Browsing by Subject "Nanotechnology"

Now showing 1 - 10 of 10
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    Bridging the gap between theory, experiments and simulations of nanochannel confined DNA
    (2020-08) Bhandari, Aditya Bikram
    The study of nanochannel confined DNA has garnered substantial attention since the early 2000's owing to its application in genome mapping, the coarse-grained counterpart to DNA sequencing, which is an indispensable tool in biological research. However, our understanding of the physics behind confined DNA is rather simplified and incomplete. Thus, theory, simulation and experiment have by and large been at odds with one another. The results of this dissertation are aimed at understanding and attempting to resolve the source of these discrepancies. Our strategy for this dissertation is three-pronged. First, we revisit a historically cited explanation for the discrepancies - the lack of understanding behind the wall depletion length denoting the wall-DNA electrostatic interactions. Second, we considered the intersection of theory and simulation, which recent developments have managed to bring sufficiently into accord. We found that the deviations between the fractional extension distributions predicted by an asymptotic theory and those observed experimentally, are not due to a breakdown of the theory, even for experimental conditions which typically do not strictly satisfy the asymptotic limits of the theory. This motivated a closer inspection of the theories to determine a missing link between theory and experiment. Finally, by studying a recently generated dataset of fractional extensions spanning a wide range of the experimental parameter space, we were able to isolate this missing link as the effect of long-range electrostatics in the system which are typically ignored in the simplified theories, wherein the DNA is assumed as a neutral polymer confined in a channel of a reduced effective channel size. We believe that our findings within this dissertation will provide a better understanding of confined polymers and, in particular, the nanochannel confined DNA system used in genome mapping, as well as provide new directions of study in the future.
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    Coupling of far-infrared light to the surface phonon-polaritons in Transition metal dichalcogenides
    (2021-05) Saha, Subhodip
    Enhanced light-matter interactions through a plethora of dipole-typepolaritonic excitations started to emerge in two-dimensional (2D) layered materials in recent years. 2D Van der Waals (vdWs) polar crystals sustaining phonon-polaritons (PhPs) have opened up new avenues for fundamental research and optoelectronic applications within the mid-infrared (mid-IR) to terahertz ranges. One of the fundamental hurdles in polaritonics is the trade-off between electromagnetic field confinement and the coupling efficiency with free-space light, a consequence of the large momentum mismatch between the excitation source and polaritonic modes. Our group recently demonstrated the fundamental problem of momentum mismatch can be overcome with a graphene acoustic plasmon resonator with nearly perfect absorption (94%) of incident mid-infrared light. This high efficiency is achieved by utilizing a two-stage coupling scheme: free-space light coupled to conventional graphene plasmons, which then couple to ultraconfined acoustic plasmons. To date, experimental demonstration of excitation of the surface phonon-polaritons (SPhPs) in transition metal dichalcogenides (TMDs) remains unexplored, so here we demonstrate novel strategies for dynamically controlling of far-infrared light using unique optical properties of TMDs in particular ZrS2. In comparison to other vdW materials, the phonon modes of these TMDs are much softer and exhibits phonon peaks within the far-infrared (far-IR) regime. Here we experimentally demonstrate the excitation of SPhPs in ZrS2 acoustic resonator by the far-IR absorption spectroscopy. The surface optical (SO) phonon modes of these TMDs were tuned and tailored to lie anywhere within the reststrahlen band, by controlling the ribbon width, which brings extreme tunability. In addition, the absorption can be pushed beyond 90% with the integration of gold reflectors and can become promising material for far-IR biosensing. The results demonstrate TMDs as a new platform for studying phonon-polaritons exhibiting good quality factors and excellent tunability which enable far-IR nanophotonics devices. Recently our group demonstrated ultra strong coupling (USC) between polar phonons and mid-IR light in coaxial nanocavities. Here we push the boundary further up to the far-IR range and we propose to demonstrate USC coupling between polar phonons and far-IR light using the coaxial nanocavity platform. Our numerical simulation predicts a level splitting of strongly coupled polaritons of 95% of the resonant frequency, enabled by epsilon-near-zero (ENZ) responses in the far-IR of the ZrS2 filled coaxial nanocavities. The ability to reach the USC regime in mass-produced nanocavity systems can open up new avenues to explore non-perturbatively coupled light-matter systems, multiphoton effects, as well as higher-order nonlinear effects, which may lead to novel applications in sensing, spectroscopy, and nanocavity optomechanics.
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    Crystallographic Information Files (CIF) with atomistic models of interacting double-walled carbon nanotubes.
