Patent Publication Number: US-2015076412-A1

Title: Manufactured product with optically encoded particle tag and id method

Description:
PRIORITY CLAIM AND REFERENCE TO RELATED APPLICATION 
     This application is a continuation of and claims priority under 35 U.S.C. §120 from prior co-pending application Ser. No. 10/503,217 filed Aug. 2, 2004, which was a 35 U.S.C. §371 application from PCT application PCT US 03/03040, filed Jan. 31, 2003, which claimed priority under 35 U.S.C. §119 from prior provisional application Ser. No. 60/335,234, which was filed Feb. 7, 2002. 
    
    
     TECHNICAL FIELD 
     A field of the invention is encoding. Additional exemplary fields of the invention include the life sciences, security, product marking, food processing, agriculture, and chemical detection. 
     BACKGROUND ART 
     A well-appreciated need for labeling exists in society. Labeling is a fundamental basis for tracking and identifying. Encoding can be used as a form of labeling understood by persons or equipment, as in the case of bar coding. At the microscale, however, labeling/encoding itself becomes difficult. 
     Strategies to encode microscale materials have accordingly received increased attention for such uses as high-throughput screening in the fields of drug discovery, genetics screening, biomedical research, and biological and chemical sensing. Concurrent research strategies for measuring an increased number of analytes while minimizing the necessary sample volume have focused on either on-chip spatially differentiated arrays or encoded beads. Large arrays have been developed for biological and/or chemical sensing purposes by making use of positional encoding to register specific analyte responses. The main advantage of using an array over a conventional single analyte sensor is the ability to process and analyze a large number of analytes simultaneously. Positional arrays, however, can suffer from slow diffusion rates and limits on the concentration ranges of analytes being sensed. An alternative approach is to use individually encoded beads. 
     Early attempts to encode particles used fluorescent or infrared-active molecules as binary markers. More recently, cadmium selenide quantum dots have been demonstrated as viable candidates for particle encoding based on their unique fluorescent properties. Quantum dots have the advantage over organic molecules of increased stability towards photobleaching, sharper fluorescence peaks, improved solubility characteristics, and large excitation frequency ranges. With six colors (limited to the peak width of the fluorescence in the visible range) and ten intensity levels, 10 6  particles could theoretically be encoded. In practice, this number is difficult to obtain because of spectral overlap and sample inhomogeneities. Also, despite the increased photostability of quantum dots, fluorescence quenching is still possible, casting uncertainty on using relative intensity measurements as a reliable encoding method. 
     Another encoding strategy has used sub-micron metallic rods. The sub-micron metallic rods are prepared by electrodeposition of metals on a porous membrane in alternating strips of controlled thickness. Different reflection characteristics of the various metals are used as a barcode for identification purposes. Reflection spectroscopy does not have the disadvantage of photobleaching inherent with fluorophores. Additionally, fluorescent analytes do not interfere with the particle signal. Deposition of rods is a relatively complex process, however, and may be difficult to apply as an encoding strategy where, for example, a large number of codes is desirable because each rod must be brought into focus in an optical reader (such as a microscope) in order to read out the codes. There remains a need for encoding strategies at the microscale. 
