Solid-state nanopores are a versatile class single-molecule sensors to electrically characterize a range of biological molecules. Nanopores operate on the simple premise that when a voltage is applied across a pore immersed in a salt solution, the passage of a biomolecule results in a transient blockage in the ionic current that provide information about the translocating molecule. This thesis presents studies employing various DNA nanostructures with solid-state nanopore electrical readout for the development of high sensitivity digital single-molecule assays to detect low-abundance biomarkers. Toward this ultimate goal, work presented in this thesis use nanopores to probe DNA nanostructures, their assembly, mechanical properties, and monitor their dynamics with time and temperature. DNA nanostructures are self-assembled via specific base pairing of DNA, their programmability make them particularly useful for applications including drug delivery, molecular computation and biosensing. Here, I first show results of translocation profiles and discuss folding characteristics, mobility, and molecular configuration during passage for different DNA nanostructures such as the short star-shaped DNA nanostructures and large helix-bundle DNA origami structures under various experimental conditions in an effort to understand the passage characteristics through nanopores of these structures before using them in biological assays. I conclude by presenting a magnetic bead-based immunoassay scheme using a digital solid-state nanopore readout. Nanopore has the ability to count molecules one at a time, this allows accurate and precise determination of the concentration of a biomarker in solution. Coupled with the use of specific choice of DNA nanostructures, as proxy labels for proteins of interest, I establish that nanopores sensors can reliably quantify the concentration of a protein biomarker from complex biofluids and overcome the traditional challenges associated with nanopore-based protein sensing, such as specificity, sensitivity, and consistency. I demonstrate the quantification of thyroid stimulating hormone (TSH) with a high degree of precision down to the femtomolar range by using a nanoparticle-based signal amplification strategy. The proposed assay scheme is generalizable to a framework for the detection and quantification of a wide range of target proteins, and given that its performance can further be improved with the use of parallelization, preconcentration, or miniaturization, it opens up exciting opportunities for the development of ultra-sensitive digital assay in a format that is compatible for point-of-care.

Class II cytokine receptors are important pleiotropic regulators of the immune system that play a central role in pathogen defense, tumor surveillance and immune system homeostasis. Most of these activities are very promising for biomedical applications, which, however, have so far failed to succeed due to severe undesired side effects resulting from the pleiotropic nature of these cytokine receptors. Controlling the functional plasticity of class I/II cytokine receptor signaling by engineered cytokines has recently emerged as a promising approach to selectively reduce such side effects. In this context, systematic studies on the IFNalpha/beta receptor and other systems have identified that the binding kinetics of the ligand-receptor interaction play an important role in defining signaling specificity. This has been explained by altered equilibrium and dynamics of the signaling complex in the plasma membrane. In this work, I have investigated how the spatiotemporal organization and dynamics of signaling complexes regulate activation and signaling specificity of other members of the class II cytokine receptors. I focused on the type II IFN and IL-10 systems that supposedly form hexameric ligand-receptor signaling complexes in the plasma membrane. To this end, we developed an orthogonal multicolor anti-GFP nanobody-based labeling strategy, that allowed imaging of up to four different class II cytokine receptor subunits simultaneously. Using this labeling strategy, I investigated the spatiotemporal dynamics of IFNGR and IL-10R complex assembly by co-localization and co-tracking of single receptor subunits. Thereby, I did show that unliganded receptor subunits of IFNGR and IL-10R remain monomeric at the cell surface, whereas binding of the ligand led to fast and efficient receptor homo- and hetero-dimerization, verifying a ligand-induced receptor complex assembly model for both cytokine receptors. Moreover, I verified the hexameric ligand-receptor complex structure in cellulo. Analysis of single molecule trajectories and co-trajectories revealed a decrease in mobility and diffusion of IFNGR and IL-10R subunits upon ligand stimulation indicating receptor confinement and endocytosis. In this context, I identified an abnormal diffusion behavior of IL-10R2 that was dependent on the length of its transmembrane helix. We used partial agonists for both receptor complexes to systematically alter receptor binding stoichiometry and complex stability in the plasma membrane and correlated these with downstream signaling responses. Our analysis revealed a minor contribution of the second low affinity receptor subunit and its associated kinase to the overall signaling activity. However, the second high affinity binding subunit was indispensable to acquire full signaling potential. We managed to obtained decoupling of gene expression for both hexameric class II cytokine receptors by utilizing engineered ligands with altered receptor binding affinities. Our findings could pave the way for new biomedical approaches with engineered IFNgamma and IL-10 in the future. Furthermore, we uncovered pathogenic mechanisms behind the IFNGR2-T168N mutant and auto-IFNgamma antibodies, both of which prominently cause the Mendelian Susceptibility to Mycobacteria Disease (MSMD) syndrome, showing that both interfere with IFNGR activation by preventing recruitment of IFNGR2 into receptor complexes.

