R-3 Repository :: Browsing by Author "Landes, Christy F"

Browsing by Author "Landes, Christy F"

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Conformational Dynamics of the Glutamate Receptors via single Molecule Förster Resonance Energy Transfer
(2015-04-21) Cooper, David; Landes, Christy F; Clementi, Cecilia; Phillips, George
Glutamate receptors perform a critical role in the nervous system, mediating synaptic transmission through cellular membranes. These proteins have developed a quick response to agonist presence and, when activated, undergo a conformational shift that allows calcium ion transport across the membrane. In a number of neurological diseases, genetic variants can cause mutations that disrupt the balance between fast binding response and desensitization resulting in over- or under- signaling in affected cells. Herein it describes the use of single molecule Förster resonance energy transfer to observe the bound form of the glutamate receptors and subsequent dynamics. For a complete understanding of the dynamics involved in the conformational landscape, the response of the receptor to a variety of known full and partial agonists is tested. Additionally multiple receptor types are investigated to determine if the conformational pathway is conserved between the different types of glutamate receptors. The results from this project allows for a more complete understanding of the relationship between conformation and functionality of glutamate receptors.
Enhanced super-resolution microscopy by phase modulation
(2016-08-12) Wang, Wenxiao; Landes, Christy F; Kelly, Kevin F
Super-resolution microscopy typically achieves high 2D spatial resolution but the detection of depth is always difficult. At the same time the temporal resolution remains low and obstructs most biological and chemical researches. In this thesis, I firstly introduced the depth detection method via phase modulation with a 4f system. In the Fourier domain, a phase mask encodes the depth information with a specific phase pattern, double helix phase mask. The final point spread functions deviates from the standard Gaussian point spread functions and the depth information can be measured with high precision by fitting the corresponding double helix point spread functions. Based on the 4f system, I modified the instrument and propose a novel technique Super Temporal-Resolved Microscopy (STReM) to improve the temporal resolution of 2D super-resolution microscopy. The fundamental basis for STReM is the utilization of a double helix phase mask which is rotated at fast speeds to encode temporal information in Fourier domain. The signal can be analyzed either by single emitter fitting or a l_1norm constrained optimization process, which is based on dynamic properties of emitter movement. STReM has been verified using both simulated and experimental 2D data for adsorption/desorption and 2D transport. The temporal resolution has been improved roughly 20 times when comparing traditional methods to that of the novel method of STReM presented in this thesis.
Gold Nanorod Size Prediction from Spectra Assisted by Machine Learning
(2022-06-07) Shiratori, Katsuya; Link, Stephan; Landes, Christy F; Rossky, Peter J
Electron microscopy is often required to correlate the size and shape of plasmonic nanoparticles with their optical properties. Eliminating the need for electron microscopy is one crucial step toward in situ sensing applications, especially for complicated sample conditions such as during irreversible chemical reactions or when particles are embedded in a matrix. In this thesis, we show that a machine learning (ML) decision tree can accurately predict gold nanorod dimensions over a wide range of sizes. The model is trained by using around 450 nanorod geometries and corresponding scattering spectra obtained from finite-difference time-domain (FDTD) simulations. We test the model using a set of experimental spectra and sizes obtained from correlated scanning electron microscopy images, resulting in predictions of the dimensions of gold nanorods within around 10% of their true values (root-mean- squared percentage error) over a large range of sizes. Analysis of the decision tree structure reveals that a relationship with resonance energy and line width of the localized surface plasmon resonance (LSPR) is suffcient to predict nanorod dimensions, notably outperforming more complicated models. Our findings illustrate the advantages of using ML models to infer single particle structural features from their optical spectra.
