Abstract:
The present invention provides an automated analyzer system for performing chemical, biochemical or biological assays using changes/no changes in diffraction of light by the presence/absence of analytes which may or may not be present in a sample binding to their analyte specific receptors laid out in a preselected pattern in a disposable sensor. The analyzer is a modular, bench-top instrument that compactly integrates subsystems for sample dispensing, liquid handling, and optical generation of laser light beams and detectors for detecting for diffracted light. An internal processor is included for automating the instrument, and a user interface to provide communication with the operator.

Description:
CROSS REFERENCE TO RELATED U.S. APPLICATIONS 
     This patent application relates to, and claims the priority benefit from, U.S. Provisional Patent Application Ser. No. 60/798,719 filed on May 9, 2006, in English, entitled AUTOMATED ANALYZER USING LIGHT DIFFRACTION, and which is incorporated herein by reference in its entirety. 
    
    
     FIELD OF THE INVENTION 
     The present invention is related to an automated analyzer particularly for applications for analyte detection using diffractive optics technology. 
     BACKGROUND OF THE INVENTION 
     Recently, automated analyzers for performing chemical, biological and biochemical assays have become widespread for use by diagnostic &amp; research laboratories for the rapid and reliable detection of analytes in a variety of biological samples. Analyzers are routinely used to perform a wide variety of assays, most of which involve immunoassays where the high affinity and selectivity of an antibody for its antigen is exploited. Many of these systems are based on measurement of emitted light such as chemiluminescence caused by reactions in the assay. 
     For example, in many instances, it is desirable to determine the presence and the amount of a specific material in solution (the ‘medium’). Surface-based assays rely on the interaction of the material to be assayed (the ‘analyte’) with a surface that results in a detectable change in any measurable property. For the purpose of this patent application, the term ‘analyte’ refers to the material to be assayed. Examples of analytes include: an ion; a small molecule; a large molecule or a collection of large molecules such as a protein or DNA; a cell or a collection of cells; an organism such as a bacterium or virus. ‘Analyte-specific receptor, or ‘recognition element’ refers to that complementary element that will preferentially bind its partner analyte. This could include: a molecule or collection of molecules; a biomolecule or collection of biomolecules, such as a protein or DNA; a groove on the substrate that has the complementary geometry and/or interaction. In general, in order to assay for a specific analyte, the surface is modified so as to offer the appropriate chemical interaction. 
     In immunoassays, for example, one takes advantage of the specificity of the antibody-antigen interaction: A surface can be coated with an antigen in order to assay for the presence of its corresponding antibody in the solution or vice versa. Similarly, a strand of deoxyribonucleic acid (DNA) can be attached to a substrate and used to detect the presence of its complementary strand in solution. In any of these cases, the occurrence of binding of the analyte to its recognition element on the surface, which thus identifies the presence of the specific analyte in solution, is accompanied by a detectable change. For example, the binding can produce a change in the index of refraction at the interfacial layer; this can be detected by ellipsometry or surface plasmon resonance. Alternatively, the bound analyte molecules may emit light; this emission can be collected and detected, as is the case for fluorescence-based sensors. Non-optical signals may also be used, as in the case of radio immunoassays and acoustic wave sensing devices. 
     Diffraction is a phenomenon that occurs due to the wave nature of light. When light hits an edge or passes through a small aperture, it is scattered in different directions. But light waves can interfere to add (constructively) and subtract (destructively) from each other, so that if light hits a non-random pattern of obstacles, the subsequent constructive and destructive interference will result in a clear and distinct diffraction pattern. A specific example is that of a diffraction grating, which is of uniformly spaced lines, typically prepared by ruling straight, parallel grooves on a surface. Light incident on such a surface produces a pattern of evenly spaced spots of high light intensity. This is called Bragg scattering, and the distance between spots (or ‘Bragg scattering peaks’) is a unique function of the diffraction pattern and the wavelength of the light source. There is a unique correspondence between a pattern and its diffraction image, although in practice, diffraction is best illustrated by using periodic patterns, because these yield easily recognized diffraction images of clearly defined regions of high and low light intensity. 
     There is therefore a need for an analyzer which is based on diffraction of light that that offers ease of use, minimal sample handling, low consumable cost and assay versatility in a compact instrument. 
     SUMMARY OF THE INVENTION 
     The present invention addresses the need for an automated analyzer for diffraction-based screening of fluids such as liquids for analytes. 