Polymer flooding is one of the most used chemical methods for enhanced oil recovery(EOR). However, laboratory studies and field applications of polymer injections often encounter polymer-induced clogging due to polymer transport and entrapment, leading to permeability reduction and diminished recovery performance. In this work, we focus on understanding polymer flow behavior using microfluidics devices and fluorescence microscopy. Microfluidic devices were designed to mimic and replicate the pore-network structures of oil-bearing conventional reservoir rocks. We present various flow experiments to study polymer transport and the underlying mechanisms of polymer retention in porous media. We assess the polymer-induced clogging of partially hydrolyzed polyacrylamides - HPAMs, using tracers. Afterward, we use a commercially available fluorescent polymer with microfluidics and single-molecule microscopy to give insights into individual molecule dynamics. Furthermore, we perform numerical simulations to replicate and extend the experimental work. As these experiments were conducted using commercially fluorescent polymer of low molecular weight and due to limitations of tracers to track polymers, we extended this work to investigate the transport of HPAMs, which is the most used polymer for EOR, at molecule-scale. However, existent methods in the literature are not suitable for fluorescently labeling ultra-high molecule weight polymers. Therefore, we present a novel method for synthesis of dye-labeled polymers that successfully tagged the HPAMS. Finally, we assessed the conformation and flow dynamics of the fluorescently labeled HPAM molecules. The findings highlight a limitation in some polymer screening workflows in the industry that suggest selecting the candidate polymers based solely on their molecular size and the size distribution of the rock pore-throats. Moreover, we present, for the first time, direct visualization of the three main mechanisms underlying polymer retention in porous media. We bring the first molecular evidence of polymer pore-clogging and permeability reduction reversibility, which sheds light on the controversy in the literature. In addition, we propose a new method for fluorescent labeling water-soluble ultra-high molecular weight polyacrylamides-based polymers that preserves their viscosifying properties. The method can be extended to any polymers containing carboxyl groups or groups that can be functionalized into carboxyls, and therefore, the applicability covers any fields that employ polymers.

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The prominent features of single molecule magnets (SMMs), such as the quantum tunneling of the magnetization (QTM), are conventionally understood through the giant spin approximation (GSA) which considers the molecule as a single rigid spin. This model often requires the inclusion of high order anisotropy terms in the Hamiltonian, a manifestation of admixing of low lying excited states that can be more naturally understood by employing a multi-spin (MS) description i.e. considering the individual spins and the interactions between ions within the molecule. However, solving the MS Hamiltonian for high nuclearity molecules is not feasible due to the enormous dimensions of the associated Hilbert space that put it beyond the capability of existing computational resources. In contrast, low nuclearity systems permit the complete diagonalization of the MS Hamiltonian required to sample the effect of internal degrees of freedom, such as exchange interactions and single ion anisotropies, on the QTM. This dissertation focuses on the study of low nuclearity SMMs in view of understanding these subtle quantum effects. To accomplish this, we have developed a series of magnetic characterization techniques, such as integrated microchip sensors resulting from the combination of two dimensional electron gas (2DEG) Hall-Effect magnetometers and microstrip resonators, capable of performing measurements of magnetization and EPR spectroscopy simultaneously. The thesis bases on a comparative study of two low nuclearity SMMs with identical magnetic cores (Mn4 dicubane) but differing ligands. Notably, one of these SMMs lacked solvent molecules for crystallization; a characteristic that gives rise to extremely sharp resonances in the magnetization loops and whose basic QTM behavior can be well explained with the GSA. On the contrary, the second SMM exhibited mixed energy levels, making a MS description necessary to explain the observations. We have also examined the role of internal degrees of freedom on more subtle QTM phenomena, leading to the explanation of asymmetric Berry-phase interference patterns observed in a Mn4 SMM in terms of a competition between different intermolecular magnetic interactions, i.e. non-collinear zero-field splitting tensors and intramolecular dipolar iii interactions, resulting in astonishing manifestations of the structural molecular symmetry on the quantum dynamics of the molecular spin.

