Classifications

• • H—ELECTRICITY
  • H01—ELECTRIC ELEMENTS
  • H01S—DEVICES USING THE PROCESS OF LIGHT AMPLIFICATION BY STIMULATED EMISSION OF RADIATION [LASER] TO AMPLIFY OR GENERATE LIGHT; DEVICES USING STIMULATED EMISSION OF ELECTROMAGNETIC RADIATION IN WAVE RANGES OTHER THAN OPTICAL
  • H01S3/00—Lasers, i.e. devices using stimulated emission of electromagnetic radiation in the infrared, visible or ultraviolet wave range
  • H01S3/05—Construction or shape of optical resonators; Accommodation of active medium therein; Shape of active medium
  • H01S3/06—Construction or shape of active medium
• • H—ELECTRICITY
  • H01—ELECTRIC ELEMENTS
  • H01S—DEVICES USING THE PROCESS OF LIGHT AMPLIFICATION BY STIMULATED EMISSION OF RADIATION [LASER] TO AMPLIFY OR GENERATE LIGHT; DEVICES USING STIMULATED EMISSION OF ELECTROMAGNETIC RADIATION IN WAVE RANGES OTHER THAN OPTICAL
  • H01S3/00—Lasers, i.e. devices using stimulated emission of electromagnetic radiation in the infrared, visible or ultraviolet wave range
  • H01S3/05—Construction or shape of optical resonators; Accommodation of active medium therein; Shape of active medium
  • H01S3/06—Construction or shape of active medium
  • H01S3/07—Construction or shape of active medium consisting of a plurality of parts, e.g. segments
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
  • B01J19/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
  • B01J19/0046—Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
  • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
  • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
  • B01J2219/00277—Apparatus
  • B01J2219/00351—Means for dispensing and evacuation of reagents
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
  • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
  • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
  • B01J2219/00277—Apparatus
  • B01J2219/00457—Dispensing or evacuation of the solid phase support
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
  • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
  • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
  • B01J2219/00277—Apparatus
  • B01J2219/00497—Features relating to the solid phase supports
  • B01J2219/005—Beads
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
  • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
  • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
  • B01J2219/00277—Apparatus
  • B01J2219/0054—Means for coding or tagging the apparatus or the reagents
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
  • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
  • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
  • B01J2219/00277—Apparatus
  • B01J2219/0054—Means for coding or tagging the apparatus or the reagents
  • B01J2219/00565—Electromagnetic means
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
  • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
  • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
  • B01J2219/00583—Features relative to the processes being carried out
  • B01J2219/00585—Parallel processes
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
  • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
  • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
  • B01J2219/00583—Features relative to the processes being carried out
  • B01J2219/00603—Making arrays on substantially continuous surfaces
  • B01J2219/00646—Making arrays on substantially continuous surfaces the compounds being bound to beads immobilised on the solid supports
• • B—PERFORMING OPERATIONS; TRANSPORTING
  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
  • B01J2219/00—Chemical, physical or physico-chemical processes in general; Their relevant apparatus
  • B01J2219/00274—Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
  • B01J2219/00583—Features relative to the processes being carried out
  • B01J2219/00603—Making arrays on substantially continuous surfaces
  • B01J2219/00659—Two-dimensional arrays
• • C—CHEMISTRY; METALLURGY
  • C40—COMBINATORIAL TECHNOLOGY
  • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
  • C40B60/00—Apparatus specially adapted for use in combinatorial chemistry or with libraries
  • C40B60/14—Apparatus specially adapted for use in combinatorial chemistry or with libraries for creating libraries
• • C—CHEMISTRY; METALLURGY
  • C40—COMBINATORIAL TECHNOLOGY
  • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
  • C40B70/00—Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
• • H—ELECTRICITY
  • H01—ELECTRIC ELEMENTS
  • H01S—DEVICES USING THE PROCESS OF LIGHT AMPLIFICATION BY STIMULATED EMISSION OF RADIATION [LASER] TO AMPLIFY OR GENERATE LIGHT; DEVICES USING STIMULATED EMISSION OF ELECTROMAGNETIC RADIATION IN WAVE RANGES OTHER THAN OPTICAL
  • H01S3/00—Lasers, i.e. devices using stimulated emission of electromagnetic radiation in the infrared, visible or ultraviolet wave range
  • H01S3/05—Construction or shape of optical resonators; Accommodation of active medium therein; Shape of active medium
  • H01S3/06—Construction or shape of active medium
  • H01S3/063—Waveguide lasers, i.e. whereby the dimensions of the waveguide are of the order of the light wavelength
  • H01S3/067—Fibre lasers
• • H—ELECTRICITY
  • H01—ELECTRIC ELEMENTS
  • H01S—DEVICES USING THE PROCESS OF LIGHT AMPLIFICATION BY STIMULATED EMISSION OF RADIATION [LASER] TO AMPLIFY OR GENERATE LIGHT; DEVICES USING STIMULATED EMISSION OF ELECTROMAGNETIC RADIATION IN WAVE RANGES OTHER THAN OPTICAL
  • H01S3/00—Lasers, i.e. devices using stimulated emission of electromagnetic radiation in the infrared, visible or ultraviolet wave range
  • H01S3/05—Construction or shape of optical resonators; Accommodation of active medium therein; Shape of active medium
  • H01S3/08—Construction or shape of optical resonators or components thereof
  • H01S3/08086—Multiple-wavelength emission
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
  • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
  • Y10T436/00—Chemistry: analytical and immunological testing
  • Y10T436/13—Tracers or tags

Definitions

• This invention relates generally to beads and other structures typically used in combinatorial chemistry applications, as well as to structures capable of emitting electromagnetic radiation, and to optical encoding techniques and to techniques for reading out and detecting encoded information.
