Single molecule fluorescence techniques have contributed considerably to our understanding of a variety of biological systems. Unfortunately, single molecule techniques are fundamentally limited by the concentration of fluorescent species and volume being observed. Nanofabricated structures have emerged as ideal tools for volume confinement in fluorescence spectroscopy. This has allowed the extension of single molecule techniques to high concentration regimes. Zero Mode Waveguides, nanometer scale holes in a thin metal film produce observation volumes in the attoliter to zeptoliter range. These structures have been used to measure protein kinetics in the micro molar concentration range as well as for observations of polymerase incorporating single nucleotide bases. We have investigated the optical properties of these structures using a combination of fluorescence spectroscopy, scanning electron microscopy and optical transmission measurements in an effort to accurately model the optical properties of these structures. These measurements have allowed a detailed characterization of the optical behavior of sub-wavelength apertures in a thin metal film.
Microarrays are being widely used in genomic, proteomic, and diagnostic applications. The binding events to the microarrays are measured with fluorescent labels. Fluorescent microarray readers offer high sensitivity and normalization of the reference and test samples. The use of labels increases the number of steps involved in array testing, concerns about storage labels, and cost of additional labeling steps. This paper describes an alternative approach that does not require the use of fluorescent or other labels. The binding events on the microarray introduce changes in polarization of the illuminated light which is measured to determine the concentrations of biomolecules bound to the microarray. Oligonucleotide microarrays were synthesized and tested on the imaging microarray reader. The refractive index changes of 0.006 and changes in thickness of 1 nm are demonstrated at a spatial resolution of 20 μm over a field of view of 1 cm2. This ellipsometric technique offers an attractive alternative to fluorescence-based measurement and could be very valuable in some of the genomic, proteomic, diagnostic, and sensing applications.
We demonstrate dome-shaped, radio frequency, micromechanical resonators with integrated thermo-elastic actuators. Such resonators can be used as the frequency-determining element of a local oscillator or as a combination of a mixer and IF filter in a superheterodyne transceiver.
The dome resonators (shallow shell segments clamped on the periphery) are fabricated utilizing pre-stressed thin polysilicon film over sacrificial silicon dioxide. The shell geometry enhances the rigidity of the structure, providing a resonant frequency several times higher than a flat membrane of the same dimensions. The finite curvature of the shell also couples out-of-plane deflection with in-plane stress, providing an actuation mechanism. Out-of-plane motion is induced by employing non-homogeneous, thermomechanical stress, generated in plane by local heating. A metal resistor, lithographically defined on the surface of the dome, provides thermal stress by dissipating 4 μW of Joule heat.
The diminished heat capacity of the MEMS device enables a heating/cooling rate comparable to the frequency of mechanical resonance and allows operation of the resonator by applying AC current through the microheater. Resistive actuation can be readily incorporated into integrated circuit processing and provides significant advantages over traditional electrostatic actuation, such as low driving voltages, matched 50-ohm impedance, and reduced cross talk between drive and detection.
We show that when a superposition of two AC signals is applied to the resistive heater, the driving force can be detected at combinatory frequencies, due to the fact that the driving thermomechanical stress is determined by the square of the heating current. Thus the thermoelastic actuator provides frequency mixing while the resonator itself performs as a high quality (Q~10,000) intermediate frequency filter for the combinatory frequencies. A frequency generator is built by closing a positive feedback loop between the optical detection of the mechanical motion of the dome and the resistive drive. We demonstrate self-sustained oscillation of the dome resonator with frequency stability of 1.5 ppm and discuss the phase noise of the oscillator.
High frequency and high quality factor, Q, (defined as a half-width of the resonant peak) are the key factors that determine applications of microelectromechanical (MEMS) oscillators for supersensitive force detection or as elements for radio frequency signal processing. By shrinking the dimensions of MEMS resonators to the sub-micron range one increases the resonant frequency of the devices. Shrinking the devices, however, also increases the surface-to-volume ratio leading to a significant degradation of the quality factor (to below 5,000) due to the increased contribution of surface-related losses.
