Rapid fabrication of a microfluidic device with integrated optical waveguides for DNA fragment analysis

The fabrication and performance of a microfluidic device with integrated liquid-core optical waveguides for laser induced fluorescence DNA fragment analysis is presented. The device was fabricated through poly(dimethylsiloxane) (PDMS) soft lithography and waveguides are formed in dedicated channels through the addition of a liquid PDMS pre-polymer of higher refractive index. Once a master has been fabricated, microfluidic chips can be produced in less than 3 h without the requirement for a cleanroom, yet this method provides an optical system that has higher performance than a conventional confocal optical assembly. Optical coupling was achieved through the insertion of optical fibers into fiber-to-waveguide couplers at the edge of the chip and the liquid-fiber interface results in low reflection and scattering losses. Waveguide propagation losses are measured to be 1.8 dB cm(-1) (532 nm) and 1.0 dB cm(-1) (633 nm). The chip displays an average total coupling loss of 7.6 dB due to losses at the optical fiber interfaces. In the electrophoretic separation and detection of a BK virus PCR product, the waveguide system achieves an average signal-to-noise ratio of 570 +/- 30 whereas a commercial confocal benchtop electrophoresis system achieves an average SNR of 330 +/- 30. To our knowledge, this is the first time that a waveguide-based system has been demonstrated to have a SNR comparable to a commercially available confocal-based system for microchip capillary electrophoresis.     

Fluorescent liquid-core/air-cladding waveguides towards integrated optofluidic light sources

We have demonstrated fluorescent liquid-core/air-cladding (LA) waveguides suitable for use as integrated optofluidic light sources. These waveguides were fabricated by conventional soft lithography using poly(dimethylsiloxane) (PDMS). Two-phase stratified flows of air and ethylene glycol with fluorescent dye were generated along the PDMS channel. Compared to the liquid-core/liquid-cladding (L(2)) waveguide, the larger refractive index contrast of the LA waveguide resulted in stronger optical confinement. Specifically, the larger refractive index contrast led to experimentally achievable captured fractions (the amount of light to be coupled into the liquid core) as high as 22.8% and the measured propagation losses as low as 0.14 dB cm(-1). Furthermore, in our LA waveguides, diffusional mixing of the core and cladding fluids did not occur and the size of the core stream could be reversibly tuned simply by adjusting the flow rates of the two contiguous phases.     

Dual-color fluorescence cross-correlation spectroscopy on a planar optofluidic chip

Fluorescence cross-correlation spectroscopy (FCCS) is a highly sensitive fluorescence technique with distinct advantages in many bioanalytical applications involving interaction and binding of multiple components. Due to the use of multiple beams, bulk optical FCCS setups require delicate and complex alignment procedures. We demonstrate the first implementation of dual-color FCCS on a planar, integrated optofluidic chip based on liquid-core waveguides that can guide liquid and light simultaneously. In this configuration, the excitation beams are delivered in predefined locations and automatically aligned within the excitation waveguides. We implement two canonical applications of FCCS in the optofluidic lab-on-chip environment: particle colocalization and binding/dissociation dynamics. Colocalization is demonstrated in the detection and discrimination of single-color and double-color fluorescently labeled nanobeads. FCCS in combination with fluorescence resonance energy transfer (FRET) is used to detect the denaturation process of double-stranded DNA at nanomolar concentration.     

Polymer waveguide backplanes for optical sensor interfaces in microfluidics

A polymer optical backplane capable of generic luminescence detection within microfluidic chips is demonstrated using large core polymer waveguides and vertical couplers. The waveguides are fabricated through a new process combining mechanical machining and vapor polishing with elastomer microtransfer molding. A backplane approach enables general optical integration with planar array microfluidics since optical backplanes can be independently designed but still integrated with planar fluidic circuits. Fabricated large core waveguides exhibit a loss of 0.1 dB cm(-1) at 626 nm, a measured numerical aperture of 0.50, and a collection efficiency of 2.86% in an n = 1.459 medium, comparable to a 0.50 NA microscope objective. In addition to vertical couplers for out-of-plane collection and excitation, polymer waveguides are doped with organic dyes to provide wavelength selective filtering within waveguides, further improving optical device integration. With large core low loss waveguides, luminescence collection is improved and measurements can be performed with simple LEDs and photodetectors. Fluorescein detection via fluorescence intensity with a limit of detection (3sigma) of 200 nM in a 1 microL volume is demonstrated. Phosphorescence lifetime based oxygen detection in water in an oxygen controllable microbial cell culture chip with a limit of detection (3sigma) of 0.08% or 35 ppb is also demonstrated utilizing the waveguide backplane. Single waveguide luminescence collection performance is equivalent to a back collection geometry fiber bundle consisting of nine 500 microm diameter collection fibers.     