    (2021-07-19) Dumitrica, Traian; dtraian@umn.edu; Dumitrica, Traian; Computational Nanomechanics Laboratory
    The dataset provides Crystallographic Information Files (CIF) atomistic models of interacting double-walled carbon nanotubes diameter monodisperse and different mean diameter and standard deviations. These models can be used to reproduce Figures 6-10 of the referenced paper. The files can be visualized with molecular visualizers like OVITO and JMOL.
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    Engineered Proteins for Studying and Controlling Cellular Recognition
    (2018-08) Csizmar, Clifford
    The ability to direct cell-cell interactions has tremendous value in several therapeutic fields. While genetically-encoded artificial receptors have proven efficacious, their scope is limited by the genetic engineering that underlies the approach. To circumvent some of these limitations, our group has developed a non-genetic method to modify any cell surface with a targeted protein scaffold. First, we engineered a protein ligand based upon the human tenth type III fibronectin domain (Fn3) that binds to epithelial cell adhesion molecule (EpCAM), an overexpressed tumor antigen. Using yeast surface display, mammalian cell panning, and a novel titratable avidity-reduction selection technique, we evolved Fn3 clones exhibiting high affinity and robust selectivity for cellular EpCAM. We then incorporated these Fn3s into a multivalent chemically self-assembled nanoring (CSAN). EpCAM-targeted CSANs were anchored to cell membranes through the hydrophobic insertion of phospholipids into the lipid bilayer. The targeting elements were subsequently removed from the cell surface by disassembling the CSAN with the antibiotic, trimethoprim. Using this system, we successfully directed and reversed targeted intercellular interactions in vitro. Finally, the modular CSANs were used to study how avidity impacts the apparent affinity of a multivalent scaffold. By tuning the number of Fn3 domains on the CSAN, we quantitatively described how the apparent affinity changes as a function of ligand affinity, domain valency, and antigen expression density. These results informed the development of a CSAN capable of discriminating between cells expressing different quantities of EpCAM both in vitro and in vivo. In conclusion, we developed a diverse toolkit for directing and studying cell-cell interactions. The CSAN platform is applicable to several therapeutic arenas and, by balancing affinity and avidity, may offer advantages over current cell-directing methods.
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    Engineering metallic nanogap apertures for enhanced optical transmission
    (2016-10) Yoo, Daehan
    Physics and technology of metallic nanoapertures have been of great interest in nanophotonics. In particular, enhanced optical transmission mediated by surface plasmon waves in metallic nanoapertures has been widely studied and utilized in biochemical sensing, imaging, optical trapping, nonlinear optics, metamaterials, and optoelectronics. State-of-the-art nanotechnology enables researchers to explore optical physics in complex nanostructures. However, the high cost and tedium of conventional fabrication approaches such as photolithography, electron-beam lithography, or focused-ion-beam milling have limited the utilization of metallic nanoapertures for practical applications. This dissertation explores new approaches to enable high-throughput fabrication of sub-10-nm nanogaps and apertures in metal films. In particular, we focus on a new technique called atomic layer lithography, which turns atomic layer deposition into a lithographic patterning technique and can create ultra-small coaxial nanoapertures. The resulting nanostructures allowed us to observe extraordinary optical transmission in mid-infrared regime that originates from an intriguing physical phenomenon called the epsilon-near-zero (ENZ) condition. Subsequently, we turn this nanogap structure into a high-Q-factor plasmonic resonator, called a trench nanogap resonator, by combining a nanogap and sidewall mirrors. This structure is optimized for electrical trapping of biomolecules and concurrent optical detection, which is demonstrated experimentally via dielectrophoresis-enhanced plasmonic sensing. The fabrication technique and resulting structures demonstrated in this thesis work can facilitate practical engineering of metallic nanoapertures towards harnessing the potential of plasmonics.
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    Environmental Nanotechnology: A Universal, Green Process for the Synthesis of Functional Nanocomposites
    (2020-09) Brockgreitens, John
    Environmental nanotechnology is broadly defined as the application of nano-scale materials (10^-9 m) to environmental systems as well as the impacts of these materials on air, water, and soil quality. There are significant advantages to using nanomaterials for pollution control due to their high reactivity and ability to specifically bind to target pollutants under diverse conditions. However, nanomaterials can have negative biogeochemical and toxicological effects in natural systems. Furthermore, nanomaterials can be difficult to identify and remove in natural and engineered systems. To facilitate the application of nanomaterials to pollution control, research has turned to using nanoparticles embedded in macro-sized support materials referred to as “nanocomposites.” The work presented here builds upon preliminary work on the synthesis of selenium nanomaterials for the removal of mercury from water. The synthesis process was simplified and expanded for use with four other nanomaterials: iron, copper, titanium, and zinc. These nanomaterials were utilized as high-efficiency pollutant binding “sorbents” for dissolved phosphorus, arsenic, and organic contaminants. Furthermore, titanium and zinc nanomaterials were successfully fabricated on textile materials to enable UV resistant and antimicrobial functionalities. Collectively, this work provides a fundamental basis for scalable nanocomposite synthesis with minimal chemical inputs and the diverse application of these composite materials.
