Nanopores are apertures of nanometric dimensions in an insulating matrix. They are routinely used to sense and measure properties of single molecules such as DNA. This sensing technique relies on the process of translocation, whereby a molecule in aqueous solution moves through the pore under an applied electric field. The presence of the molecule modulates the ionic current through the pore, from which information can be obtained regarding the molecule's properties. Whereas the electrical properties of the nanopore are relatively well known, much less work has been done regarding their fluidic properties. In this thesis I investigate the effects of fluid flow within the nanopore system. In particular, the charged nature of the DNA and pore walls results in electrically-driven flows called electroosmosis. Using a setup which combines the nanopore with an optical trap to measure forces with piconewton sensitivity, we elucidate the electroosmotic coupling between multiple DNA molecules inside the confined environment of the pore. Outside the pore, these flows produce a nanofluidic jet, since the pore behaves like a small electroosmotic pump. We show that this jet is well-described by the low Reynolds number limit of the classical Landau-Squire solution of the Navier-Stokes equations. The properties of this jet vary in a complex way with changing conditions: the jet reverses direction as a function of salt concentration, and exhibits asymmetry with respect to voltage reversal. Using a combination of simulations and analytic modelling, we are able to account for all of these effects. The result of this work is a more complete understanding of the fluidic properties of the nanopore. These effects govern the translocation process, and thus have consequences for better control of single molecule sensing. Additionally, the phenomena we have uncovered could potentially be harnessed in novel microfluidic applications, whose technological implications range from lab-on-a-chip devices to personalised medicine.

Transmembrane protein ion channels can regulate intercellular transport in response to external stimulus, playing a vital role in diverse physiological functions. Replicating such stimulus-responsive behaviors in the artificial counterparts, e.g. solid-state nanopores, is of great interest in a variety of cross-disciplinary studies and applications, yet has remained challenging due to complicated structures of naturally occurring protein channels and anomalous transport phenomena of the nanoscale fluid. Current stimulus-responsive solid-state nanopores are achieved by employing functional materials and/or geometrical/surface charge asymmetry but suffer from low sensitivity, slow response, and limited reversibility. To tackle the existing challenges, this thesis investigates electromechanical coupled transport phenomena in a new type of stimulus-responsive nanopores, i.e., nanoparticle-blocked nanopores, and their potential applications in gating and sensing. The first part of this thesis describes a bio-inspired liposome-enabled nanopore gating strategy inspired by the ''ball-and-chain'' inactivation mechanism in voltage-gated protein ion channels. By manipulating the position of the liposome nanoparticles around the nanopore, we demonstrate an electromechanically gated nanopore with rapid, reversible, and complete gating response, which allows unprecedented spatial and temporal control of ion/chemical transport across the nanopore. In the second part of the thesis, we report an ultra-mechanosensitive ion transport across the single nanopore blocked by the rigid nanoparticles. The observed pressure-suppressed ion conduction partially mimics the behavior of stretch-inactivated ion channels and is rationalized with mechanical-induced particle motion. Finally, in the third part of the thesis, we further utilize the mechanosensitive ion conduction in nanoparticle-blocked nanopores to develop a nanopore-based platform for mechanical characterization of single nanoparticles. This new platform overcomes the limitations of current characterization techniques and provides an alternative nano-mechanical characterization approach in an efficient and cost-effective manner. We expect this work to provide a convenient platform to achieve natural stimulus-responsive functionalities as well as to develop emerging applications in drug delivery, biosensing, single-molecule manipulation, and ionic-based computation and storage. / 2024-01-25T00:00:00Z

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A hybrid molecular dynamics/multiparticle collision dynamics algorithm was constructed to model the pressure-driven flow of a compressible fluid through a nanoscopic channel of square cross-sectional area, as well as the effect of this flow on the configuration of a polymer chain that was tethered to the surface of this nanochannel. In the process of simulating channel flow, a new adiabatic partial slip boundary condition was created as well as a modified source/sink inlet and outlet boundary condition that could maintain a specified pressure gradient across the channel without the large entrance effects typically associated with these algorithms. The results of the flow simulations were contrasted with the results from a series solution to the Navier-Stokes equation for isothermal compressible flow, and showed excellent agreement with the results from the series solution when slip-boundary conditions were applied. A finitely extendible non-linear elastic spring and bead polymer chain was used to simulate the effect of flow on the polymer chain configuration under poor solvent and θ solvent conditions. Under θ solvent conditions, the cyclical dynamics that have been previousy observed for tethered polymer chains in pure shear flows were noted, however they were restricted to the end of the polymer chain. Under poor solvent conditions, the polymer adopted a metastable helix configuration as it collapsed to a globule state. The study also examined interchain and intrachain entanglements in polymers using the granny knot and overhand knot. The mechanisms by which these tangles untied themselves were determined. At low flow rates, the tangles unravelled by the end of the chain migrating through the loops of the tangle. At high flow rates, the tangles behaved like an entrained object as they reptated towards the end of the chain.

