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`PROVISIONAL APPLICA TION FOR PA TENT COVER SHEET
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`INVENTOR(S
`
`Given Name (first and middle [if any])
`John A.
`Martin A.
`Tuo
`AlanD.
`
`Family Name or Surname
`Moon
`Putnam
`Li
`Kersey
`
`Residence
`(City and either State or Foreign Counlryl
`Wallingford, Connecticut 06492
`Cheshire, Connecticut 06410
`East Lyme, Connecticut 06333
`South Glastonbury, 06073
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`-0 '1
`o
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`D Additional inventors are bemg named on thE~~ separately numbered sheets attached hereto
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`TITLE OF THE INVENTION (280 characters max)
`
`Improved Optical Identification Element
`
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`United States Government.
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`Respectfully subml VI!
`SIGNATU:SUb~ ~~
`TYPED or~~lNAME Gerald l. DePardo
`
`I
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`50-0260
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`I
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`$160.00
`
`Date
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`I 9/12/02 I
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`Page 1
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`

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`Improved Digital Optical Identification Element
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`Technical Field
`
`This invention relates to optical identification, and more particularly to optical
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`5
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`elements used for digital identification or coding.
`
`Background Art
`
`Many industries have a need for very small, uniquely identifiable objects, for
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`sorting, tracking, and/or identification. Existing technologies, such as bar codes,
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`10
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`electronic microchips/transponders, RFID, and fluorescence and other optical
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`techniques, are often inadequate. For example, current technology may be too large
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`for certain applications or do not provide enough different codes or cannot withstand
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`harsh temperature or chemical environments.
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`Some current techniques are described in US Patents, 6,417,010, "Methods
`
`15
`
`and Apparatus for Synthesizing Labeled Combinatorial Chemistry Labraries", to
`
`Cargill et ai, 6,340,588, "Matrices with Memories", to Nova et aI, 6,329,139,
`
`"Automated Sorting System for Martices with Memory", to Nova et ai, 5,961,923,
`
`"Matrices with Memories and Uses Thereof', to Nova et aI, 6,087,186, "Methods and
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`Apparatus for Sythesizing Labeled Combinatorial Chemistry Libraries", to Cargill et
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`20
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`aI, 6,025,129 "Remotely Prgrammable Matrices with Memories and Uses Thereof', to
`
`Nova et aI, 5,841,528, "Anti-Counterfeit Apparatus", to Lewis et aI, 6,355,431,
`
`"Detection of Nucleic Acid Amplification Reactions Using Bead Arrays", to Chee et
`
`aI, 6, 396,995, "Method and Apparatus for Retaining and Presneting at least one
`
`Microsphere array to Solutions and/or to Optical Imaging Systems", to Stue1pnage1 et
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`25
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`ai, 4,767,205, "Composition and Method for Hidden Identification", to Schwartz et ai,
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`6,268,222, "Micropartic1es Attached to Nanoparticles Labeled with Fluorescent Dye",
`
`to Chandler et aI, 6,057,107 "Methods and Compositions for Flow Cytometric
`
`Determination of DNA Sequences", to Fulton, 6,387,623, "Screening of Drugs from
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`Chemical Combinatorial Libraries Employing Transponders", to Mandecki,
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`tl~'T!J' a: h
`... H 'il"'l1 unTO""> ~l H '-nIl
`1,1>
`11,;,p lImn '~'''it'' ,.,n .. iI~ If
`•• :,Jl , .. uti": ... Il"
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`TI'~'l! 1t ... ··'!
`
`IH JJ,:,H ";tn i
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`.. f!
`-='''tt it'''<U "-"'J-
`Ii", Ii, • H-."H H,~ n
`
`6,376,187, "Electronically-Indexed Solid Phase Assay for Biomolecules", to
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`Mandecki, 6,361,950, "Multiplex Assay for Nucleic Acids Employing Transponders",
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`to Mandecki, 6,046,003, "Method of Determining The Sequence of Nucleic Acidds
`
`Employing Solid Phase Particles Carrying Transponders", to Mandecki, 5,981,166,
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`5
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`"Screening of Soluble Chemical Compounds for their Phamacological Properties
`
`Using Transponders, to Mandecki, 6,214,560 "Analyte Assay Using Particulate
`
`Labels" to Y guerabide et ai, 6,312,914 "Up-Converting Reporters For Biological and
`
`other Assays" to Kardos et ai, 5,609,907, "Self-Assembled Metal Colloid
`
`Monolayers" to Natan, which are incorporated herein by reference in their entirety.
