In this thesis, underlying concepts of transport phenomena through generated nanopores on a cell membrane during electroporation were studied. A comprehensive literature review was performed to find the pros and cons of the previous works and consequently extensive studies were accomplished to explain shortcomings of the former studies on this topic. The membrane permeabilization of the single cell located in the microchannel was studied, and the effects of microchannel’s wall and electrode size were investigated on cell electroporation. It was studied how the electrical (e.g., strength of the electric pulse) and geometrical parameters (e.g., microchannel height and electrode size) affect size, location, and number of created hydrophilic pores on the cell membrane. Because of a transmembrane potential, the electrokinetic effects have decisive influence on the transport process through the created nanopores. A comprehensive study was performed to explain the electrokinetic transport through the nanochannels. Effects of surface electric charge and radius of the nanochannel on the electric potential, liquid flow, and ionic transport were investigated. Unlike microchannels, the electric potential field, ionic concentration field, and velocity field are strongly size-dependent in the nanochannels. They are also affected by the surface electric charge of the nanochannel. More counter ions than co-ions are transported through the nanochannel. The ionic concentration enrichment at the entrance and the exit of the nanochannel is completely evident from the simulation results. The study also shows that the fluid velocity in the nanochannel is higher when the surface electric charge is stronger, or the radius of the nanochannel is larger. The obtained model of the electrokinetic effects in the nanochannels was utilized to examine the ionic mass transfer and the fluid flow through the generated hydrophilic nanopores of the cell membrane during electroporation. The results showed how the electric potential, velocity field, and ionic concentration vary with the size and angular position of the generated nanopores of the cell membrane. It was also shown that, in the presence of the electric pulse, the electrokinetic effects (the electroosmosis and the electrophoresis) had significant influences on the ionic mass transfer through the nanopores, while the effect of diffusion on the ionic mass flux was negligible in comparison with the electrokinetics. Increasing the radius of the nanopores intensified the effect of convection (electroosmosis) in comparison with the electrophoresis on the ionic flux. Furthermore, the electrokinetic motion of the nanoparticle through the nanochannel was investigated to mimic inserting the nanoscale biological samples, such as QDots and DNAs, through the created nanopores on the cell membrane. It was proved that, because of the large applied electric field over the nanochannel, the impact of the Brownian force was negligible in comparison with the electrophoretic and the hydrodynamic forces. It was demonstrated that increasing the bulk ionic concentration or the surface charge of the nanochannel will increase the electroosmotic flow, and hence affect the particle’s motion. It was also shown that, unlike the microchannels with thin EDL, the change in the nanochannel size will change the EDL field and the ionic concentration field in the nanochannel, affecting the particle’s motion. If the nanochannel size is fixed, a larger particle will move faster than a smaller particle under the same conditions. Finally, it was examined how the nanoscale biological samples (nanoparticles) reach openings of the generated nanopores on the cell membrane during electroporation. It was examined what forces (electrophoresis, diffusion, and convection) brings the nanoparticles into the nanopores and how the size and the surface electric charge of the nanoparticle affect its transport to the opening of the nanopores.

