On-chip integrated label-free optical biosensing

This thesis investigates the design and implementation of a label-free optical biosensing system utilizing a robust on-chip integrated platform. The goal has been to transition optical micro-resonator based label-free biosensing from a laborious and delicate laboratory demonstration to a tool for the analytical life scientist. This has been pursued along four avenues: (1) the design and fabrication of high-$Q$ integrated planar microdisk optical resonators in silicon nitride on silica, (2) the demonstration of a high speed optoelectronic swept frequency laser source, (3) the development and integration of a microfluidic analyte delivery system, and (4) the introduction of a novel differential measurement technique for the reduction of environmental noise.

The optical part of this system combines the results of two major recent developments in the field of optical and laser physics: the high-$Q$ optical resonator and the phase-locked electronically controlled swept-frequency semiconductor laser. The laser operates at a wavelength relevant for aqueous sensing, and replaces expensive and fragile mechanically-tuned laser sources whose frequency sweeps have limited speed, accuracy and reliability. The high-$Q$ optical resonator is part of a monolithic unit with an integrated optical waveguide, and is fabricated using standard semiconductor lithography methods. Monolithic integration makes the system significantly more robust and flexible compared to current, fragile embodiments that rely on the precarious coupling of fragile optical fibers to resonators. The silicon nitride on silica material system allows for future manifestations at shorter wavelengths. The sensor also includes an integrated microfluidic flow cell for precise and low volume delivery of analytes to the resonator surface. We demonstrate the refractive index sensing action of the system as well as the specific and nonspecific adsorption of proteins onto the resonator surface with high sensitivity. Measurement challenges due to environmental noise that hamper system performance are discussed and a differential sensing measurement is proposed, implemented, and demonstrated resulting in the restoration of a high performance sensing measurement.

The instrument developed in this work represents an adaptable and cost-effective platform capable of various sensitive, label-free measurements relevant to the study of biophysics, biomolecular interactions, cell signaling, and a wide range of other life science fields. Further development is necessary for it to be capable of binding assays, or thermodynamic and kinetics measurements; however, this work has laid the foundation for the demonstration of these applications.

Linear chirp control of infrared signal in a biased semiconductor thin film

Ultrashort light-matter interactions between a linear chirped pulse and a biased semiconductor thin film GaAs are investigated. Using different chirped pulses, the dependence of infrared spectra on chirp rate is demonstrated for a 5 fs pulse. It is found that the infrared spectra can be controlled by the linear chirp of the pulse. Furthermore, the infrared spectral intensity could be enhanced by two orders of magnitude via appropriately choosing values of the linear chirp rates. Our results suggest a possible scheme to control the infrared signal.

The local-field corrective effect on Rabi oscillation of ultrashort pulse excitation in semiconductor GaAs

Rabi oscillation of the thin bulk semiconductor GaAs, which takes into account the effect of the local-field correction induced by the interacting excitons, is investigated by numerically solving the semiconductor Bloch equations. It is found, for a 2 pi few-cycle pulse excitation, that two incomplete Rabi-floppings emerge due to the competition between the Rabi frequency of the incident pulse and the internal-field matrices. Furthermore, for a sub-cycle 2 pi pulse excitation a complete Rabi-flopping can occur because of the absolute phase effect. We ascribe these characteristics of the Rabi oscillation to the renormalized Rabi frequency.

Third harmonic enhancement due to Fano interference in semiconductor quantum well

We investigate the emission spectra of the semiconductor quantum well for few-cycle and sub-cycle pulse exciting. We find that Fano interference may induce third harmonic enhancement. Third harmonic enhancement varies with the magnitude and duration of the incident pulse, and may be enhanced by approximately one order of magnitude for the low intensity region of the sub-cycle incident pulse exciting.