A hybrid molecular dynamics/multiparticle collision dynamics algorithm was constructed to model the pressure-driven flow of a compressible fluid through a nanoscopic channel of square cross-sectional area, as well as the effect of this flow on the configuration of a polymer chain that was tethered to the surface of this nanochannel. In the process of simulating channel flow, a new adiabatic partial slip boundary condition was created as well as a modified source/sink inlet and outlet boundary condition that could maintain a specified pressure gradient across the channel without the large entrance effects typically associated with these algorithms. The results of the flow simulations were contrasted with the results from a series solution to the Navier-Stokes equation for isothermal compressible flow, and showed excellent agreement with the results from the series solution when slip-boundary conditions were applied. A finitely extendible non-linear elastic spring and bead polymer chain was used to simulate the effect of flow on the polymer chain configuration under poor solvent and θ solvent conditions. Under θ solvent conditions, the cyclical dynamics that have been previousy observed for tethered polymer chains in pure shear flows were noted, however they were restricted to the end of the polymer chain. Under poor solvent conditions, the polymer adopted a metastable helix configuration as it collapsed to a globule state. The study also examined interchain and intrachain entanglements in polymers using the granny knot and overhand knot. The mechanisms by which these tangles untied themselves were determined. At low flow rates, the tangles unravelled by the end of the chain migrating through the loops of the tangle. At high flow rates, the tangles behaved like an entrained object as they reptated towards the end of the chain.

This work revolves around the development of microfluidic technology for use in biomedical diagnostics with a specific focus on analyte concentration. At the reduced scale inherent with microfluidic technologies the sensing of target species can be difficult since the sample volume is reduced to nanolitres leading to low amounts of target species. This necessitates the need to preconcentrate samples prior to the sensing step. The exclusion-enrichment phenomenon associated with concentration polarization has been used within microfluidic platforms for the purpose of analyte concentration though methods have all been inherently 1-D, axial configurations. Within this work a novel radial concentration strategy based on a single microfluidic layer on a uniform nanoporous film is presented. The active nanostructured region is defined by the microfluidics, providing flexibility and opening opportunities beyond the single-channel axial configurations to date. Radial geometries have not been previously shown operating as CP based concentration devices, though the unique geometry offers enhanced flux at the perimeter and the capability to focus samples down to small central regions. This focusing ability allows the concentration to take place on a separate layer and does not compete for space with other analysis fluidics. This radial configuration is numerically modeled and experimentally demonstrated.