• a large number of so-called solid supports or beads are provided so as to have a matrix or growth matrix phase (also referred to as a functionalized support) to which various compounds can adhere during the synthesis of diverse new compounds, some of which have, ideally, useful physiological or other properties.
• a problem in the use of such beads is in providing an identification for the beads that facilitates the subsequent screening and identification of, for example, an oligomer sequence that is synthesized.
• a structure in accordance with an aspect of this invention can include a core or other substrate, at least one and preferably a plurality of optical gain medium films disposed about said core for providing a plurality of characteristic emission wavelengths.
• the structure may further include a functionalized support suitable for the synthesis therein or thereon of a chemical compound.
• Various structure geometries are disclosed, such as disks and spheres, as well as several suitable pump sources and detectors.
• a technique for fabricating planar-type structures is also disclosed, wherein a micro-laser bead structure contains a plurality of areas or dots of optical gain material and is contained between protective substrates using, for example, a solvent resistant cross- linked polymer adhesive.
• At least one of the protective substrates is substantially transparent (at the excitation and emission wavelengths of interest) and is disposed between a substrate surface that bears the micro-laser dots and the environment.
• a method employs a head with one or more orifices for selectively printing optical gain material into the areas, and a mechanism for causing relative motion between the head and the substrate.
• the step of depositing may deposit a full complement of optical gain material into each of the plurality of areas.
• the method includes a step of selectively removing (e.g., mechanically removing or laser or photo-ablating) or deactivating (e.g. optically photo-bleaching) the optical gain material within selected ones of the areas.
• the substrate may have a large size for fabricating many micro-laser bead structures, which are then physically separated by sawing or dicing, in a manner similar to that used in integrated circuit fabrication.
• Information is encoded into the bead using only wavelength encoding, or by using both wavelength encoding and signal level encoding.
• the information may be encoded using one of a single level encoding or multi-level encoding.
• Fig. 1A is an enlarged elevational view of a micro-lasing cylindrical bead structure
• Fig. 2 is a graph that depicts an exemplary lasing emission from the micro-lasing cylindrical bead structure
• Fig. 3 is an enlarged cross-sectional view of a micro- lasing cylindrical bead structure capable of emitting three distinct wavelengths and including a functionalized support.
• Fig. 4 is an enlarged cross-sectional view of a spherical geometry micro-lasing structure, in accordance with one embodiment, or a top view of a disk-shaped micro-lasing structure in accordance with another embodiment;
• Figs. 5-9 each depict an embodiment of a laser-based optical system that employs Raman Scattering for generating all or some of multiple pump wavelengths;
• Fig. 10 is a schematic diagram of a Raman laser module using a Nd:YLF pump laser
• Fig. 11 is a graph that illustrates a typical output spectrum of the Raman laser module of Fig. 10;
• Fig. 12 is a graph that plots power out versus power in, and thus illustrates a slope efficiency curve for the Raman laser module of Fig. 10;
• Fig. 13 is a block diagram of an embodiment of a pump source/reader system
• Fig. 14 is a block diagram of a lasing bead structure fabrication print step
• Fig. 15 is an enlarged cross-sectional view of a lasing bead structure laminate with a solvent resistant cross- linked polymer
• Fig. 16 shows further lasing bead structure fabrication steps, wherein Fig. 16A shows an integrated solid support, Fig. 16B shows attachment of resins, such as commercially available LLC Dynospheres, by flexographic, intaglio, or a reverse analox roll process, and Fig. 16C shows direct grafting of the functionalized support;
• Fig. 16A shows an integrated solid support
• Fig. 16B shows attachment of resins, such as commercially available LLC Dynospheres, by flexographic, intaglio, or a reverse analox roll process
• Fig. 16C shows direct grafting of the functionalized support
• Fig. 16D depicts a further embodiment wherein resin beads are placed into wells and fixed in place with a mesh structure, while Fig. 16D shows a multi-chip composite structure;
• Fig. 17 is a top view of wafer containing a plurality of lasing bead structures, and a wavelength calibration and slicing of the wafer into individual lasing bead structures ;
• Fig. 18 depicts an exemplary Lawn Assay readout technique in accordance with an aspect of this invention
• Fig. 19 illustrates a substrate having embedded fibers or threads that emit narrow-band light, when exited by an optical source such as a laser, containing one or more characteristic wavelengths;
• Fig. 20A illustrates a planchette embodiment of a bead suitable for use in a combinatorial chemistry, or other application, in accordance with the teachings of this invention
• Fig. 20B illustrates a filament or fiber embodiment of a bead in accordance with the teachings of this invention, and which is suitable for embodying the threads shown in Fig. 19;
• Fig. 20C illustrates a distributed feedback (DFB) embodiment of a bead in accordance with the teachings of this invention
• Fig. 20D illustrates a top view of a planchette, as in Fig. 20A, or an end view of fiber, wherein the planchette or fiber is sectored and capable of outputting multiple wavelengths;
• Fig. 20E illustrates a top view of a planchette, as in Fig. 20A, or an end view of fiber, wherein the planchette or fiber is radially structured so as to be capable of outputting multiple wavelengths;
• Fig. 21 is an enlarged, cross-sectional view of an embodiment of a bead that is also suitable for embodying the threads shown in Fig. 19;
• Fig. 22 is an enlarged, cross-sectional view of an other embodiment of the bead of Fig. 21;
• Fig. 23 depicts the emission peak of a selected dye in any of the embodiments of Figs. 20A-20E, before (B) and after (A) a spectral collapse;
• Fig. 24 shows characteristic emission peaks for a thread comprised of a plurality of constituent polymeric fibers, each of which emits at a characteristic wavelength;
• Fig. 28 depicts emission wavelength signal amplitude and is useful in explaining an embodiment of this invention wherein both wavelength and signal level amplitude coding are employed.
