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.

Biophysical and network mechanisms of high frequency extracellular potentials in the rat hippocampus

A fundamental question in neuroscience is how distributed networks of neurons communicate and coordinate dynamically and specifically. Several models propose that oscillating local networks can transiently couple to each other through phase-locked firing. Coherent local field potentials (LFP) between synaptically connected regions is often presented as evidence for such coupling. The physiological correlates of LFP signals depend on many anatomical and physiological factors, however, and how the underlying neural processes collectively generate features of different spatiotemporal scales is poorly understood. High frequency oscillations in the hippocampus, including gamma rhythms (30-100 Hz) that are organized by the theta oscillations (5-10 Hz) during active exploration and REM sleep, as well as sharp wave-ripples (SWRs, 140-200 Hz) during immobility or slow wave sleep, have each been associated with various aspects of learning and memory. Deciphering their physiology and functional consequences is crucial to understanding the operation of the hippocampal network.

We investigated the origins and coordination of high frequency LFPs in the hippocampo-entorhinal network using both biophysical models and analyses of large-scale recordings in behaving and sleeping rats. We found that the synchronization of pyramidal cell spikes substantially shapes, or even dominates, the electrical signature of SWRs in area CA1 of the hippocampus. The precise mechanisms coordinating this synchrony are still unresolved, but they appear to also affect CA1 activity during theta oscillations. The input to CA1, which often arrives in the form of gamma-frequency waves of activity from area CA3 and layer 3 of entorhinal cortex (EC3), did not strongly influence the timing of CA1 pyramidal cells. Rather, our data are more consistent with local network interactions governing pyramidal cells' spike timing during the integration of their inputs. Furthermore, the relative timing of input from EC3 and CA3 during the theta cycle matched that found in previous work to engage mechanisms for synapse modification and active dendritic processes. Our work demonstrates how local networks interact with upstream inputs to generate a coordinated hippocampal output during behavior and sleep, in the form of theta-gamma coupling and SWRs.

星间相干光通信中的光学锁相环

在相干体制下,二进制相移键控(BPSK)信号调制的零差接收机可实现理论上的最高灵敏度,是星间相干光通信的研究和应用重点。零差接收机要求本振波和信号波严格相位同步,常用的相位同步技术是光学锁相环(OPLL)。阐述了光学锁相环的基本原理,介绍了近20年来光学锁相环的发展,在此基础上总结了各种类型锁相环的性能和适用范围。回顾了欧洲国家在星间相干光通信计划中通信终端使用光学锁相环的情况。最后对光学锁相环技术进行了总结,对该技术的前景进行了展望。

两根掺镱大芯双包层光纤激光器获得113W同相输出功率

利用一个自成像共焦腔和一个空间滤波器实现了两掺Yb大芯光纤激光器的位相锁定。观测到稳定的具有高对比度的干涉条纹。相干条纹的对比度为59%，而非相干时对比度为6%。中心条纹的宽度与理论计算结果吻合得很好。对同相模式而言，位相锁定激光器阵列输出达到113W，对应的斜率效率为38.5%。

Beam combination of a radial laser array: Flat-topped beam

An analytical expression of a radial laser array for flat-topped beam is derived based on the generalized Collins formula. The intensity distribution of the resulting beam focused by a lens at the focus plane, for phase-locked and nonphase-locked cases, is studied numerically. The effect of the Fresnel number and normalized radius on intensity distribution for phase-locked and nonphase-locked cases is also presented. It is found that intensity distribution for nonphase-locked case is much less sensible to the Fresnel number and normalized radius than that of phase-locked case. (C) 2008 Elsevier Ltd. All rights reserved.

Rhythm generation in monkey motor cortex explored using pyramidal tract stimulation.

