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Full-Text Articles in Nanoscience and Nanotechnology

Minimalistic Peptide-Based Supramolecular Systems Relevant To The Chemical Origin Of Life, Daniela Kroiss Sep 2019

Minimalistic Peptide-Based Supramolecular Systems Relevant To The Chemical Origin Of Life, Daniela Kroiss

All Dissertations, Theses, and Capstone Projects

All forms of life are based on biopolymers, which are made up of a selection of simple building blocks, such as amino acids, nucleotides, fatty acids and sugars. Their individual properties govern their interactions, giving rise to complex supramolecular structures with highly specialized functionality, including ligand recognition, catalysis and compartmentalization. In this thesis, we aim to answer the question whether short peptides could have acted as precursors of modern proteins during prebiotic evolution. Using a combination of experimental and computational techniques, we screened a large molecular search space for peptide sequences that are capable of forming supramolecular complexes with adenosine ...


Incorporation Of Egfr And Ron Receptors Into Nanodiscs, Cristina Flores-Cadengo Apr 2019

Incorporation Of Egfr And Ron Receptors Into Nanodiscs, Cristina Flores-Cadengo

Biomedical Engineering ETDs

Understanding the structure-function relationship of membrane receptors is essential to comprehend the crosstalk between key signaling pathways. Aberrant trans-activation between receptors can lead to tumorigenesis. Two of these receptors known to be involved in cancer development are receptor tyrosine kinases (RTKs), RON (Recepteur d'Origine Nantais) and EGFR (Epidermal Growth Factor Receptor). There has been evidence of heterodimerization and crosstalk between these two receptors based on co-immunoprecipitation, however the structural requirements behind these interactions remain unknown. Structural studies could provide insights into these RTKs’ modes of dimerization and structure-function relationship. However, structural studies of full-length membrane proteins are often difficult ...


Potential Of Nanoscale Elements To Control Fusarium Wilt Disease In Tomato (Solanum Lycopersicum), Enhance Macronutrient Use Efficiency, And Increase Its Yield, Ishaq Olarewaju Adisa Jan 2019

Potential Of Nanoscale Elements To Control Fusarium Wilt Disease In Tomato (Solanum Lycopersicum), Enhance Macronutrient Use Efficiency, And Increase Its Yield, Ishaq Olarewaju Adisa

Open Access Theses & Dissertations

Nanotechnology has a great potential in ensuring food production, security and safety globally. Over the past decade, research on the use of nanomaterials to supply nutrient elements and protect plants from pest and diseases has significantly increased. Tomato (Solanum lycopersicum) is one of the most consumed vegetables in the world and United State is one of its largest producers globally generating billions of dollars annually in revenue.. Tomato plants are affected worldwide by Fusarium wilt caused by Fusarium oxysporum f. sp. Lycopersici. There is growing concern about excessive use of conventional pesticides in controlling Fusarium and other diseases in tomato ...


State Dependent Function And Dynamics In Cerebral Cortical Networks, Leila Fakhraei May 2018

State Dependent Function And Dynamics In Cerebral Cortical Networks, Leila Fakhraei

Theses and Dissertations

Cerebral cortex exhibits vigorous ongoing, internal neural activity even with no sensory input is present or the animal is minimally engaged in a task or behavior. This internal ongoing activity is not static; the ‘cortical state’ varies ranging from synchronous and highly correlated activity to asynchronous and weakly correlated neural activity. The main goal of the work presented here is to understand how changes in cortical states effect several aspects of cortical function and dynamics.

To meet this goal, we did three separate projects. First, we compared the predictability of neuronal network dynamics across cortical states in somatosensory cortex of ...