Dissipation is an inevitable property of a mechanical system and influences the dynamical behavior and device performance. It is, therefore, crucial to study and understand the sources of dissipation in mechanical systems in order to control the dissipation present in the system. These sources of dissipation can be broadly classified in two groups: extrinsic and intrinsic mechanisms. Extrinsic mechanisms are independent of material properties and influenced by the external properties of the system, such as geometry, pressure, and temperature. Intrinsic mechanisms on the other hand, are independent of external conditions and arise from the intrinsic properties of the device material, such as defects in the bulk and the surface of the material. In this work, we closely study two extreme limits of dissipation at the opposite ends of the spectrum. First, at the high dissipation limit where extrinsic mechanisms dominate dissipation, spectral properties of the thermal noise force giving rise to Brownian fluctuations of a continuous mechanical system — namely, a doubly clamped nanomechanical beam resonator — immersed in a viscous liquid are investigated. To this end, two separate sets of experiments are performed. The power spectral density (PSD) of the Brownian fluctuations of the resonator around its fundamental mode are measured at the center of the resonator. Then, the frequency-dependent linear response of the resonator is measured, again at its center, by driving it with a harmonic force, via an electrothermal transducer, that couples well to the fundamental mode. These two separate measurements are then used to determine the PSD of the Brownian force acting on the structure in its fundamental mode. The PSD of the force noise extracted from multiple resonators with varied lengths spanning a broad frequency range displays a ``colored spectrum'' and follows the viscous dissipation of a cylinder oscillating in a viscous liquid by virtue of the fluctuation-dissipation theorem. In the second application, which is at the ultra-low dissipation limit at low temperature where intrinsic mechanisms dominate dissipation, we design and fabricate high-frequency aluminum nitride (AlN) piezo-optomechanical resonators. Furthermore, an acoustic radiation shield consisting of periodic phononic crystals is designed and implemented to further decrease dissipation. Fabrication and design of both the optomechanical cavity and phononic crystals are discussed in detail. Room temperature characterization of the ring resonator is presented and out-of-plane thickness mode of the AlN resonators has been identified. With microwave mechanical frequency and high Quality factor mechanical response, these resonators can be cooled down to quantum ground state with direct cooling methods such as dilution fridge cooling. These type of resonators can achieve efficient conversion between electrical, optical, and mechanical signals which can be utilized for quantum information science and sensing applications in the field of nanoelectromechanical systems. / 2023-09-24T00:00:00Z

The microcantilever has become a ubiquitous tool for surface science, chemical sensing, biosensing, imaging, and energy harvesting, among many others. It is a device of relatively simple geometry with a static and dynamic response that is well understood. Further, because of it's small size, it is extremely sensitive to small external perturbations. These characteristics make the microcantilever an ideal candidate for a multitude of sensing applications. In this thesis dissertation we use the microcantilever to conduct numerous physical measurements and to study fundamental phenomena in the areas of fluid dynamics, turbulence, and biology. In each area we use the cantilever as a sensitive transducer in order to probe fluctuating forces. In micro and nanometer scale flows the characteristic length scale of the flow approaches and is even exceeded by the fluid mean free path. This limit is beyond the applicability of the Navier-Stokes equations, requiring a rigorous treatment using kinetic theory. In our first study, we conduct a series of experiments in which we use a microcantilever to measure gas dissipation in a nanoscopically confined system. Here, the distance between the gas molecules is of the same order as the separation between the cantilever and the walls of its container. As the cantilever is brought towards the wall, the flow becomes confined in the gap between the cantilever and the wall, affecting the resonant frequency and dissipation of the cantilever. By carefully tuning the separation distance, the gas pressure, and the cantilever oscillation frequency, we study the flow over a broad range of dimensionless parameters. Using these measurements, we provide an in-depth characterization of confinement effects in oscillating nanoflows. In addition, we propose a scaling function which describes the flow in the entire parameter space and which unifies previous theories based on the slip boundary condition and effective viscosity. In our next study, we seek to gain a better understanding of the transition to turbulence in a channel flow. We use a cantilever embedded in the channel wall to perform two sets of experiments: first, we study transition to turbulence triggered by the natural imperfections of the channel walls and second, we study transition under artificially added inlet noise. Our results point to two very different paths to turbulence. In the first case, wall effects lead to an extremely intermittent transitional flow and in the second case, broadband fluctuations originating at the inlet lead to less intermittent flow that is more reminiscent of homogeneous turbulence. The two experiments result in random flows in which high-order moments of near-wall fluctuations differ by orders of magnitude. Surprisingly however, the lowest order statistics in both cases appear qualitatively similar and can be described by a proposed noisy Landau equation. The noise, regardless of its origin, regularizes the Landau singularity of the relaxation time and makes transitions driven by different noise sources appear similar. Our results provide evidence of the existence of a finite turbulent relaxation time in transitional flows due to the persistent nature of noise in the system. In our last study, we turn to biologically-driven fluctuations from bacterial motion. Recent studies suggest that the motion of living bacteria could serve as a good indicator of bacteria species and resistance to antibiotics. To gain a better understanding of these fluctuations, we measure the nanomechanical motion of bacteria adhered to a chemically functionalized silicon microcantilever. A non-specific binding agent is used to attach E. coli to the surface of the device. The motion of the bacteria couples efficiently to the cantilever well below its resonance frequency, causing a measurable increase in its mechanical fluctuations. We vary the bacterial concentration over two orders of magnitude and are able to observe a corresponding change in the amplitude of fluctuations. Additionally, we administer antibiotics (Streptomycin) to kill the bacteria and observe a decrease in the fluctuations. A basic physical model is used to explain the observed spectral distribution of the mechanical fluctuations. These results lay the groundwork for understanding the motion of microorganisms adhered to surfaces and for developing micromechanical sensors for rapid bacterial identification and antibiotic resistance testing.