• cylindrical dielectric sheet structures are equivalent to a closed two dimensional slab waveguide and support a resonant mode. Modes with Q values exceeding 10 6 are possible with active layer thicknesses of l-2 ⁇ m and D ⁇ 5 ⁇ m-50 ⁇ m.
• the structure may be constructed in a similar manner to that described by Frolov et al . so as to include a LCP layer or film.
• the presence of amplifying media in the guiding region results in laser oscillation with emission spectra narrower than about 1 Angstrom.
• the lasing emission signature of the micro- lasing bead is non-saturable and leads to detection with high signal to noise ratios.
• the cylindrical geometry is ideal for producing multi-wavelength (e.g., ⁇ ., , ⁇ 2 , ⁇ 3 ) laser emission from micro-lasing beads.
• the core region can be metallic, polymeric or scattering.
• the cylindrical geometry allows for the use of economic extrusion and coating techniques in the manufacturing of each micro-lasing bead code.
• the bead includes a solid-state functionalized support layer or region, making it suitable for use in combinatorial chemistry applications such as the one described above.
• a possible constraint of a 50 ⁇ m transverse dimension, along with a waveguide isolation region ( ⁇ l ⁇ m) leads to N ⁇ 6 possible wavelengths from a single bead.
• the lasing optical bit number (M) for micro-lasing beads is set by the excitation sources, detection range, and the required wavelength spacing ( ⁇ lnm) .
• M the lasing optical bit number
• ⁇ lnm the required wavelength spacing
• a generally spherical geometry can be provided, in an "onion-skin" embodiment, with one or more gain material layers and isolation layers.
• Each generally spherical micro-lasing bead can be used in a combinatorial chemistry or some other application.
• the structure could be manufactured in an elongated fiber form and then cut into disk-shaped structures.
• a minimum disk thickness would be on the order of one half wavelength.
• Any suitable pump source can be employed.
• one or more pump sources may be required, or a single pump source that is capable of emitting a plurality of wavelengths.
• a dye laser is one such example.
• another suitable multi-wavelength pump source employs efficient stimulated Raman Scattering in narrow linewidth, high Raman cross- section salts such as Ba(N0 3 ) 2 , Ca(C0 3 ) and NaN0 3 (in general: R ⁇ (M0 3 ) y ).
• Such a source can be used to create an all solid state, compact, low cost and low maintenance pump source for exciting the bead structures.
• the preferred crystals have Raman gains of the order of 10-50 cm/GWatt and exhibit excellent transparencies with typical shifts in the 1000-1100 cm "1 range (e.g., Ba(N0 3 ) 2 gives 1047cm '1 ).
• the Raman process is not phase matched so that the source is extremely insensitive to crystal vibrations, translations and rotations. Typical costs for such crystals can be as $1000 or less, and simple single pass gain or resonant cavity designs are adequate for most if not all applications. Furthermore the use in some embodiments of a robust Nd:YAG laser to drive all of the required wavelengths results in greatly improved life and service requirements .
• Fig. 5 shows a first embodiment of an all solid state optical source 10 for that is capable of providing red- green-blue (RGB) pump wavelengths.
• the source 10 uses a single Q-switches Nd:YAG laser that outputs 1.06 micrometer light, an external frequency doubler, such as a KTP crystal to produce 532 nm light, a further non-linear crystal to generate 355 nm light, and two resonant cavity Raman Scattering structures each using a selected one of a R v (M0,) crystal to generate the red and the blue light.
• the green light is generated directly from the 532 nm frequency doubled Nd:YAG output.
• Fig. 6 shows a second embodiment of an all solid state optical source 20 that uses an intra-cavity doubled Q- switched Nd:YAG laser and a separate Q-switched NdrYAG laser.
• the two lasers are electrically and delay synchronized such that combined pulses are applied to a non-linear crystal in the blue light Raman channel.
• the red light is generated by a second Raman scattering resonant cavity structure from the 532 nm light, while the green light is obtained directly from the 532 nm light.
• This approach is capable of providing higher powers than the embodiment of Fig. 5.
• the embodiment 30 of Fig. 7 uses only 532 nm light and Coherent Anti-Stokes Raman Scattering (CARS) to produce the blue emission.
