Optical Fiber Array Research Articles

Combinatorial decoding: an approach for universal DNA array fabrication.

A fiber optic microsphere-based oligonucleotide array is described that employs the sequence of the oligonucleotide probe attached to each microsphere as positional identifiers. Each microsphere serves as an immobilized array feature, functionalized with a unique single-stranded oligonucleotide sequence and randomly distributed into an array of microwells. To determine the sequences attached to individual microspheres, a series of fluorescently labeled combinatorial-pooled oligonucleotide target solutions was designed. Each combinatorial decoding solution is intended to identify the nucleotide at a particular position on every microsphere in the array. The combinatorial target solutions were synthesized by linking the four possible nucleotides at each position to four different fluorescent reporter dyes. As such, when the solutions were hybridized to the array, one of four possible fluorescent responses was generated for each position on a microsphere probe sequence. Adjusting the stringency of hybridization enabled single-base mismatch discrimination, and the signal with the highest intensity corresponded to the perfect nucleotide match. By consecutively exposing the array to a series of combinatorial decoding pool solutions, it was possible to simultaneously determine the sequence of every randomly positioned oligonucleotide-functionalized microsphere in the array. Once mapped, the microsphere array can be used for any typical genomic microarray experiment.

A three-dimensional MEMS optical switching module having 100 input and 100 output ports

This paper describes an optical switching module based on microelectromechanical systems (MEMS) two-axis tilt mirror arrays and low-cost highly accurate free-space optics. The MEMS mirror arrays are integrated on single-crystal silicon wafers and provide reliable switching operation at a low driving voltage. The free-space optics consists of two-dimensional optical fiber and microlens arrays based on low-cost and highly accurate polymer-based components. They provide a compact switching module (approximately 80/spl times/60/spl times/35 mm [170 cc]) and are assembled passively by using dowel pins. A prototype switch module with 100-ch optical fiber I/O has a low coupling loss of 4.0 dB, a low crosstalk within -60 dB, and switching time of 3 ms.

Fiber-Optic Sensor Arrays for Permanent Offshore Applications

This article, written by Assistant Technology Editor Karen Bybee, contains highlights of paper OTC 15072, "Requirements, Constraints, and Advantages of Fiber-Optic Sensor Arrays for Permanent Offshore Applications," by M.H. Houston, SPE, Northrop Grumman, originally presented at the 2003 Offshore Technology Conference, Houston, 5-8 May.

High-density fiber optic array technology and its applications in functional genomic studies

High-density fiber optic array technology and its applications in functional genomic studies

High-precision characterization of single-mode optical fiber arrays

A precise method of measuring core center dispersion in single-mode fiber arrays is presented. This approach dispenses with the use of high-precision linear translation stages and is based on a direct comparison of the fiber core center position to a simple lithographically patterned template. Combining image recognition and efficient processing algorithm, the fiber-core center positions of fiber arrays can be determined with precision of order of 0.1 /spl mu/m, in both longitudinal and transversal directions. Complementary information about the position of fibers within v-grooves as well as bending of multifiber arrays can be also obtained.

Plasticizer-free microspheres for ionophore-based sensing and extraction based on a methyl methacrylate-decyl methacrylate copolymer matrix