Biochemical interaction analysis on ATR devices: a wet chemistry approach for surface functionalization

A new generic device suitable for the investigation of ligand-receptor interactions is presented. In particular, the research focused on optical waveguides constituted by an attenuated total internal reflection (ATR) element, transparent in the infrared and whose surfaces were activated in view of covalently binding a receptor. Silicon and germanium ATR elements were considered. The original method is based on the grafting of bifunctional spacer molecules directly at the surface of the germanium crystal, avoiding the deposition of an intermediate metal layer. The grafting of these binding molecules (under their N-hydroxysuccinimidyl ester forms) was performed either by wet chemistry or by photochemistry. The functionalized surfaces, which allow the binding of molecules bearing peripherical NH2 groups, were successfully used, e.g., for the detection of proteins (streptavidin) or of small molecules (biotin). In the latter case, the biotin was readily detected for concentrations as low as 10(-12) M.     

Polymers for Electro‐Optical Modulation

Second‐order nonlinear optical (NLO) properties of polymeric materials have been attracting a lot of attention, especially for such potential applications as fast waveguides electrooptic (EO) modulation and frequency‐doubling devices. For these photonic applications, the performance of the NLO materials has to be optimized. This requires not only a fundamental knowledge of inter‐relationship between their chemical and NLO properties, but new technologies competitive or superior to existing ones as well. This review focuses on the synthesis of NLO polymers including chromophore design, and the comparison among comprehensive EO polymer systems. Moreover, characterization and device fabrication of electro‐optical polymer planar waveguides are also reported in this review.     

Integrated wavelength-selective optical waveguides for microfluidic-based laser-induced fluorescence detection

We demonstrate the fabrication and characterization of a novel, inexpensive microchip capable of laser induced fluorescence (LIF) detection using integrated waveguides with built-in optical filters. Integrated wavelength-selective optical waveguides are fabricated by doping poly(dimethysiloxane) (PDMS) with dye molecules. Liquid-core waveguides are created within dye-doped PDMS microfluidic chips by filling channels with high refractive index liquids. Dye molecules are allowed to diffuse into the liquid core from the surrounding dye-doped PDMS. The amount of diffusion is controlled by choosing either polar (low diffusion) or apolar (high diffusion) liquid waveguide cores. The doping dye is chosen to absorb excitation light and to transmit fluorescence emitted by the sample under test. After 24 h, apolar waveguides demonstrate propagation losses of 120 dB cm(-1) (532 nm) and 4.4 dB cm(-1) (633 nm) while polar waveguides experience losses of 8.2 dB cm(-1) (532 nm) and 1.1 dB cm(-1) (633 nm) where 532 and 633 nm light represent the excitation and fluorescence wavelengths, respectively. We demonstrate the separation and detection of end-labelled DNA fragments using polar waveguides for excitation light delivery and apolar waveguides for fluorescence collection. We demonstrate that the dye-doped waveguides can provide performance comparable to a commercial dielectric filter; however, for the present choice of dye, their ultimate performance is limited by autofluorescence from the dye. Through the detection of a BK virus polymerase chain reaction (PCR) product, we demonstrate that the dye-doped PDMS system is an order of magnitude more sensitive than a similar undoped system (SNR: 138 vs. 9) without the use of any external optical filters at the detector.     