We investigated whether stimulation of the pyramidal tract (PT) could reset the phase of 15-30 Hz beta oscillations observed in the macaque motor cortex. We recorded local field potentials (LFPs) and multiple single-unit activity from two conscious macaque monkeys performing a precision grip task. EMG activity was also recorded from the second animal. Single PT stimuli were delivered during the hold period of the task, when oscillations in the LFP were most prominent. Stimulus-triggered averaging of the LFP showed a phase-locked oscillatory response to PT stimulation. Frequency domain analysis revealed two components within the response: a 15-30 Hz component, which represented resetting of on-going beta rhythms, and a lower frequency 10 Hz response. Only the higher frequency could be observed in the EMG activity, at stronger stimulus intensities than were required for resetting the cortical rhythm. Stimulation of the PT during movement elicited a greatly reduced oscillatory response. Analysis of single-unit discharge confirmed that PT stimulation was capable of resetting periodic activity in motor cortex. The firing patterns of pyramidal tract neurones (PTNs) and unidentified neurones exhibited successive cycles of suppression and facilitation, time locked to the stimulus. We conclude that PTN activity directly influences the generation of the 15-30 Hz rhythm. These PTNs facilitate EMG activity in upper limb muscles, contributing to corticomuscular coherence at this same frequency. Since the earliest oscillatory effect observed following stimulation was a suppression of firing, we speculate that inhibitory feedback may be the key mechanism generating such oscillations in the motor cortex.

Fluid mechanics of pulse pressure-gain combustors

The fluid dynamic operation of a valveless pulse combustor has been studied experimentally and numerically. Through phase-locked chemiluminescence and pressure measurements it is shown that mechanical energy is created periodically in the flame surface, with an efficiency of 1.6%. This mechanical energy leaves the pulse combustor through unsteady jets at the aerovalve inlet and the tailpipe exit stations. Two thermodynamically distinct flows are identified: a flow that is transported from inlet to exit and participates in combustion along the way, and a flow that is ingested and then ejected from the combustor without undergoing combustion. It is the latter of these two flows which has the greatest quantity of net work done on it. Copyright © 2008 by the American Institute of Aeronautics and Astronautics, Inc.

Improving the performance of a valveless pulse combustor using unsteady fuel injection

This paper describes an experimental investigation into the effect of unsteady fuel injection on the performance of a valveless pulse combustor. Two fuel systems were used. The first delivered a steady flow of ethylene through choked nozzles, and the second delivered ethylene in discrete pulses using high-frequency fuel injectors. Both fuel systems injected directly into the combustion chamber. The high-frequency fuel injectors were phase locked to the unsteady pressure measured on the inlet pipe. The phase and opening pulse width of the injectors and the time-averaged fuel mass flow rate through the injectors were independently varied. For a given fuel mass flow rate, it is shown that the maximum pressure amplitude occurs when fuel is injected during flow reversal in the inlet pipe, i.e. flow direction is out of the combustor. The optimal fuel injection pulse width is shown to be approximately 2/9th of the cycle. It should, however, be noted that this is the shortest time in which the injectors can reliably be fully opened and closed. It is shown that by using unsteady fuel injection the mass flow rate of fuel needed to achieve a given amplitude of unsteady pressure can be reduced by up to 65% when compared with the steady fuel injection case. At low fuel mass flow rates unsteady fuel injection is shown to raise the efficiency of the combustor by a factor of 7 decreasing to a factor of 2 at high fuel mass flow rates. Copyright © 2008 by the American Institute of Aeronautics and Astronautics, Inc.

Clustering behaviors in networks of integrate-and-fire oscillators

Clustering behavior is studied in a model of integrate-and-fire oscillators with excitatory pulse coupling. When considering a population of identical oscillators, the main result is a proof of global convergence to a phase-locked clustered behavior. The robustness of this clustering behavior is then investigated in a population of nonidentical oscillators by studying the transition from total clustering to the absence of clustering as the group coherence decreases. A robust intermediate situation of partial clustering, characterized by few oscillators traveling among nearly phase-locked clusters, is of particular interest. The analysis complements earlier studies of synchronization in a closely related model. © 2008 American Institute of Physics.