     An embodiment of an analyzer for performing chemical, biochemical or biological assays using diffraction of light, comprises: 
     a disposable sensor including at least one sample well and at least one pre-selected pattern of analyte-specific receptors bound to a surface of said at least one sample well; 
     at least one sensor station for receiving said disposable sensor; 
     a fluid holding sample container for holding assay fluids used in performing said assays and samples being tested for presence or absence of analytes which bind to said analyte-specific receptors; 
     a fluid flow and handling system in flow communication with said at least one sensor, sources of said samples and sources of said assay fluids used in performing said assays configured to deliver said samples and fluids to said at least one well in said disposable sensor and said fluid holding sample container, said fluid flow and handling system including fluid pump configured to pump fluids and samples from their respective sources to said disposable sensor, to said fluid holding sample container and to fluid waste containers, said fluid flow and handling system including a fluid dispenser configured to dispense samples and fluids to said fluid holding sample container and to dispense samples and assay fluids from said fluid holding sample container to said at least one sensor; 
     a robotic manipulator connected to said fluid holding sample container configured to pre-position said fluid holding sample container with respect to said fluid dispenser; 
     a temperature controller for controlling a temperature of an interior of the analyzer; 
     an optical system for producing and directing a coherent beam of light toward said at least one sensor station to impinge on said surface of said at least one sample well containing said at least one pre-selected pattern of analyte-specific receptors bound thereto, said optical system including a first optical detector configured to measure diffracted light signals from said at least one pre-selected pattern of analyte-specific receptors; 
     a scanning mechanism for scanning said coherent beam of light with respect to said at least one sample well containing said at least one pre-selected pattern of analyte-specific receptors bound thereto; and 
     a microprocessor controller connected to said scanning mechanism, said scanning mechanism being configured to scan said coherent light beam across said surface in a controlled manner, and said microprocessor controller being programmed with instructions to scan said coherent light beam across pre-selected portions of said at least one pre-selected pattern of analyte-specific receptors prior to flowing sample containing the analytes into said disposable sensor, and based on qualities of signals received from said pre-selected portions, the microprocessor being programmed with instructions to determine a selected region in said at least one pre-selected pattern of analyte-specific receptors to subsequently monitor said diffracted light signals after sample has been admitted into said disposable vessel;
         said microprocessor controller also being connected to
           said temperature controller, and programmed to control the temperature controller to control the temperature in said analyzer,   said robotic manipulator, and programmed to pre-position said fluid holding sample container with respect to said fluid dispenser,   said fluid flow and handling system, and programmed to control sample and assay fluid flow routes through said fluid control system,   said optical system, and programmed to control parameters of said coherent light beam, said optical detector being configured to analyze said measured diffracted light signals from said at least one pre-selected pattern of analyte-specific receptors for determining a presence or absence of analytes in said sample based on the presence or absence of a change in diffraction pattern before and after sample has been admitted into said disposable vessel; and   said microprocessor controller including a user interface enabling interaction between the analyzer and an operator.   
               

     A further understanding of the functional and advantageous aspects of the invention can be realized by reference to the following detailed description and drawings. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       The invention will be more fully understood from the following detailed description thereof taken in connection with the accompanying drawings, which form a part of this application, and in which: 
         FIG. 1  shows a schematic view of a sensor for analyte-specific detection used in the apparatus of the present invention where A) shows two substrates with analyte-specific receptors, B) shows the interrogation of the receptors with nothing bound, and C) shows the interrogation of the receptors with analyte bound; 
         FIG. 2  shows a perspective drawing of the analyzer apparatus; 
         FIG. 3A  shows schematic layout of the fluidic control module forming part of the analyzer in  FIG. 2 ; 
         FIG. 3B  shows a close up view of a portion of the two-axis fluid handling robot and a portion of the fluid control module; 
         FIG. 4  shows an assembled view of an embodiment of a disposable sensor according to the present invention; 
         FIG. 5  shows an exploded view of a part of the disposable sensor shown in  FIG. 4 ; 
         FIG. 6  shows an enlarged view of a part of the disposable sensor shown in  FIG. 4 ; 
         FIG. 7  shows an isometric view of the optics subsystem of the present analyzer; 
         FIG. 8  shows an exploded view of the optics subsystem shown in  FIG. 7 ; 
         FIG. 9  shows an exploded view of the main structure assembly forming part of the optical subsystem shown in  FIG. 7 ; 
         FIG. 10  shows a schematic cross sectional view of a sensor receiving structure with a part of the sensor in place; 
         FIGS. 11A ,  11 B,  11 C and  11 D show multiple schematic views of the optical path implemented in the analyzer by the components of the optical subsystem shown in  FIG. 7  and a disposable sensor shown in  FIG. 4 ; 
         FIG. 12  shows multiple views of the optical block which a component of the optical subsystem shown in  FIG. 7 ; 
         FIGS. 13A and 13B  show schematic cross sectional views of the optical subsystem illustrating the workings of the system interlocks; 
         FIG. 14  shows a) an assembled view of the latch side assembly which positions and/or seals the disposable sensors in the analyzer and b) an exploded view thereof; 
         FIG. 15  show a schematic cross sectional view of an exemplary optical element and relevant angles and optical paths for obtaining total internal reflection given the particular materials being used for the optical element and analyte-receptors patterns. 