     SUMMARY OF THE INVENTION 
     The invention concerns an article of manufacture having a manufactured product marked with a microparticle and a method of marking a manufactured product. The microparticle tag includes a predetermined code embedded in its physical structure by refractive index changes between different regions of the particle. The particle has a diameter of a few hundred microns or less and has a plurality of layers. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1  is a schematic diagram of a multi-layer encoded particle of the invention; 
         FIGS. 2A and 2B  illustrate a preferred embodiment Fourier transform particle decoding; 
         FIG. 3A  illustrates an exemplary etching waveform for a preferred embodiment method of Rugate particle encoding; 
         FIG. 3B  illustrates a preferred embodiment Rugate particle decoding; 
         FIG. 4  illustrates a preferred embodiment method of fabricating encoded particles; 
         FIG. 5  shows the optical reflectivity spectrum of a single preferred embodiment encoded particle in laboratory air (solid line) and in air containing a small amount of ethanol vapor (dashed line); 
         FIG. 6  shows the intensity of reflected laser light (632 nm) from a preferred embodiment encoded porous silicon Rugate particle measured for three exposure/evacuation cycles using (from bottom to top as indicated) acetone, ethanol, toluene and water analytes at their saturation vapor pressures; 
         FIG. 7  is an image of exemplary preferred embodiment encoded particles formed in a wafer by a spatially defined, periodically varying etch; 
         FIG. 8  plots the reflectivity spectra from 15 separately coded exemplary preferred embodiment sample particles; 
         FIG. 9A  plots the reflectivity spectra from exemplary preferred embodiment single Rugate encoded sample particles and triply encoded Rugate sample particles; 
         FIG. 9B  is a schematic diagram of an exemplary preferred embodiment multiple Rugate encoded particle; and 
         FIG. 10  plots decoding results for exemplary preferred embodiment single Rugate encoded particles prepared for biological screening. 
     
    
    
     BEST MODE OF CARRYING OUT THE INVENTION 
     The invention concerns a particle having a code embedded in its physical structure by refractive index changes between different regions of the particle. A change in the refractive index is preferably obtained by varying porosity formed in the particle. Reflections taken from the particles produce an optical signature, in the visible and/or non-visible wavelengths. In preferred embodiments, the number of peaks, their locations, and intensities can be used to produce a high number of unique optical signatures. In preferred embodiment formation methods, a multi-layer porous encoded structure is produced by an etching process during which the etching conditions are varied during pore formation. A dicing may be conducted to form individual encoded particles having a range of small sizes, e.g., from hundreds of nanometers to hundreds of microns. 
     Methods and particles of the invention are applicable to a variety of industries, including but not limited to drug discovery, biological screening, chemical screening, biological labeling, chemical labeling, in vivo labeling, security identification and product marking. Various attributes of the particles and methods of the invention enable a wide range of applications in various industries. The small size of the particles facilitates ready incorporation into various hosts, e.g., products, test kits, assays, powders (such as explosives for identification), pastes, liquids, glass, paper, and any other host or system that can accept small particles. In vivo detection is enabled by biocompatible particles of the invention, which may then be queried, for example, through tissues using near infrared and infrared wavelengths that penetrate tissues. 
     In accordance with the aforementioned exemplary aspects and applications of the inventions, preferred embodiment particles are identified by the code inherent to the reflectivity spectrum of their varying porous structure. In another aspect of the invention, matter, e.g., biological or chemical matter, is hosted by the porous structure and the particle becomes a tag identifying the matter hosted by the pores. In another aspect of the invention, a variance in the reflectivity spectrum of an encoded particle can indicate the presence, absence or quantity of matter within the particle&#39;s pores. 
     Referring to  FIG. 1 , a preferred embodiment encoded particle  10  is shown in cross-section. The encoded particle  10  includes a multi-layer porous thin film having layers or regions  12   1 - 12   N . Multi-layer, as used herein, means that there must be a plurality of regions having distinct porosity. Transitions between porosity in some embodiments may be gradual. This means that multi-layer encompasses both structures having multiple gradual transitions of porosity and structures having multiple abrupt transitions of porosity. Consistent with this definition, the layers  12   1 - 12   N  are defined by varying porosity, which may change gradually or abruptly. Also, the use of “layer” encompasses separate deposits, for example, but also encompasses continuous structures having the varying porosity. In other words, “layer” includes but does not solely imply separate formation processes or depositions. The multi-layer porous thin film structure of layers or regions  12   1 - 12   N  having varying porosity is shown in  FIG. 1  as being formed on a substrate  14 . However, embodiments of the invention include particle structures of multi-layer thin films such as the layers  12   1 - 12   N  released from a substrate upon or from which they were initially formed. The porous layers  12   1 - 12   N  are encoded to produce an interference pattern in the reflectivity spectrum that forms an optical signature. Light reflected at the interfaces between the porous layers  12   1 - 12   N  interferes with light from interfaces between other ones of the layers to generate an interference pattern in the reflectivity spectrum. Particles  10  of the invention may be specifically encoded by controlling etching conditions and layer thicknesses during formation of the particle  10 . The refractive index at layer interfaces, chemical composition, and thickness of each layer  12   1 - 12   N  affects the optical signature generated by a particular particle. Thus, varying the relative porosity between layers in an individual particle (to affect the refractive index) and varying the layer thickness during formation of the particle  10  permits the tailoring of particular optical signatures in the reflectivity spectrum. Porosity also affects the intensity of peaks in the reflectivity spectrum, providing additional encoding potential. 