• CARS Coherent Anti-Stokes Raman Scattering
• the embodiment 40 of Fig. 8 uses Raman shifting for both the blue and red emissions.
• a Photonics Industry Nd:YLF laser is operated at a PRR of 300 Hz and a PW of 200 nsec.
• Fig. 11 is a graph that illustrates a typical output spectrum of the Raman laser module of Fig. 10; and Fig. 12 is a graph that plots power out versus power in, and thus illustrates a slope efficiency curve for the Raman laser module of Fig. 10.
• a device 70 for reading the emission wavelengths can be comprised of a spectrometer, preferably a monolithic spectrometer 72.
• Such a device may comprise an optical fiber 74 and a prism or grating 76 for enabling individual wavelengths emitted by a single lasing structure or bead to be resolved and identified through the use of a multi-pixel detector 78, such as a CCD array.
• a look-up table (LUT) 80 can be used to output a code or bead identification (bead ID) corresponding to the detected wavelength (s) .
• the laser source 82 for the reader device could be any one of the various sources referred to above.
• One suitable spectrometer is one referred to as a S2000 Miniature Fiber Optic Spectrometer that is available from Ocean Optics, Inc.
• the teachings of this invention also encompass the use of a reader with a search phase, a targeting, or pointing phase, and a laser excitation phase (i.e., Search, Point and Shoot (or SPS) , such as one based on or similar to the ones described in commonly assigned U.S. Patent Application Serial Number 09/197,650, filed 11/23/98, entitled “Self- Targeting Reader System for Remote Identification” by William Goltsos, the disclosure of which is incorporated by reference herein in its entirety.
• This type of reader system may be used to quickly read out the results of any "reporter” assay in a one, two, or three dimensional field.
• a Lawn Assay using E-coli (or other bacteria) and a reporter gene can be used to provide an optical signature correlated to a specific target, when a compound-containing solid support is placed on it.
• a reporter gene e.g. , a green fluorescent protein or a chemiluminescent assay
• Optically coded beads with synthesized material are deposited at random on the medium (e.g., agar), resulting in about a 6mm to 8mm zone of activity that arises from a successful assay.
• the SPS system can then read the Lawn Assay at a rate of about 20 msec/bead, a time which is several orders of magnitude faster than is possible with currently available millimeter or submillimeter scale element or solid support bead.
• no handling is required to read the code, such as manipulation for chemical or mass spectroscopy deconvolution.
• the method can use thresholding to set the level of assay activity, allowing for the screening of different levels of activity. This allows users to refine their understanding of which molecular parameters (e.g., ring position) create activity for a specific (drug) target.
• molecular parameters e.g., ring position
• the search phase can be replaced by any source of coordinates.
• beads located in sample plate and other types of wells can be read out by coordinates which are supplied to the point and shoot stages.
• coordinates can be obtained from CCD arrays (e.g. , those comprised of amorphous silicon) or from scintillation plates to create a signal for the optical point phase.
• CCD arrays e.g. , those comprised of amorphous silicon
• scintillation plates e.g. , those comprised of amorphous silicon
• Other assays which create temperature changes can also be used with patterned calorimetric, piezoelectric or thermoelectric sensors to create a coordinate location for the point and shoot phases of the optical code readout.
• FIG. 18 there is depicted an exemplary Lawn Assay where exemplary fluorescent GFP rings (R) result at bead sites with assay activity.
• a UV source 92 is used to illuminate the micro-lasing beads in accordance with embodiments of this invention.
• UV irradiated GFP or chemiluminescent assays radiate and provide input to a suitable sensor 94 (possibly thresholded) for the Search phase of the SPS system.
• the bead coordinates are then provided to a laser 96 (L) having a pointable beam, and the laser 96 then targets in turn specific beads (e.g., 9, 11, 22) with the pointable interrogation beam 96a.
• a detector (D) 98 that is capable of discriminating the various possible emission wavelengths ( ⁇ s) that result from the laser excitation, such as the monolithic spectrometer 72 of Fig. 13, sends a list of the detected wavelengths to an associated processor (P) 100.
• the processor 100 which may include the lookup table (LUT) 80 of Fig. 13, outputs the bead identification (ID) based on the detected emission wavelengths that encode the bead ID, thereby identifying the beads of interest.
• the Search phase can be calibrated to detect activity levels via multiple threshold levels, and is not limited to a single threshold (binary, yes/no) necessary to deal with the slow rates of bead deconvolution.
• the Search phase can be sensitive to the presence of a particular region or ring of fluorescent or chemiluminescent emission, as well as to the size of the region (or the diameter of the ring) .
• This aspect of the invention thus provides a system and method for identifying a particular bead in a combinatorial chemistry, or similar application.
• the method includes a first step of providing a population of beads, where each bead includes a functionalized support and a means for optically encoding bead identification information.
• a second step uses the sensor 94 that is responsive to a desired bead activity for identifying a location of one or more beads of interest within the population of beads.
• a third step uses the identified location to aim an interrogation beam 96a at a particular bead, and another step determines, using the detector 98, processor 100 and LUT 80, an identification of the particular bead from a plurality of wavelengths emitted by the particular bead in response to the interrogation beam 96a.
• the sensor 94 can be comprised of at least one of an optical energy detector, an ionizing radiation detector, or a thermal energy detector. The sensor 94 may be capable of operating with more than one sensitivity threshold.