     
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     Generally speaking, the systems described herein are directed to an automated analyzer using light diffraction. As required, embodiments of the present invention are disclosed herein. However, the disclosed embodiments are merely exemplary, and it should be understood that the invention may be embodied in many various and alternative forms. The Figures are not to scale and some features may be exaggerated or minimized to show details of particular elements while related elements may have been eliminated to prevent obscuring novel aspects. Therefore, specific structural and functional details disclosed herein are not to be interpreted as limiting but merely as a basis for the claims and as a representative basis for teaching one skilled in the art to variously employ the present invention. For purposes of teaching and not limitation, the illustrated embodiments are directed to an automated analyzer using light diffraction. 
     As used herein, the term “about”, when used in conjunction with ranges of dimensions of particles or other physical properties or characteristics, is meant to cover slight variations that may exist in the upper and lower limits of the ranges of dimensions so as to not exclude embodiments where on average most of the dimensions are satisfied but where statistically dimensions may exist outside this region. It is not the intention to exclude embodiments such as these from the present invention. 
     The present invention provides an automated or user operated bench-top instrument intended for use in analyte detection and/or examining binding events using diffractive optics technology which may be used in research or diagnostic applications. Diffraction occurs due to the wave nature of light: when light hits a non-random pattern of obstacles, the resulting constructive and destructive interference will result in a clear diffraction image. Referring to  FIG. 1A , an when proteins, antibodies, or other molecules are deposited on a surface in a specific pattern, a diffractive optical element is created that, when interrogated with a laser as in  FIG. 1B , diffracts light into diffractive orders. Binding of analyte to the pattern will increase its mean height, thickness, density, and/or a combination thereof, thereby causing a change in the intensity of diffracted light as in  FIG. 1C  which is different from intensity in  FIG. 1B . This technique is not limited to detection of binding events per se but could also include interactions involving dissociation of bound materials, confirmational changes, compositional changes, and/or a combination thereof. 
     If the pattern is placed on the surface of properly constructed, optically clear prism, light can interrogate the pattern by total internal reflection (TIR), without passing through the sample. Since the technique can be performed in TIR the analyzer does not require clear solutions. 
     Details of the method of determining the absence or presence of analytes in a sample using changes in diffraction patterns by the analytes binding to their analyte specific receptors is disclosed in U.S. Pat. No. 7,008,794 issued to Goh et al. on Mar. 7, 2006 entitled: Method And Apparatus For Assay For Multiple Analytes, which is incorporated herein in its entirety by reference. 
     The instrument constructed in accordance with the present invention is shown generally at  10  in  FIG. 2 , and includes a housing  12 , an integrated computer (microprocessor controller) mounted within the housing  12 , in communication with a wireless-keyboard  15 , and a monitor  14 . The computer is configured with control and processing software which allows coordinated control and monitoring of the fluidic control module  16 , the optical subsystem (partially shown at  460 ), a the two-axis sample handling robot  20 , data recording, display, and processing, communication to external devices and networks, and a user interface through which the user can define assay protocols or select and utilize pre-configured assay protocols. 
     Four sensor stations  19  are shown integrated into the optical subsystem  460 , to be described hereinafter, for receiving disposable sensors. The integrated fluidic control module  16  configured to provide delivery of samples, reagents, buffers and the like to the disposable sensors to monitor and subsequently analyze and otherwise conduct assays on samples using a multiplicity of reagents. The two-axis sample handling robot  20  provides walk away automation, sample and reagent loading, accepts microtiter plates or tubes and includes a wash station provided to clean the liquid delivery probes  340 . 
     The instrument will be more comprehensively described beginning with the fluidic control module  16 . 
     Fluid Control Module 
     The instrument  10  is provided with the automated and integrated fluid control module  16  ( FIG. 3A ) which is configured to provide delivery of samples, reagents, buffers and the like to sensors  316  to monitor and subsequently analyze and otherwise conduct assays on samples using a multiplicity of reagents. 