Fabrication of monodisperse asymmetric colloidal clusters by using contact area lithography (CAL)

We report a new fabrication method of asymmetric colloidal clusters by using contact area lithography with site-selective growth. Nanometric surface patterns (approximately 44, 60, and 81 nm in diameter) were prepared by coating surfaces with self-assembled monolayers (SAMs; octadecyltrichlorosilane (OTS) in this study) except the contact area either between colloidal particles or between colloids and substrate. Nanoscale site-specific heterogeneous nucleation and growth of oxide materials of titanium were studied using the patterns of OTS-SAMs onto the either flat or curved surfaces of SiO2. Experimental results suggest that a combination of the large difference in the surface energy between the growing and surrounding surfaces and the diffusion-controlled growth leads to complete nanoscale site specificity. We also fabricated superstructrures of silica spheres with hemispheres of titania (<20 nm in dimension) on their surfaces and discussed the optical properties of colloidal films consisting of the monodisperse asymmetric colloidal clusters in terms of photonic band gap.     

Laser densification of channel waveguides in gel-silica substrates

Channel waveguides are important components in optical signal processing. A new method is described for producing such waveguides with high design flexibility. The channel waveguides are produced using CO₂ laser densification of partially densified gel-silica matrices (Type VI optical silica). Critical processing conditions include pore size and initial density of the matrix, laser power, translational speed of the sample, distance between sample and focusing lens, and ambient humidity.Channel waveguides less than 500 µm wide were produced in gel-silica substrates of different pore sizes and bulk densities throgh laser densification. Optically transparent waveguides were obtained for speeds of the sample over 1.4 cm/s and laser power settings ranging between 12 and 16 mA. Substrates with three different pore sizes were analyzed, i.e, 12, 30 and 45 Å, with densities varying from 1.1 g/cc to 2.1 g/cc. Fourier transform infrared microspectrometry of the densified regions showed that IR shifts ranging from 1 to 38 cm^–1 in the peak position of the Si-O-Si stretching vibrational mode were achieved. This corresponds to changes of index of refraction ranging from 0.01 to 0.20. The experiments show also that the larger the pore size the wider is the range of parameters for producing effective waveguides.     

Viscosity and refractive index adjustment of poly(methyl methacrylate‐co‐ethyleneglycol dimethacrylate) for application in microoptics

Polymer optical components like waveguides or lenses are gaining more and importance as passive or active devices enabling the formation of a sensor and detector platform, e.g. for monitoring the health of large area functional surfaces, which are difficult to access like the wings of an off‐shore wind energy plant. With respect to low‐loss waveguiding and the use of chemical and mechanical stable polymers there is a need to tailor the optical as well as the thermomechanical properties. The given approach describes the addition of electron‐rich small organic molecules like phenanthrene to a poly(methyl methacrylate)‐based polymer matrix enabling a significant refractive index increase from 1.49 up to almost 1.55 (@589 nm). As undesirable side effects the optical transmittance in the visible range at higher guest molecule content is reduced, and a pronounced plasticizing occurs. Both hamper the application of the mixture, e.g. as optical waveguide material. The plasticizing and the accompanied drop of the glass transition temperature, determining the maximum operation temperature, can be partially compensated by the copolymerization of the methyl methacrylate monomer (MMA) with the difunctional monomer ethyleneglycol dimethacrylate (EGDMA) at certain crosslinker content. The resulting new developed guest–host mixtures enable the realization of optical devices with adjusted rheological behavior prior to curing and tailored optical properties after polymerization. Copyright © 2015 John Wiley & Sons, Ltd.     

Solid-state bonding technique for template-stripped ultraflat gold substrates

A simple procedure using gold diffusion bonding for the preparation of template-stripped gold (TSG) surfaces is described. TSG surfaces are useful for surface studies because a very consistent flat gold surface with few defects can be easily prepared. We have developed a method of producing TSG surfaces that relies only on gold diffusion bonding rather than epoxies. The resulting substrates are free from concerns of solvent compatibility, heat stability, and impurities. Bonding of centimeter-sized substrates is performed at 300 degrees C for 2 h using a vise and aluminum foil.     