Comparison of acoustic velocity perturbation measurements using PIV vs. two-microphone technique

Understanding combustion instabilities requires accurate measurements of the acoustic velocity perturbation into injectors. This is often accomplished via the use of the two microphone technique, as this only requires two pressure transducers. However, measurements of the actual velocities emerging from the injectors are not often taken, leaving questions regarding the assumptions about the acoustic velocity. A comparison of velocity measured at downstream of the injector with that of two-microphone technique can show the accuracy and limitations of two-microphone technique. In this paper, velocity measurements are taken using both particle image velocimetry (PIV) and the two-microphone technique in a high pressure facility designed for aeroengine injector measurements. The flow is excited using an area modulation device installed on the choked end of the combustion chamber, with PIV measurements enabled by optical access downstream of the injector through a quartz tube and windows. Acoustic velocity perturbations at the injector are determined by considering the Fourier transformed pressure fluctuations for two microphones installed at a known distance upstream of the injector. PIV measurements are realized by seeding the air flow with micrometric water particles under 2.5 bar pressure at ambient temperature. Phase locked velocity fields are realized by synchronizing the acquisition of PIV images with the revolution of the acoustic modulator using the pressure signal measured at the face of injector. The mean velocity fluctuation is calculated as the difference between maximum and minimum velocities, normalized by the mean velocity of the unforced case. Those values are compared with the peak-to-peak velocity fluctuation amplitude calculated by the two-microphone technique. Although the ranges of velocity fluctuations for both techniques are similar, the variation of fluctuation with forcing frequencies diverges significantly with frequency. The differences can be attributed to several limitations associated with of both techniques, such as the quality of the signal, the signal/noise ratio, the accuracy of PIV measurements and the assumption of isentropic flow of the particle velocity from the plenum through the injector. We conclude that two-microphone methods can be used as a reference value for the velocity fluctuation in low order applications such as flame transfer functions, but not for drawing conclusions regarding the absolute velocity fluctuations in the injector. Copyright © 2013 by ASME.

A multi-standard active-RC filter with accurate tuning system

A low-power, highly linear, multi-standard, active-RC filter with an accurate and novel tuning architec-ture is presented. It exhibits 1EEE 802. 11a/b/g (9.5 MHz) and DVB-H (3 MHz, 4 MHz) application. The filter exploits digitally-controlled polysilicon resistor banks and a phase lock loop type automatic tuning system. The novel and complex automatic frequency calibration scheme provides better than 4 comer frequency accuracy, and it can be powered down after calibration to save power and avoid digital signal interference. The filter achieves OIP3 of 26 dBm and the measured group delay variation of the receiver filter is 50 ns (WLAN mode). Its dissipation is 3.4 mA in RX mode and 2.3 mA (only for one path) in TX mode from a 2.85 V supply. The dissipation of calibration consumes 2 mA. The circuit has been fabricated in a 0.35μm 47 GHz SiGe BiCMOS technology; the receiver and transmitter filter occupy 0.21 mm~2 and 0.11 mm~2 (calibration circuit excluded), respectively.

Anti-cyclonic eddies northwest of Luzon in summer-fall observed by satellite altimeters

Anti-cyclonic eddies northwest of Luzon of the Philippines in summer-fall are identified in the merged data products of satellite altimeters of Topex/Poseidon, Jason-1 and European Research Satellites. The generation and propagation of the anti-cyclonic eddies, which are confirmed by satellite ocean color data, are found to be a seasonal phenomenon that is phase-locked to the onset of the southwesterly monsoon and the relaxation of the cyclonic wind curl in the northeastern South China Sea. The eddies originate from northwest of Luzon in summer, move across the northeastern South China Sea to reach the China continental slope in fall, and propagate southwestward along the continental slope in fall-winter, inducing shelfbreak current variations in the western South China Sea in fall-winter. The anti-cyclonic eddy discovered by Li et al. (1998) in the northern South China Sea is found to originate from northwest of Luzon and carry primarily the South China Sea waters. It does not appear to be an eddy shed from the Kuroshio in the Luzon Strait area as alluded by Li et al. (1998) and others.