Plasticizer-free methyl methacrylate-decyl methacrylate (MMA-DMA) microspheres were prepared under mild, non-reactive conditions using a high-throughput particle generator. The particles were perfectly smooth and monodisperse, with a particle diameter of approximately 10.0 μm. In order to evaluate the suitability of the polymer as a matrix for bulk extraction processes, lipophilic sensing components were incorporated into the particles. Particles contained either a H +-selective chromoionophore (ETH 5294) only (type 1), or a K +-selective ionophore (BME-44), anionic sites (NaTFPB), and ETH 5294 (type 2). Type 1 particles responded according to an anion–proton coextraction mechanism and demonstrated Hofmeister selectivity by showing a preference for more lipophilic sample anions (ClO 4 −>NO 3 −>Cl −). Particles of type 2 functioned by way of an ion-exchange equilibrium and demonstrated a functional response for K +, with a dynamic range from 10 −1–10 −4 M K +. These particles also exhibited selectivity comparable to that previously reported for analogous particles made from bis(2-ethylhexyl sebacate) (DOS)-plasticized poly(vinyl chloride) (PVC) and DMA-DOS. In addition, the behavior of both types1 and 2 particles was in agreement with analogous thin film optical sensors (optodes) prepared from MMA-DMA. With the advent of ionophore-based plasticizer-free microspheres a wide variety of ions may potentially be assessed using various popular bead-based sensing strategies, such as lab-on-a-chip technologies, bundled optical fiber arrays, and flow cytometry, without experiencing the deleterious effects resultant of plasticizer leaching.

Development of a charge exchange recombination spectroscopy method for determination of ion temperature from Hα line broadening in the Hanbit mirror device

Ion temperatures can be determined from Hα line broadening measured by charge exchange recombination spectroscopy on Hanbit, a mirror device. Since the Hα line emission from hydrogen atoms in plasma edges is much larger than that of the charge exchange recombination emission of ions, the line shape of the latter is submerged into the former when measured by an array detector such as a CCD detector. Thus, a notching filter in front of a detector is needed to block out the central region of the emission line. An optical fiber array detector, which works as a notching filter as well as an array detector, has been developed, since the transmission characteristics of commercial notching filter are not suitable for the line-broadening measurements. The design concept of the optical fiber array detector is described, and the feasibility to determine ion temperatures from the Hα line broadening measurements is estimated.

Large-scale remotely interrogated arrays of fiber-optic interferometric sensors for underwater acoustic applications

The fiber-optic interferometric acoustic sensor array has established itself as a potential alternative to the conventional sonar array based on electroceramic transducers. In this paper, we discuss all the aspects of a large-scale fiber-optic interferometric sensor array. We review the basic operating principles of the fiber-optic interferometric sensor, signal processing, and multiplexing techniques, we present results from a noise model for a full size system, and we determine the benefit of incorporating a remotely-pumped optical amplifier in the array. As a practical example we describe the design and construction of a prototype array with 96 hydrophones incorporating a remotely pumped erbium-doped fiber amplifier, called the fiber-optic bottom mounted array, which is based on a dense wavelength division and time division multiplexed architecture. These arrays have applications in military sonar and seismic surveying.

Onedimensional imaging system for the diagnosis of the Zpinch xray radiation

A temporalspatial resolution system, which is composed of a slit, infra scintillator, optical fibre array, streak camera, image intensifier, etc., is constructed for the diagnosis of the Zpinch plasma. This system can effectively shield visible light and has an advantage of gaining flat response in the interested region of xray energy. The designed parameters and experimental results of gaspuff Zpinch are presented in this paper.

R&D Status of Neutral Beam Assisted Diagnostics on the Hanbit Mirror Device

Two types of neutral beam sources have been developed in order to measure plasma parameters on the Hanbit mirror device. The first source is a diagnostic neutral beam (DNB) which consists of a hydrogen neutral beam with a beam energy of 30 keV and a total beam current of ca. 1 A. The ion temperature profile can be determined by measuring directly the broadening of the Hα line emitted from hydrogen neutrals produced through the charge exchange recombination reaction with the DNB in the plasma. A fibre optic array detector, which works as an ideal notching filter, was developed to filter out the intense Hα line emitted from the cold hydrogen atoms in the plasma edge. The second source is a hyperthermal neutral beam (HNB) which consists of neutral particles with an energy of 1-100 eV. The HNB can be used to measure electron temperature and density profiles in the region between the core and the outer edge. This region cannot be covered either by Thomson scattering or by electrostatic probes. The feasibility of obtaining profiles of electron density and temperature by means of a helium HNB with a collisonal radiative equilibrium code has been performed.