An optically driven pump for microfluidics

We demonstrate a method for generating flow within a microfluidic channel using an optically driven pump. The pump consists of two counter rotating birefringent vaterite particles trapped within a microfluidic channel and driven using optical tweezers. The transfer of spin angular momentum from a circularly polarised laser beam rotates the particles at up to 10 Hz. We show that the pump is able to displace fluid in microchannels, with flow rates of up to 200 microm(3) s(-1) (200 fL s(-1)). The direction of fluid pumping can be reversed by altering the sense of the rotation of the vaterite beads. We also incorporate a novel optical sensing method, based upon an additional probe particle, trapped within separate optical tweezers, enabling us to map the magnitude and direction of fluid flow within the channel. The techniques described in the paper have potential to be extended to drive an integrated lab-on-chip device, where pumping, flow measurement and optical sensing could all be achieved by structuring a single laser beam.     

Anomalous spreading with Marangoni flow on agar gel surfaces

We have experimentally observed anomalous spreading of aqueous alcohol solutions on flat and rough fractal agar gel surfaces. On flat agar gel surfaces, extremely fast spreading [θ(D)(t) ∝ t(-0.92)] that differs from Tanner's law [θ(D)(t) ∝ t(-0.3)] was observed when the liquid contained over 9 wt % of 1-propanol in which strong Marangoni flow was observed as a fluctuation on the liquid surface. However, on fractal gel surfaces, different spreading dynamics [θ(D)(t) ∝ t(-0.58)] were observed, although Marangoni flow still occurred. We found the surface-dependent spreading can be discussed in terms of competition between Marangoni flow and the pinning effect due to surface roughness.     

Monolithic integration of optical waveguides for absorbance detection in microfabricated electrophoresis devices.

The fabrication and performance of an electrophoretic separation chip with integrated optical waveguides for absorption detection is presented. The device was fabricated on a silicon substrate by standard microfabrication techniques with the use of two photolithographic mask steps. The waveguides on the device were connected to optical fibers, which enabled alignment free operation due to the absence of free-space optics. A 750 microm long U-shaped detection cell was used to facilitate longitudinal absorption detection. To minimize geometrically induced band broadening at the turn in the U-cell, tapering of the separation channel from a width of 120 down to 30 microm was employed. Electrical insulation was achieved by a 13 microm thermally grown silicon dioxide between the silicon substrate and the channels. The breakdown voltage during operation of the chip was measured to 10.6 kV. A separation of 3.2 microM rhodamine 110, 8 microM 2,7-dichlorofluorescein, 10 microM fluorescein and 18 microM 5-carboxyfluorescein was demonstrated on the device using the detection cell for absorption measurements at 488 nm.     

Microfluidic immunosensor with integrated liquid core waveguides for sensitive Mie scattering detection of avian influenza antigens in a real biological matrix

This work presents the use of integrated, liquid core, optical waveguides for measuring immunoagglutination-induced light scattering in a microfluidic device, towards rapid and sensitive detection of avian influenza (AI) viral antigens in a real biological matrix (chicken feces). Mie scattering simulations were performed and tested to optimize the scattering efficiency of the device through proper scatter angle waveguide geometry. The detection limit is demonstrated to be 1 pg mL⁻¹ in both clean buffer and real biological matrix. This low detection limit is made possible through on-chip diffusional mixing of AI target antigens and high acid content microparticle assay reagents, coupled with real-time monitoring of immunoagglutination-induced forward Mie scattering via high refractive index liquid core optical waveguides in close proximity (100 μm) to the sample chamber. The detection time for the assay is <2 min. This device could easily be modified to detect trace levels of any biological molecules that antibodies are available for, moving towards a robust platform for point-of-care disease diagnostics.     

Near infrared photopolymer for micro-optics applications

Near infrared (NIR) activable photopolymers suitable for versatile fabrication of micro-optical elements were developed. The first main objective of this article is to show that these new photopolymers can be used for microfabrication and investigate the parameters governing the microfabrication process. The impact of photonic, physico-chemical, and chemical parameters is discussed. High quality microstructures with a good control over their size and shape are demonstrated. The second main objective is to show practical examples of microlenses and waveguides implemented on single core and multiple core optical fibers, VCSELs, and glass slides are then presented. The NIR photosensitivity of this negative tone photoresists allows using the device source itself as to start the crosslinking process, which constitutes a convenient approach for micro-optics self-positioning on NIR sources and justifies the interest of such NIR photopolymer for the fabrication micro-optical elements and optical interconnects.     