Gold Nanorod Size Prediction from Spectra Assisted by Machine Learning
(2022-06-07) Shiratori, Katsuya; Link, Stephan; Landes, Christy F; Rossky, Peter J
Electron microscopy is often required to correlate the size and shape of plasmonic nanoparticles with their optical properties. Eliminating the need for electron microscopy is one crucial step toward in situ sensing applications, especially for complicated sample conditions such as during irreversible chemical reactions or when particles are embedded in a matrix. In this thesis, we show that a machine learning (ML) decision tree can accurately predict gold nanorod dimensions over a wide range of sizes. The model is trained by using around 450 nanorod geometries and corresponding scattering spectra obtained from finite-difference time-domain (FDTD) simulations. We test the model using a set of experimental spectra and sizes obtained from correlated scanning electron microscopy images, resulting in predictions of the dimensions of gold nanorods within around 10% of their true values (root-mean- squared percentage error) over a large range of sizes. Analysis of the decision tree structure reveals that a relationship with resonance energy and line width of the localized surface plasmon resonance (LSPR) is suffcient to predict nanorod dimensions, notably outperforming more complicated models. Our findings illustrate the advantages of using ML models to infer single particle structural features from their optical spectra.
Hybrid and Molecular Plasmonics for Strongly Coupled Nanosystems and Photoelectrochemical Devices
(2015-12-04) Schlather, Andrea E; Halas, Naomi J; Nordlander, Peter; Landes, Christy F
The field of nanophotonics has realized rapid growth over the past several decades, as novel nanoscale materials are consistently being developed and researched for a wide variety of promising light-driven applications. Plasmonics is a particularly fascinating subset of nanomaterials research, owing to the unique ability of metallic nanostructures to interact with light from areas larger than their physical size, effectively focusing it to dimensions below the diffraction limit. This interaction, called a localized surface plasmon, arises when the electric field of light induces a coherent oscillation of the conduction electrons in the metal. Tuning the geometry and near-field environment of metallic nanostructures allows for controlled light scattering and absorption across a broad spectral range. Moreover, the strong spatial confinement of electric fields near the metal surface can remarkably enhance a host of molecular processes, motivating the development of plasmonic nanomaterials for single molecule sensing, photocatalysis and photoelectrochemical devices. This thesis will focus on two sets of interactions between plasmonic metal nanostructures and molecules in their local environment. Using spectroscopic and electrochemical techniques, the experimental far-field responses are correlated to the calculated near-field properties of the metal nanostructures. This is followed by a demonstration that molecules themselves may sustain plasmon resonances through active electrochemical charging. In the first part of this thesis, the near-field coupling of plasmons and molecular excitons are studied at the single-particle level. Polarization-dependent hyperspectral dark field microspectroscopy is used to probe the far-field scattering response of plasmonic dimers, which is influenced by strong near-field coupling to molecular J-aggregates located in the dimer junction. The coupling strengths are quantified and a rigorous theoretical investigation reveals that the plexcitonic coupling is dependent on the intensity of the plasmonic field enhancement in the dimer junction, which can be tuned by varying the polarization of incident light. These nanostructures represent a class of hybrid plasmonic materials that show reversible, all-optical spectral modulation, a necessary feature for a number of applications ranging from ultrafast optical switches to tactical obscurants. The next part of this thesis investigates the factors influencing the efficiency and kinetics of plasmonic hot carrier- driven redox reactions in an photoelectrochemical cell. Multi-layered Au-SiO2-Au nanoparticles, called nanomatroyshkas (NMs), serve as nano-electrodes due to their interesting optical properties. Strong light absorption by the NM electrodes leads to the formation of energetic hot electron-hole pairs that can be utilized to drive chemical reactions of surface adsorbates. The photooxidation of citrate by plasmonic hot holes and subsequent reduction of water by hot electrons on the surface of the NM electrodes is studied as a function of excitation wavelength, electrode potential and incident laser power. A qualitative system for optimizing plasmon-enabled photoelectrochemical reactions is presented by considering the interplay between plasmonic absorption and the energy alignment of hot carriers with molecules at the metal-solution interface. This result is an important step toward the ultimate goal of designing optimized nanomaterials for efficient photoelectrochemical devices. In the last part of this thesis, a new class of carbon-based plasmonic materials is proposed by reconsidering our understanding of the nature of optical transitions in charged polycyclic aromatic hydrocarbons (PAHs). 2D- graphene doped with charge carriers has been shown to support a surface plasmon resonance that is optically- and electrically-tunable in the mid-infrared (IR) and terahertz regimes. This study confirms theoretical predictions that spatial confinement of graphene to its smallest dimensions, that is, to individual PAH molecules containing only a few tens of atoms, can result in visible optical transitions when the molecules are charged with single electrons. A custom spectroelectrochemical setup is built to study the visible resonances of a series of PAH molecules in their reduced state, sustained by the absence of water or oxygen in a non-aqueous electrochemical cell. Time-dependent density functional theory (TDDFT) calculations provide insight into the origins of the broad, intensely-absorbing experimental optical spectra, which are concluded to be a superposition of light-induced electronic and vibronic transitions that are dipolar in nature. While efforts to fully understand these polarizable molecular transitions are ongoing, a number of research possibilities and potential applications arise from the addition of PAH molecules to the nanophotonics toolbox.