     The porous layers  12   1 - 12   N  may be formed of any porous semiconductor or insulator. In preferred embodiment particles of the invention, porous silicon is used to form the layers  12   1 - 12   N . Controlled anodic etching of crystal silicon in hydrofluoric acid solution permits control of both the porosity and thickness of porous layers  12   1 - 12   N . The time of etching controls the thickness of a porous layer, while the etching current density controls the porosity. The thicknesses and porosities of layers  12   1 - 12   N  are varied with respect to each other to produce a particular optical signature. 
     Variance in the porosity and thicknesses may in some embodiments be arbitrary, and in other embodiments follow a periodic pattern. In some embodiments, the porosity may vary gradually and in others the porosity may change abruptly from layer to layer. Porous silicon is a preferred material for the layers  12   1 - 12   N . Porous silicon has a number of demonstrated advantages. For example, porous silicon has been demonstrated to be biocompatible. In addition, the surface chemistry of oxidized porous silicon is effectively that of silica. Accordingly, the surface chemistry is well understood for biochemical derivatization and ligand immobilization. 
     In preferred embodiments, the layers  12   1 - 12   N  are formed to include a receptor material within the porous structure. The purpose of the receptor is to bind a particular analyte of interest. Exemplary receptors (also referred to as binders) are disclosed, for example, in U.S. Pat. No. 6,248,539 entitled “Porous Semicoductor Based Optical Interferometric Sensor”. Receptor molecules may be adsorbed or otherwise associated with the porous silicon layers  12   1 - 12   N  by any approach that leads to the tethering of the receptor molecules to the porous layers  12   1 - 12   N . This includes, without limitation, covalently bonding the receptor molecules to the semiconductor, ionically associating the receptor molecules to the layers, adsorbing the receptor molecules onto the surface of the layers, or other similar techniques. Association can also include covalently attaching the receptor molecules to another moiety, which is in turn covalently bonded to the porous layers  12   1 - 12   N , or binding the target molecule via hybridization or another biological association mechanism to another moiety which is coupled to the porous layers  12   1 - 12   N . Specific additional examples include receptor ligands that have been attached to porous silicon layers to produce biosensors. An analyte bound to a particle  10  of the invention becomes identifiable and traceable by the encoding provided by the particle  10 . 
     Encoding is possible for both intensity and wavelength properties of multi-layer films  12   1 - 12   N . A preferred embodiment is a particle  10  having multi-layer films  12   1 - 12   N  that have mismatched optical thicknesses. Optical thickness is defined as the refractive index of a layer multiplied by its metric thickness. Referring to  FIGS. 2A and 2B , a particle  10  encoded in such a manner reveals an optical signature in a Fourier transform of the resulting reflectivity interference spectrum. An exemplary resulting interference spectrum is shown in  FIG. 2A . The Fourier transform shown in  FIG. 2B  reveals an optical signature with well-resolved peaks. Particles  10  may be set to have a distinct series of peaks (a, b, c). 
     The intensity of peaks in the reflectance spectrum is controlled by the refractive index at interfaces between layers  12   1 - 12   N , determined by a change in porosity between adjacent layers. Such change may be gradual or sharp. The position of peaks is controlled by adjusting layer thicknesses. Additional encoding is possible by variation of the relative intensities of each reflectivity peak, which can be engineered into particles  10  of the invention by adjustment of the electro chemical etch parameters to control porosity of the layers  12   1 - 12   N . Accordingly, an N-layer particle  10  having A resolvable positions for each peak and B resolvable intensities can encode (A*B) N  particles. Additionally, a particle  10  having N peaks with A resolvable positions for each peak with any combination of order of relative intensities can encode one of N!(A) N . 
