Biological and Chemical Physics Commons^™

Fundamental Limits In Measuring The Anisotropic Rotational Diffusion Of Single Molecules, Weiyan Zhou, Tingting Wu, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Many biophysical techniques, such as single-molecule fluorescence correlation spectroscopy, Förster resonance energy transfer, and fluorescence anisotropy, measure the translation and rotation of biomolecules to quantify molecular processes at the nanoscale. These methods often simplify data analysis by assuming isotropic rotational diffusion, e.g., that molecules wobble within a circular cone. This simplification ignores the anisotropy present in many biological contexts that may cause molecules to exhibit different degrees of diffusion in different directions. Here, we loosen this assumption and establish a theoretical framework for describing and measuring anisotropic rotational diffusion using fluorescence imaging. We show that anisotropic wobble is directly quantified …

An Analysis Of (Hu)Manid Using The Usf Donated Skeletal Collection: Estimating Sex And Ancestry For Edentulous Individuals, Natalie S. Wise

USF Tampa Graduate Theses and Dissertations

The Human Mandible Identification program, (hu)MANid©, enables anthropologists to estimate the sex and ancestry of unidentified skeletal remains from metric and morphoscopic variables from the mandible. The program is suitable for a variety of anthropological contexts, including forensic casework and bioarchaeological or paleoanthropological analyses. The purpose of this research project is to test the accuracy and applicability of the (hu)MANid program on edentulous mandibles. While the authors of (hu)MANid warn against data collection for edentulous mandibles, there are many circumstances in applied forensic casework where the unidentified person is edentulous. Edentulous individuals experience alveolar resorption, which is the loss of …

Single-Molecule Orientation Imaging Reveals The Nano-Architecture Of Amyloid Fibrils Undergoing Growth And Decay, Brian Sun, Tianben Ding, Weiyan Zhou, Tara S. Porter, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Amyloid-beta (Aβ42) aggregates are characteristic Alzheimer’s disease signatures, but probing how their nanoscale architectures influence their growth and decay remains challenging using current technologies. Here, we apply time-lapse single-molecule orientation-localization microscopy (SMOLM) to measure the orientations and rotational “wobble” of Nile blue (NB) molecules transiently binding to Aβ42 fibrils. We correlate fibril architectures measured by SMOLM with their growth and decay over the course of 5 to 20 min visualized by single-molecule localization microscopy (SMLM). We discover that stable Aβ42 fibrils tend to be well-ordered and signified by well-aligned NB orientations and small wobble. SMOLM also shows that increasing order …

Assigning The Ch Stretch Overtone Spectrum Of Benzene And Naphthalene With Extension To Anthracene And Tetracene Using 2- And 3-Quanta Anharmonic Quantum Chemical Computations, Vincent J. Esposito, Ryan C. Fortenberry, Christiaan Boersma, Louis J. Allamandola

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The CH stretch overtone region (5750–6300 cm⁻¹) of benzene and naphthalene is assigned herein using anharmonic quantum chemical computations, and the trend of how this extends to larger polycyclic aromatic hydrocarbons (PAHs) is established. The assignment of all experimental bands to specific vibrational states is performed for the first time. Resonance polyads and the inclusion of 3-quanta vibrational states are both needed to compute accurate vibrational frequencies with the proper density-of-states to match the experimental band shape. Hundreds of 3-quanta states produce the observed band structure in naphthalene, anthracene, and tetracene, and this number is expected to increase …

Positron Emission Tomography In Oncology And Environmental Science, Samantha Delaney

Dissertations, Theses, and Capstone Projects

The last half century has played witness to the onset of molecular imaging for the clinical assessment of physiological targets. While several medical imaging modalities allow for the visualization of the functional and anatomical properties of humans and living systems, few offer accurate quantitation and the ability to detect biochemical processes with low-administered drug mass doses. This limits how physicians and scientists may diagnose and treat medical issues, such as cancer, disease, and foreign agents.

A promising alternative to extant invasive procedures and suboptimal imaging modalities to assess the nature of a biological environment is the use of positron emission …

Simulation Of Polymerization On Surfaces: Implications For Abiogenesis, Sylvia Greene

Macalester Journal of Physics and Astronomy

How did life arise from the prebiotic conditions of the early earth? This problem has vexed scientists for decades with no consensus on its solution. Significant spontaneous formation of biopolymers such as proteins and nucleic acids in the aqueous phase appears to be improbable due to thermodynamic constraints. It has been proposed that mineral surfaces could have served as a catalyst for the initial formation of biopolymers. However, the feasibility of this mechanism has not been thoroughly studied. In this study, a particle simulation of polypeptide formation on surfaces is developed to assess the feasibility of this mechanism. Elementary processes …