• the senor 94 particularly when detecting ionizing radiation energy (e.g., alpha, beta, gamma) or thermal energy, may be integrated into or placed beneath the plate, dish or other type of container holding the beads, as indicated generally by the sensor 94'.
• the sensor 94" could be, by example, a scintillation type imager or a CCD for ionizing radiation, or a bolometer or other type of thermal energy detector.
• the sensor 94 ' is spatially patterned or differentiated in some manner so as to provide a desired degree of spatial resolution when detecting a location of a bead or bead of interest.
• the detector could be sensitive to fluorescent or a chemiluminescent emission from beads of interest, or in some embodiments to a lack of an optical emission (e.g., the beads normally fluoresce, and the fluorescence is deactivated by a desired bead assay activity.)
• the system 90 can instead search for "dark spots" in a fluorescent background, and may then aim the interrogation laser at the dark spots.
• Figs. 14-17 show various fabrication-related steps for the micro-lasing beads, also referred to as laser bead structures, in accordance with further embodiments of the teachings of this invention.
• Fig. 14 is a block diagram of a lasing bead structure fabrication print step, wherein an N 'color* head 102 is controlled by a head controller 104 and a computer 106.
• a substrate 110 such as a one meter by one meter polymeric (e.g., a cross-linked polystyrene) or glass substrate (or other suitable material) , is placed on an X-Y stage 108 beneath the head 102.
• the head 102 includes a capillary dispenser 102a, preferably capable of movement along a Z- axis, for controllably placing or printing "dots" of selected gain medium material, such as one or more of those listed previously, onto a surface region of the substrate 110.
• Each dot can be considered to be a micro-laser capable of a laser-like emission at a predetermined wavelength or 'color'.
• the illustrated embodiment shows three dots for emitting at ⁇ ⁇ ⁇ 2 , and ⁇ 3 . Each region would thus contain a plurality of dots and would be capable of emitting with a plurality of distinguishable wavelengths.
• Fig. 15 is an enlarged cross-sectional view of a lasing bead structure laminate with a solvent resistant cross- linked polymer.
• a bead structure 120 containing the three micro-laser dots of Fig. 14 is contained between protective substrates 122, 124 using a solvent resistant cross-linked polymer adhesive 126.
• at least one of the protective substrates is substantially transparent (at the excitation and emission wavelengths of interest) and is disposed between the surface that bears the micro-laser dots and the environment.
• Fig. 16 shows further lasing bead structure fabrication steps, wherein Fig. 16A shows an integrated solid support, wherein a functionalized support 130 (or growth matrix) is attached or directly grafted, Fig. 16B shows an attachment of resin particles 132 (i.e., the growth matrix or functionalized support in a particulate form) , such as a functionalized support commercially available from LLC Dynospheres, with a cross-linked adhesive 126 by flexographic, intaglio, or a reverse analox roll process, and Fig. 16C shows an embodiment employing direct grafting of the functionalized support (growth matrix 130) onto the protective substrate (122 or 124).
• resin particles 132 i.e., the growth matrix or functionalized support in a particulate form
• Fig. 16C shows an embodiment employing direct grafting of the functionalized support (growth matrix 130) onto the protective substrate (122 or 124).
• Suitable polymers for the protective layer 122 include Poly (styrene- oxyethylene) (PS-PEG) , Aminomethylated polystyrene-PS, Hydroxyethylmethacrylate-PE, Methacrylic acid/ dimethylacrylamide-PE, and Polyvinyl-glass/polystyrene- glass.
• PS-PEG Poly (styrene- oxyethylene)
• Aminomethylated polystyrene-PS Hydroxyethylmethacrylate-PE
• Methacrylic acid/ dimethylacrylamide-PE Methacrylic acid/ dimethylacrylamide-PE
• Polyvinyl-glass/polystyrene- glass Polyvinyl-glass/polystyrene- glass.
• Fig. 16D depicts a top and side view of a further embodiment 140 wherein a functionalized support comprised of resin beads 144 are placed into wells formed in a frame 142 in combination with a coded film 146. The beads 144 are held in the well with a polymer mesh structure 148.
• Fig. 16E shows a multi-chip composite structure comprising a plurality of wells covered with the mesh structure 148. The mesh structure 148 allows the beads 144 to be contacted by chemicals .
• Figs. 16D and 16E allows the use of almost any commercial resin bead, and there is no need to fix the reaction medium to the coded substrate.
• a well headspace is provided to allow for resin swelling, and the well size/volume can be adjusted to accommodate almost any desired loading.
• the embodiment of Figs. 16D and 16E provides a relatively simple construction.
• the functionalized support preferably in the form of the resin particles, can be sprayed onto a sticky or "tackified” coded substrate layer (as in the embodiment of Fig. 16B) , while in another embodiment the resin particles can be fluidized in air, and combined with "tackified” optically encoded substrates. In either case the resin particles adhere to the tackified surface of the substrate.
• Fig. 17 is a top view of the substrate or wafer 110, such as that shown in Fig. 14, which contains a plurality of regions each defining one of the lasing bead structures, and further shows wavelength calibration and slicing of the wafer into individual lasing bead structures 110a.