Ion acceleration with mixed solid targets interacting with circularly polarized lasers

The interaction of a circularly polarized laser pulse with a mixed solid target containing two species of ions is studied by particle in cell simulations and analytical model. After the interaction tends to be stable, it is demonstrated that the acceleration is more efficient for the heavier ions than that in plasmas containing a single kind of heavy ion and the acceleration efficiency is higher when its proportion is lower. To obtain monoenergetic heavy-ion beams, a sandwich target with a thin mixed ion layer between two light ion layers and a microstructured target are proposed. The influences of parameters of the laser pulse and target on ion acceleration are discussed in detail. It is found that, when the target is thick enough, a cold target is more appropriate for heavy-ion acceleration than a warm target, and the velocity of the reflected heavy ions is proportional to the laser amplitude.

Ultrafast dynamics in ZnO thin films irradiated by femtosecond lasers

The damage morphologies, threshold fluences in ZnO films were studied with femtosecond laser pulses. Time-resolved reflectivity and transmissivity have been measured by the pump-probe technique at different pump fluences and wavelengths. The results indicate that two-phase transition is the dominant damage mechanism, which is similar to that in narrow band gap semiconductors. The estimated energy loss rate of conduction electrons is 1.5 eV/ps. (c) 2005 Elsevier Ltd. All rights reserved.

Application of microwave diagnostics to copper chloride and carbon dioxide lasers

Part A

A problem restricting the development of the CuCl laser has been the decrease in output power with increases of tube temperature above 400°C. At that temperature the CuCl vapor pressure is about .1 torr. This is a small fraction of the buffer gas pressure (He at 10 torr).

The aim of the project was to measure the peak radiation temperature (assumed related to the mean energy of electrons) in the laser discharge as a function of the tube temperature. A 24 gHz gated microwave radiometer was used.

It was found that at the tube temperatures at which the output power began to deteriorate, the electron radiation temperature showed a sharp increase (compared with radiation temperature in pure buffer).

Using the above result, we have postulated that this sudden increase is a result of Penning ionization of the Cu atoms. As a consequence of this process the number of Cu atoms available for lasing decrease.

PART B

The aim of the project was to study the dissociation of CO₂ in the glow discharge of flowing CO₂ lasers.

A TM₀₁₁ microwave (3 gHz) cavity was used to measure the radially averaged electron density n_e and the electron-neutral collision frequency in the laser discharge. An estimate of the electric field is made from these two measurements. A gas chromatograph was used to measure the chemical composition of the gases after going through the discharge. This instrument was checked against a mass spectrometer for accuracy and sensitivity.

Several typical laser mixtures were .used: CO₂-N₂-He (1,3,16), (1,3,0), (1,0,16), (1,2,10), (1,2,0), (1,0,10), (2,3,15), (2,3,0), (2,0,15), (1,3,16)+ H₂O and pure CO₂. Results show that for the conditions studied the dissociation as a function of the electron density is uniquely determined by the STP partial flow rate of CO₂, regardless of the amount of N₂ and/or He present. The presence of water vapor in the discharge decreased the degree of dissociation.

A simple theoretical model was developed using thermodynamic equilibrium. The electrons were replaced in the calculations by a distributed heat source.

The results are analyzed with a simple kinetic model.

Topics in LIGO-related physics: interferometric speed meters and tidal work

In the quest to develop viable designs for third-generation optical interferometric gravitational-wave detectors, one strategy is to monitor the relative momentum or speed of the test-mass mirrors, rather than monitoring their relative position. The most straightforward design for a speed-meter interferometer that accomplishes this is described and analyzed in Chapter 2. This design (due to Braginsky, Gorodetsky, Khalili, and Thorne) is analogous to a microwave-cavity speed meter conceived by Braginsky and Khalili. A mathematical mapping between the microwave speed meter and the optical interferometric speed meter is developed and used to show (in accord with the speed being a quantum nondemolition observable) that in principle the interferometric speed meter can beat the gravitational-wave standard quantum limit (SQL) by an arbitrarily large amount, over an arbitrarily wide range of frequencies . However, in practice, to reach or beat the SQL, this specific speed meter requires exorbitantly high input light power. The physical reason for this is explored, along with other issues such as constraints on performance due to optical dissipation.

