Development of Microfluidic Devices with the Use of Nanotechnology to Aid in the Analysis of Biological Systems Including Membrane Protein Separation, Single Cell Analysis, and Genetic Markers

Computation technology has dramatically changed the world around us; you can hardly find an area where cell phones have not saturated the market, yet there is a significant lack of breakthroughs in the development to integrate the computer with biological environments. This is largely the result of the incompatibility of the materials used in both environments; biological environments and experiments tend to need aqueous environments. To help aid in these development chemists, engineers, physicists and biologists have begun to develop microfluidics to help bridge this divide. Unfortunately, the microfluidic devices required large external support equipment to run the device. This thesis presents a series of several microfluidic methods that can help integrate engineering and biology by exploiting nanotechnology to help push the field of microfluidics back to its intended purpose, small integrated biological and electrical devices. I demonstrate this goal by developing different methods and devices to (1) separate membrane bound proteins with the use of microfluidics, (2) use optical technology to make fiber optic cables into protein sensors, (3) generate new fluidic devices using semiconductor material to manipulate single cells, and (4) develop a new genetic microfluidic based diagnostic assay that works with current PCR methodology to provide faster and cheaper results. All of these methods and systems can be used as components to build a self-contained biomedical device.

Experimental, Numerical and Analytical Studies of the MHD-driven plasma jet, instabilities and waves

This thesis describes a series of experimental, numerical, and analytical studies involving the Caltech magnetohydrodynamically (MHD)-driven plasma jet experiment. The plasma jet is created via a capacitor discharge that powers a magnetized coaxial planar electrodes system. The jet is collimated and accelerated by the MHD forces.

We present three-dimensional ideal MHD finite-volume simulations of the plasma jet experiment using an astrophysical magnetic tower as the baseline model. A compact magnetic energy/helicity injection is exploited in the simulation analogous to both the experiment and to astrophysical situations. Detailed analysis provides a comprehensive description of the interplay of magnetic force, pressure, and flow effects. We delineate both the jet structure and the transition process that converts the injected magnetic energy to other forms.

When the experimental jet is sufficiently long, it undergoes a global kink instability and then a secondary local Rayleigh-Taylor instability caused by lateral acceleration of the kink instability. We present an MHD theory of the Rayleigh-Taylor instability on the cylindrical surface of a plasma flux rope in the presence of a lateral external gravity. The Rayleigh-Taylor instability is found to couple to the classic current-driven instability, resulting in a new type of hybrid instability. The coupled instability, produced by combination of helical magnetic field, curvature of the cylindrical geometry, and lateral gravity, is fundamentally different from the classic magnetic Rayleigh-Taylor instability occurring at a two-dimensional planar interface.

In the experiment, this instability cascade from macro-scale to micro-scale eventually leads to the failure of MHD. When the Rayleigh-Taylor instability becomes nonlinear, it compresses and pinches the plasma jet to a scale smaller than the ion skin depth and triggers a fast magnetic reconnection. We built a specially designed high-speed 3D magnetic probe and successfully detected the high frequency magnetic fluctuations of broadband whistler waves associated with the fast reconnection. The magnetic fluctuations exhibit power-law spectra. The magnetic components of single-frequency whistler waves are found to be circularly polarized regardless of the angle between the wave propagation direction and the background magnetic field.

Plasma loop and strapping field dynamics: reproducing solar eruptions in the laboratory

Coronal mass ejections (CMEs) are dramatic eruptions of large, plasma structures from the Sun. These eruptions are important because they can harm astronauts, damage electrical infrastructure, and cause auroras. A mysterious feature of these eruptions is that plasma-filled solar flux tubes first evolve slowly, but then suddenly erupt. One model, torus instability, predicts an explosive-like transition from slow expansion to fast acceleration, if the spatial decay of the ambient magnetic field exceeds a threshold.

We create arched, plasma filled, magnetic flux ropes similar to CMEs. Small, independently-powered auxiliary coils placed inside the vacuum chamber produce magnetic fields above the decay threshold that are strong enough to act on the plasma. When the strapping field is not too strong and not too weak, expansion force build up while the flux rope is in the strapping field region. When the flux rope moves to a critical height, the plasma accelerates quickly, corresponding to the observed slow-rise to fast-acceleration of most solar eruptions. This behavior is in agreement with the predictions of torus instability.

Historically, eruptions have been separated into gradual CMEs and impulsive CMEs, depending on the acceleration profile. Recent numerical studies question this separation. One study varies the strapping field profile to produce gradual eruptions and impulsive eruptions, while another study varies the temporal profile of the voltage applied to the flux tube footpoints to produce the two eruption types. Our experiment reproduced these different eruptions by changing the strapping field magnitude, and the temporal profile of the current trace. This suggests that the same physics underlies both types of CME and that the separation between impulsive and gradual classes of eruption is artificial.