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    Improving Neural Recording Technology at the Nanoscale
    (2011-08) Ferguson, John
    Neural recording electrodes are widely used to study normal brain function (e.g., learning, memory, and sensation) and abnormal brain function (e.g., epilepsy, addiction, and depression) and to interface with the nervous system for neuroprosthetics. With a deep understanding of the electrode interface at the nanoscale and the use of novel nanofabrication processes, neural recording electrodes can be designed that surpass previous limits and enable new applications. In this thesis, I will discuss three projects. In the first project, we created an ultralow-impedance electrode coating by controlling the nanoscale texture of electrode surfaces. In the second project, we developed a novel nanowire electrode for long-term intracellular recordings. In the third project, we created a means of wirelessly communicating with ultra-miniature, implantable neural recording devices. The techniques developed for these projects offer significant improvements in the quality of neural recordings. They can also open the door to new types of experiments and medical devices, which can lead to a better understanding of the brain and can enable novel and improved tools for clinical applications.
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    Signals and Systems Tools for Advanced Nanoscale Investigation with Atomic Force Microscopy
    (2017-03) Ghosal, Sayan
    The atomic force microscope (AFM) is one of the major advancements in recent science that has enabled imaging of samples at the nanometer and sub-nanometer scale. Over the years, different techniques have been developed to improve the speed, resolution and accuracy of imaging using AFM. Further, the application spectrum of AFMs has extended beyond topography imaging, examples of which include material characterization, probe based data storage systems, and also single molecule force spectroscopy. In spite of the remarkable achievements by AFM technologies, many challenges exist. While majority of this thesis aims to address important challenges that exist with state of the art AFM methodologies using tools from signal processing and systems theory, it also reports some surprising new phenomena that are observed from AFM based mechanical characterization of protein molecules. The techniques developed in each chapter are extensively verified with simulation and experimental results. A key issue that remains largely unaddressed in the AFM literature is the assessment of fidelity of the measurement data. The first contribution of this thesis is to develop a quantitative measure for the fidelity of images obtained from a fast dynamic mode AFM technique. The developed paradigm facilitates user specific priority for either detection of sample features with high decision confidence or on not missing detection of true features. The fidelity measures developed in this thesis are suitable for real-time implementation. The second contribution of this thesis is to develop and compare the performance of different methods to characterize mechanical properties of materials utilizing the dynamic mode of AFM operation. The dynamic mode AFM is particularly suitable for investigating soft-matter. Here, an important enabler is the viewpoint of an equivalent cantilever. The parameters of the equivalent cantilever need to be estimated to derive material properties. In this thesis, we develop a new steady-state based estimation of equivalent parameters (SEEP) and compare it with the recursive estimation of equivalent parameters (REEP). We show that the SEEP is considerably simpler to implement, however, SEEP is a low bandwidth method when compared to REEP. Both methods yield material parameters that quantitatively agree in the domain of validity of the methods. This thesis also streamlines the process of material identification and outlines the key pitfalls that need to be avoided for quantitative estimation of material parameters. Extensive design of a system identification module is reported which implements the REEP algorithm on modern field programmable gate arrays (FPGA). The step by step design procedure of the module explained in this thesis is employable to the development of a wide variety of FPGA based signal processing systems. The third contribution of this thesis is a new system model detection technique called the innovations squared mismatch. Such detection of a model from a set of models that best describes the behavior of a system is of primary importance in many applications. Here, two discriminating signals are derived from measurements for a plant that switches between two model behaviors, where the transfer functions from inputs to the two signals are identical when one model is effective while they are negative of one another when the other model is effective. Further, we report sequence based detection approaches to extend the use of the signals for high bandwidth applications. In such applications the plant behavior can switch from one model to another at high rates and the transients from a previous behavior affect the current behavior causing inter-symbol interference (ISI). Methods developed are specialized for probe based data storage where experimental data demonstrates that they offer significant advantages over current methods. The fourth contribution of this thesis is the first ever characterization of mechanical properties of utrophin protein molecule and its different terminal fragments using AFM based force spectroscopy experiments. Utrophin and its homologue dystrophin are proteins which are believed to play vital roles in mechanically stabilizing the muscle cells during stretch and relax cycles. These proteins are also under active research for finding possible cure for the disease muscular dystrophy. In this thesis we report markedly different mechanical characteristics for the utrophin constructs where previous thermodynamic studies measured identical thermal denaturation profiles. Our findings signify the need for force spectroscopy based characterization of molecules that are believed to play important mechanical roles in human body.