• the particular wavelength signature of each bead structure 110a can be readout by illuminating with a suitable excitation source (e.g., a laser), detecting the emitted wavelengths, and then cataloging and storing (possible in the LUT 80) the wavelength signature.
• a suitable excitation source e.g., a laser
• the slicing of the wafer into individual laser bead structures can be accomplished by, for example, scribing and breaking, mechanical sawing, or by laser cutting, i.e., by using techniques based on or similar to those employed in the semiconductor chip fabrication arts.
• the embodiment od Fig. 14 depicts a technique to essentially print the desired individual micro-lasers onto the substrate surface.
• a sub-set of nine different micro-lasers are individually printed from a set of, for example, 25 micro- lasers.
• the complete set of 25 micro-lasers could be provided on each laser bead structure (e.g., on the wafer), and then some number selectively removed or deactivated.
• a silk- screening process could be used to simultaneously form some large number of laser bead structures on the wafer (see Fig. 17) , with each laser bead structure initially comprising a full compliment of micro-lasers.
• some suitable process such as laser-driven photo-bleaching or ablation, can be used to selectively deactivate or remove selected ones of the micro-lasers in each laser bead structure, resulting in each laser bead structure exhibiting its characteristic multi-wavelength emission signature.
• This aspect of the invention employs bead structures that contain an optical gain medium that is capable of exhibiting laser-like activity (e.g., emission in a narrow band of wavelengths when excited by a source of excitation energy) .
• the bead structures in accordance with the teachings of this invention do not require the presence of a scattering phase or scattering sites to generate the narrow band of emissions.
• the optical gain medium that provides the amplified spontaneous emission in response to the illumination is responsive to, for example, size constraints, structural constraints, geometry constraints, and/or index of refraction mis-matches for emitting the narrow band of emissions.
• the size constraints, structural constraints, geometry constraints, and/or index of refraction mis-matches are used to provide for at least one mode in the bead structure that favors at least one narrow band of wavelengths over other wavelengths, enabling emitted energy in the narrow band of wavelengths to constructively add.
• the size constraints, structural constraints, geometry constraints, and/or index of refraction mis-matches are used to provide for an occurrence of amplified spontaneous emission (ASE) in response to a step of illuminating.
• ASE amplified spontaneous emission
• ASE may occur in homogeneously and inhomogeneously broadened medium.
• the structure tends to confine and possibly guide the electromagnetic radiation output from the amplifying (gain) phase, and may favor the creation of at least one mode, or the creation of amplified spontaneous emission (ASE) . In either case the output may be contained in a narrow range of wavelengths, e.g., a few nanometers in width, and is considered herein as a narrowband emission.
• the matrix phase may comprise the material that forms the bead structure, such as a polymeric planchette that contains the electromagnetic radiation amplifying (gain) phase.
• a substrate such as a polymer or glass substrate 10
• the threads 212 exhibit electro-optic properties consistent with laser action; i.e., an output emission that exhibits both a spectral linewidth collapse and a temporal collapse at an input pump energy above a threshold level.
• the threads 212 In response to illumination with laser light, such as frequency doubled light (i.e., 532 nm) from a Nd:YAG laser 214, the threads 212 emit a wavelength ⁇ that is characteristic of the chromic dye or other material that comprises the illuminated threads 212.
• a reflective coating can be applied so as to enhance the emission from the threads 212.
• An optical detector 214 which may include a wavelength selective filter, can be used to detect the emission at the wavelength ⁇ . The emission may also be detected visually, assuming that it lies within the visible portion of the spectrum. In either case, the detection of the emission at the characteristic wavelength ⁇ indicates at least the presence of the bead structure, and possible also an identity of the bead structure.
• the addition of multiple wavelength emission enables a larger number of beads to be individually encoded and identified.
• the threads 212 can be selected from different sets of threads, with each set having a characteristic emission wavelength.
• Fig. 25 illustrates a number of exemplary dyes that are suitable for practicing this invention, and shows their relative energy output as a function of wavelength. The teaching of this invention is not limited for use with only the dyes shown in Fig. 25.
• Fig. 20A is an enlarged elevational view of a small disk- shaped structure, also referred to as a planchette 212A.
• the planchette 212A can be provided with a functionalized support layer or region and can be used as a bead structure, or it can be added to a substrate material of a larger bead structure for optically encoding the larger bead structure.
• the planchette 212A has, by example, a circular cylindrical shape with a diameter (D) and a thickness (T) that is less than the dimensions of the substrate material to which the planchette will be added.
• D and T can be significantly less than 100 microns.
• a planchette can also be designed so that ASE across the thickness T creates a narrowband emission, or such that ASE along an internal reflection path, such as the perimeter, leads to narrowband emission.
• Fig. 20B depicts a fiber embodiment, wherein the diameter (DM) of fiber 212B is made to have a value that is a function of the desired emission wavelength, such as one half wavelength or some multiple of one half wavelength.
• the fiber 212B is comprised of a polymer, or a glass, or some other suitable material, which contains an optical emitter, such as one of the dyes shown in Fig. 25.
• the index of refraction (n) of the fiber 212B be different from the index of refraction (n 1 ) of the desired substrate material so that the fiber 212B is non-index matched to the surrounding substrate.
• the electromagnetic radiation that is emitted by the dye is confined to the fiber and propagates therein. Due at least in part to the diameter of the fiber 212B one narrowband of wavelengths is preferred over other wavelengths, and energy in this band of wavelengths builds over time, relative to the other wavelengths.