Liquid Crystals Formed By Short Dna Oligomers And The Origin Of Life, Gregory Patrick Smith Jan 2018

Liquid Crystals Formed By Short Dna Oligomers And The Origin Of Life, Gregory Patrick Smith

Physics Graduate Theses & Dissertations

When dissolved in water, base paired DNA oligomers form double helices with sufficient structural rigidity that, if they are at high enough concentration, can undergo a phase transition into chiral nematic or hexagonal columnar liquid crystalline (LC) order. Within these LC phases, constrained orientation allows these rods to stack more efficiently by hydrophobic forces than they would otherwise, building them into long double helical aggregates that can be chemically glued together (ligated) to further increase their lengths. Even in absence of chemical ligation, this stacking effect is strong enough that short DNA oligomers, which are otherwise too short to form ...


Surface And Structural Modification Of Carbon Electrodes For Electroanalysis And Electrochemical Conversion, Yan Zhang Jan 2018

Surface And Structural Modification Of Carbon Electrodes For Electroanalysis And Electrochemical Conversion, Yan Zhang

Theses and Dissertations--Chemistry

Electrocatalysis is key to both sensitive electrochemical sensing and efficient electrochemical energy conversion. Despite high catalytic activity, traditional metal catalysts have poor stability, low selectivity, and high cost. Metal-free, carbon-based materials are emerging as alternatives to metal-based catalysts because of their attractive features including natural abundance, environmental friendliness, high electrical conductivity, and large surface area. Altering surface functionalities and heteroatom doping are effective ways to promote catalytic performance of carbon-based catalysts. The first chapter of this dissertation focuses on developing electrode modification methods for electrochemical sensing of biomolecules. After electrochemical pretreatment, glassy carbon demonstrates impressive figures-of-merit in detecting small, redox-active ...


Experiment-Based Quantitative Modeling For The Antibacterial Activity Of Silver Nanoparticles, Mohammad Aminul Haque Aug 2017

Experiment-Based Quantitative Modeling For The Antibacterial Activity Of Silver Nanoparticles, Mohammad Aminul Haque

Theses and Dissertations

Silver (Ag) has been well known for its antimicrobial activity for a long time. Recent research showed the potential of Ag nanoparticles as emerging antimicrobial agents. However, little quantitative analysis has been performed so far to decipher the mechanism of interaction between nanoparticles and bacteria. Here, a detailed analysis based on kinetic growth assay and colony forming unit assay has been carried out to study the antimicrobial effect of Ag nanoparticles against Escherichia coli (E. coli) bacteria. It was observed that the presence of Ag nanoparticles increased the lag time of bacterial growth while not affecting the maximum growth rate ...


Advances In Single Molecule Microscopy: Protein Characterization, Force Analysis And Fluorescence Localization, Chi-Fu Yen Jan 2017

Advances In Single Molecule Microscopy: Protein Characterization, Force Analysis And Fluorescence Localization, Chi-Fu Yen

Graduate Theses and Dissertations

Recent advances in single molecule techniques have allowed scientists to address biological questions which cannot be resolved by traditional ensemble measurements. In this dissertation, I integrate single molecule and bulk measurements to establish a direct link between copper exposure and neurotoxicity in prion disease. Furthermore, I develop a new analysis method to improve the accuracy of kinetic parameter estimation in single molecule Atomic Force Microscope (AFM) experiments. Finally, I develop a new fluorescence localization microscopy to identify the axial position of a single fluorescent object with sub-nanometer accuracy.

Prion diseases are characterized by the misfolding and oligomerization of prion protein ...


Characterization Of The Influence Of External Stimulus On Protein-Nucleic Acid Complex Through Multiscale Computations, Agnivo Gosai Jan 2017

Characterization Of The Influence Of External Stimulus On Protein-Nucleic Acid Complex Through Multiscale Computations, Agnivo Gosai

Graduate Theses and Dissertations

The concomitant detection, monitoring and analysis of biomolecules have assumed utmost importance in the field of medical diagnostics as well as in different spheres of biotechnology research such as drug development, environmental hazard detection and biodefense. There is an increased demand for the modulation of the biological response for such detection / sensing schemes which will be facilitated by the sensitive and controllable transmission of external stimuli. Electrostatic actuation for the controlled release/capture of biomolecules through conformational transformations of bioreceptors provides an efficient and feasible mechanism to modulate biological response. In addition, electrostatic actuation mechanism has the advantage of allowing ...