     Another encoding strategy involves periodic structures. Exemplary periodic structures include particles  10  having layers  12   1 - 12   N  configured by porosity and thickness to form a Bragg stack or a Rugate filter. Bragg stacks, for example, may be generated by alternating layers having matched optical thicknesses. A Bragg stack defined by varying porosity layers  12   1 - 12   N  in a particle  10  of the invention will produce peaks in the reflectivity spectrum with full width half maximum peaks in the reflectivity spectrum that are very well resolved, e.g., ˜10 nm. Rugate filters produced by variation of the refractive index of the interfaces through multi-layer structures  12   1 - 12   N  also generate similarly narrow peaks in the reflectivity spectrum while also suppressing side bands and higher order reflections. 
       FIGS. 3A and 3B  illustrate a preferred embodiment Rugate particle encoding strategy. A Rugate encoded particle may be created by etching a semiconductor or insulator with a periodic variance of etching conditions, such that the refractive index in the material varies in a sinusoidal (or apodised sinusoidal) function. The structures can be generated by etching the silicon wafer with a pseudo-sine current waveform.  FIG. 3A  indicates that a period for an exemplary sine wave variation of etching current density (n) in an etch used to produce the exemplary embodiment was 18 seconds. As seen in  FIG. 3B , a well-resolved narrow peak results from the encoding. The intensity and location of the peak can be varied with layer thickness and refractive index. 
     Referring now to  FIG. 4 , a preferred method for forming an encoded porous particle  10  is shown. A suitable semiconductor or insulator, e.g., a silicon wafer, is selected for processing (step  14 ). For example, silicon wafers may be cut to size and be masked to have portions exposed for etching. An exemplary suitable silicon material is a single crystalline silicon wafer. Spatial encoding is then defined (step  16 ). The spatial encoding defines a range of codes over the material to be etched. Conducting a spatially resolved etch allows codes to be programmed in particle-sized sections of the wafer. An exemplary spatially resolved etch is disclosed in U.S. Pat. No. 5,318,676, entitled “Photolithographic fabrication of luminescent images on porous silicon structures”, published Jun. 7, 1994. In an alternative process, the step of spatial defining (step  16 ) is omitted. For example, a single wafer or an area of wafer could be etched to include particles having a single code. In that case, other wafers could be etched to have particles having a different code. Anodic etching is then commenced, for example, in an aqueous solution of hydrofluoric acid and ethanol (step  18 ). Etching is then conducted with etching conditions varying according to the defined encoding strategy (step  20 ). A code or codes of the invention are etched into the wafer. The traverse (vertical direction in  FIG. 1 ) encoded but still connected particles may be lifted off from the silicon wafer (step  22 ), for example by a high level of electropolishing current. Areas between spatially defined etch sections may be cut to separate differently encoded wafer sections. Individual particles are then separated (step  24 ) in a dicing that may be conducted, for example, by mechanical agitation or ultrasonic fracturing. The particle separation (step  24 ) preferably produces micron-sized particles, e.g., particles in a range from a few hundred nanometers to a few hundred micrometers. A step of particle designation (step  26 ) may be conducted after the particle separation (step  24 ) or subsequent to step  20  or step  22 . Particle designation may comprise, for example, chemical modification of the porous multi-layer structure  12   1 - 12   N  for specific biological, biomedical, electronic, or environmental applications. As an example, the particles can be modified with a receptor for a desired analyte or with a targeting moiety (such as a sugar or a polypeptide). Additionally, binding can be signaled, for example, by fluorescence labeling of analytes or analyte autofluoresence. In use of particle  10 , the particle can be identified by its optical signature upon binding of the designated targeted analyte. This step of designation may also be omitted in embodiments of the invention. 