Optically monitoring the electrochemical stability of single metallic nanocrystals in complex electrolyte environments
(2018-05-03) Flatebo, Charlotte; Landes, Christy F
Recent developments in life sciences technology, such as electrochemical biosensing, harness the unique properties of metallic nanocrystals. The localized surface plasmon resonance (LSPR) scattering spectra of gold nanocrystals are effective electrochemical sensors of both biological and organic molecules; however, the LSPR is directly related to the size and shape of the gold nanocrystals and the local environment. Changes in these parameters drastically affect gold nanocrystal functionality. Hyperspectral dark-ﬁeld analysis and correlated scanning electron microscopy demonstrate that the ionic composition of complex electrolyte solutions containing predominantly chloride anions signiﬁcantly inﬂuences the morphological stability of gold nanorods (AuNRs). The introduction of small concentrations of oxoanions with increasing numbers of hydroxyl groups drastically alters the dissolution onset potential and the dissolution pathway of single AuNRs. At high concentrations of chloride ions, both bicarbonate and phosphate ions prevent dissolution until applying highly anodic potentials. Applying an anodic bias to single anion chloride environments causes a drastic average red-shift. As the number of hydroxyl groups of the competing oxoanion increases, the magnitude of the shift decreases and then begins to blue-shift. Understanding the impact of complex anion solutions on the stability of metal nanocrystal modiﬁed electrodes improves capabilities of electrochemical biosensing by increasing the potential window for sensing of new species.
Phase modulation in super-resolution microscopy
(2018-12-18) Wang, Wenxiao; Landes, Christy F
Phase modulation attracts arising attention in super-resolution studies because of the convenience and efficiency in encoding the information. Current super-resolution microscopy typically achieves high spatial resolution, but the temporal resolution remains low and obstructs most physical and chemical studies. Based on phase modulation, the novel technique Super Temporal-Resolved Microscopy is proposed to compress time information and thus improve the temporal resolution of 2D super-resolution microscopy. The fundamental basis for STReM is the utilization of a double helix phase mask that is rotated at fast speed to encode temporal information in the Fourier domain. Complicated movement can be also dissolved and reconstructed through an L1 norm constrained optimization process. STReM has been verified using both simulated and experimental 2D data and the temporal resolution is improved 20 times when comparing traditional methods to that of the novel method of STReM presented in this thesis. Besides the application to boost the temporal resolution, phase modulation is also applied to extract depth information in super-resolution microscopy. Most physical and chemical processes occur in 3D space and the underlying mechanism is usually unavailable or misleading due to the poor depth detection ability. Recently, phase modulation is reported as a promising solution to 3D imaging in super-resolution microscopy. Various functions have been achieved through phase modulation such as improving the axial spatial localization precision and expanding the axial detection range. However, a current challenge is the lack of a robust and efficient algorithm to design a phase mask for arbitrary desired point spread function patterns in 3D continuous space. In this thesis the phase mask design algorithm is proposed using a phase retrieval scheme. Multiple algorithms were studied and compared for solving the phase retrieval, including Gerchberg Saxton, stochastic gradient decent, and Gauss-Newton methods. The Gauss-Newton method is proved to be the best by reaching the minima of the phase retrieval optimization. Several phase mask patterns for 3D super-resolution microscopy are proposed, and their corresponding PM patterns are successfully designed and experimentally fabricated with light lithography. Finally, by combining both depth and time modulations, phase modulation is proposed to encode the information simultaneously in 4D space, which will definitely benefit super-resolution studies in the future.