Chapter 3 proposes a more sophisticated version of a speed meter. This new design requires only a modest input power and appears to be a fully practical candidate for third-generation LIGO. It can beat the SQL (the approximate sensitivity of second-generation LIGO interferometers) over a broad range of frequencies (~ 10 to 100 Hz in practice) by a factor h/h_SQL ~ √W^(SQL)_(circ)/W_circ. Here W_circ is the light power circulating in the interferometer arms and W_SQL ≃ 800 kW is the circulating power required to beat the SQL at 100 Hz (the LIGO-II power). If squeezed vacuum (with a power-squeeze factor e^-2R) is injected into the interferometer's output port, the SQL can be beat with a much reduced laser power: h/h_SQL ~ √W^(SQL)_(circ)/W_circe^-2R. For realistic parameters (e^-2R ≃ 10 and W_circ ≃ 800 to 2000 kW), the SQL can be beat by a factor ~ 3 to 4 from 10 to 100 Hz. [However, as the power increases in these expressions, the speed meter becomes more narrow band; additional power and re-optimization of some parameters are required to maintain the wide band.] By performing frequency-dependent homodyne detection on the output (with the aid of two kilometer-scale filter cavities), one can markedly improve the interferometer's sensitivity at frequencies above 100 Hz.

Chapters 2 and 3 are part of an ongoing effort to develop a practical variant of an interferometric speed meter and to combine the speed meter concept with other ideas to yield a promising third- generation interferometric gravitational-wave detector that entails low laser power.

Chapter 4 is a contribution to the foundations for analyzing sources of gravitational waves for LIGO. Specifically, it presents an analysis of the tidal work done on a self-gravitating body (e.g., a neutron star or black hole) in an external tidal field (e.g., that of a binary companion). The change in the mass-energy of the body as a result of the tidal work, or "tidal heating," is analyzed using the Landau-Lifshitz pseudotensor and the local asymptotic rest frame of the body. It is shown that the work done on the body is gauge invariant, while the body-tidal-field interaction energy contained within the body's local asymptotic rest frame is gauge dependent. This is analogous to Newtonian theory, where the interaction energy is shown to depend on how one localizes gravitational energy, but the work done on the body is independent of that localization. These conclusions play a role in analyses, by others, of the dynamics and stability of the inspiraling neutron-star binaries whose gravitational waves are likely to be seen and studied by LIGO.

Effect of cerium oxide on the precipitation of silver nanoparticles in femtosecond laser irradiated silicate glass

We investigated the effect of cerium oxide on the precipitation of Ag nanoparticles in silicate glass via a femtosecond laser irradiation and successive annealing. Absorption spectra show that Ce3+ ions may absorb part of the laser energy via multiphoton absorption and release free electrons, resulting in an increase of the concentration of Ag atoms and a decrease of the concentration of hole-trapped color centers, which influence precipitation of the Ag nanoparticles. In addition, we found that the formed Ag-0 may reduce Ce4+ ions to Ce3+ ions during the annealing process, which inhibits the growth of the Ag nanoparticles.

Investigations of charge-carrier dynamics at semiconductor/liquid interfaces

Theoretical and experimental investigations of charge-carrier dynamics at semiconductor/liquid interfaces, specifically with respect to interfacial electron transfer and surface recombination, are presented.

Fermi's golden rule has been used to formulate rate expressions for charge transfer of delocalized carriers in a nondegenerately doped semiconducting electrode to localized, outer-sphere redox acceptors in an electrolyte phase. The treatment allows comparison between charge-transfer kinetic data at metallic, semimetallic, and semiconducting electrodes in terms of parameters such as the electronic coupling to the electrode, the attenuation of coupling with distance into the electrolyte, and the reorganization energy of the charge-transfer event. Within this framework, rate constant values expected at representative semiconducting electrodes have been determined from experimental data for charge transfer at metallic electrodes. The maximum rate constant (i.e., at optimal exoergicity) for outer-sphere processes at semiconducting electrodes is computed to be in the range 10^-17-10^-16 cm⁴ s^-1, which is in excellent agreement with prior theoretical models and experimental results for charge-transfer kinetics at semiconductor/liquid interfaces.