We demonstrate that local annealing performed by focused low-power laser beams can improve the quality factor of MEMS resonators by more than an order of magnitude, which we attribute to the alteration of the surface state. Quality factors over 150,000 were achieved after laser annealing 3.1 MHz disc-type oscillators (radius R=10 micrometers, thickness h=0.25 micrometer) compared with a Q=6,000 for the as-fabricated device. The mushroom-type design of our resonator (a single-crystal silicon disc supported by a thin silicon dioxide pillar at the center) provides low heat loss and also confines the electron-hole gas created by laser excitation, enhancing light absorption. The combined power of a red HeNe laser (Pred=4mW) and a blue Ar+ ion laser (Pblue=5mW) focused on the periphery of the mushroom provides enough energy for surface modification. The post-treatment quality factor, exceeding 100,000 for MHz-range resonators, boosts the performance of MEMS to be comparable to that of lower frequency single-crystal quartz devices. The local nature of laser annealing, safe for surrounding electronics, is a crucial element for integration of MEMS resonators into an integrated circuit environment.
Shell-type micromechanical resonators operating in radio frequency range were fabricated utilizing mechanical stress that is built into polysilicon thin films. Significant increase of the resonant frequency (in comparison with flat, plate-type resonators of the same size) and the rich variety of vibrating modes demonstrate great potential for "2.5-Dimensional" MEMS structures. A finite curvature of the shell also provides a mechanism for driving resonators by coupling in plane stress with out of plane deflection. By modulating the intensity of a low power laser beam (P~10μWatts) focused on the resonator we introduced a time-variable, in-plane, thermomechanical stress. This stress modulation resulted in experimentally observed, large amplitude, out-of-plane, vibrations for a dome-type resonator.
A double laser beam experimental setup was constructed where mechanical motion of a shell-type resonator was actuated by a modulated, sharply focused Ar+ ion (blue) laser beam and detected by a red HeNe laser using an interferometric setup. A positive feedback loop was implemented by amplifying the red laser signal (related to the oscillator deflection) and applying it to modulate the blue (driving) laser beam. Stable self-sustained vibrations were observed providing that the feedback gain was high enough. Employing a frequency selective amplifier in the feedback loop allowed excitation of different modes of vibrations. Fine frequency tuning was realized by adjusting the CW component of either lasers' intensity or a phase shift in the feedback loop. Frequency stability better than 1 ppm (10-6) at 9 MHz was demonstrated for self-sustained vibrations for certain modes of the dome-shaped oscillators.
High-frequency microoptoelectromechanical systems (MOEMS) are proposed as active devices for radio frequency signal processing. Parametric amplification (PA), generation, frequency modulation and frequency conversion on the micromechanical level were demonstrated at MHz range by microfabricated single-crystal silicon mechanical resonators. A focused laser beam was used to pump energy into the motion of the oscillator, to control the frequency response and to provide a carrier signal for the frequency up-conversion. Laser light interaction with the microelectromechanical system (MEMS) was realized through the stress pattern induced within the microfabricated structure by the focused laser beam. Stress-induced stiffening of the oscillator provides control over the effective spring constant and leads to a parametric mechanism for amplification of mechanical vibrations. Periodic modulation of the laser intensity synchronized with the driving force allowed us to demonstrate a degenerate (phase-sensitive) PA scheme with gain in access of 30dB. Design of the oscillator as a part of the built-in Fabry-Perot cavity provides auto-modulation of the effective spring constant as a result of the position-dependent absorption of the light by the oscillator. The auto-modulation mechanism allows a parametric self-excitation induced by continuous wave (CW) laser beam. Self-sustained generation was observed when laser power exceeded a threshold of few hundred microWatts. Nonlinear effects cause frequency dependence vs. laser power, providing a mechanism for frequency modulation of the self-generated vibrations. The same type of optical scheme can also work as an ideal frequency mixer, which combines the self-generated response with an external high-frequency modulation of the laser intensity.
We have used an embossed plastic microfluidic system for the electrophoretic separation of relatively small molecules followed by electro spray ionization of the analytes. Th separation of dyes has been also visualized in microfluidic systems. A lithographically produced silicon master was used to emboss channels in ZEONOR 1020R plastic. An oxygen plasma was used to convert the plastic channel surface from hydrophobic to hydrophilic characteristics for the separation of molecules in aqueous solution.
Micromechanical oscillators in the radio frequency (rf) range were fabricated in the form of silicon discs supported by a SiO2 pillar at the disc center. Effective spring constant of this oscillator can be controlled within the range (Delta) f/f approximately 10-4 by a low power laser beam, (Plaser approximately 100 (mu) W), focused at the periphery of the disc. Parametric amplification of the disc's vibrations was achieved through a double frequency modulation of the laser power. An amplitude gain of up to 30 was demonstrated, with further increase limited by non-linear behavior and self-generation. Phase dependence, inherent in degenerate parametric amplification, was also observed. Self- modulation of the CW laser beam (Plaser approximately 100 (mu) W) provided by placing the disc oscillator into an interference pattern setup can lead to parametric self- excitation.