     More particularly  FIG. 3A  shows a schematic drawing of the fluid control module  16  forming part of the analyzer  10  and includes a fluid or liquid dispensing station having two syringe pumps  300  and  302  both including a multi-port valve. A multi-port rotary valve  308  is connected to the two syringe pumps  300  and  302  through a three-port connector  310 . The interconnecting tubing  307  is preferably Teflon tubing with a flangeless ferrule and M6 male nut fitting at each termination. Tubes  313  lead from four ports of the multi-port rotary valve  308  and terminate at the system side of a manifold  312 . Three ports  315 ,  317 , and  319  allow for bulk reagents from liquid containers  311 ,  306  and  309 , respectively, to enter the system through valve  308  (from container  311 ) and through pumps  302  and  300 . The sensor side of the manifold  312  is fitted with quick-connect fittings  314 , one for each of the four sensors  316 , with a format that mates with an injection molded fitting  318  that is glued to a length of PVC tubing (0.060″ O.D., 0.020″ I.D.)  320  leading to the system side port  322  of each of the sensors  316  where they are permanently connected using glue or some other means of retention, for example, solvent bonding, friction fit, etc. 
     The sensors  316  include lengths of PVC tubing (0.060″ O.D., 0.020″ I.D.)  320  and  330  connected to injection molded fittings  318  and  332 , respectively. Each injection molded fitting  318  and  332  mate to one quick connect fitting  314  and  334  (partially visible in  FIG. 7   b ) respectively. Quick connect fittings  334  are located on a stationary structure referred to as the arm  338 . Each of the four quick connect fittings  334  mounted to the arm  338  make a fluidic coupling to one probe  340  that protrudes beneath the arm  338  and is positioned on a spacing appropriate to access the sample containers  350  which are situated on a two-axis fluid handling robot  20  shown in  FIG. 2 . It should be noted that probes  340  may be re-usable or disposable. 
     The entirety of the disposable sensor as shown in  FIG. 4  includes the tubes  320  and  330 , the injection molded fittings  318  and  332 , the upper lid  402 , and the patterned prism  400 . The instrument  10  can be readily configured to accept alternative constructions of the disposable sensors  316  described hereinafter. 
       FIG. 3B  shows the sample containers  350  loaded onto an aluminum sample rack  360  which makes contact with a temperature control plate  362 . The temperature control plate  362  maintains the aluminum sample rack  360 , thereby sample container  350 , and thus the fluids held within the sample container  350  at the user defined temperature setpoint. The temperature of the temperature control plate  362  may be controlled by means of resistive heating, thermoelectric elements, or circulating temperature control fluids. Exemplary temperature control characteristics of the temperature control plate  362  are: 
     Range: 4-40 deg C. 
     Precision: +/−1 deg C. 
     Accuracy +/−2 deg C. 
     In addition to the sample container  350  on the two axis fluid handling robot  20  ( FIG. 1 ) there is a drip-well  364  ( FIG. 2 ) which captures fluids which may escape from the probes  340  when the injection molded fittings  332  are removed from the quick connect fittings  334 . Referring to  FIG. 3A  a wash/waste station  344  is provided with a construction that may include a 125 mL Nalgene bottle with a custom injection molded cap. The functionality of the wash/waste station  344  is to provide; a wash-station  370 , including four wash wells  376  which receive wash solution from probes  340  after the probes have been aligned with their associated wash wells  376 . The four wash wells  376  are individually separable from the others, allowing for individual configurations such that the washing characteristics may be matched to different configurations of the probes  340 . 
     The inside walls and outside walls of each of the probes  340  can be washed using wash buffers that are delivered through the probes  340 . A trough  372  allows for waste fluids exiting the probes  340  to be directed toward the waste bottle (not shown) situated directly beneath the waste/wash station  344 , and attached to the waste/wash station. Optionally a port  380  allows wasted buffer flowing through tube  342 , from the pumps  300  and  302 , and valve  308  without passing through the sensors  316  or probes  340  to be collected in the waste bottle (not shown). 
     The configuration of the waste/wash station  344  and the sample container  350  is such that they may be readily removed and replaced manually or using simple laboratory robotic systems. 
     The two-axis fluid handling robot  20 , the temperature controlled sample container  350 , a drip-well  364  ( FIG. 2 ), and the waste/wash station  344  ( FIGS. 2 and 3A ) is a separate sub assembly that can easily be separated from the rest of the instrument. This modularity is very advantageous to allow removal and disposal in the event of biohazardous contamination. 
     The present apparatus may use several different sample containers, including 96 well micro-titre plates and 48 well micro-titre plates both compliant with SBS standards, 1.8 mL BD Freezer vials, 1.0 mL Eppendorf tube and 0.5 mL Eppendorf tube. 