`
`10
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`Therefore, it would be desirable to obtain a coding element or platform that
`
`provides the capability of providing many codes (e.g., greater than 1 million codes),
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`are very small and/or are intrinsic to the element or device.
`
`Summary of the Invention
`
`15
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`Objects of the present invention include provision of an optical coding
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`element that allows for a large number (> 1 million) of codes.
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`According to the present invention, an optical identification element,
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`comprises an optical substrate; and at least a portion of said substrate having at least
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`one Bragg grating disposed therein, said Bragg grating having a plurality of (or at
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`20
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`least one) refractive index pitches superimposed at a common location; and the Bragg
`
`grating having a digital code that is detected when illuminated by a source light
`
`signal.
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`According further to the present invention, the substrate is il1uminated either
`
`from the side or from an axial end.
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`25
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`The present invention provides a dense holographically coded microbeads
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`Massively Parallel Assay Applications
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`plurality of co-located Bragg gratings (or a single Bragg grating having a
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`plurality of co-located index spacings or pitches) disposed in an optical element,
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`which may be an optical waveguide or fiber, or other optical structure that can contain
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`a Bragg grating.
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`Alternatively, for a disc design, each grating region can have one or more
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`gratings disposed therein.
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`5
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`The element may be made of a glass material, such as silica or other glasses,
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`or may be made of plastic, or any other material capable of having a Bragg grating (or
`
`variation of refractive index) disposed therein. The element may be cylindrical in
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`shape or have other geometries. The element may be illuminated from the side or
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`axial end with one (or more) wavelengths.
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`10
`
`The invention allows for a high number of uniquely identifiable codes (e.g., 64
`
`mi11ion codes demonstrated, and billions are possible). Also, the elements may be
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`made very small "microbeads" for small applications (e.g., about 150 microns diam. x
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`300 microns long or smaller), or larger "macrobeads" (ID discs or ID rods) for larger
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`applications (e.g., 1-100 mm diameter or larger). Also, the elements are rugged and
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`15
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`may be disposable if desired. The codes are embedded inside the element and may be
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`permanent non-removable codes that can operate in harsh environments (chemical,
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`temperature, etc.). The codes are not visible with the naked eye. Also, they may be
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`sterilized without losing the codes.
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`The elements are inexpensive to manufacture and the codes are easy and
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`20
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`inexpensive to imprint into the element. The codes are digitally readable and easily
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`adapted to optical coding techniques. Thus, the optical readout is very simple and
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`inexpensive to implement. The code is not affected by spot imperfections, scratches,
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`cracks or breaks. In addition, splitting or slicing an element axially produces more
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`elements with the same code; therefore, when a bead is axially split-up, the code is
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`25
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`not lost, but instead replicated in each piece. Unlike electronic ID elements, the
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`elements of the present invention are not affected by nuclear or electromagnetic
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`radiation.
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`The invention may be used in many areas such as drug discovery, auto(cid:173)
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`identification, functionalized substrates, biology, proteomics, manufacturing!
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`production product identification, animal/people/plant identification, peptide
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`synthesis, combinatorial chemistry, DNA analysis/tracking/sorting/tagging,
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`biochemical synthesis, materials development (coatings, phosphors, etc), security
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`(marking & tracking), chemical sensor arrays, isolation and purification of target
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`5
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`macromolecules, capture and detection of macromolecules for analytical purposes,
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`selective removal of contaminants, enzymatic catalysts, cell sorting, sensors, drug
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`delivery, chemical modification, as well as tagging of molecules, biological particles,
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`matrix support materials, immunoassays, receptor binding assays, scintillation
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`proximity assays, radioactive or non-radioactive proximity assays, and other assays,
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`10
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`(including fluorescent, mass spectroscopy), geno-typing (eg. SNP discovery, and high
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`throughput applications of known SNP's), gene expression, protein to protein
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`interactions, "split and pool", directed sorting, HTS, high throughput drug/genome
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`screening, and/or massively parallel assay applications. The invention provides
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`uniquely identifiable beads with reaction supports by active coatings for reaction
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`15
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`tracking.
