Kari Kataja

Multiplexed Quantification of Bacterial 16S rRNA by Solution Hybridization with Oligonucleotide Probes and Affinity Capture

Multiplexed and quantitative analysis of nucleic acid sequences in complex mixtures is essential in various applications of microbiological research. We have developed a method based on solution hybridization between biotinylated nucleic acid targets and multiple fluorophore-labeled oligonucleotide probes of distinct sizes. The biotin–nucleic acid–probe complexes are captured on magnetic streptavidin-coated microparticles and washed. The hybridized probes are eluted and their identity and quantity are determined by capillary electrophoresis. The signal intensities of the recorded probes correspond to the amount of target nucleic acid in the mixture, and the size indicates the target. Based on this principle and 16S rRNA–specific oligonucleotide probes, we set up an application for the relative quantification of different groups of clostridia and related organisms in a mixed bacterial population. The lower detection limit is 0.05 ng of total RNA and the linear range of measurement is 102. The method allowed accurate and highly repeatable quantification of the proportion of clostridia in human feces. Further, we discuss other applications of the method such as quantitative transcriptional analysis of eukaryotic microorganisms, which can be performed without conversion of mRNA to cDNA.

Light transmission through a high index dielectric-filled sub-wavelength hole in a metal film.

We investigate transmission of a normally incident, linearly polarized plane wave through a circular sub-wavelength hole in a metal film filled by a high index dielectric medium. We demonstrate for the first time that the trans-mission efficiency of such holes exhibits a Fabry-Pérot like behaviour versus thickness of the metal film, similar to that exhibited by sub-wavelength slits in metal films illuminated by TM-polarized plane waves. We show that by reducing the imaginary part of the propagation constant of the hybrid HE11 mode and by fortifying the Fabry-Pérot resonance, the high index dielectric filling can greatly enhance light transmission through a circular sub-wavelength hole.

Embedded optical interconnect on printed wiring board

Integration of high-speed parallel optical interconnects into printed wiring boards (PWB) is studied. The aim is a hybrid optical-electrical board including both electrical wiring and embedded polymer waveguides. Robust optical coupling between the waveguide and the emitter/detector should be achieved by the use of automated pick-and-place assembly. Different coupling schemes were analyzed by combining non-sequential ray tracing with Monte-Carlo tolerance simulation of misalignments. A modular demonstrator was designed based on three different kind of optical coupling schemes: butt-coupling and couplings based on microlens arrays and on micro ball lenses. The optical front-ends were implemented with PIN and flip-chip-VCSEL arrays as well as 10-Gb/s/channel electronics onto LTCC-based (low-temperature co-fired ceramic) transmitter and receiver modules, which were surface mounted on high-speed PWBs. An electrical simulation model was developed for the design of a VCSEL-based transmitter circuit. Polymer waveguides were fabricated on separate FR-4 boards to allow characterization of alignment tolerances with different waveguides. Optical and adhesion properties of several potential waveguide materials were characterized. The simulations and experiments suggest that, with optimized optomechanical structures and with low loss waveguides, it is possible to achieve acceptable total path loss and yield with the accuracy of automated assembly.

Light transmission through a high index dielectric hole in a metal film surrounded by surface corrugations.

We analyze transmission of a normally incident plane wave through a 100nm diameter hole in a silver film that is filled with a high index dielectric and is surrounded by 300nm wide surface grooves. Specifically, we study the dependency of the transmission efficiency on the number of grooves, groove depth, and the horizontal distance between the groove and the central hole. We observe that the investigated structure exhibits over five orders of magnitude larger transmission efficiency versus a single hole without the dielectric filling.

Extremely short external cavity lasers: the use of wavelength tuning effects in near field sensing

An adjustable extremely short external cavity (ESEC; cavity length 0...50 microns) can be used to tune the wavelength of an edge emitting Fabry-Perot semiconductor laser up to two percents. This means about 30 nm tuning range for the 1550-nm lasers and about 15 nm tuning range for the 800-nm lasers. In addition to the use in WDM and other tunable laser applications, this phenomenon can be directly used in realizing wavelength tuning sensitive near field sensors. In this paper, we discuss the ESEC laser tuning mechanism by using various numerical models and experimentation. We show simulations and experimental results for two different wavelength tuning schemes: a single mirror tuning, and tuning by using a micromachined Fabry Perot interferometer. In addition, we discuss and show results on wavelength tuning enhanced readout in near field optical data storage, and on near field surface profilometry via laser wavelength tuning.