High-density fiber optic array technology and its applications in functional genomic studies

High-density fiber optic array technology and its applications in functional genomic studies

Automatic decoding of sensor types within randomly ordered, high-density optical sensor arrays.

In this paper automatic sensor identification of sensor classes within a high-density randomized array, without a priori knowledge of sensor locations, is demonstrated. Two different fluorescence-based sensor types, with hundreds of replicates each, were randomly distributed into an optical imaging fiber array platform. The sensor element types were vapor-sensitive microspheres with the environmentally-sensitive fluorescent dye Nile Red adsorbed on their surface. Nile Red undergoes spectral changes when exposed to different microenvironmental polarity conditions, e.g. microsphere surface polarity or odor exposure. These reproducible sensor spectral changes, or sensor-response profiles, enable sensors within a randomized array to be grouped into categories by optical decoding methods. Two computational decoding methods (supervised and unsupervised) are introduced; equal classification rates were achieved for both. By comparing sensor responses from a randomized array with those obtained from known (control) arrays, 587 sensors were correctly classified with 99.32% accuracy. Although both methods were equally effective, the unsupervised method, which uses sensor response changes to odor exposure, is a better decoding model for the vapor-sensitive arrays studied, because it relies only on the odor-response profiles. Another decoding technique employed the emission spectra of the sensors and is more applicable to other types of multiplexed fluorescence-based arrays and assays. The sensor-decoding techniques are compared to demonstrate that sensors within high-density optical chemosensor arrays can be positionally-registered, or decoded, with no additional overhead in time or expense other than collecting the sensor-response profiles.

Simultaneous Recording of Event-Related Auditory Oddball Response Using Transcranial Near Infrared Optical Topography and Surface EEG

Near infrared optical topography (OT) is the measurement of hemoglobin absorption simultaneously from an array of optical fibers on the scalp to construct maps of cortical activity. We demonstrate that OT can be used to simultaneously detect and characterize the hemodynamic responses associated with an “oddball” auditory stimulus and that corresponding electrical event related potentials can be acquired simultaneously using conventional scalp recordings. In addition to the measured electrical response, the hemodynamic localization is consistent with fMRI studies, which show significant activation in the temporal and parietal cortical regions. The event-related response of total hemoglobin showed relatively slow peak latencies (5.8 ± 0.3 s), which were also consistent with fMRI. The current study shows the regions of peak hemodynamic activity that are in closest proximity to areas of peak electrical activity. This is the first demonstration of simultaneous ERP electrical recording and non-invasive optical mapping in human subjects, which promises to be an important tool in the characterization of both normal and abnormal brain function.

Novel optical fiber sensor for simultaneous measurement of temperature and salinity

The paper describes a new optic fiber sensor developed for simultaneous seawater temperature and salinity measurement. Temperature-dependent semiconductor absorption at the band edge is used as the principle of the temperature measurement, and the sensor exploits beam deviation caused by refraction due to the salinity of seawater at the receiving end face of the optical fiber array. The measured optical signals are reflected and transmitted through a sequentially linear arranged fibers array, and then the light intensity peak value and its deviant are detected by a charge-coupled device (CCD). The sensor probe is composed of an intrinsically pure GaAs single crystal, a right angle prism, a partitioned water cell, the emitting fiber with an attached self-focused lens and the linear arranged receiving fibers array. Theoretical analysis and simulations verify the feasibility of the proposed system.

Superfluidity versus Disorder in the Discrete Nonlinear Schrödinger Equation

We study the discrete nonlinear Schrödinger equation (DNLS) in an annular geometry with on-site defects. The dynamics of a traveling plane-wave maps onto an effective nonrigid pendulum Hamiltonian. The different regimes include the complete reflection and refocusing of the initial wave, solitonic structures, and a superfluid state. In the superfluid regime, which occurs above a critical value of nonlinearity, a plane wave travels coherently through the randomly distributed defects. This superfluidity criterion for the DNLS is analogous to (yet very different from) the Landau superfluidity criteria in translationally invariant systems. Experimental implications for the physics of Bose-Einstein condensate gases trapped in optical potentials and of arrays of optical fibers are discussed.