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`The invention can be used in combinatorial chemistry, such as solid phase
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`chemical and biochemical synthesis, used to synthesis large numbers of compounds
`
`for drug screening, active coating and functionalized polymers, as well as
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`immunoassays, and hybridization reactions. The invention may enable millions of
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`20
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`parallel chemical reactions, enable large-scale repeated chemical reactions, increase
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`productivity and reduce time-to-market for drug and other material development
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`industries.
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`The invention may also be used for tracking, tagging, and/or sorting fluids
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`(liquids and/or gasses) in an open or closed conduit to determine the path, source or
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`25
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`composition of certain chemicals or fluids. The invention may be used to identify
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`microscope slides or test tubes by writing codes directly into the material, or by
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`embedding microbeads into same. The invention may also be used for tracking,
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`tagging, and/or sorting powders (e.g., gunpowder, anthrax, detergent, dirt, or any
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`other powders). The invention may also be used for tracking, tagging, and/or sorting
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`powders currency, credit cards, micron or nanometer size products (such as,
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`mircocircuits or nanocircuits, or other products).
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`The beads may be coated with any material useful for identifying reactions or
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`combinations, e.g., oligos, complementary DNA (cDNA), antibodies, other.
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`5
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`In addition, other features and advantages include, beads may be placed
`
`directly into sample solution of DNA rather bringing samples to sensor. One can use
`
`very small sample sizes. Beads can be inserted directly into a conventional DNA
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`synthesizer and the desired sequence can be built up base by base using
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`phosphoramidite chemistry. Preformed oligo-nucleotides may be added directly to
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`10
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`surface activated beads. Glass substrate as opposed to metal or polystyrene may lend
`
`to reuse. No fluorophores required for ID tag. Solution based advantages: diffusion
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`ofanalytes to surface. Large number of unique codes: demonstrated over 60 million.
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`Single sample identification: ensemble statistics not required for identification.
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`Enables TRUE combinatorial chemistry techniques with large number combinations.
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`15
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`Rapid Read Out: about 50/sec or faster. Low Cost: between about $0.01 to $0.05 per
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`bead. Small Size 80 um x 150 um or smaller (but may made be larger than current 10
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`urn polystyrene beads). Low cost technique for making 100- 1000 simultaneous
`
`measurements many times.
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`The invention is a significant improvement over chip based assay and existing
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`20
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`bead assay technology, as discussed above.
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`The foregoing and other objects, features and advantages of the present
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`invention will become more apparent in light of the following detailed description of
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`exemplary embodiments thereof.
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`25
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`Brief Description of the Drawings
`
`Fig. 1 is a side view of an optical identification element, in accordance with
`
`the present invention.
`
`Fig. 2 is a side view of an optical identification element illuminated from the
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`side, in accordance with the present invention.
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`Fig. 3 is a graph ofa plurality of wavelengths making up a Bragg grating
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`written into an optical identification element, in accordance with the present
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`invention.
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`Fig. 4 is a diagram of an image on a CCD camera from a side illuminated
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`5
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`optical identification element, in accordance with the present invention.
`
`Fig. 5 is a graph of a plurality of spatial locations indicative of a digital code
`
`embedded in an optical identification element, in accordance with the present
`
`invention.
`
`Fig. 6 is a graph of an optical spectrum of 26 co-located gratings written into a
`
`10
`
`2mm large diameter waveguide of an optical identification element, in accordance
`
`with the present invention.
`
`Fig. 7 is a graph of an optical spectrum of 11 co-located gratings written into a
`2mm large diameter waveguide having a predetermined code spacing of 226 for an
`
`optical identification element, in accordance with the present invention.
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`15
`
`Fig. 8 is a diagram showing a side illuminated image imaged onto a CCD
`
`camera for the grating shown in Fig. 7, for an optical identification element, in
`
`accordance with the present invention.