Integrated tunable liquid optical fiber

We present an integrated tunable liquid-core/liquid-cladding (L2) optical fiber, based on a novel three-dimensional hydrodynamic focusing scheme that enables the production of a tunable circular liquid core located in the center of the channel, regardless of the flow-rate ratio of the cladding and core liquids.     

Synthesis of Duloxetine Intermediate (S)-3-Chloro-1-(2-thienyl)-1-propanol with Liquid-Core Immobilized Candida pseudotropicalis 104

(S) -3-Chloro-1-(2-thienyl)-1-propanol was synthesized by the asymmetric reduction of 3-chloro-1-(2-thienyl)propanone with liquid-core immobilized Candida pseudotropicalis 104. The optimum time was 28?h for the re-cultivation of immobilized cells. The optimum film solvent for the liquid-core capsule was 0.3?% chitosan (M _w 1.0?×?10⁵). Conversion decreased with the increase of the liquid-core capsule diameter and with the addition of more substrates at the same reduction time. The immobilized cells show good reduction ability in a potassium phosphate buffer (pH 6.6~7.2). The material outside the spread speed of immobilized cells was not restricted when the shaking speed was higher than 160?r/min. Liquid-core immobilized cells can be reused 11 times. Compared with the batch reduction, the continuous reduction of 3-chloro-1-(2-thienyl)propanone in the membrane reactor with liquid-core immobilized cells as catalyst can relieve the inhibition from a high-concentration substrate. Conversion and enantiometric excess of (S)-3-chloro-1-(2-thienyl)-1-propanol reached 100?% and >99?% in a continuous reduction of 12?g/L 3-chloro-1-(2-thienyl)propanone for 10?days.     

Fabrication of ordered mesoporous thin films for optical waveguiding and interferometric chemical sensing

Planar optical waveguides with a propagation loss of 2.9 dB/cm at 633 nm were fabricated using ordered mesoporous thin films of TiO2-P2O5 nanocomposite deposited on the tin-rich surfaces of float glass slides. The resulting waveguides show substantial sensitivity to parts-per-million-level ammonia gas at room temperature on the basis of single-beam polarimetric interferometry.     

Microfluidic system for simultaneous optical measurement of platelet aggregation at multiple shear rates in whole blood

Thrombosis is the pathological formation of platelet aggregates which occlude blood flow causing stroke and heart attack-the leading causes of death in developed nations. Instrumentation for diagnosing and exploring treatments for pathological platelet aggregation thus has the potential for major clinical impact. Most current thrombosis methods focus on single flow conditions, non-occlusive platelet adhesion, or low shear rates and so are limited in their application to comparative studies involving multiple, pathological test conditions (e.g., shear rate, stenotic geometries that mimic arteries, and rapid platelet accumulation to occlusion). The field could benefit from a low volume, high throughput, short analysis time, and low cost system while minimizing sample handling. We report on the design, fabrication, testing, and application of a microfluidic device and associated optical system for simultaneous measurement of platelet aggregation at multiple initial shear rates within four stenotic channels in label-free whole blood. Following computational design, requisite shear rates were achieved in the device by micro- surface milling a mold and subsequent PDMS casting. We applied the microfluidic system to measure platelet aggregation in whole porcine blood for shear rates spanning physiological to pathological flow conditions (500-13000 s(-1)). Real-time, non-contact, label-free, microscope-free measurements of platelet aggregation were acquired using an optical system comprising a 650 nm diode laser and a linear CCD. We observed fully occlusive platelet aggregation in less than 20 min above a threshold initial shear rate of 4000 s(-1), and no occlusive platelet aggregation below 1500 s(-1) (N = 86 trials). Accumulation of thrombus was consistent between laser intensity, light microscopy, histology, and mass flow rate measurements. The amount of blood volumes producing occlusion were dependent on shear rate. Times to occlusion were not found to be dependent on shear rate above the threshold level of 4000 s(-1). This microfluidic system enables measurement of the entire process of occlusive platelet thrombosis in whole, unlabeled blood, in vitro, at multiple shear rates. Such a system may be useful as a point-of-care diagnostic tool for studying anti-platelet therapies in individual blood samples from high-risk patients.