Profiling alternative splicing on fiber-optic arrays.

The human transcriptome is marked by extensive alternative mRNA splicing and the expression of many closely related genes, which may be difficult to distinguish using standard microarray techniques. Here we describe a sensitive and specific assay for parallel analysis of mRNA isoforms on a fiber-optic microarray platform. The method permits analysis of mRNA transcripts without prior RNA purification or cDNA synthesis. Using an endogenously expressed viral transcript as a model, we demonstrated that the assay readily detects mRNA isoforms from as little as 10-100 pg of total cellular RNA or directly from a few cells. Multiplexed analysis of human cancer cell lines revealed differences in mRNA splicing and suggested a potential autocrine mechanism in the development of choriocarcinomas. Our approach may be useful in the large-scale analysis of the role of alternative splicing in development and disease.

High-Density Fiber-Optic Genosensor Microsphere Array Capable of Zeptomole Detection Limits

The detection limit of a fiber-optic microsensor array was investigated for simultaneous detection of multiple DNA sequences. A random array composed of oligonucleotide-functionalized 3.1-microm-diameter microspheres on the distal face of a 500-microm etched imaging fiber was monitored for binding to fluorescently labeled complementary DNA sequences. Inherent sensor redundancy in the microarray allows the use of multiple microspheres to increase the signal-to-noise ratio, further enhancing the detection capabilities. Specific hybridization was observed for each of three sequences in an array yielding a detection limit of 10(-21) mol (approximately 600 DNA molecules).

Intrinsic fiber-optic ultrasonic sensor array using multiplexed two-wave mixing interferometry.

An intrinsic multiplexed laser interferometer is presented that allows for the simultaneous detection of acoustic waves by an array of fiber-optic sensors. The phase-modulated signals from each sensor are demodulated by use of an adaptive two-wave mixing setup. The light from each sensing fiber in the array is mixed with a reference beam in a single photorefractive crystal (PRC), and the output beams from the PRC are imaged onto separate photodetectors to create a multiplexed two-wave mixing (MTWM) system. The sensing fibers are embedded in graphite-epoxy composite panels, and detection of both acoustic emission and ultrasonic signals in these materials is demonstrated. The intrinsic MTWM system is an effective tool for the simultaneous demodulation of signals from a large fiber sensor array. Also, the adaptive nature of the MTWM setup obviates the need for active stabilization against ambient noise.

Laser diffractometer for single-particlescattering measurements

A laser diffractometer (polar nephelometer)constructed for single-particle studies is described. It takesadvantage of an array of optical fibres and a scanning disc toallow the use of a single photomultiplier tube for thedetection of scattered light. A background subtraction schememakes the instrument especially valuable in cases where background scattering exceeds the scattering from the observedparticle, for example for living cells in aqueous media. Thesystem can be easily integrated with particle trappingequipment such as laser tweezers or an electrodynamic balance.

Determination of the line emission locations in a large helical device on the basis of the Zeeman effect.

Neutral helium He I lambda 728.1 nm (2 1P-3 1S) and lambda 667.8 nm (2 1P-3 1D) emission lines have been observed with an array of optical fibers that cover the entire poloidal cross section of the plasma. The Zeeman profile yields a magnetic field strength, and the locations of the emission regions are identified on the well-established map of the magnetic field of the plasma. It is found that the emission region forms a closed zone just outside the region, the so-called "ergodic layer," where the magnetic field line structure is chaotic. A collisional-radiative model calculation for an inward atom flux suggests a peaked emission profile of about 3.5 cm in full width at half maximum, and this is consistent with the experimental result. The inward atom flux is found to decay before reaching the last closed flux surface and this implies a screening effect of the ergodic layer.