Optical Tweezers Explorations: Dna-Mitoxantrone Interactions At 20pn, Heléna Kathryn Beeloo

Honors Program Theses and Projects

Mitoxantrone is a chemotherapy drug that treats a variety of cancers by inhibiting cancer cell replication through intercalation with DNA. Intercalation is the process by which certain small molecules slide flat planar regions in their structure between the base pairs of DNA. This increases the stacking force in the DNA double helix, preventing DNA replication by increasing the force required to separate the two strands that compose the helix. In this study, dual-beam optical tweezers were used to determine the binding kinetics and dissociation constant of Mitoxantrone to single molecules of DNA at 20 pN of force. This study utilized …

Cn Stretches Around 4.4 Microns Dominate The Ir Absorption Spectra Of Cyanopolycyclic Aromatic Hydrocarbons, Vincent J. Esposito, Ryan C. Fortenberry, Christiaan Boersma, Alexandros Maragkoudakis, Louis J. Allamandola

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Anharmonic quantum chemical computations reveal a strong, narrow (width = 0.075 μm) band in the 4.3–4.5 μm region of the absorption spectra of the cyano-substituted polycyclic aromatic hydrocarbons (CN-PAHs) cyanonaphthalene, cyanoanthracene, c yanophenanthrene, and c yanopyrene. This narro w windo w with intense IR lines implies that CN-PAHs of various shapes and sizes offer little variation in both wavelength and intensity in this region. Subsequently, this band can be used as a tracer for CN-PAHs. The distinct features making up the band are assigned to mixed vibrational states consisting of the CN stretch fundamental and various combination bands, including in-plane …

Redesign Of X-Ray Irradiator To Expand Research Of Low-Dose X-Ray Radiation, Lauren Ulbrich

All Theses

The effects of high-dose radiation are well-documented, and are understood to be harmful to the human body. On the other hand, the effects of low-dose radiation are much less understood. There is debate over whether or not there are negative, positive, or no effects at all from low-dose radiation. One of the reasons why these effects are not well known is because there aren't as many studies done on this type of radiation. It is a lot harder to classify the effects of radiation at low doses due to many external factors. However, the Clemson Medical Physics lab has been …

Fabrication And Characterization Of Black Phosphorus Terahertz Photoconductive Antennae, Katie Michelle Welch

Graduate Theses and Dissertations

Advancements in terahertz (THz) imaging systems, particularly for applications like post-surgical analysis of breast cancer, have led to the exploration of novel materials such as black phosphorus as the active material for a THz photoconductive antenna (PCA). This thesis, motivated by innovative techniques developed at the University of Arkansas, investigates the potential of black phosphorus as a material to enhance the performance of THz PCAs, focusing on generation efficiency and bandwidth. Previous implementations of BP as THz emitters have shown limitations, highlighting the need for thorough material characterization and optimized fabrication processes. Therefore, we adopted a dual-phase approach to this …

Drag Reduction In Channel Flow Configurations For Laminar And Turbulent Flow Past Superhydrophobic Surfaces, Henry Louis Ems

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

In this work, we present friction drag reduction in minichannel laminar flow past superhydrophobic metallic surfaces. Femtosecond laser surface processing (FLSP), a one-step scalable method, was used to create permanent microscale and nanoscale structures on 316 stainless steel plates. The resulting superhydrophilic plates were covered by tall (215 μm) or short (27 μm) structures. The FLSP plates were then transitioned to superhydrophobic by evaporative deposition of a fluorinated silane, a low surface energy coating. Using purified water, the friction factor was obtained by measuring pressure drop along a minichannel with a rectangular cross section for flow rates corresponding …

Charge And Strain Engineering Of Ferroic And Correlated Oxides, Yifei Hao

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

This dissertation presents a comprehensive study of the charge and strain effects on the electronic and magnetic properties of epitaxial ferroic and correlated oxide thin films and heterostructures. We perform the planar Hall effect to quantify the magnetocrystalline anisotropy (MCA) in epitaxial La_1-xSr_xMnO₃ films (x = 0.2 and 0.33) deposited on SrTiO₃ substrates. The biaxial magnetic anisotropy energy of L_0.67Sr_0.33MnO₃ is about 17% larger than La_0.8Sr_0.2MnO₃. By comparing with the theoretically predicted values, we have decoupled the doping and strain effects on …

Electrochemical Modulation Of Surface Plasmon Wave To Investigate Dna-Based Sensing Platforms And Detection Of Sars-Cov2., Anil Sharma