Double-layer corrections have been evaluated for semiconductor electrodes in both depletion and accumulation conditions. In conjuction with the Gouy-Chapman-Stern model, a finite difference approach has been used to calculate potential drops at a representative solid/liquid interface. Under all conditions that were simulated, the correction to the driving force used to evaluate the interfacial rate constant was determined to be less than 2% of the uncorrected interfacial rate constant.

Photoconductivity decay lifetimes have been obtained for Si(111) in contact with solutions of CH₃OH or tetrahydrofuran containing one-electron oxidants. Silicon surfaces in contact with electrolyte solutions having Nernstian redox potentials > 0 V vs. SCE exhibited low effective surface recombination velocities regardless of the different surface chemistries. The formation of an inversion layer, and not a reduced density of electrical trap sites on the surface, is shown to be responsible for the long charge-carrier lifetimes observed for these systems. In addition, a method for preparing an air-stable, low surface recombination velocity Si surface through a two-step, chlorination/alkylation reaction is described.

Innovations of wide-field optical-sectioning fluorescence microscopy : toward high-speed volumetric bio-imaging with simplicity

Optical microscopy has become an indispensable tool for biological researches since its invention, mostly owing to its sub-cellular spatial resolutions, non-invasiveness, instrumental simplicity, and the intuitive observations it provides. Nonetheless, obtaining reliable, quantitative spatial information from conventional wide-field optical microscopy is not always intuitive as it appears to be. This is because in the acquired images of optical microscopy the information about out-of-focus regions is spatially blurred and mixed with in-focus information. In other words, conventional wide-field optical microscopy transforms the three-dimensional spatial information, or volumetric information about the objects into a two-dimensional form in each acquired image, and therefore distorts the spatial information about the object. Several fluorescence holography-based methods have demonstrated the ability to obtain three-dimensional information about the objects, but these methods generally rely on decomposing stereoscopic visualizations to extract volumetric information and are unable to resolve complex 3-dimensional structures such as a multi-layer sphere.

The concept of optical-sectioning techniques, on the other hand, is to detect only two-dimensional information about an object at each acquisition. Specifically, each image obtained by optical-sectioning techniques contains mainly the information about an optically thin layer inside the object, as if only a thin histological section is being observed at a time. Using such a methodology, obtaining undistorted volumetric information about the object simply requires taking images of the object at sequential depths.

Among existing methods of obtaining volumetric information, the practicability of optical sectioning has made it the most commonly used and most powerful one in biological science. However, when applied to imaging living biological systems, conventional single-point-scanning optical-sectioning techniques often result in certain degrees of photo-damages because of the high focal intensity at the scanning point. In order to overcome such an issue, several wide-field optical-sectioning techniques have been proposed and demonstrated, although not without introducing new limitations and compromises such as low signal-to-background ratios and reduced axial resolutions. As a result, single-point-scanning optical-sectioning techniques remain the most widely used instrumentations for volumetric imaging of living biological systems to date.

In order to develop wide-field optical-sectioning techniques that has equivalent optical performance as single-point-scanning ones, this thesis first introduces the mechanisms and limitations of existing wide-field optical-sectioning techniques, and then brings in our innovations that aim to overcome these limitations. We demonstrate, theoretically and experimentally, that our proposed wide-field optical-sectioning techniques can achieve diffraction-limited optical sectioning, low out-of-focus excitation and high-frame-rate imaging in living biological systems. In addition to such imaging capabilities, our proposed techniques can be instrumentally simple and economic, and are straightforward for implementation on conventional wide-field microscopes. These advantages together show the potential of our innovations to be widely used for high-speed, volumetric fluorescence imaging of living biological systems.