`
`Fig. 9 is the optical bench set-up used to produce the data shown in Figs. 7 and
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`8, for an optical identification element, in accordance with the present invention.
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`20
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`Fig. 10, illustration (a) is a graph of a grating having a single spatial period,
`
`and illustrations (b)-(c) is a graph ofa grating having multiple co-located spatial
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`periods, for an optical identification element, in accordance with the present
`
`invention.
`
`Fig. II is a graph of a single grating having a spatial period, for an optical
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`25
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`identification element, in accordance with the present invention.
`
`Figs. 12-17 are side views of various alternative embodiments for optical
`
`identification elements, in accordance with the present invention.
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`Fig. 18 is a side view of an optical identification element which is illuminated
`
`from the side, in accordance with the present invention.
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`'iI'Ii ·t!>"$'h ""f!
`jlJ 'lJ n T:;II ~"i1,. tr:; ~ Ilmf! tr~.,
`
`<~'''~ii <if"'!! '~"'n
`
`Fig. 19 is a side view of an optical identification element illuminated from one
`
`axial end, in accordance with the present invention.
`
`Fig. 20 is a perspective view of a tray for holding an end-illuminated optical
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`identification element, in accordance with the present invention.
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`5
`
`Fig. 21 is a perspective view of a tray for holding a side-illuminated optical
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`identification element, in accordance with the present invention.
`
`Fig. 22 is a side view of a side-illuminated optical identification element
`
`having a reflective coating on a surface, in accordance with the present invention.
`
`Fig. 23 is an optical spectral graph of wavelengths for an example end
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`10
`
`illuminated optical identification element, in accordance with the present invention.
`
`Fig. 24 is a diagram of a process for using an optical identification element in
`
`a chemical reaction, in accordance with the present invention.
`
`Fig. 25 to Fig. 73 are additional or alternative descriptions and/or
`
`embodiments, in accordance with the present invention.
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`15
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`20
`
`Best Mode for Carrying Out the Invention
`
`Referring to Fig. 1, an optical identification element (or microbead) 8
`
`comprises a known optical substrate 10, having a Bragg grating 12 impressed (or
`
`embedded or imprinted) in the substrate 10. The substrate 10 has an outer diameter of
`
`about 125 microns and comprises silica glass (Si02) having the appropriate chemical
`composition to allow a Bragg grating 12 to be disposed therein or thereon.
`
`The optical substrate 10 may be any form of material capable of having a
`
`Bragg grating disposed therein. e.g., a larger diameter single mode waveguide (greater
`
`than 0.3 mm diameter), or a standard telecommunication single mode optical fiber
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`25
`
`(125 micron diameter or 80 micron diameter fiber). Other materials and dimensions
`
`for the optical substrate 10 may be used if desired. For example, the substrate 10 may
`
`be made of any glass, e.g., silica, phosphate glass, or other glasses, or made of glass
`
`and plastic, or solely plastic. For high temperature or harsh chemical applications, an
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`optical substrate made of a glass material is desirable.
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`Further, any type of optical waveguide may be used for the optical substrate
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`10, such as, a multi-mode, birefringent, polarization maintaining, polarizing, multi(cid:173)
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`core, or multi-cladding optical waveguide, or a flat or planar waveguide (where the
`
`waveguide is rectangular shaped), or other waveguides. Also, it is not required that
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`5
`
`the substrate 10 be an optical waveguide, i.e., be designed to guide light along itself,
`
`as long as it has a Bragg grating disposed therein.
`
`The Bragg grating 12, as is known, is a periodic or aperiodic variation in the
`
`effective refractive index and/or effective optical absorption coefficient of an optical
`
`waveguide, such as that described in US Patent No.4, 725,110 and 4,807,950, entitled
`
`10
`
`"Method for Impressing Gratings Within Fiber Optics", to Glenn et al; and US Patent
`
`No. 5,388,173, entitled "Method and Apparatus for Forming Aperiodic Gratings in
`
`Optical Fibers", to Glenn, which are hereby incorporated by reference to the extent
`
`necessary to understand the present invention. However, any grating or reflective
`
`element embedded, etched, imprinted, or otherwise formed in the substrate 10 may be
`
`15
`
`used if desired. As used herein, the term "grating" means any of such reflective
`
`elements. Further, the reflective element (or grating) 12 may be used in reflection
`
`and/or transmission of light, depending on the embodiment.
