on the bath gas. This effect is investigated by studying the …

Understanding The Plasmonic Properties Of Metallic Nanostructures With Correlated Photon- And Electron-Driven Excitations, Vighter Ozezinimize Iberi

Doctoral Dissertations

The collective oscillation of the conduction band electrons in metal nanostructures, known as plasmons, can be used to manipulate light on length scales that are smaller than the diffraction limit of visible light. In this dissertation, a correlated approach is used to probe localized surface plasmon resonances (LSPRs) in metallic nanostructures, and their application to surface-enhanced spectroscopy. This correlated approach involves the measurement of LSPRs with dark-field optical microscopy (resonance-Rayleigh scattering), and electron energy-loss spectroscopy (EELS) in a scanning transmission electron microscope (STEM). Structural parameters of the exact same nanostructures obtained from the STEM are subsequently used in performing fully …

Measurements Of Nh3 Linestrengths And Collisional Broadening Coefficients In N2, O2, Co2, And H2o Near 1103.46 Cm−1, Kyle Owen, Et-Touhami Es-Sebbar, Aamir Farooq

Dr. Et-touhami Es-sebbar

Laser-based ammonia gas sensors have useful applications in many fields including combustion, atmospheric monitoring, and medical diagnostics. Calibration-free trace gas sensors require the spectroscopic parameters including linestrengths and collisional broadening coefficients to be known. Ammonia's strong ν2 vibrational band between View the MathML source has the high absorption strength needed for sensing small concentrations. Within this band, the 1103.46 cm−1 feature is one of the strongest and has minimal interference from CO2 and H2O. However, the six rotational transitions that make up this feature have not been studied previously with absorption spectroscopy due to their small line spacing ranging from …

Effects Of N2o And O2 Addition To Nitrogen Townsend Dielectric Barrier Discharges At Atmospheric Pressure On The Absolute Ground-State Atomic Nitrogen Density, Et. Es-Sebbar, N. Gherardi, F. Massines

Dr. Et-touhami Es-sebbar

Absolute ground-state density of nitrogen atoms N (2p3 4S3/2) in non-equilibrium Townsend dielectric barrier discharges (TDBDs) at atmospheric pressure sustained in N2/N2O and N2/O2 gas mixtures has been measured using Two-photon absorption laser-induced fluorescence (TALIF) spectroscopy. The quantitative measurements have been obtained by TALIF calibration using krypton as a reference gas. We previously reported that the maximum of N (2p3 4S3/2) atom density is around 3 × 1014 cm−3 in pure nitrogen TDBD, and that this maximum depends strongly on the mean energy dissipated in the gas. In the two gas mixtures studied here, results show that the absolute N …

Temperature-Dependent Absorption Cross-Section Measurements Of 1-Butene (1-C4h8) In Vuv And Ir, Et-Touhami Es-Sebbar, Yves Benilan, Aamir Farooq

Dr. Et-touhami Es-sebbar

Vacuum ultraviolet (VUV) and infrared (IR) absorption cross-section measurements of 1-butene (1-C4H8; CH2=CHCH2CH3; Butylene) are reported over the temperature range of 296–529 K. The VUV measurements are performed between 115 and 205 nm using synchrotron radiation as a tunable VUV light source. Fourier Transform Infrared (FTIR) spectroscopy is employed to measure absorption cross-section and band strengths in the IR region between 1.54 and 25 μm (∼6500–400 cm−1). The measured room-temperature VUV and IR absorption cross-sections are compared with available literature data and are found to be in good agreement. The oscillator strength for the electronic transition (A1A′→X1A′) around 150–205 nm …

Capacitively Coupled Radio-Frequency Discharges In Nitrogen At Low Pressures, L. L Alves, L. Marques, C. D Pintassilgo, W. Wattieaux, Et. Es-Sebbar, J. Berndt, E. Kovačević, N. Carrasco, L. Boufendi, G. Cernogora

Dr. Et-touhami Es-sebbar

This paper uses experiments and modelling to study capacitively coupled radio-frequency (rf) discharges in pure nitrogen, at 13.56 MHz frequency, 0.1–1 mbar pressures and 2–30 W coupled powers. Experiments performed on two similar (not twin) setups, existing in the LATMOS and the GREMI laboratories, include electrical and optical emission spectroscopy (OES) measurements. Electrical measurements give the rf-applied and the direct-current-self-bias voltages, the effective power coupled to the plasma and the average electron density. OES diagnostics measure the intensities of radiative transitions with the nitrogen second-positive and first-negative systems, and with the 811.5 nm atomic line of argon (present as an …

Ionization Photophysics And Rydberg Spectroscopy Of Diacetylene, M. Schwell, Y. Benilan, N.. Fray, M.-C. Gazeau, Et. Es-Sebbar, F.-G. Levrel, N. Campion, S. Leach

Dr. Et-touhami Es-sebbar

Photoionization of diacetylene was studied using synchrotron radiation over the range 8–24 eV, with photoelectron-photoion coincidence (PEPICO) and threshold photoelectron–photoion coincidence (TPEPICO) techniques. Mass spectra, ion yields, total and partial ionization cross-sections were measured. The adiabatic ionization energy of diacetylene was determined as IEad = (10.17 ± 0.01) eV, and the appearance energy of the principal fragment ion C4H+ as AE = (16.15 ± 0.03) eV. Calculated appearance energies of other fragment ions were used to infer aspects of dissociation pathways forming the weaker fragment ions , C3H+, and C2H+. Structured autoionization features observed in the PEPICO spectrum of diacetylene …