Experimental and theoretical studies of the electrothermal instability in a nonequilibrium plasma

Experimental and theoretical studies have been made of the electrothermal waves occurring in a nonequilibrium MHD plasma. These waves are caused by an instability that occurs when a plasma having a dependence of conductivity on current density is subjected to crossed electric and magnetic fields. Theoretically, these waves were studied by developing and solving the equations of a steady, one-dimensional nonuniformity in electron density. From these nonlinear equations, predictions of the maximum amplitude and of the half width of steady waves could be obtained. Experimentally, the waves were studied in a nonequilibrium discharge produced in a potassium-seeded argon plasma at 2000°K and 1 atm. pressure. The behavior of such a discharge with four different configurations of electrodes was determined from photographs, photomultiplier measurements, and voltage probes. These four configurations were chosen to produce steady waves, to check the stability of steady waves, and to observe the manifestation of the waves in a MHD generator or accelerator configuration.

Steady, one-dimensional waves were found to exist in a number of situations, and where they existed, their characteristics agreed with the predictions of the steady theory. Some extensions of this theory were necessary, however, to describe the transient phenomena occurring in the inlet region of a discharge transverse to the gas flow. It was also found that in a discharge away from the stabilizing effect of the electrodes, steady waves became unstable for large Hall parameters. Methods of prediction of the effective electrical conductivity and Hall parameter of a plasma with nonuniformities caused by the electrothermal waves were also studied. Using these methods and the values of amplitude predicted by the steady theory, it was found that the measured decrease in transverse conductivity of a MHD device, 50 per cent at a Hall parameter of 5, could be accounted for in terms of the electrothermal instability.

Thermodynamic and kinetic behavior of an argon plasma jet. Decomposition of nitric oxide between 1300 - 1750 degrees K in an argon plasma

In the first part of the study, an RF coupled, atmospheric pressure, laminar plasma jet of argon was investigated for thermodynamic equilibrium and some rate processes.

Improved values of transition probabilities for 17 lines of argon I were developed from known values for 7 lines. The effect of inhomogeneity of the source was pointed out.

The temperatures, T, and the electron densities, n_e , were determined spectroscopically from the population densities of the higher excited states assuming the Saha-Boltzmann relationship to be valid for these states. The axial velocities, v_z, were measured by tracing the paths of particles of boron nitride using a three-dimentional mapping technique. The above quantities varied in the following ranges: 10¹² ˂ n_e ˂ 10¹⁵ particles/cm³, 3500 ˂ T ˂ 11000 °K, and 200 ˂ v_z ˂ 1200 cm/sec.

The absence of excitation equilibrium for the lower excitation population including the ground state under certain conditions of T and n_e was established and the departure from equilibrium was examined quantitatively. The ground state was shown to be highly underpopulated for the decaying plasma.

Rates of recombination between electrons and ions were obtained by solving the steady-state equation of continuity for electrons. The observed rates were consistent with a dissociative-molecular ion mechanism with a steady-state assumption for the molecular ions.

In the second part of the study, decomposition of NO was studied in the plasma at lower temperatures. The mole fractions of NO denoted by x_NO were determined gas-chromatographically and varied between 0.0012 ˂ x_NO ˂ 0.0055. The temperatures were measured pyrometrically and varied between 1300 ˂ T ˂ 1750°K. The observed rates of decomposition were orders of magnitude greater than those obtained by the previous workers under purely thermal reaction conditions. The overall activation energy was about 9 kcal/g mol which was considerably lower than the value under thermal conditions. The effect of excess nitrogen was to reduce the rate of decomposition of NO and to increase the order of the reaction with respect to NO from 1.33 to 1.85. The observed rates were consistent with a chain mechanism in which atomic nitrogen and oxygen act as chain carriers. The increased rates of decomposition and the reduced activation energy in the presence of the plasma could be explained on the basis of the observed large amount of atomic nitrogen which was probably formed as the result of reactions between excited atoms and ions of argon and the molecular nitrogen.

Plasma inverse scattering theory

The object of this report is to calculate the electron density profile of plane stratified inhomogeneous plasmas. The electron density profile is obtained through a numerical solution of the inverse scattering algorithm.

The inverse scattering algorithm connects the time dependent reflected field resulting from a δ-function field incident normally on the plasma to the inhomogeneous plasma density.

Examples show that the method produces uniquely the electron density on or behind maxima of the plasma frequency.

It is shown that the δ-function incident field used in the inverse scattering algorithm can be replaced by a thin square pulse.