Photonic integrated circuits for the generation of coherent optical signals

The demand for optical bandwidth continues to increase year on year and is being driven primarily by entertainment services and video streaming to the home. Current photonic systems are coping with this demand by increasing data rates through faster modulation techniques, spectrally efficient transmission systems and by increasing the number of modulated optical channels per fibre strand. Such photonic systems are large and power hungry due to the high number of discrete components required in their operation. Photonic integration offers excellent potential for combining otherwise discrete system components together on a single device to provide robust, power efficient and cost effective solutions. In particular, the design of optical modulators has been an area of immense interest in recent times. Not only has research been aimed at developing modulators with faster data rates, but there has also a push towards making modulators as compact as possible. Mach-Zehnder modulators (MZM) have proven to be highly successful in many optical communication applications. However, due to the relatively weak electro-optic effect on which they are based, they remain large with typical device lengths of 4 to 7 mm while requiring a travelling wave structure for high-speed operation. Nested MZMs have been extensively used in the generation of advanced modulation formats, where multi-symbol transmission can be used to increase data rates at a given modulation frequency. Such nested structures have high losses and require both complex fabrication and packaging. In recent times, it has been shown that Electro-absorption modulators (EAMs) can be used in a specific arrangement to generate Quadrature Phase Shift Keying (QPSK) modulation. EAM based QPSK modulators have increased potential for integration and can be made significantly more compact than MZM based modulators. Such modulator designs suffer from losses in excess of 40 dB, which limits their use in practical applications. The work in this thesis has focused on how these losses can be reduced by using photonic integration. In particular, the integration of multiple lasers with the modulator structure was considered as an excellent means of reducing fibre coupling losses while maximising the optical power on chip. A significant difficultly when using multiple integrated lasers in such an arrangement was to ensure coherence between the integrated lasers. The work investigated in this thesis demonstrates for the first time how optical injection locking between discrete lasers on a single photonic integrated circuit (PIC) can be used in the generation of coherent optical signals. This was done by first considering the monolithic integration of lasers and optical couplers to form an on chip optical power splitter, before then examining the behaviour of a mutually coupled system of integrated lasers. By operating the system in a highly asymmetric coupling regime, a stable phase locking region was found between the integrated lasers. It was then shown that in this stable phase locked region the optical outputs of each laser were coherent with each other and phase locked to a common master laser.

The synchronization of superparamagnetic beads driven by a micro-magnetic ratchet.

We present theoretical, numerical, and experimental analyses on the non-linear dynamic behavior of superparamagnetic beads exposed to a periodic array of micro-magnets and an external rotating field. The agreement between theoretical and experimental results revealed that non-linear magnetic forcing dynamics are responsible for transitions between phase-locked orbits, sub-harmonic orbits, and closed orbits, representing different mobility regimes of colloidal beads. These results suggest that the non-linear behavior can be exploited to construct a novel colloidal separation device that can achieve effectively infinite separation resolution for different types of beads, by exploiting minor differences in their bead's properties. We also identify a unique set of initial conditions, which we denote the "devil's gate" which can be used to expeditiously identify the full range of mobility for a given bead type.

High harmonic generation in the relativistic limit

The generation of extremely bright coherent X-ray pulses in the femtosecond and attosecond regime is currently one of the most exciting frontiers of physics - allowing, for the first time, measurements with unprecedented temporal resolution(1-6). Harmonics from laser - solid target interactions have been identified as a means of achieving fields as high as the Schwinger limit(2,7) (E = 1.3 x 10(16) V m(-1)) and as a highly promising route to high-efficiency attosecond (10(-18) s) pulses(8) owing to their intrinsically phase-locked nature. The key steps to attain these goals are achieving high conversion efficiencies and a slow decay of harmonic efficiency to high orders by driving harmonic production to the relativistic limit(1). Here we present the first experimental demonstration of high harmonic generation in the relativistic limit, obtained on the Vulcan Petawatt laser(9). High conversion efficiencies (eta> 10(-6) per harmonic) and bright emission (> 10(22) photons s(-1) mm(-2) mrad(-2) (0.1% bandwidth)) are observed at wavelengths <4 nm ( the 'water-window' region of particular interest for bio-microscopy).