Plasmonic Sensing and Enhancement of Electrochemical Processes at Single Gold Nanoparticle Surfaces in Aqueous Halide Electrolytes
(2018-04-12) Hoener, Benjamin Shaw; Landes, Christy F
Localized surface plasmon resonances (LSPR), the coherent oscillation of conduction band electrons confined to a nanoparticle, can be both sense and enhance electrochemical processes occurring at a metal nanoparticle surface. The spectrum of light scattered by a plasmonic nanoparticle is dependent on the properties of the LSPR. The LSPR frequency and lifetime depend on the local environment and nanoparticle morphology. Changes in refractive index, charge density, size, shape, and more can be measured through single plasmonic nanoparticle scattering spectra. In this work, single plasmonic nanoparticle spectroscopy is combined with electrochemistry to optically study various electrochemical processes on plasmonic nanoparticles. At less positive potential, the effect of charge density tuning on gold nanoparticle (AuNP) LSPRs was isolated from the effect of reactive halide anion adsorption. The capacitive charging regime was then used to study the nanoparticle morphology effects on sensitivity to change in charge density. As positive potential and anion reactivity were increased, anion adsorption and AuNP dissolution reactions occurred. The onset of these adsorption and dissolution reactions at single nanoparticles was determined by correlating spectral shifts with electrochemical potential. Plasmonic enhancement of the dissolution reaction was studied by comparing dissolution onset potential and rate with and without plasmon excitation.
Point cloud analysis underlies unbiased adaptive single particle tracking methods
(2021-02-26) Zepeda, Jorge Arturo; Landes, Christy F
Single particle tracking (SPT) methods assume predetermined motion models that affect tracking analysis. I present an unbiased SPT algorithm, Knowing Nothing Outside Tracking (KNOT), that utilizes the point clouds provided by iterative deconvolution to educate particle localization and trajectory linking between frames for 2-D and 3-D tracking. Retaining the information between point clouds fuels a machine learning paradigm that predicts the next particle position using an adaptive per-particle motion model, avoiding the motion biases present in other SPT methods. KNOT competes with or surpasses other methods presented in the 2012 International Symposium on Biomedical Imaging (ISBI) particle tracking challenge. Further, we apply KNOT to lysozyme adsorption on polymer surfaces and early endosome transport in live cells, distinguishing motion types and preferred directions of motion. KNOT can differentiate motion between transported and diffused vesicles in the cellular environment crucial to understanding transitions in cellular structure and chemistry that precedes metastasis.
Relating chromatogram lineshape to microscale surface interactions using stochastic theory and chemometrics
(2021-04-01) Bishop, Logan D.C.; Landes, Christy F
Pharmaceutical separations are necessary to mass-produce novel treatments for emerging diseases. Rare, heterogeneous surface chemistry hampers separations by generating chromatographic tails that cause peak overlap. The chemical source of tailing is thoroughly detailed in microscopic terms by the stochastic theory but difficult to assess from macroscale measurements that guide optimization. Chemometric-driven chromatogram analysis that achieves a microscale understanding of surface chemistry could help direct tuning of column chemistry to reduce tailing. Here, we improve upon previous graphical metrics with our own metric, the Distribution Function Ratio (DFR), which is compatible with stochastic theory and capable of bridging the gap between macroscale chromatograms and microscale surface chemistry. Further, we prove the DFR can provide predictive analysis of surface chemistry, an application that could be used in online chromatographic instruments. Establishing an analytical metric that is simple to implement provides mechanistic, chemometric guidance for future development of surface chemistry in chromatographic columns.