     In other embodiments of the invention, encoded particles can be placed into a suitable hosts, namely any liquid, powder, dust, or other material that will hold encoded micron sized particles of the invention. Particles placed in hosts, for example, could be used to identify the source of a manufactured powder such as an explosive. Another potential host is an animal. Particles of the invention being biocompatible may be implanted in vivo into an animal host. The reflectivity spectrum of preferred embodiment porous silicon particles  10  of the invention, for example, encompasses the visible, near infrared, and infrared spectra. This presents the opportunity to sense the code of a particle of the invention through barriers such as living tissue. 
     Example Embodiments and Experimental Data 
     Example embodiments of the invention will now be discussed. Experimental data is included for the purpose of illustrating to artisans the potential of the invention. Where given, equipment is specified only to allow artisans to understand experimental data reported herein. Commercial embodiment devices of the invention may take substantially different form, permitting low cost mass manufacturing, for example. 
     A first example embodiment is stand-off detection. This is a chemical detection technique to identify an analyte from a distance. A particle  10  of the invention includes a receptor to sense a particular analyte. Both the code of the particle and an indication of binding of the analyte can be detected in the reflectivity spectrum, for example, with use of a low power laser. The receptor, for example, can be specific to sense biomolecules or to attach the encoded particle to a cell, spore, or pollen particle. 
     A test of stand-off detection was conducted with exemplary encoded multi-layer porous silicon films. The multi-layered porous silicon films were prepared by an electrochemical etch of a (100) oriented polished Si wafer (p ++ -type, B doped, &lt;1 mΩ-cm resistivity) in a 1:3 ethanol:48% aqueous HF solution. The etching current density was modulated periodically with a pseudo-sine wave (between 11.5 and 34.6 mA/cm 2 ) to generate a sinusoidally varying porosity gradient. The films were removed from the substrate by applying a 30 second electropolishing pulse of current density of 600 mA/cm 2 . The freestanding films were then made into particles by mechanical grinding or by ultrasonic fracture to produce particles of sizes ranging from several hundred nanometers to a few hundred microns. The optical reflectivity spectrum in  FIG. 5  approximates a Rugate filter, displaying a sharp reflection maximum at a wavelength and source-sample-detector angle that satisfies the Bragg equation and appropriate phase matching condition. 
     The particles were immobilized on a glass plate and mounted in a gas dosing chamber fitted with an optical window and Baratron pressure gauge. The particles were illuminated with a 10 MW He/Ne laser. The as-formed particles strongly reflect the 632 nm light of the He/Ne laser at a wavelength in air, as seen in  FIG. 5 . The spectral position of the laser used to acquire the data presented in  FIG. 5  is shown for comparison (vertical arrow). The data were taken using an Ocean Optics CCD visible spectrometer at the focal plane of an optical microscope. When exposed to analyte vapors, capillary condensation causes the reflectivity spectrum of the particles to shift to longer wavelengths due to an increase in the refractive index of the porous medium and the particles are observed to go dark. 
     The relative change in light intensity simultaneously reflected from many of the particles was quantified at a fixed wavelength (632 nm) for a series of condensable analyte vapors, as seen in  FIG. 6 . The vapor pressure at 25° C. for each of these analytes is 222, 60, 28, and 24 Torr, respectively. Relative reflected light intensity was measured as the photocurrent from an amplified Si photodiode mounted at the objective of the 8-inch Schmidt-Cassegrain collection optics. The sample was 20 m from the laser and detection optics. Spectra are offset along the y-axis for clarity. The vapors were all introduced to the exposure chamber at their saturation vapor pressures. The intensity of reflected light was measured at a distance of 20 m in the presence of normal fluorescent room lighting using chopped light and phase-sensitive detection (Stanford Instruments SR-510 lock-in amplifier). No other optical or electronic filtering was used. The specificity of adsorption and/or microcapillary condensation at porous Si surfaces depends dramatically on the surface chemistry, and the hydrogen-terminated, hydrophobic as-formed material used in the experiments has a much greater affinity for hydrophobic versus hydrophilic analytes. Thus, the particles are relatively insensitive to water vapor at a partial pressure comparable to that used for the more hydrophobic organic analytes. No attempt was made to provide acoustic or vibrational isolation of the sample or optics, and most of the noise observed in the data is attributed to laboratory vibrations. Sensitivity should be further enhanced using a near infrared laser light source, where background radiation and atmospheric adsorption and scattering are less significant. 