Coarse-Grained Simulations Of The Self-Assembly Of Dna-Linked Gold Nanoparticle Building Blocks, Charles Wrightsman Armistead Dec 2016

Coarse-Grained Simulations Of The Self-Assembly Of Dna-Linked Gold Nanoparticle Building Blocks, Charles Wrightsman Armistead

Theses and Dissertations

The self-assembly of nanoparticles (NPs) of varying shape, size, and composition for the purpose of constructing useful nanoassemblies with tailored properties remains challenging. Although progress has been made to design anisotropic building blocks that exhibit the required control for the precise placement of various NPs within a defined arrangement, there still exists obstacles in the technology to maximize the programmability in the self-assembly of NP building blocks. Currently, the self-assembly of nanostructures involves much experimental trial and error. Computational modeling is a possible approach that could be utilized to facilitate the purposeful design of the self-assembly of NP building blocks ...


Thermodynamics And Kinetics Of The Three-Way Junction Of Phi29 Motor Prna And Its Assembly Into Nanoparticles For Therapeutic Delivery To Prostate Cancer, Daniel W. Binzel Jan 2016

Thermodynamics And Kinetics Of The Three-Way Junction Of Phi29 Motor Prna And Its Assembly Into Nanoparticles For Therapeutic Delivery To Prostate Cancer, Daniel W. Binzel

Theses and Dissertations--Pharmacy

The emerging field of RNA nanotechnology necessitates creation of functional RNA nanoparticles, but has been limited by particle instability. Previously, it was found the three-way junction (3WJ) of the Phi29 DNA packaging motor pRNA was found to be ultra-stable and assemble in solution without the presence of metal ions. The three-way junction is composed of three short oligo RNA strands and proven to be thermodynamically stable. Here the assembly mechanism, thermodynamic and enzymatic stabilities, and kinetics are examined in order to understand the stability behind this unique motif. Thermodynamic and kinetics studies found that the pRNA 3WJ formed out of ...


Morphological And Material Effects In Van Der Waals Interactions, Jaime C. Hopkins Jan 2016

Morphological And Material Effects In Van Der Waals Interactions, Jaime C. Hopkins

Doctoral Dissertations

Van der Waals (vdW) interactions influence a variety of mesoscale phenomena, such as surface adhesion, friction, and colloid stability, and play increasingly important roles as science seeks to design systems on increasingly smaller length scales. Using the full Lifshitz continuum formulation, this thesis investigates the effects of system materials, shapes, and configurations and presents open-source software to accurately calculate vdW interactions.

In the Lifshitz formulation, the microscopic composition of a material is represented by its bulk dielectric response. Small changes in a dielectric response can result in substantial variations in the strength of vdW interactions. However, the relationship between these ...


In Vitro Studies Of Gold And Gold Silica Nanoparticle Radiosensitization With Kilovoltage X-Rays, Gregory Colarch May 2015

In Vitro Studies Of Gold And Gold Silica Nanoparticle Radiosensitization With Kilovoltage X-Rays, Gregory Colarch

UNLV Theses, Dissertations, Professional Papers, and Capstones

Technological advances in the ability to construct and manipulate nanoscale particles have opened up the possibility of using solid metallic nanoparticles and mixed metal nanoshells as a means to increase dose enhancement and treatment efficacy to tumors. In order for nanoparticles to be an effective form of treatment, they must be delivered to tumors in sufficient concentrations so that there is a dose enhancement factor due to ionizing radiation, as well as being essentially non-toxic to healthy cells. Gold nanoparticles and silica-gold nanoshells fit these requirements. Gold has a high atomic number (Z=79), which gives a larger cross section ...