<p>In this thesis, a theory of fluid--structure interaction (FSI) between an oscillatory Newtonian fluid flow and a compliant conduit is developed for  canonical geometries consisting of a 2D channel with a deformable top wall and an axisymmetric deformable tube. Focusing on hydrodynamics, a linear relationship between wall displacement and  hydrodynamic pressure is employed, due to its suitability for a leading-order-in-slenderness theory. The slenderness assumption also allows the use of lubrication theory, which is used to relate flow rate  to the pressure gradient (and the tube/wall deformation) via the classical solutions for oscillatory flow in a channel and in a tube (attributed to Womersley). Then, by two-way coupling the oscillatory flow and the wall deformation via the continuity equation, a one-dimensional nonlinear partial differential equation (PDE) governing the instantaneous pressure distribution along the conduit is obtained, without \textit{a priori} assumptions on the magnitude of the oscillation frequency (i.e., at arbitrary Womersley number).The PDE is solved numerically to evaluate the pressure distribution as well as the cycle-averaged pressure at several points along the length of the channel and the tube. It is found  that the cycle-averaged pressure (for harmonic pressure-controlled conditions) deviates from the expected steady pressure distribution, suggesting the presence of a streaming flow. An analytical perturbative solution for a weakly deformable conduit is also obtained to rationalize how FSI induces such streaming. In the case of a compliant tube, the results obtained from the proposed reduced-order PDE and its perturbative solutions are validated against three-dimensional, two-way-coupled direct numerical simulations. A good agreement is shown  between theory and simulations for a range of dimensionless parameters characterizing the oscillatory flow and the FSI, demonstrating the validity of the proposed theory of oscillatory flows in compliant conduits at arbitrary Womersley number.</p>

Nanofluidic devices have been of great interest due to their applications in variety of fields, including energy conversion and storage, water desalination, biological and chemical separations, and lab-on-a-chip devices. Although these applications cross the boundaries of many different disciplines, they all share the demand for understanding transport in nanoscale conduits. In this thesis, different elusive aspects of molecule and particle transport through nanofluidic conduits are investigated, including liquid and ion transport in nanochannels, diffusion- and reaction-governed enzyme transport in nanofluidic channels, and finally translocation of nanobeads through nanopores. Liquid or solvent transport through nanoconfinements is an essential yet barely characterized component of any nanofluidic systems. In the first chapter, water transport through single hydrophilic nanochannels with heights down to 7 nm is experimentally investigated using a new measurement technique. This technique has been developed based on the capillary flow and a novel hybrid nanochannel design and is capable of characterizing flow in both single nanoconduits as well as nanoporous media. The presence of a 0.7 nm thick hydration layer on hydrophilic surfaces and its effect on increasing the hydraulic resistance of the nanochannels is verified. Next, ion transport in a new class of nanofluidic rectifiers is theoretically and experimentally investigated. These so called nanofluidic diodes are nanochannels with asymmetric geometries which preferentially allow ion transport in one direction. A nondimensional number as a function of electrolyte concentration, nanochannel dimensions, and surface charge is derived that summarizes the rectification behavior of this system. In the fourth chapter, diffusion- and reaction-governed enzyme transport in nanofluidic channels is studied and the theoretical background necessary for understanding enzymatic activity in nanofluidic channels is presented. A simple analytical expression that describes different reaction kinetics is derived and confirmed against available experimental data of reaction of Trypsin with Poly-L-lysine. Finally, in the last chapter translocation of nanobeads through synthetic nanopores is experimentally investigated using resistive pulse sensing. The emphasis is placed on elucidating the effect of nanobead size on the translocation current and time. The key goals pursued in this study are multiplex detection of different nanobead sizes in a mixture of nanobeads as well as determining the concentration of each component. This problem other than its fundamental significance paves the way for developing new biosensing mechanisms for detection of biomolecules. This thesis further explores the molecule and particle transport in nanoscale conduits and serves for better characterization and development of nanofluidic devices for various applications.