`
`The substrate 10 has an inner region 20 where the grating 12 is located, which
`
`may be the core of an optical waveguide. The inner region may be photosensitive to
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`20
`
`allow the writing of the grating 12. The substrate 10 has an outer region 18 which is
`
`does not have the grating 12 in it.
`
`The optical substrate 10 with the grating 12 has a length L and an outer
`
`diameter Dl, and the inner region (or core) has a diameter D, e.g., 10 microns. The
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`length L can range from small (about 100-300 microns or smaller) to large (greater
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`25
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`than 1.0 - 100 mm or greater). In addition, the diameter D 1 can range from small (less
`
`than 80 microns) to large (greater than 1.0 - 100.mm). Other lengths L and diameters
`
`D I may be used if desired. The invention is not limited by the dimensions. Also,
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`geometries other than a cylinder may be used, e.g., rectangular, square, D-shaped,
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`spherical, and others.
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`The dimensions Land D 1, materials, and material properties of the substrate
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`10 are selected such that the desired optical and material properties are met for a
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`given application. The resolution and range for the optical codes are scalable by
`
`controlling these parameters (discussed more hereinafter).
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`5
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`For any of the embodiments described herein, the axial end faces of the
`
`substrate 10 may be coated with a material that reduces optical scatter if desired. Also,
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`the end faces need not be perfectly straight and perpendicular to the sides for side
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`illumination.
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`The grating 12 has a length Lg of about the length of the substrate.
`
`10
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`Alternatively, the length L of the substrate 10 may be longer than the length Lg of the
`
`grating 12. Other dimensions and lengths for the substrate 10 and the grating 12 may
`
`be used.
`
`Referring to Fig. 2, an incident light 24 of a wavelength Ai, e.g., 632 nm (from
`
`a Helium-Neon laser) is incident on the grating 12 in the substrate 10. Other input
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`15
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`wavelengths can be used if desired.
`
`A portion of the light 24 passes straight through the grating 12 as indicated by
`
`lines 25. The rest of the light 24 is reflected by the grating 12 and forms a plurality of
`
`beams 26-36, each having a different angle indicative of the pitches (AI-An) existing
`
`in the grating 12. The Bragg grating 12 is actually a combination of a plurality of co-
`
`20
`
`located individual gratings, each located at the same location on the substrate and
`
`each having a unique grating spacing or pitch or spatial period A of the refractive
`
`index variation (discussed more hereinafter). The resultant combination is the Bragg
`
`grating 12 having a plurality of possible spatial periods (AI-An). The code is
`
`determined by which spatial periods exist for a given grating 12.
`
`25
`
`The reflected light 26-36 is passed through a lens which provides focussed
`
`beams 46-56 which are imaged onto a CCD camera 60. Fig. 3 shows a plurality of
`
`reflection spectrum wavelengths that exist in the co-located Bragg grating 12.
`
`Referring to Fig. 4, the image on the CCD camera 60 is a series of stripes indicating
`
`ones and zeros of a digital pattern of the code in the optical identification element (or
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`microbead) 8. Fig. 5 is a digitized version of the image of Fig. 4 as indicated in
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`spatial periods (A I-An).
`
`Referring to Fig. 6, a 2 mm single mode waveguide can easily support 26 co(cid:173)
`located gratings, corresponding to 226 (or about 67 million) codes. Referring to Fig. 7,
`
`5
`
`a sample spectral 23 bit code written for the grating 12 is shown and Fig. 8 shows the
`
`corresponding image on the CCD (Charge Coupled Device) camera 60 for a 23 bit
`
`digital pattern of: 10010100100111101000101 for a given microbead element 8.
`
`Fig. 9 shows the lab bench set up used to provide the data shown in Figs. 7-8.