Resonance Energy Transfer and Charge Density Tuning at Plasmonic Interfaces
(2023-04-12) Searles, Emily Kay; Landes, Christy F
When photoexcited, plasmons decay through multiple pathways including surface scattering and photoluminescence. Spectroscopic investigation at the single-particle level can provide insight to decay dynamics. The plasmon’s spectral response is sensitive to changes in dielectric environment, charge density, and the chemical interface which can be tuned in-situ. In this thesis, plasmonic-polymeric hybrids are used to increase the electron-hole pair lifetime through interfacial redistribution. Single-particle spectroscopy is used to characterize the energy transfer efficiencies of the hybrid structures by recording changes to the homogenous plasmon linewidth upon acceptor polymerization and dynamic pH tuning. Specifically, non-radiative energy transfer efficiencies > 45% are achieved for Au nanorod-metallated phthalocyanine hybrids while dynamic tuning of resonance energy transfer is achieved in Au nanorod-polyaniline hybrids. We complement results from single-particle scattering and photoluminescence measurements of resonance energy transfer in nanohybrids with the comparison of plasmon modulation at applied potentials. While changes in dark-field scattering during electrochemical charging are well understood, changes to the photoluminescence of plasmonic nanoparticles under similar conditions are less studied and may offer a tool to monitor chemical transformation at hybrid interfaces. We find that changes in the emission of a single gold nanorod during charge density tuning of intraband photoluminescence can be attributed to changes in the Purcell factor and absorption cross-section. While the modulation of interband photoluminescence provides an additional constructive observable, giving promise for establishing dual channel sensing in spectroelectrochemical measurements. The understanding of resonance energy transfer and charge density tuning at the plasmon interface will lead to control and tunability of plasmonic enhancement in ensemble nanocomposites.
Single Molecule Studies of Dynamics at Polymeric Film Interfaces
(2016-04-21) Tauzin, Lawrence J; Landes, Christy F
Filtration and separations play large roles in many industries yet no complete mechanistic interpretation of these phenomena exists. The development of experimental methods capable of characterizing dynamics at the single molecule level has opened the door to reexamining these heavily studied processes. By overcoming ensemble averaging mechanistic understandings that account for heterogeneities in these systems can be formulated. In this work, single molecule spectroscopic methods along with advanced particle tracking and localization algorithms are used to directly observe the interaction of single molecule probes with polymer films. The electrostatic contribution to interfacial interactions was evaluated by using the post-assembly tunability of polyelectrolyte multilayers and probes of varying charge. Multimodal transport mechanisms of protein interactions with functionalized nylon membranes were also discovered. Finally, the groundwork for a kinetic model of protein adsorption to a thin film was developed. A major conclusion was that even in ion-exchange systems in which electrostatic interactions are considered the most important variable, complex interactions between the adsorbents and the substrate are not insignificant in polymer membrane based systems. Additionally, interfacial transport in nearly all systems is characterized, not by 2 dimensional surface diffusion or activated hop diffusion, but by desorption mediated diffusion involving repeat adsorption events punctuated by periods of immobilization, the extent of which can be controlled using solution conditions.
Single Molecule Studies of Ion-Exchange Chromatography
(2015-04-20) Kisley, Lydia; Landes, Christy F; Weisman, R. Bruce; Pasquali, Matteo
As the pharmeceutical industry moves away from traditional small organic molecules towards biologically-based treatments, ion-exchange separation methods must be investigated to improve the cost and time required for protein purification. Several new single molecule, super-resolution techniques are presented to offer a mechanistic experimental understanding of chromatography unachievable through traditional ensemble-averaged methods. Super-resolution analysis visualizes single protein adsorption kinetics to single, super-resolved ligands, allowing for the first experimental validation of the statistical mechanical stochastic theory of chromatography. Imperative results on the spatial charge-distribution of ligands, reduction of heterogeneity by ionic strength, and tuning of protein/stationary phase interfacial interactions by pH are observed. A common finding that the sterics of the agarose support induces separation heterogeneity leads to super-resolution imaging of the agarose structure and diffusion properties. Finally, the single molecule techniques are applied to several applications beyond protein chromatography to demonstrate the potential for future materials research. Overall, we have shown that single molecule spectroscopy can aid in the mechanistic experimental and theoretical understanding of the ion-exchange chromatographic separation of proteins.