Interactions Of Nanomaterials With Biological Systems: A Study Of Bio-Mineralized Nanoparticles And Nanoparticle Antibiotics, Jennifer Chappell Gifford Jan 2015

Interactions Of Nanomaterials With Biological Systems: A Study Of Bio-Mineralized Nanoparticles And Nanoparticle Antibiotics, Jennifer Chappell Gifford

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

Nature is continually able to out-perform laboratory syntheses of nanomaterials with control of specific properties under ambient temperatures, pressures and pH. The investigation of existing biomolecule-mediated nanoparticle synthesis provides insight and knowledge necessary for duplicating these processes. In this way, peptides or proteins with nanomaterial mediation capabilities can be: 1) explored to further understand the ways in which biomolecules create specific nanoparticles then 2) used to create genetically encodable tags for use in electron tomography. The goal of designing such a tag was to assist in closing the resolution gap that exists in current imaging techniques between approximately 5 nm ...


Carbon Nanopipettes For Advanced Cellular Probing And Microinjection, Sean Eric Anderson Jan 2015

Carbon Nanopipettes For Advanced Cellular Probing And Microinjection, Sean Eric Anderson

Publicly Accessible Penn Dissertations

Carbon nanopipettes (CNPs) consist of a pulled-quartz micropipette with a thin layer of amorphous carbon deposited along its entire interior surface via chemical vapor deposition. The micropipette maintains a continuous fluidic pathway from its nanoscopic tip to its distal macroscopic end, while the insulated carbon film provides an electrical path to the tip that can be used as a working electrode. The quartz at the tip of the CNP can be chemically etched to expose a desired length of a carbon pipe to control the size and characteristics of the electrode. CNPs are inexpensive, batch- fabricated, and can be made ...


Photoelectric Characterization Of Bacteriorhodopsin Reconstituted In Lipid Bilayer Membrane, Joel Kamwa Dec 2014

Photoelectric Characterization Of Bacteriorhodopsin Reconstituted In Lipid Bilayer Membrane, Joel Kamwa

Theses and Dissertations

The objective of this work was to conduct basic research in biologically inspired energy conversion solutions. A photosynthetic protein (Bacteriorhodopsin) was reconstituted in a bi-layer membrane. Then, when a laser beam was shined on the membrane, the photon energy was used by the protein to pump protons across the membrane. The translocation of protons across the membrane was measured as photocurrent. For this purpose, a system was built to characterize the lipid bilayer membranes and to measure the photocurrent. The lipid bilayer membrane was characterized by its capacitance and resistance. A picoampere photocurrent was observed when Bacteriorhodopsin protein was present ...


Hierarchical Cell Fluid Extracellular Matrix Interaction In Cell Microenvironment, Soham Ghosh Oct 2014

Hierarchical Cell Fluid Extracellular Matrix Interaction In Cell Microenvironment, Soham Ghosh

Open Access Dissertations

Hierarchical structural interactions between components of cell microenvironment, the extracellular matrix (ECM), cytoplasm, nucleus and fluid, are important phenomena that decide cell level physiological process and tissue engineering applications. One of those tissue engineering modalities is freezing of biomaterials, important in a wide variety of biomedical applications including cryopreservation and cryosurgeries. In order to design these applications, freezing-induced changes of the cells and tissues and corresponding biophysical mechanisms need to be well understood. Although the effects of freezing on cells in suspension have been extensively studied, the intracellular mechanics of cells embedded in the extracellular matrix (ECM) during freezing are ...