Molecular magnets with different dimensionality, whether they are zero-dimensional singlemolecule magnets (SMM) or one-dimensional single-chain magnets (SCM) are very interesting, since they allow probing the fundamental aspects bordering quantum and classical physics at the nanoscale level. This dissertation covers experimental studies of two Mn-based exchangecoupled molecule-based magnets and two Co-based single-chain magnets, using both dc Halleffect magnetometry and electron paramagnet resonance (EPR) techniques. In these multidimensional systems, the spin of the molecule exhibits quantum mechanical behavior at low temperature. It is quite interesting to observe the effect of magnetic exchange interactions on the magnetic properties of various complexes; hence they strongly affect the magnetic behavior. In this dissertation, the research is initiated with the study of low-magnetic-nuclearity molecules, starting with a spectroscopic study of a significantly anisotropic Mn(IV) monomer. At low temperature the molecule possesses easy-plane type anisotropy of a remarkable magnitude. Although the molecule is not a single-molecule magnet, the remarkable anisotropy can initiate synthesis of newer and better molecular magnets with Mn(IV) as the main building block. Furthermore, the interplay between the magnetic anisotropy and the inter-ion exchange interactions (J) within the molecule are probed for a dimer and a trimer where the magnetic core is comprised of two and three ions respectively. In the Mn-based case of the dimer, the low coupling between the atoms leads to significant state mixing, thus making it impossible to assign the individual spin states to the dimer or to the respective individual Mn(II) ions. In the case of iv the trimer, lowering of the symmetry achieved by fine tuning of the inter-ion exchange interactions leads to relieving of frustration in the antiferromagnetic (AF) triangular Mn(III) system, resulting in a well defined ground state and significant zero field splitting. Also a clear hysteretic behavior observed in this system demonstrates its SMM nature at low temperature. Finally, high-field high-frequency magnetic and spectroscopic studies performed on two cobalt-based SCMs reveal that formation of magnetic domains by exchange interactions within the chain are strongly influenced by thermal fluctuations. The chain possesses a uniaxial anisotropy with the quantization axis lying along the length of the chain. Moreover it is shown that modulation of the magnitude of inter- and intra-chain interactions results in a threedimensional dynamics in one of the samples. Interestingly, detailed dc magnetic studies show a tunable crossover between one- and three-dimensional magnetic dynamics as a function of temperature and/or magnetic field sweep rate. Our voyage through several molecular systems of different dimensionality have allowed us to expand our understanding of the role of exchange interactions on the magnetic behavior in molecular magnetism

Optical microscopy is the oldest form of microscopy that has been visually aiding scientific research. In our research, I have reported here two such optical microscopy techniques for two different projects. In the first project, we re-developed an instrumentation of a cost-effective, high-performing, single-molecular localization super-resolution microscopy setup that breaks the diffraction limitation barrier. Then we use a stochastic image capturing technique to capture the best precision image positions of gold nanoparticles. In our second project, we apply confocal microscopy technique to image DNA molecular nanoscale structural alterations of chromatin in cell nuclei of gut tissues caused by total body irradiation (TBI). We then quantify these alterations using a light localization technique called inverse participation ratio (IPR) using the confocal micrographs of the sample. Our results show radiation causes reduction and saturation of DNA spatial mass density fluctuations that were observed for different durations of post-irradiation.

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