`
`For the above results, the grating was 1.5 mm long, but it can easily be made 200-300
`
`10
`
`microns long. Each grating in the array has slightly different spatial frequencies, thus
`
`producing an array of N unique Bragg conditions (Bragg diffraction angles). When
`
`the element (or microbead) 8 is illuminated from the side, in the region of the grating
`
`12, at the appropriate angle, with a monochromatic (single wavelength) source, the
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`pattern diffracted beams 26-36 is generated. In this experiment, we imaged these
`
`15
`
`beams to infinity onto the CCD camera 60 to produce a pattern that looks much like a
`
`bar code. A digital binary code is generated by varying the spatial frequencies in a
`
`periodic manner. For example, in the experiment above, the pitch A was varied
`
`between adjacent gratings by about 0.2%, then either created a grating (binary 1) or
`
`did not create a grating (binary 0) at a particular pitch. For light having a wavelength
`
`20
`
`of about 1553 nanometers (nm), a pitch change of about 0.2% is corresponds to a
`
`Bragg wavelength change of about 6 nanometers between adjacent bits.
`
`The invention will work equally well for a standard telecommunications
`
`optical fiber having a diameter of 125 or 80 microns. Other smaller or lager diameter
`
`fibers or cane waveguides may be used if desired.
`
`25
`
`Referring to Fig. 10, illustration (a), the grating pitch A is the axial spatial
`
`period of the variation in the refractive index n in the substrate 10 along the axial
`
`length of the Bragg grating. Referring to Fig. 10, illustration (b), shows a composite
`
`Bragg grating comprising three individual Bragg gratings (or 3 periodic variations in
`
`the refractive index of the glass) that are co-located (i.e., disposed on top of each other
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`"u'o-'l'! ~ .... ~! .... u u""h 'IF"!! ~u"'h
`'I-l",Jl •• ~:~ "IL'll"':m 'fl,,;H IT,~..-
`
`.,Tll
`
`at the same location), each individual grating having slightly different pitches, AI,
`
`A2, A3, respectively, the difference between each pitch being about 10% of the
`
`period. Referring to Fig. 10, illustration (b), shows three co-located Bragg gratings,
`
`each having slightly different pitches, AI, A2, A3, respectively, the difference
`
`5
`
`between each pitch being about 0.2% of the spatial period. The gratings are shown to
`
`all start at 0 for illustration purposes; however, it should be understood that each
`
`separate grating may not be and need not be in phase at any point along the grating
`
`12.
`
`Referring to Figs. 11 and 18, the number of codes that are achievable is
`
`10
`
`primarily a function of the length L of the grating 12 (and element 10), the diameter
`
`or thickness of the grating region, the beam divergence angle SR. Bragg condition is
`8i = 80; Diffraction condition is: Sin 8i + Sin 80 = Ail AB. Beam divergence angle 8 R
`= Ai/(nw); where Ai is the input wavelength, w = beam half-width, at lIe2 *1 at point
`
`of incidence on the element 8; Bragg divergence is 6SB::::; ~K*D, where K is the
`wavenumber and ~K = KB - (Kin + Kout); Therefore, the number of discernable bits
`
`15
`
`N ::::; 68B/8 R and 68B::::; Ai/(n*Sin(Si)*D); Therefore, N ::::; nw/(n*(Sin(8i)*D). This is for
`a monochromatic readout only. Using multiple read-out wavelengths, the limitation in
`
`the number of bits N is the number of gratings which can be superimposed.
`
`See the below table 1 for values ofN, where the grating thickness D and Bead
`
`20
`
`length is in microns.
`
`25
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`

`
`.t"~l Hum !t if .... »
`i1
`'11"'h j-1
`'!lIt'
`"~n
`!I,,;n It.-AI .. ·~W~.; II, 'It,,~I';', H "'~r' ",-It.
`
`... tt
`'l!''',h l1"'-tl
`='~!l ~~'Hh ,UOHf:j
`;l!"iH · ... ;:!f ~,lL, lL .... n ;.!! fh-:'"
`
`n
`
`========== Table 1 =========
`
`5
`
`10
`
`'--------------------v-------------------~
`N
`
`The substrate 10 may be coated with a plastic material or other material that
`
`may be used in a chemical process. If the coating does not allow sufficient light to
`
`pass through transversely for adequate optical detection using side illumination, the
`
`15
`
`substrate may be illuminated axially as described herein.