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    A systems approach to identify skill needs for agrifood nanotechnology: a mixed methods study
    (2013-05) Yawson, Robert Mayfield
    The purpose of this study was to identify skill needs for the emerging agrifood nanotechnology sector and to determine how agricultural education can contribute to human resource and workforce development for this sector. As nanotechnology continues to advance in food and agriculture, there is the need for pragmatic decisions as to how to prepare the workforce. This mixed methods study incorporated disparate fields of systems and complexity theories; nanoscience and nanotechnology; science policy; agricultural education; human resource development and workforce education. The study followed a four-step process involving different methods and approaches. The first phase involved a comprehensive systematic evidence review (SER) and analysis of the literature. This phase of the study also helped to identify key experts and formulate questions for the in-depth and semi-structured interviews and also quantitative survey instruments. A comprehensive stakeholder analysis was done using primary data obtained from experts.The second phase of the study used multi-criteria approaches for value elicitation (which included qualitative and quantitative data) from key stakeholders and experts to identify current and future skill needs in the agrifood nanotechnology sector. The third phase of the study included quantitative analysis, Qualitative Systems Analysis (QSA) and Strategic Flexibility Analysis (SFA) of evidence from the literature review and the multi-criteria value elicitation of experts and stakeholders. The final phase of the study created a generic systems model from the quantitative analysis, QSA and SFA to describe holistically the current and future skill needs for agrifood nanotechnology workers as well as how educational practice and policy can meet these needs. The main conclusions from this study are that: (1) future shortages and skills gaps in agrifood nanotechnology are expected to increase but at the same time there is still quite a lot of uncertainty about future developments and impacts of nanotechnology in the agrifood sector to accurately determine future demand and supply of agrifood nanoskilled workforce. (2) Extra demands in high qualified workers with a background in sciences and engineering (PhD, MSc) will be needed. (3) STEM education at the K-12 levels is even more important than ever and that K-12 nanotechnology programs should be a seamless part of the overall STEM initiative. And most importantly STEM education should not be devoid of employability skills. (4) In addition to various types of technical skills that come with advances in any technology, and thus nanotechnology, employability skills and competencies such as problem solving and ability to work in an interdisciplinary context are considered very important.
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    Toward therapeutic nanoassemblies: the design and modeling of protein-protein interactions.
    (2009-11) White, Brian Richard
    Unraveling the nanoscale processes of biological pathways via the testing, replication, and visualization of the underlying mechanisms remains a persistent challenge in the study of these critical life-governing systems. Recent advances in the field of chemically induced dimerization have unlocked multiple tools for the exploration of these facets of biology, including the development of switchable signaling systems, assertion of control over protein localization in the cell, and regulation of gene expression. An additional revelation through protein complexation by chemical induction is the construction of multivalent protein-based nanostructures, capable of bearing multiple targeting agents. However, stochastic assembly of these proteins has proven unsatisfactory in generating homogeneous populations. Herein, we have taken the initial steps toward developing a protein-based biomolecular language for nanostructural assembly. Through gel filtration analysis, we have characterized the ability of interfacial point mutations to modulate the stability of a bis-methotrexate (bis-MTX) induced E. coli dihydrofolate reductase (DHFR) dimer over a dynamic range of 1.5 kcal/mol. Furthermore, we have employed single-molecule fluorescence assays to demonstrate the stabilization of a heterodimeric DHFR dimer, yielding 4-fold selectivity for the heterodimer over either corresponding homodimer. In addition to our experimental characterization of the chemically induced DHFR dimer, we have also taken steps toward the construction of a tripartite computational model of dimerization in an effort to predict the effects of further mutations. We have tested a number of molecular mechanics force fields against quantum mechanical benchmarks and discovered that the MMFF94, OPLS2005, and AMBER force fields yield the most accurate electrostatic and configurational treatment of the complex bis-MTX dimerizer. While initial attempts at calculating the binding free energy of the macromolecular complex have been unsuccessful, we have gleaned important insights into the complexities of modeling this three-body system. The advances described within the following work delineate important aspects of protein interface remodeling in a chemically induced system and provide an avenue toward the further development of both a computational model of protein interactions and the future directed assembly of protein based materials and therapeutic nanostructures.