Single-Molecule Studies of Proteins at Polymer based Chromatographic Interfaces
(2020-01-14) Moringo, Nicholas A; Landes, Christy F
The worldwide pharmaceutical landscape has witnessed a large influx of biological-based therapeutics, termed ‘biologics’, for the successful treatment of diseases and illnesses. The downstream separation and purification of promising biologics via chromatography dominates the total production cost leading to market entry. A mechanistic examination of protein interactions at the interface of stationary phase materials can improve and enable predictive chromatographic separation optimization. Single-molecule imaging techniques, inspired by the advances of super-resolution microscopy, can capture the highly dynamic interactions of proteins at stationary phase materials. It is observed that nanoscale protein dynamics can explain experimentally observed increases in separation efficiencies. We uncover how the suppression of anomalous surface diffusion, which leads to improved separations, can be tuned with stationary phase surface chemistries, polymer packing, and ionic salt conditions. Overall, we have shown that single-molecule imaging can relate protein dynamics at the nanoscale to improved protein separations at the interface of synthetic polymer materials.
Single-particle absorption spectroscopy by photothermal contrast
(2014-11-21) Nizzero, Sara; Link, Stephan; Landes, Christy F; Nordlander, Peter J; Kelly, Kevin F
Independent characterization of absorption of nano-objects is fundamental to the understanding of non-radiative properties of light matter interaction. To resolve heterogeneity in the response due to local effects, orientation or rare interactions, a single particle approach is necessary. Currently, there are very few methods that attempt to do so. Furthermore, they are limited in the type of structures and the spectral range for which they succeed. This work presents the first general and broad band method to measure the pure absorption spectrum of single particles. Photothermal microscopy is combined with a supercontinuum pulsed fiber optic tunable laser to detect a signal proportional to the pure absorption cross section of single particles at different excitation wavelengths. For the first time, a method is available to measure the pure absorption spectra of single nano-structures that exhibit spectral features from the visible to the near IR. This method is used to resolve the radiative and non-radiative properties of simple gold nanostructures, revealing the heterogeneity present in the response.
Spectroelectrochemistry of Plasmonic Nanoantennas
(2015-11-30) Byers, Chad; Landes, Christy F; Link, Stephan; Verduzco, Rafael
The optical properties of metal nanoparticles make them useful in the fundamental study of light-matter interactions at the nanoscale. These nanoparticles can behave as antennas for optical electromagnetic radiation and can be used to investigate nanoscopic processes by measuring the optical spectral response of individual nanoantennas. In this thesis, original research is presented that expands our knowledge and understanding of how plasmonic nanoantennas respond to electrochemical potential control. In addition to minor spectral shifts from charge density tuning, nanoparticle plasmons respond very strongly to potential-controlled chemical reactions at the nanoparticle surface. With this knowledge, nanostructures were engineered to produce desired optical characteristics that are switchable via electrochemistry. The optical responses can then be used to either sense electrochemical processes occurring at the nanoscale or to create desired optical phenomena. Two engineered systems were studied to this end. First, single nanospheres and pairs of closely spaced nanospheres called dimers were placed onto two working electrode substrates and the effects of the substrate on sensitivity to potential-controlled electroadsorption of sulfate anions was investigated. The most sensitive nanoantenna geometry was then used to develop and demonstrate a single-nanoantenna analog to bulk electrochemistry’s cyclic voltammogram (CV). Using this technique, the single-nanoantenna CV analog was used to detect the potential controlled adsorption and desorption of sulfate, acetate, and perchlorate anions. A simpler intensity-based alternate method was also tested to increase the accessibility and applicability of the single-nanoantenna technique. In another application, a core/shell strategy was employed in which the shell was electrochemically switchable between a semiconductor and a pure metal. This method was employed for both Au nanospheres and dimers. In the case of a dimer fused by an Ag bridge, the bridge was found to be electrochemically switchable between electrically conductive and nonconductive, allowing a change in the plasmonic coupling mechanism using only electrochemical potential control. The scattering spectra of these dimers experienced large changes during this switching process and dynamic measurements allowed the observation of the first in situ switchable and tunable charge transfer plasmon resonance mode. In sum, the work presented in this thesis demonstrates the value of single-nanoantenna spectroelectrochemistry both for fundamental research and application.

Browsing by Author "Landes, Christy F"

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