Oriented Collagen And Applications Of Waveguide Evanescent Field Scattering (Wefs) Microscopy, Qamrun Nahar Apr 2014

Oriented Collagen And Applications Of Waveguide Evanescent Field Scattering (Wefs) Microscopy, Qamrun Nahar

Electronic Thesis and Dissertation Repository

In this thesis, Waveguide Evanescent Field Scattering (WEFS) microscopy is developed as a non-invasive, label-free live cell imaging technique. This new high-contrast imaging can be employed to study the first hundred nanometers from the surface as it utilizes the evanescent field of a waveguide as the illumination source. Previously, waveguide evanescent field fluorescence (WEFF) microscopy was developed as a fluorescence imaging technique comparable to the total internal reflection fluorescent (TIRF) microscopy. Both the WEFF and WEFS technique utilizes the same fundamental concepts except in WEFS microscopy imaging is accomplished without the application of any fluorescent labeling. In this work, bacterial ...


Real-Time Single-Molecule Observations Of Proteins At The Solid-Liquid Interface, Blake Brianna Langdon Jan 2014

Real-Time Single-Molecule Observations Of Proteins At The Solid-Liquid Interface, Blake Brianna Langdon

Chemical & Biological Engineering Graduate Theses & Dissertations

Non-specific protein adsorption to solid surfaces is pervasive and observed across a broad spectrum of applications including biomaterials, separations, pharmaceuticals, and biosensing. Despite great interest in and considerable literature dedicated to the phenomena, a mechanistic understanding of this complex phenomena is lacking and remains controversial, partially due to the limits of ensemble-averaging techniques used to study it. Single-molecule tracking (SMT) methods allow us to study distinct protein dynamics (e.g. adsorption, desorption, diffusion, and intermolecular associations) on a molecule-by-molecule basis revealing the protein population and spatial heterogeneity inherent in protein interfacial behavior. By employing single-molecule total internal reflection fluorescence microscopy ...


Synthesis And Functionalization Of Gold Nanoparticles Using Chemically Modified Ssdna, Philip Gerard Calabrese Jan 2014

Synthesis And Functionalization Of Gold Nanoparticles Using Chemically Modified Ssdna, Philip Gerard Calabrese

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

In the first part of this thesis, methods for functionalizing spherical gold nanoparticles with nucleic acid binding ligands (aptamers) that target the VEGF receptor complex were developed. In order to provide a multiplexed labeling strategy for imaging the VEGF receptor complex in electron microscopy, gold nanoparticles of distinct sizes were conjugated to modified ssDNA aptamers that target the VEGF-A cytokine, the VEGFR-2 RTK receptor and a membrane associated co-receptor, Nrp-1. The modified ssDNA gold nanoparticle conjugates were applied to a human lung carcinoma cell line (A549) which has been shown to express each of these proteins and used as a ...


The Geometry And Sensitivity Of Ion-Beam Sculpted Nanopores For Single Molecule Dna Analysis, Ryan Connor Rollings May 2013

The Geometry And Sensitivity Of Ion-Beam Sculpted Nanopores For Single Molecule Dna Analysis, Ryan Connor Rollings

Theses and Dissertations

In this dissertation, the relationship between the geometry of ion-beam sculpted solid-state nanopores and their ability to analyze single DNA molecules using resistive pulse sensing is investigated. To accomplish this, the three dimensional shape of the nanopore is determined using energy filtered and tomographic transmission electron microscopy. It is shown that this information enables the prediction of the ionic current passing through a voltage biased nanopore and improves the prediction of the magnitude of current drop signals when the nanopore interacts with single DNA molecules. The dimensional stability of nanopores in solution is monitored using this information and is improved ...


Design Of Novel Nano-Carriers For Multi-Enzyme Co-Localization, Feng Jia Jan 2013

Design Of Novel Nano-Carriers For Multi-Enzyme Co-Localization, Feng Jia

Graduate Theses and Dissertations

The widely existing MECs in Nature have inspired researchers to design synthetic analogs to promote the overall catalytic efficiency in vitro by co-localizing multiple enzymes to mimic the MECs' unique functionalities. A number of efforts have been devoted to designing synthetic MECs in the past couples of decades. This thesis work has focused on developing novel strategies based on enzyme immobilization to design nano-carriers for multi-enzyme co-localization to realize kinetics enhancement and strong control of spatial arrangement of the enzymes. Three distinct approaches have been designed using different attachment methods and platforms.

