DNA sequencing in a lab-on-a-chip aims at providing cheap, high-speed analysis of low reagent volumes to, e.g., identify genomic deletions or insertions associated with genetic illnesses. Detecting single base-pair insertions/deletions from DNA fragments in the diagnostically relevant range of 150−1000 base-pairs requires a sizing accuracy of S < 10-3. Here we demonstrate S = 4×10-4. A microfluidic chip was post-processed by femtosecond-laser writing of an optical waveguide. 12 blue-labeled and 23 red-labeled DNA fragments were separated in size by capillary electrophoresis, each set excited by either of two lasers power-modulated at different frequencies, their fluorescence detected by a photomultiplier, and blue/red signals distinguished by Fourier analysis. Different calibration strategies were tested: a) use either set of DNA molecules as reference to calibrate the set-up and identify the base-pair sizes of the other set in the same flow experiment, thereby eliminating variations in temperature, wall-coating and sieving-gel conditions, and actuation voltages; b) use the same molecular set as reference and sample with the same fluorescence label, flown in consecutive experiments; c) perform cross-experiments based on different molecular sets with different labels, flown in consecutive experiments. From the results we conclude: Applying quadratic instead of linear fit functions improves the calibration accuracy. Blue-labeled molecules are separated with higher accuracy. The influence of dye label is higher than fluctuations between two experiments. Choosing a single, suitable dye label combined with reference calibration and sample investigation in consecutive experiments results in S = 4×10-4, enabling detection of single base-pair insertion/deletion in a lab-on-a-chip.
We report on the use of femtosecond laser pulses to fabricate photonic devices (waveguides and interferometers) inside
commercial CE chips without affecting the manufacturing procedure of the microfluidic part of the device. The
fabrication of single waveguides intersecting the channels allows one to perform absorption or Laser Induced
Fluorescence (LIF) sensing of the molecules separated inside the microchannels. Microfluidic channels, with access
holes, are fabricated using femtosecond laser irradiation followed by chemical etching. Mach-Zehnder interferometers
are used for label-free sensing of the samples flowing in the microfluidic channels by means of refractive index changes
detection.
In the last years much effort has been taken to arrive at optical integrated circuits with high complexity and advanced functionality. For this aim high index contrast structures are employed that allow for a large number of functional elements within a given chip area: VLSI photonics. It is shown that optical microresonators can be considered as promising basic building blocks for filtering, amplification, modulation, switching and sensing. Active functions can be obtained by monolithic integration or a hybrid approach using materials with thermo-, electro- and opto-optic properties and materials with optical gain. Examples are mainly taken from work at MESA+.
In our recent published works we reported that the propagation length dependence of the conversion efficiency of the Cerenkov second harmonic generation (CSHG) in planar waveguides with a nonlinear substrate follows quite strict rules depending on an actual waveguide geometry together with the wavelength of the pump radiation. Namely, simple integral expressions show that the propagation length exponent may vary continuously from zero to a quadratic dependence. In this contribution, we generally analyze the propagation length dependence of CSHG for some specific arrangements. We also study, for the first time, the effect of pump depletion together with the influence of the pump wavelength and the effective refractive index. It is shown that the length dependence can thus be described by several categories, where the conversion efficiency is - with respect to the propagation length - linearly proportional and quadratic, but also the length exponent may continuously vary from 1 to 2 (for the classical phase-matching), including the so-called Cerenkov peak region, where the length exponent is equal to 3/2.
Integrated optics micoresonators (μ-resonators) are microstructures with dimensions typically in the order of tens of
microns down to a few microns, whose response depends critically on optical wavelength and material properties. Recent experimental studies have shown that they are suitable as refractive index sensors, absorption sensors, and microresonator-assisted single and two-photon fluorescence. The absorption and fluorescence spectra are material-specific properties, that the devices can readily detect by using different excitation wavelengths. Therefore, the devices
are suitable for non-specific agent detection. Due to their inherent small size and the ease of cascading several microresonators, they are suitable building blocks for a sensing array allowing sensing/detection of multiple quantities/agents on a single chip, by e.g., using different chemo-optical transduction layers on top of the
microresonators. Such devices have a chip-area of only a few 100 μm2, making them suitable for sensing ultra-small analyte volumes (which is advantageous for bio-chemical sensing). In this contribution, sensing arrays based on integrated optics microresonators and their prospects for Homeland Security applications are discussed. Several device-concepts based on integrated optics microresonators will be treated. Their performance is analyzed using realistic parameters and experimental results of microresonator devices realized in silicon oxynitride (SiON) technology. The potential integration of theses devices with microelectronics, micro-mechanics and micro total analysis systems is
discussed.
Abnormal reflecting mirror (ARM) structures, consisting of a corrugated optical waveguide structure, can serve as a narrow band reflection filter in which strong field enhancement may occur by excitation of the guided mode. The latter is quite interest for SHG. We report experimental results of a first prototype, which exhibits CSHG in the ARM structure.
The curriculum in Electrical Engineering at the University of Twente has been recently adjusted in order to increase the proficiency in optics of the graduates, providing a general background and preparing especially for integrated optics and optical communication techniques. This involves mainly three undergraduate courses during the second through fourth year of the five-year curriculum. Two of these courses involve intensive use of computer aids. In the first one, Electrodynamics, Maple worksheets are extensively used for diminishing the tedium of the mathematics and for visualizing (using animation) of traveling and standing wave patterns. In the last course, computer programs (a slab mode solver and an implementation of the beam propagation method) are used as design tools. We describe the aims, contents, and the relationship between the courses and some organizational issues. It is concluded that the courses meet our requirements: undergraduate students become productive quite fast in the field of integrated optics when they work in an internship or in their MSc-project. The background thus provided to our graduates seems to be well received in the relevant industry.
A method to construct modal fields for an arbitrary one- or two-dimensional intensity dependent refractive index structure is described. An arbitrary starting field is propagated along a complex axis using the slowly varying envelope approximation for the Finite Difference Beam Propagation Method. By suitably choosing the complex value of the propagation step, one mode is maximally increased in amplitude. The applicability of the method is discussed and illustrated by a one-dimensional cross section test example with Kerr- type nonlinearity.
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