"This dissertation is devoted to the computational investigation of supersonic gas flows in rectangular nanochannels with scales between 100 nm and 1000 nm, using an unstructured three-dimensional Direct Simulation Monte Carlo (U3DSMC) methodology. This dissertation also contributes to the computational mathematics background of the U3DSMC method with validations and verifications at the micronscale and nanoscale, as well as with the investigation of the statistical fluctuations and errors associated with U3DSMC simulations at the nanoscale. The U3DSMC code is validated by comparisons with previous two dimensional DSMC simulations of flows in micron-scale rectangular channels. The simulation involves the supersonic flow of nitrogen into a microchannel with height of 1.2 m and width of 6 m. The free stream conditions correspond to a pressure of 72,450 Pa, Mach number , Knudsen number and mean free path nm. The U3DSMC centerline temperature, heat flux to the wall, and mean velocity as a function of the transverse direction are in very good agreement with previous 2D results. Statistical fluctuations and errors in U3DSMC have added significance in nanoscale domains because the number of real particles can be very small inside a computational cell. The effect of the number of samples, the number of computational particles in a Delaunay cell, and the Mach number on the fractional errors of density, velocity and temperature are investigated for uniform and pressure-driven nanoscale flows. The uniform nanoflow is implemented by applying a and free stream boundary condition with m-3, K, nm in a domain that requires resolution of a characteristic length scale nm. The pressure-driven flows consider a nanochannel of 500 nm height, 100 nm width and 4 m length. Subsonic boundary conditions are applied with inlet pressure 101,325 Pa and outlet pressure of 10132.5 Pa. The analysis shows that U3DSMC simulations at nanoscales featuring 10-30 particles per Delaunay cell result in statistical errors that are consistent with theoretical estimates. The rarefied flow of nitrogen with speed ratio of 2, 5, and 10, pressure of 10.132 kPa into rectangular nanochannels with height of 100, 500 and 1000 nm is investigated using U3DSMC. The investigation considers rarefaction effects with =0.481, 0.962, 4.81, geometric effects with nanochannel aspect ratios of (L/H) from AR=1, 10, 100 and back-pressure effects with imposed pressures from 0 to 200 kPa. The computational domain features a buffer region upstream of the inlet and the nanochannel walls are assumed to be diffusively reflecting at the free stream temperature of 273 K. The analysis is based on the phase space distributions as well as macroscopic flow variables sampled in cells along the centerline. The phase space distributions show the formation of a disturbance region ahead of the inlet due to slow particles backstreaming through the inlet and the formation of a density enhancement with its maximum inside the nanochannel. The velocity phase-space distributions show a low-speed particle population generated inside the nanochannel due to wall collisions which is superimposed with the free stream high-speed population. The mean velocity decreases, while the number density increases in the buffer region. The translational temperature increases in the buffer region and reaches its maximum near the inlet. For AR=10 and 100 nanochannels the gas reaches near equilibrium with the wall temperature. The heat transfer rate is largest near the inlet region where non-equilibrium effects are dominant. For =0.481, 0.962, 4.81, vacuum back pressure, and AR=1, the nanoflow is supersonic throughout the nanochannel, while for AR=10 and 100, the nanoflow is subsonic at the inlet and becomes sonic at the outlet. For =0.962, AR=1, and imposed back pressure of 120 kPa and 200 kPa, the nanoflow becomes subsonic at the outlet. For =0.962 and AR=10, the outlet pressure nearly matches the imposed back pressure with the nanoflow becoming sonic at 40 kPa and subsonic at 100 kPa. Heat transfer rates at the inlet and mass flow rates at the outlet are in good agreement with those obtained from theoretical free-molecular models. The flows in these nanochannels share qualitative characteristics found in microchannels ad well as continuum compressible flows in channels with friction and heat loss. The rarefied flow of nitrogen with speed ratio of 2, 5, 10, at an atmospheric pressure of 101.32 kPa into rectangular nanochannels with height of 100 and 500 nm is investigated using U3DSMC. The investigation considers rarefaction effects with =0.0962 and 4.81, geometric effects with nanochannel aspect ratios of (L/H) of AR=1 and 10 and vacuum back-pressure. Phase plots and sample-averaged macroscopic parameters are used in the analysis. Under vacuum back pressure the centerline velocity decreases in the buffer region from its free stream value. For 0.481, 0.0962 and AR=1 the Mach number is supersonic at the inlet and remains supersonic throughout the nanochannel. For 0.481, 0.0962 and AR=10, the flow becomes subsonic at the inlet and shows a sharp increase in pressure. The Mach number, subsequently, increases and reaches the sonic point at the outlet. For 0.481, 0.0962 and AR=1 the translational temperature reaches a maximum near the inlet and decreases monotonically up to the outlet. For 0.481, 0.0962 and AR=10, the translational temperature reaches a maximum near the inlet and then decreases to come in near equilibration with the wall temperature of 273 K. "

Electrokinetic flows within an overlapped Electrical Double Layer (EDL), which are not well-understood, were theoretically investigated in this study with the particular attention on the consideration of hydronium ions in the EDL. Theoretical models for fully-developed steady pressure-driven flow for salt-free water or a binary salt solution in a slit-like nanochannel connecting to two reservoirs were developed. The transient flow in such a domain was also simulated from static state to the final steady state. In these models, the Poisson equation and the Nernst-Planck equation were solved either by analytic methods or by the finite element method. Surface adsorption-desorption equilibrium and water equilibrium were considered to account for the proton exchange at the surface and in the fluid. These models were the first to include those comprehensive processes that are uniquely important for overlapped EDL scenarios. This study improves the understanding of electrokinetic flows within an overlapped EDL by demonstrating the profound impact of hydronium ions on the EDL structure. In the steady flow of potassium chloride solutions, hydronium ions are more enriched than potassium ions by up to 2~3 orders of magnitude, making the electrokinetic effects greatly depressed. The unequal enrichment effects of counterions were omitted in the traditional theory partially because the transient is extremely slow. The simulation results show that a concentration hump of hydronium ions initially forming at the channel entrance gradually expands over the whole channel in a way similar to the concentration plug flow moving downstream. The time required for the flow to reach the steady state could be as long as thousands of times the hydraulic retention time, dependent on the degree of the EDL overlap. This study improves the fundamental understanding for nanofluidic flows.