Simulation of imaging system's performance

In this paper, an imaging system simulation tool is presented. With the tool, it is possible to simulate the performance (quality) of an imaging system. Furthermore, the system allows optimization of the lens system for a given image sensor. Experiments have shown that the tool is useful in actual lens design.

Parallel optical interconnect between surface-mounted devices on FR4 printed wiring board using embedded waveguides and passive optical alignments

Technologies to design and fabricate high-bit-rate chip-to-chip optical interconnects on printed wiring boards (PWB) are studied. The aim is to interconnect surface-mounted component packages or modules using board-embedded optical waveguides. In order to demonstrate the developed technologies, a parallel optical interconnect was integrated on a standard FR4-based PWB. It consists of 4-channel BGA-mounted transmitter and receiver modules as well as of four polymer multimode waveguides fabricated on top of the PWB using lithographic patterning. The transmitters and receivers built on low-temperature co-fired ceramic (LTCC) substrates include flip-chip mounted VCSEL or photodiode array and 4x10 Gb/s driver or receiver IC. Two microlens arrays and a surface-mounted micro-mirror enable optical coupling between the optoelectronic device and the waveguide array. The optical alignment is based on the marks and structures fabricated in both the LTCC and optical waveguide processes. The structures were optimized and studied by the use of optical tolerance analyses based on ray tracing. The characterized optical alignment tolerances are in the limits of the accuracy of the surface-mount technology.

Optical interconnect on printed wiring board

Integration of high-speed parallel optical interconnects into printed wiring boards (PWB) is studied. The aim is a hybrid optical-electrical board including both electrical wiring and embedded polymer waveguides. Robust optical coupling between the waveguide and the emitter/detector should be achieved by the use of automated pick-and-place assembly. Different coupling schemes were analyzed by combining non-sequential ray tracing with Monte-Carlo tolerance simulation of misalignments. The simulations demonstrate that, with optimized optomechanical structures and with very low loss waveguides, it is possible to achieve acceptable total path loss and yield with the accuracy of automated assembly. A technical demonstrator was designed and realized to allow testing of embedded interconnects based on three different kind of optical coupling schemes: butt-coupling, and couplings based on micro-lens arrays and on micro-ball lenses. They were implemented with PIN and flip-chip-VCSEL arrays as well as 10-Gb/s/channel electronics onto LTCC-based (low-temperature co-fired ceramic) transmitter and receiver modules, which were surface mounted on high-speed PWBs. The polymer waveguides were on separate FR-4 boards to allow testing and characterization of alignment tolerances with different waveguides. With micro-lens array transmitter, the measured tolerances (±10 μm) were dominated by the thickness of the waveguides.

Fabrication and characterization of hybrid-glass-based axicons

We introduce a process for applying directly UV photopattern- able materials and processing methods for the fabrication of binary dif- fractive optical elements. We design and model a binary axicon—an optical element that produces an almost diffraction free beam at a speci- fied distance from the element. We also synthesize sol-gel-based hybrid glass materials and tailor their processing parameters to fit to the de- mands of the axicon design. A grating periodicity of 2 mm, an 850-nm structure depth, and certain morphological properties are required to meet the design parameters. The materials are synthesized using zirco- nium(IV)isopropoxide, methacrylic acid and methacryloxypropyltri- methoxysilane as deposition material precursors. We determine the mor- phological and shape characteristics of the fabricated axicons as a function of the lithographic exposure parameters. The optical character- istics of the axicons are measured in terms of the axial and radial inten- sity profiles. The difference between the modeled and measured results is explained.

On surface plasmon enhanced near-field transducers

General design principles for near-field transducers that are based on the excitation of surface plasmon polaritons in planar structures are presented. The transmission of normally incident plane waves through thin Ag film containing a very small (sub-wavelength diameter) cylindrical hole that is surrounded by a set of concentric circular grooves is analyzed via the BOR-FDTD method. We find that surface corrugations can substantially enhance light transmission through the central sub-wavelength aperture.