Electronic Theses and Dissertations

This study offers a thorough comparative analysis of optical and electrical signaling strategies for assessing the electrochemical properties of different redox-labeled DNA-based biosensing platforms. In addition, it illustrates the development of an optical interrogation technique with electrochemical modulation of surface plasmon waves (ECM-SPW) as a route for analyzing and implementing DNA-based hybridization sensors. For those quantitative analyses, we chose a model sensing platform composed of a methylene blue (MB)-modified single-stranded DNA (ssDNA) signaling probe and an unlabeled capture ssDNA probe that complements the signaling probe. Two types of signaling probes were employed in this work: one with MB attached to …

Computational Modeling Of Retinal Damage Thresholds, Payton Hoffman, Eos Shapland, Alan Enriquez

SACAD: Scholarly Activities

The Scalable Effects Simulation Environment(SESE), is the computational Biophysics software contracted by Nanohmics we used for our research. The goal was to find the minimum energy necessary to damage the retina from 2 laser sources, a 532 nm He-Ne source, and Supercontinuum Laser(SCL) source at 400-1400nm. We needed a 10 times damage ratio for significance. Our data did not show this trend.

Float Like A Butterfly, Sting Like A Bee!, Kobe D. Rome

SACAD: Scholarly Activities

By injecting an electron into the empty pie* molecular orbital (LUMO) of Amino Acids in gas phase, we measure the Vertical Attachment Energies (VAEs) for the formation of short-lived anion states of these species using electron transmission spectroscopy (ETS). Our ETS study, a first of its kind to measure the VAE for the simplest of proteins, Glycine-Glycine (Gly-Gly), is currently in progress. Based on our previous measurements for several Amino Acids including Glycine, we expect a common range of attachment energy (1.50 – 2.00 eV) for Gly-Gly.

Predicting Biomolecular Properties And Interactions Using Numerical, Statistical And Machine Learning Methods, Elyssa Sliheet

Mathematics Theses and Dissertations

We investigate machine learning and electrostatic methods to predict biophysical properties of proteins, such as solvation energy and protein ligand binding affinity, for the purpose of drug discovery/development. We focus on the Poisson-Boltzmann model and various high performance computing considerations such as parallelization schemes.

The Infrared Absorption Spectrum Of Phenylacetylene And Its Deuterated Isotopologue In The Mid- To Far-Ir, Vincent J. Esposito, Pierro Ferrari, Wybren Jan Buma, Ryan C. Fortenberry, Christiaan Boersma, Alessandra Candian, Alexander G. G. M. Tielens

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Anharmonicity strongly influences the absorption and emission spectra of polycyclic aromatic hydrocarbon (PAH) molecules. Here, IR–UV ion-dip spectroscopy experiments together with detailed anharmonic computations reveal the presence of fundamental, overtone, as well as 2- and 3-quanta combination band transitions in the far- and mid-infrared absorption spectra of phenylacetylene and its singly deuterated isotopologue. Strong absorption features in the 400–900 cm⁻¹ range originate from CH(D) in-plane and out-of-plane wags and bends, as well as bending motions including the C≡C and CH bonds of the acetylene substituent and the aromatic ring. For phenylacetylene, every absorption feature is assigned either directly or …

Resolving The Nanoscale Structure Of Β-Sheet Peptide Self-Assemblies Using Single-Molecule Orientation–Localization Microscopy, Weiyan Zhou, Conor L. O'Neill, Tianben Ding, Oumeng Zhang, Jai S. Rudra, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Synthetic peptides that self-assemble into cross-β fibrils are versatile building blocks for engineered biomaterials due to their modularity and biocompatibility, but their structural and morphological similarities to amyloid species have been a long-standing concern for their translation. Further, their polymorphs are difficult to characterize using spectroscopic and imaging techniques that rely on ensemble averaging to achieve high resolution. Here, we utilize Nile red (NR), an amyloidophilic fluorogenic probe, and single-molecule orientation-localization microscopy (SMOLM) to characterize fibrils formed by the designed amphipathic enantiomers KFE8^L and KFE8^D and the pathological amyloid-beta peptide Aβ42. Importantly, NR SMOLM reveals the helical (bilayer) …

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.

Spectralomics – Towards A Holistic Adaptation Of Label Free Spectroscopy, Hugh Byrne

Articles

Vibrational spectroscopy, largely based on infrared absorption and Raman scattering techniques, is much vaunted as a label free approach, delivering a high content, holistic characterisation of a sample, with demonstrable applications in a broad range of fields, from process analytical technologies and preclinical drug screening, to disease diagnostics, therapeutics, prognostics and personalised medicine. However, in the analysis of such complex systems, a trend has emerged in which spectral analysis is reduced to the identification of individual peaks, based on reference tables of assignments derived from literature, which are then interpreted as biomarkers. More sophisticated analysis attempts to unmix the spectrum …