A nanofluidic biosensor using surface-enhanced Raman scattering (SERS) was developed to detect the β-amyloid (Aβ) protein, one of the biomarkers of Alzheimer’s disease (AD). Recent studies have indicated that investigating changes in relative concentrations of structure specific Aβ oligomers in cerebral spinal fluid (CSF) during the progression of AD could be important indicators for diagnosing AD pre-mortem. However, there is no definitive pre-mortem diagnosis of AD thus far because of the lack of technology available for sensitive Aβ detection. Hence, the development of a system for detecting the structure specific Aβ oligomers, along with the concentrations of these oligomers in CSF, would be useful in the investigation of the molecular mechanisms of Aβ cytotoxicity associated with AD. In this thesis, a nanofluidic trapping device trapping system for detecting biomolecules at sub-picomolar concentrations was developed for using SERS. The device, with a microchannel leading to a nanochannel, carries out dual functions: encouraging sizedependent trapping of gold nanoparticles (60nm) at the entrance of the nanochannel as well as restricting the target molecules between the gaps created by the aggregated nanoparticles. Initially, the trapping capability of the nanofluidic device was tested using fluorescent polystyrene and gold nanoparticles. UV-vis absorption spectroscopy was used to characterize the gold nanoparticle clusters at the entrance to the nanochannel. The device established controlled, reproducible, SERS active sites within the interstices of gold nanoparticle clusters and shifted the plasmon resonance to the near infrared, in resonance with incident laser light. Two strongly Raman active molecules, adenine and Congo red, were used to test the feasibility of the SERS nanofluidic device as a platform for the detection of multiple analytes. The results showed that strong SERS signals were obtained from the nanoparticle clusters at the nanochannel entrance. Once the feasibility of the approach was determined with strong Raman molecules, Aβ was detected using this nanofluidic SERS platform. Distinct surface-enhanced Raman spectra of Aβ was observed in different conformational states as a function of concentration and structure (monomer versus oligomer form) due to Aβ refolding from α-helical to a predominantly β-pleated sheet form. The sensor was also shown to potentially distinguish Aβ from insulin and albumin, confounder proteins in cerebral spinal fluid. Thus, a novel platform was developed to detect picomoler levels of Aβ with the ultimate goal of facilitating the diagnosis and understanding of Alzheimer’s disease by means of detecting structure specific oligomers of Aβ.

Nanochannel devices have been explored over the years with wide applications in bio/chemical analysis. With a dimension comparable to many bio-samples, such as proteins, viruses and DNA, nanochannels can be used as a platform to manipulate and detect such analytes with unique advantages. As a prerequisite to the development of nanochannel devices, various nanofabrication techniques have been investigated by many researchers for decades. In this dissertation, three different fabrication approaches for nanochannels are discussed, including a novel scanning coaxial electrospinning process, a heat-induced stretching approach and a standard contact photolithography process. The scanning coaxial electrospinning process is established based on conventional electrospinning process. A coaxial jet, with the motor oil as the core and spin-on-glass-coating/PVP solution as the shell, is deposited on the rotating collector as oriented coaxial nanofibers. These nanofibers are then annealed to eliminate the core material and form the hollow interior. Silica nanochannels with an inner diameter as small as 15 nm were obtained. The heat-induced stretching approach includes using commercially available fused silica tubings to create nanochannels by thermal deforming. This method and the electrospinning technique both focus on fabricate one-dimensional nanochannels with a circular opening. Fluorescent dye was used as a testing sample for single molecule detection and electrokinetic analysis in the resultant nanochannels. Another nanochannel device described in this dissertation has a deep-shallow step structure. It was fabricated by standard contact lithography, followed by etching and bonding. This device was applied as a powerful detection platform for surface-enhanced Raman spectroscopy (SERS). The experiment results proved that it is able to highly improve the sensitivity and efficiency of SERS. The SERS enhancement factor obtained from the device is 108. Moreover, the molecule enrichment effect of this device provides an extra 105 enhancement. The detection can be efficiently finished within minutes after simply loading the mixture of analytes solution and gold nanoparticles in the device. The sample consumption is in micro-liter range. Potential applications in diagnostics, prognositics and water pollutants detection could be achieved using this device.

abstract: Nanofluidic devices in which one single-walled carbon nanotube (SWCNT) spans a barrier between two fluid reservoirs were constructed, enabling direct electrical measurement of the transport of ions and molecules. Ion current through these devices is about 2 orders of magnitude larger than that predicted from the bulk resistivity of the electrolyte. Electroosmosis drives excess current, carried by cations, and is found to be the origin of giant ionic current through SWCNT as shown by building an ionic field-effect transistor with a gate electrode embedded in the fluid barrier. Wetting of inside of the semi-conducting SWCNT by water showed the change of its electronic property, turning the electronic SWCNT field-effect transistor to "on" state. These findings provide a new method to investigate and control the ion and molecule behavior at nanoscale. / Dissertation/Thesis / Ph.D. Physics 2011