`
`The substrate 10 may have end-view cross-sectional shapes other than
`
`circular, such as square, rectangular, elliptical, clam-shell, or other shapes, and may
`
`have side-view sectional shapes other than rectangular, such as circular, square,
`
`elliptical, clam-shell, or other shapes. Alternatively, the substrate 10 may have a
`
`20
`
`geometry that is a combination of one or more of the foregoing shapes.
`
`Referring to Figs.12, 13,14, alternatively, two or more substrates 10,250, each
`
`having at least one grating therein, may be attached together to form the element 8,
`
`e.g., by an adhesive, fusing or other attachment techniques. In that case, the gratings
`
`12,252 may have the same or different ID codes.
`
`25
`
`Referring to Figs. 15,17, alternatively, the substrate 10 may have more than
`
`one region with codes. For example, there may be two grating side-by-side, or spaced
`
`end-to-end, such as that shown in Figs. 15,17.
`
`In Fig. 16, the element may be short and have a large diameter, such as a plug
`
`or puck or wafer.
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`Referring to Figs. 19 -20, the light may be incident on an axial end instead of
`
`from the side. In that case, the wavelength spectrum sets the code, as shown in Fig.
`
`23.
`
`Referring to Fig. 22, one side may be coated with a reflection coating to allow
`
`5
`
`light to be reflected back in the same side from which the incident light came.
`
`In Fig. 21, the elements may be placed in a tray with grooves 205 to allow the
`
`elements 10 to be aligned in a predetermined direction. Alternatively, the grooves
`
`may have holes 210 that provide suction to keep the microbeads 8 in position.
`
`The light 14 is incident on the grating 12 which reflects a portion thereof as
`
`10
`
`indicated by a line 16 having a predetermined wavelength band of light centered at a
`
`reflection wavelength A.b, and passes the remaining wavelengths of the incident light
`
`14 (within a predetermined wavelength range), as indicated by a line 18.
`
`Referring to Fig. 24, the substrate 10 may be coated with a material
`
`(functionalized) and used in a chemical reaction or as an attractant for certain
`
`15
`
`chemicals. In that case, the tag or optical identification element (bead) is produced,
`
`the surface is then functionalized, e.g., coated with a material that will react in a
`
`predetermined way with other chemicals. Then an assay is run with many different tag
`
`ID's at the same time. Then, the fluorescence of the microbead 8 is analyzed and the
`
`tag is read to determine information about the chemical reaction.
`
`20
`
`The microbead 8 may be placed in a tube for easier handling if desired.
`
`Referring to Figs. 25 - 26, there are shown some techniques for reading out the
`
`code on the microbead.
`
`Alternatively, the bead can be magnetically doped or coated with magnetic
`
`material, which may ease handling and/or alignment. The bead may be coated with
`
`25
`
`conductive material, e.g., metal coating on inside of holy fiber. Such a conductive
`
`coating will cause beads to align in a non-uniform electric field. Alternatively, the
`
`bead can be doped with a fluorescent element or compound, e.g., a rare earth dopant
`
`(such as Erbium, or other rare earth dopant). In that case, fluorescence may aid in
`
`finding beads if they are widely scattered.
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`

`
`,fl'-
`
`tt=·U!l ti "';1 il"~h fjU" ~fl~tl
`•• ij
`II;"j! n .• 1' · .... 11 ... ~lL •. lle II _ .. I' ·4j .. ~il.
`
`. tf"''ti<l:tU ¥ ... U
`'~"$-lI'ilT"!l~un'h
`,'j 11 .. ,11 .... :11 ",ll" .. j>;", 1]".11 II;""
`
`5
`
`Also, after initial manufacturing of the beads, the beads may be post processed
`
`to alter the size or shape, e.g., made smaller or rounded, by placing them in
`
`hydrofluoric acid (HF) or other etching or dissolving or melting solution or process.
`
`Some Advantages of Cylindrical Geometry I Assay on stick format
`
`Referring to Fig. 27, the cylindrical geometry of the Cidra micro beads lends
`
`itself to a few notable advantages over other spherical bead based formats. One very
`
`important aspect of any assay format is the ability to efficiently use the available
`
`sample ma