• the diameter DM is made a function of the emission wavelength of the selected dye. The end result is a narrowband emission from the fiber 212B, when the dye contained in the matrix material of the fiber 212B is stimulated by an external laser source.
• a plurality of different fibers 212B, each having a characteristic emission wavelength, can be added to the substrate material of a bead for optically encoding the bead identification.
• Fig. 20C depicts a distributed feedback (DFB) embodiment of the bead structure or an emitting structure that is intended to be incorporated within a larger bead structure.
• DFB distributed feedback
• a periodic structure comprised of regions of first and second indices of refraction (n 1 and n 2 ) alternate along the length of the DFB structure 212C.
• n is not equal to n 2 , and neither are equal to n' .
• the thickness of each of the regions may be one quarter wavelength, or a multiple of one quarter wavelength, of the desired emission wavelength to provide a mode for the desired emission wavelength.
• Fig. 23 depicts the emission peak of the selected dye in any of the embodiments of Figs. 20A-20E, before (B) and after (A) the spectral collapse made possible by the structure having a predetermined size, or structural features, or geometry, and/or an index of refraction that differs from the index of refraction of the substrate or environment within which the structure is intended for use.
• the structure can include a propagating mode, and the mode can help guide the electromagnetic radiation, but the mode is not necessary for ASE to occur.
• FIG. 20D illustrates a top view of a planchette 212A, as in Fig. 20A, or an end view of fiber 212B, wherein the planchette or fiber is sectored (e.g. , four sectors) and is capable of outputting multiple wavelengths ( ⁇ 1 - ⁇ 4 ) .
• Fig. 20E illustrates a top view of a planchette 212A, as in Fig. 20A, or an end view of fiber 212B, wherein the planchette or fiber is radially structured so as to be capable of outputting multiple wavelengths.
• Such multiple wavelength embodiments lend themselves to the wavelength encoding of information, such as bead identification information, as was discussed above and will be discussed in further detail below.
• Fig. 21 illustrates an embodiment of a structure wherein a one or more regions (e.g. three) 222, 224, 226 each include, by example, one or more dyes either alone or in combination with one or more rare earths that are selected for providing a desired wavelength ⁇ .,, ⁇ 2 , ⁇ 3 .
• An underlying substrate such as a thin transparent polymer layer 228, overlies a reflective layer 230.
• the reflective layer 230 can be a thin layer of metal foil, and may be corrugated or otherwise shaped or patterned as desired.
• the structure can be cut into thin strips which can be used to form the threads 212 shown in Fig. 19.
• a characteristic broad band fluorescent emission e.g., some tens of nanometers or greater
• the structure when excited by the laser 214 the structure emits a characteristic narrowband emission (e.g. , less than about 10 nm) at each of the wavelengths ⁇ 1 , ⁇ 2 , ⁇ 3 .
• the presence of these three wavelengths can be detected with the detector or detectors 216, in combination with suitable optical passband filters (see also Fig. 26) , thereby providing also for the identification of the bead containing the structure.
• a spectrum analyzer see also Fig.
• a suitable coating 232 can be applied to the regions 222, 224 and 226.
• the coating 232 can provide, for example, UV stability and/or protection from abrasive forces.
• a thin transparent UV absorbing polymer coating is one suitable example, as are dyes, pigments and phosphors.
• the coating can be selected to be or contain a fluorescent material.
• the coating 232 can be excited with a UV source to provide the broadband emission.
• the threads 212 may be comprised of fibers such as nylon-6, nylon 6/6, PET, ABS, SAN, and PPS.
• a selected dye may be selected from Pyrromethene 567, Rhodamine 590 chloride, and Rhodamine 640 perchlorate.
• the selected dye may be compounded with a selected polymer resin and then extruded. Wet spinning is another suitable technique for forming the fibers.
• a suitable dye concentration is 2 X 10 '3 M.
• Extrusion at 250 "C followed by cooling in a water bath is one suitable technique for forming the fibers 212. When used in a planar substrate the diameter is sized accordingly, and in accordance with the selected emission wavelength (s) .
• a suitable excitation (pump 212) fluence is in the range about 5 mJ/cm 2 and greater.
• Two or more fibers, each containing a different dye, can be braided together or otherwise connected to provide a composite fiber that exhibits emission at two or more wavelengths.
• the sectored embodiment of Fig. 20D can be employed, or the radial embodiment of Fig. 20E. It should be realized that simply slicing fibers so constructed can be used to create the planchettes 212A.
• Fig. 24 illustrates the emission from a braided pair of nylon fibers, excited at the 532 nm line of a frequency doubled Nd:YAG laser 212, containing 2 X 10 "3 M Pyrromethene 567 and Rhodamine 640 perchlorate with emission peaks at 552 nm and 615 nm, respectively.
• the resulting composite fibers or threads 212 make it possible to optically encode information, such as the bead identification and/or some other information concerning the bead.
• the characteristic emission lines may be more narrowly spaced than shown in Fig. 24.
• the emission lines of individual ones of the fibers are of the order of 4 nm, one or more further emission wavelengths can be spaced apart at about 6 nm intervals.