     Another preferred exemplary application of the invention is for biomolecular screening via the encoded particle  10  of the invention. Millions of codes are possible with a small number of layers. A simple antibody-based bioassay using fluorescently tagged proteins has been tested. Periodic Rugate style encoding was used as described above with respect to the exemplary chemical sensing embodiments. By masking the wafer before etching, well-defined slabs of particles were generated, as seen in  FIG. 7 . 
     The  FIG. 7  particles were prepared to display a photonic spectral maximum at 632 nm. The scale in the inset (reproduced above the figure for clarity) corresponds to 2 μm per small division. The multi-layered encoded particles generated in this fashion display a very sharp line in the optical reflectivity spectrum. This line can appear anywhere in the visible to near-infrared spectral range, depending on the waveform used in the programmed etch. 
     Exemplary waveforms for 15 separate codes are shown in  FIG. 8 .  FIG. 8  shows the reflectivity spectra of 15 porous-silicon multi-layered samples prepared using a sinusoidal etch (Rugate encoded structure). Each of the samples contains a single Rugate frequency code. Spectra were obtained using a Cambridge Instruments microscope with a 70× objective. The sample was illuminated using a tungsten lamp, and the reflected light spectrum was measured with an Ocean Optics SD2000 CCD (charge-coupled device) spectrometer. The sample particles were prepared by anodically etching p ++  type, B-doped, (100)-oriented silicon (resistivity&lt;1 mΩ-cm 2 ) in a solution of 48% aqueous HF:ethanol (3:1 by volume). Typical etch parameters for a Rugate structure used in a pseudosinusoidal current waveform oscillating between 11.5 and 19.2 mA cm −2  with 50 repeats and a periodicity of 18 s. Films were removed from the substrate using a current pulse of 460 mA cm −2  for 40 s. Lithographically defined particles were prepared by applying an S-1813 photoresist (Shipley) to the wafer before the electrochemical etch (spin coated at 4,000 r.p.m. for 60 s, soft-baked at 90° C. for 2 min., ultraviolet-exposed using a contact mask aligner, hard-baked at 120° C. for 30 min. before development). The spectral features exemplified by  FIG. 8  can be much narrower than the fluorescence spectrum obtained from a molecule or core-shell quantum dot. 
       FIG. 9A  shows the reflectivity spectra of porous silicon Rugate encoded particles etched with a single periodicity (bottom) and with three separate periodicities (top).  FIG. 9B  schematically illustrates a preferred embodiment multiple encoded particle  10   a , wherein there are three sets of encoded layers  12 ,  16 , and  18 . Multiple Rugate codes may be separated spatially, but also may be etched in the same physical location, as sets of multi-layers formed at different depths, each forming a separate Rugate encoding. Each of the layer sets  12 ,  16 , and  18  includes a periodically varying porosity to produce a separate Rugate, or alternatively, Bragg, code. 
     The example particles display peaks in the reflectivity spectrum characteristic of their multi-layered structures. The sample represented in the bottom spectrum was etched using a sinusoidal current variation between 11.5 and 19.2 mA cm −2  with 50 repeats and a periodicity of 18 s. The triply encoded particle (triple Rugate) represented by the top spectrum was prepared using a sinusoidal current variation oscillating between 11.5 and 34.6 mA cm −2  with a periodicity of 10 s for 20 periods (520 nm), 12 s for 45 periods (610 nm), and 14 s for 90 periods (700 nm). The approximate thickness of this sample is 15 μm. Spectra are offset along the y axis for clarity. 