First, the multifunctional polystyrene nanoparticles were designed for ...


Rna Mediated Assembly Of Nanostructures, Jessica Lynn Rouge Jan 2012

Rna Mediated Assembly Of Nanostructures, Jessica Lynn Rouge

Chemistry & Biochemistry Graduate Theses & Dissertations (1986-2018)

The first chapter of this work presents a comprehensive look at RNA mediated nanoparticle formation. The overall goal of this research is to gain a deeper understanding of the RNA-particle formation mechanism and the basic properties of the materials selected by modified RNA molecules. Understanding such RNA-substrate interactions and how they translate into the physical and chemical characteristics of the nanoparticles they create are important fundamental concepts when considering these biotemplated materials as potential chemical catalysts. The RNA sequences discussed in the first chapter (referred to as Pdases) were discovered using RNA in vitro selection techniques. These Pdases were found ...


Structural Basis Of Substrate Recognition In Thimet Oligopeptidase And Development Of Nanoparticles For Therapeutic Enzyme Delivery, Jonathan Mark Wagner Jan 2012

Structural Basis Of Substrate Recognition In Thimet Oligopeptidase And Development Of Nanoparticles For Therapeutic Enzyme Delivery, Jonathan Mark Wagner

Theses and Dissertations--Molecular and Cellular Biochemistry

Neuropeptidases are responsible for degradation of signaling peptides in the central nervous system and periphery. Some neuropeptidases have also been shown to play a role as part of the cell’s hydrolytic machinery responsible for breaking down proteins and peptides into amino acids, and these enzymes therefore influence small peptide availability for antigen presentation. A better understanding of how neuropeptidases recognize their substrates could lead to therapeutics that modulate the activity of these important enzymes. Alternatively, re-engineering these enzymes to selectively hydrolyze undesirable peptides could make them attractive as therapeutics themselves. A key question in understanding the activity of these ...


Mucopolysaccharidosis Type Iiib And Galnac Transferase Double Knockout Mice And Additional Studies In Gene Therapy And Animal Models To Assess Pathogenesis And Therapy, Eman Elsayed Abass Mohammed Jan 2012

Mucopolysaccharidosis Type Iiib And Galnac Transferase Double Knockout Mice And Additional Studies In Gene Therapy And Animal Models To Assess Pathogenesis And Therapy, Eman Elsayed Abass Mohammed

Graduate Theses and Dissertations

The Mucopolysaccharidoses (MPSs) are a class of lysosomal storage diseases characterized by lysosomal accumulation of glycosaminoglycan (GAG). Understanding the pathogenesis of the neuropathic forms of MPS and improving treatment options for these disorders are major areas of research in the laboratory of Dr. Ellinwood. The neuropathic MPSs include MPS I, II, III (A-D), and VII, all of which have primary storage of heparan sulfate (HS), and a secondary accumulation of GM2 and GM3 gangliosides. Clinically patients with the severe forms of these disorders have central nervous system defects. Mucopolysaccharidosis III, also known as Sanfilippo syndrome, has four subtypes designated as ...


Artificial And Natural Nucleic Acid Self Assembling Systems, Marcus Wood Jan 2011

Artificial And Natural Nucleic Acid Self Assembling Systems, Marcus Wood

Wayne State University Dissertations

Nucleic acids are good candidates for nanomachine construction. They participate in all the processes of life, and so can function as structural building blocks and dynamic catalysts. However, to use nucleic acids as nanomachines, a better understanding of their material properties, how to design structures using them, and their dynamics is needed. We have tried to address these issues, in a small way, with nucleic acid force field development, an attempt at nanostructural design and synthesis using DNA, and a study of the RNA/protein regulatory dynamics of the tryptophan regulatory attenuation protein.