Quantification and prediction of capillary fluid flow in planar nanochannels is essential to the development of many emerging nanofluidic technologies. Planar nanochannels are typically produced using the standard nanofabrication processes of thermal bonding or sacrificial etching. Both approaches may yield nanochannels that are bowed and/or exhibit non-uniform (i.e. non-planar) wall spacing. These variations in wall spacing affect the transient dynamics of a liquid plug filling the nanochannel, causing deviations from the classical behavior in a parallel-plate channel as described by the Washburn model. Non uniform wall spacing impacts the overall frictional resistance and influences the meniscus curvature. In this thesis, a new analytical model that predicts the meniscus location over time in micro- and nanochannels as a function of channel height was compared to experimental filling data of well-characterized channels with different heights. The wall-to-wall spacing of the utilized nanochannels exhibited height variations between 60 and 300 nm. The model was also validated with microscale channels that were fabricated with a linear variation in the wall-to-wall spacing from 100 µm to 400 µm. The filling speed and meniscus shape during the filling process were determined by dynamic imaging of the meniscus front for several different liquids. A modified Washburn equation that utilizes an effective channel height to predict the filling speed corresponding to the location of the tallest height within a channel was derived. A model was also developed to predict the meniscus distortion encountered in a non-constant height channel, provided the cross-sectional channel heights and the distance from the channel entrance are known. The models developed herein account for induced transverse pressure gradients created by non-constant channel heights. The models are compared to experimental data derived from both nanoscale and microscale channels with good qualitative agreement. These results demonstrate that the capillary flow in nanochannels with non-parallel-plate, linear tapered, or parabolic cross sections can be predicted.

The main objective of this thesis is to study the fundamental behaviour of multi-component gas mixture flows in micro/nano-channels undergoing catalytic chemical reactions on the walls. This work is primarily focused on nano-scale reacting flows seen in related applications; especially, miniaturized energy sources such as micro-fuel cells and batteries. At these geometries, the order of the characteristic length is close to the mean free path of the flowing gas, making the flow highly rarefied. As a result, non-equilibrium conditions prevail even the bulk flow and therefore, continuum assumptions are not held anymore. Hence, discrete methods should be adopted to simulate molecular movements and interactions described by the Boltzmann equation. The Direct Simulation Monte Carlo (DSMC) method was employed for the present research due to its natural ability for simulating a broad range of rarefied gas flows, and its flexibility to incorporate surface chemical reactions. In the first step, fluid dynamics and the heat transfer of H₂/N₂ and H₂/N₂/CO₂ gas mixture slip flows in a plain micro-channel are simulated. The obtained results are compared to the corresponding data achieved from Navier-Stokes equations with slip/jump boundary conditions. Generally, very good agreements are observed between the two methods. It proves the ability of DSMC in replicating the fluid properties of multi-component gas mixtures even when high mass discrepancies exist among the species. Based on this comparison, the proper parameters are set for the prepared DSMC code, and the appropriate intermolecular collision model is identified. It is also found that stream variables should be calculated more accurately at flow boundaries in order to simulate the intense upstream diffusion emerging at low velocity flows frequently seen in micro/nano-applications. Therefore, in the second step, a novel pressure boundary condition is introduced for gas mixture flows by substituting the commonly used Maxwell velocity distribution with the Chapman-Enskog distribution function. It is shown that this new method yields better results for lower velocity and higher rarefaction level cases. In the last step, a new method is proposed for coupling the flow field simulated by DSMC and surface reactions modelled by the species conservation ODE system derived from the reaction mechanism. First, a lean H₂/air slip flow subjected to oxidation on platinum coated walls in a flat micro-channel 4μm in height is simulated as a verification test case. The results obtained are validated against the solutions of the Navier-Stokes equations with slip/jump boundary conditions and very good conformity is achieved. Next, several cases undergoing the same reaction with Reynolds numbers ranging from 0.2 to 3.6 and Knudsen numbers ranging from 0.025 to 0.375, are simulated using the verified code to investigate the effects of the channel height ranging from 0.5μm to 2μm , the inlet mass flow rate ranging from 5 kg/m².s to 25 kg/m².s, the inlet temperature ranging from 300K to 700K, the wall temperature ranging from 300K to 1000K, and the fuel/air equivalence ratio ranging from 0.28 to 1.5. Some of the findings are as follows: (1) increasing the surface temperature from 600K to 1000K and/or the inlet temperature from 300K to 700K results in negligible enhancement of the conversion rate, (2) the optimum value of the equivalence ratio is on the fuel lean side (around 0.5), (3) the efficiency of the reactor is higher for smaller channel heights, and (4) increasing the inlet mass flux elevates the reaction rate especially for the smaller channels; this effect is not linear and is more magnified for lower mass fluxes.

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