• the dye can also be incorporated by a dyeing process of polymers with active sites and specifically designed dyes that bind to the active sites.
• Rhodamine 640 is excited at 532 nm.
• the Rhodamine 640 emits 620 nm radiation with is absorbed by Nile Blue, which in turn emits at 700 nm.
• Fig. 22 illustrates an embodiment wherein the polymer substrate 228 of Fig. 21 is removed, and the regions 222, 224 and 226 are disposed directly over the patterned metal or other material reflector layer 230.
• a thickness modulation of the gain medium regions occurs, enabling multiple wavelengths to be produced if multiple dyes are included.
• Fig. 26 illustrates an embodiment of a suitable apparatus for reading bead identifications in accordance with one aspect of this invention.
• the bead reading system 250 includes the laser 214, such as but not limited to a frequency doubled Nd:YAG laser, that has a pulsed output beam 214a.
• Beam 214a is directed to a mirror M and thence to bead structure 210 to be read (such as one of the planar bead structures shown in Figs. 14-17) .
• the structure 210 may be disposed on a support 252.
• One or both of the mirror M and support 252 may be capable of movement, enabling the beam 212a to be scanned over a population of the bead structures 210.
• one or more emission wavelengths are generated.
• a suitable passband filter F can be provided for each emission wavelength of interest (e.g. , Fl to Fn) .
• the output of each filter Fl-Fn is optically coupled through free space or through an optical fiber to a corresponding photodetector PD1 to PDn.
• the electrical outputs of PD1 to PDn are connected to a controller 254 having an output 254a for indicating bead identification (s) .
• the bead identification can be declared when all of the expected emission wavelengths are found to be present, i.e., when all or some subset of PD1 to PDn each output an electrical signal that exceeds some predetermined threshold.
• a further consideration can be an expected intensity of the detected wavelength (s) and/or a ratio of intensities of individual wavelengths one to another.
• the photodetector (s) or imaging array (s) exhibit a suitable electrical response to the wavelength or wavelengths of interest.
• the emission wavelengths e.g., the emission wavelengths can be spaced about 6 nm apart. This enables a plurality of emission wavelengths to be located within the maximum responsivity wavelength range of the selected detector(s) .
• the controller 254 can be connected to the laser 214, mirror M, support 252, and other system components, such as a rotatable wedge that replaces the fixed filters Fl-Fn, for controlling the operation of these various system components.
• the beads could also be located in a flow channel and flowed past the beam 212a, If only a counting function is used then a minimum of one wavelength (and hence one photodetector) need be employed, assuming that only one type of bead is to be counted.
• One wavelength could also be employed in the identification case, if it were assumed that a desired type of bead emits a predetermined wavelength while other beads do not emit at all, or emit at a different wavelength.
• the diverter mechanism 253 may be activated either if the expected emission is present or is not present.
• the coding of various substrates can be accomplished by a strictly binary wavelength domain code, or by an approach that also includes the amplitude of the signals.
• An increased coding capacity can be obtained by allowing for more bits to be associated with each wavelength. This may be accomplished by considering the signal levels at each wavelength, as is indicated in Fig. 28 for a specific wavelength ⁇ 0 .
• the signal level may be directly controlled by the density of each of the coding emitters in each substrate. For example, three bits at a given ⁇ o can be created as:
• emission at a signal strength A
• emission at a signal strength B>A
• the information encoded at ⁇ 0 can be as follows:
• bead structures which are considered to be a ulti- component material, fibers, such as polymer filaments and textile threads, as well as planchettes, which may be disklike round or polygonal bodies that are placed into the substrate, and which may include a coating having the optical emitter.
• This invention thus teaches a bead structure comprising a gain medium coupled to a structure that supports the creation of at least one mode for electromagnetic radiation.
• This invention further teaches a bead structure comprising a gain medium coupled to a structure having a dimension or length in one or more directions for producing and supporting amplified spontaneous emission (ASE) .
• ASE amplified spontaneous emission
• This invention further teaches a bead structure comprising an optical gain medium and a structure having boundaries that impart an overall geometry to the structure that, in combination with at least one material property of the structure, supports an enhancement of electromagnetic radiation emitted from the gain medium for favoring the creation of at least one mode that enhances an emission of electromagnetic radiation within a narrow band of wavelengths.
• Suitable, but not limiting, shapes for the structure comprise elongated, generally cylindrical shapes such as filaments, a sphere shape, a partial-sphere shape, a toroidal shape, a cubical and other polyhedral shape, and a disk shape.
• the structure is preferably comprised of at least one of a monolithic structure or a multi-layered structure or an ordered structure that may provide for distributed optical feedback.
• the disclosed multi-wavelength emitting structures can be used for product authentication and counterfeit detection, in paper for secure document and currency authentication and coding, and in textiles.
• the laser bead structures of this invention may be used for the detection and screening of Single Nucleotide Polymorphisms, or SNPs, and for the detection and identification of genomic targets and products.
• the functionalized support can be any suitable commercially available substance, such as a resin, so long as it is capable of binding to or attaching with a desired substance.
• the desired substance can be, by example, an organic or inorganic chemical compound, a genomic product or polymorphism, a fragment of DNA or RNA, a bacterium, a virus, a protein, or, in general, any desired element, compound, or molecular or cellular structure or sub-structure.

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• 1999
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