Fluidic devices with sub-micrometer dimensions provide new opportunities in manipulation and analysis of various biomolecules, such as deoxyribonucleic acid (DNA). As an example of such devices, a microchannel with an array of entropic traps is introduced. The existence of sub-100nm constriction causes long double-stranded DNA molecules to be entropically trapped, and the length-dependent escape of DNA from the trap enables a band separation of DNA. Entropic traps are also used to manipulate and collect many DNA molecules into a narrow, well-defined initial band for electrophoresis launching. In addition to its speed and compactness, another important advantage of this artifical separation device over conventional gel electrophoresis is the ability to modify and control the device precisely for the optimization of a separation process. The similar device could be used to analyze proteins or other biopolymers.
We are investigating fabrication techniques that can be used to form arbitrarily shaped fluid capillaries at dimensions below 1 micrometers . We are also considering processes and materials for forming optical waveguides in the same devices with the same fabrication processes. The intent is to develop fabrication methods that can be used to make optical/fluid-flow systems for greater miniaturization, integration and parallelism of optical excitation and detection systems, for the sampling of small volumes. We have demonstrated fabrication processes that enable the creation of functional fluid channels and waveguide in a single step. The independent operation of capillary channels and waveguides has been demonstrated and a system is designed for future testing of in-plane optical excitation of fluorescence. Capillaries with widths below 1 micrometers dimensions have been fabricated using photolithography and reactive ion etching in glass and silicon substrates. We have driven dye labeled DNA molecules electrophoretically through the micrometer size channels and observed individual molecules fluorescence. Surface energy on the high relative surface area channels is significant in the filling of the channels with aqueous solutions and treatment of the liquid contacting surfaces has influence on the system behavior. Light is coupled into the waveguide through gratings fabricate by electron-beam lithography.
A new technique for fabricating 2D artificial gels for DNA electrophoresis is presented. The technique differs from previous approaches in that the entire device is fabricated as a monolithic unit using exclusively planar processing techniques borrowed from semiconductor electronics fabrication. The height of the fluid gap between the dielectric floor and ceiling is determined by the thickness of a sacrificial layer which is removed by a wet chemical etch. This allows precise control and excellent uniformity of the gap over an entire silicon wafer. Gap control better than 5 nm has been demonstrated for floor-to-ceiling height for the fluid gap. The lateral resolution which can be attained is limited only by available lithographic techniques. In this work, 1 micrometers diameter pillars are defined with i-line photolithography. Fluid interconnects are established with a liquid meniscus to the hedge of the device.
To assess the effect of surface topography on cell attachment, central nervous system (astroglial cells) cells were grown on surfaces patterned with two different types of texture. Reactive ion etching (RIE) was used to induce nanometer-scale roughness in silicon wafers. In a subsequent wet etch, photo-patterned resist protected selected areas of the surface, resulting in a pattern of modified and unmodified texture. Scanning electron microscopy (SEM) showed that the RIE-roughened 'primary' surface consists of randomly positioned columnar structures (diameter approximately equals 50 nm, height approximately equals 250 nm). The wet-etched 'secondary' surfaces had shorter and more sparsely distributed projections, controlled to a degree by wet etch duration. Confocal microscopy and SEM demonstrated that transformed astroglial (LRM55) cells preferred secondary surfaces. The morphology of cells on secondary surfaces depended on wet etch duration. with brief wet etch, cells hade stellate or mounded morphology and were not closely adherent to the surface. With long wet etch, cells had an epithelial-like morphology and were closely adherent to substrates. Under all conditions, cells discriminated between primary and secondary surfaces. In contrast to LRM55 cells, astrocytes in primary cell culture preferred primary surfaces. Thus changes in surface topography produce cell-specific selectivity and change cell attachment characteristics.
Four- and eight-level diffractive optical elements (DOES) are fabricated in silicon using electron beam lithography and reactive ion etching. An f/1.9. 1-mm diameter, four-phase level, reflective off-axis, imaging DOE is fabricated for use in a free-space optical interconnect. The absolute first-order efficiency of the DOE is 73%. Eight-level linear gratings are fabricated to determine processing tolerances for DOEs with first order-diffraction efficiencies greater than 90%.
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