     To test the reliability of the encoding approach in a biological screening application, we prepared two different batches of encoded particles as single Rugate structures. Both batches of particles were ozone-oxidized to improve their stability in aqueous media and to provide a hydrophilic surface. The particles were oxidized in a stream of O 3  diluted with compressed air. Control particles coded with a 750-nm spectral feature were treated with concentrated BSA (Sigma, 5 g in 100 ml of double-distilled water) and incubated at 37° C. under 5% CO 2  in air for three hours. The 540-nm-encoded test particles were exposed to 50 μg ml −1  rat albumin in coating buffer (2.93 g NaHCO 3 , 1.61 g Na 2 CO 3  in 1,000 ml double-distilled water), and incubated at 37° C. under 5% CO 2  for two hours. The test particles were then exposed to a 1:100 dilution of primary rabbit anti-rat-albumin antibody in a concentrated solution of BSA at 37° C. under 5% CO 2 , for one hour. Both batches of particles were then mixed together and incubated for one hour in the presence of FITC-(fluorescein isothiocyanate) conjugated goat anti-rabbit immunoglobulin-G in a BSA solution. Detection of analyte binding to the encoded particles was then performed by fluorescence and spectral reflectance microscopy. 
     Decoding results are shown in  FIG. 10 . Decoding, performed on 16 particles, yielded the following results: among eight green fluorescent particles, eight particles were positively decoded as belonging to the functionalized rat albumin batch (plot A in  FIG. 10 ). Among the eight non-luminescent particles, six particles were correctly decoded (plot B in  FIG. 10 ), one particle displayed the incorrect code and one particle was unreadable. Presumably, the particle that displayed the incorrect code belonged to the first batch but was not sufficiently functionalized with rat albumin to generate fluorescence in the antibody assay. This is understandable because in the experiment the rat albumin was not covalently attached to the silica-coated particles. A variety of stable chemical modification chemistries have been developed for oxidized and non-oxidized porous silicon, and some of these have been demonstrated with specific antibodies or receptors. Thus, the issue of immobilizing biochemical or chemical components is easily addressable. Additionally, chemical modification can prevent corrosion in aqueous media, which may otherwise lead to undesirable shifts in the optical code and/or unreadable particles. In the conducted experiments, no passivating chemical treatments, other than ozone oxidation to generate a layer of silica, were performed, and upon immersion in basic aqueous media the spectral codes were observed to shift between 0 and 50 nm depending on the incubation times. 
     The layered porous-silicon encoded structures offer several advantages over existing encoding methodologies. Porous-silicon encoded structures can be constructed that display features spanning the visible, near-infrared and infrared regions of the spectrum. In addition, the reflectivity spectra of Rugate filters can exhibit much sharper spectral features than can be obtained from a gaussian ensemble of quantum dots. Thus, more codes can be placed in a narrower spectral window with the porous encoded structures. Unlike encoding schemes based on stratified metallic nanorods, fluorescence or vibrational signatures, encoded particles of the invention can be probed using light diffraction techniques; thus it is not necessary to use imaging optics in order to read the codes. Encoded particles may be assayed using a conventional fluorescence tagging technique, and sensitive chemical and biochemical detection can also be built into the optical structure of the encoded particles, eliminating the need for fluorescent probes and focusing optics. In addition, because preferred embodiment oxidized porous-silicon encoded particles present a silica-like surface to the environment, they do not readily quench luminescence from organic chromophores, and they can be handled and modified using the chemistries developed for glass bead bioassays. Silicon-based encoded particles may be readily integrated with existing chip technologies. 
     The use of encoded silicon particles of the invention in medical diagnostic applications has advantages over organic dyes or quantum dots. In vivo studies have shown the biocompatibility of porous silicon, as well as the long-term stability of reflectance data from multilayer structures. Additionally, the possibility of optically addressing particles at near-infrared, tissue-penetrating wavelengths without the losses associated with low fluorescence quantum yields makes these materials amenable to in vivo diagnostics. Finally, because the porous codes are an integral and orderly part of the porous structure, it is not possible for part of the code to be lost, scrambled or photobleached, as can occur with quantum dots or fluorescent molecules. 
     While specific embodiments of the present invention have been shown and described, it should be understood that other modifications, substitutions and alternatives are apparent to one of ordinary skill in the art. Such modifications, substitutions and alternatives can be made without departing from the spirit and scope of the invention, which should be determined from the appended claims. 
     Various features of the invention are set forth in the appended claims.