     The fluids can flow through the fluid control module  16  in user configured specified routes or combinations thereof, of which the following are four non-limiting examples: 
     1) From the bulk reagent bottles  306 ,  309 , and  311 , through the tubing  307  multi-port valve  308  and/or pumps  300  and  302 , and through the waste line  342  directly to the wash/waste station  344 . 
     2) From the bulk reagent bottles  306 ,  309 , and  311 , through the multi-port valve  308  and/or pumps  300  and  302 , through one or more of the four sensors  316 , through one of the four probes  340 , and into the waste station  372 . 
     3) From the bulk reagent bottles  306 ,  309  and  311 , through the six-way valve  308  and/or pumps  300  and  302 , through one or more of the four sensors  316 , through one or more of the four probes  340 , and into the wash station  370 . 
     4) Samples or small volume reagents can be aspirated (pumped) back to the sensors  316  through tubes  330  from the sample containers  350 , and delivered to, and incubated in, one or of the sensors  316 , and subsequently dispensed from one or more of the four probes  340  into the waste station  372 . 
     It will be clear to those skilled in the art that alternate fluid handling sequences can be supported using the existing hardware, for example, dilutions, combinations, mixing, reclamation of effluent samples/reagents, and the like. 
     While the fluid control module  16  has been described with various components these are only exemplary and may be substituted with other components. For example syringe pumps  300  and  302  may be replaced with peristaltic pumps, other types of piston or rotary pumps, electro-osmotics devices, pressurized fluid delivery means, and/or multi-channel pipetting systems. The functions of the various valves, connectors, and manifolds in the instrument  10  can be replicated using networks of two-way valves, integrated manifold based systems, micro-fluidic systems, and combinations thereof. 
     Sample and reagent introduction is accomplished by the user loading samples and any required reagents into a SBS  96  well microtiter plates and/or bulk buffer containers and executing a prepared assay protocol which delivers fluids at desired volumes, times and flow rates to the disposable sensor  316 . Protocols may be user determined within the constraints of system hardware. 
     The control software may be configured so that assays may be run in the four sensors  316  sequentially (one protocol completes before initiation of another) or interleaved (the protocol for each sensor  316  is started when system hardware is available). 
     Data is represented graphically on screen  14  as it is generated as detector output plotted on a time scale. The user can determine the details of presentation choosing for example to show data from all analyte-receptor patterns  412  on all sensors  316  or selecting specific assay locations for onscreen presentation. Data files are generated corresponding to each sensor position and are exportable in standard formats for off line analysis in standard programs (MS Excel™, GraphPad Prism™, or in customized data analysis programs). 
     Sensors 
     The sensors  316  each include a molded plastic housing and are preferably constructed as a consumable with one or more preselected patterns on a planar surface of the consumable as disclosed in United States Patent Publication No. US-2005-01480635-A1 with a publication date of Jul. 7, 2005 entitled: DISPOSABLE REACTION VESSEL WITH INTEGRATED OPTICAL ELEMENTS, which is incorporated herein in its entirety by reference. 
       FIG. 4  shows an assembled view of the disposable sensor  316  with the liquid tubes  320  and  330 , and the fluidic fittings  318  and  332 , respectively, coupled thereto and an upper lid  402  designed to mate with patterned prism  400 . More specifically  FIG. 5  shows an exploded view of a portion of disposable sensor  316  wherein it is illustrated that upper lid  402  mates with patterned  400  which when assembled forms a defined interior chamber to allow flow of fluids across the analyte-receptor patterns  412 . 
     Upper lid  402  includes a lip  406  which in this embodiment helps define the chamber and provides alignment features for assembling lid  402  with patterned prism  400 .  FIG. 6  shows a slightly enlarged view of the bottom of upper lid  402  The tubes  320  and  330  provide connection to the lid  402  to provide the fluid connection to the chamber in sensor  316 . This described structure allows connection to fluid control module  16  described in detail previously. Patterned prism  400  as shown in this exemplary embodiment includes an integrally formed optical element  410  through which light accesses the analyte-receptor patterns  412  ( FIG. 1A ) within sensor  316  from the optical subsystem described hereinafter and from which emerges the diffracted light beams which then enters the detector in the optical subsystem. 
     Referring to the schematic drawing of the interior of the optical element  410  as shown in  FIG. 1A  it can be seen that the inner surface of optical element  410  has one or more analyte-receptor patterns  412  formed thereon, which may be identical for redundancy or they may be different patterns and/or different receptors. 
     In an embodiment of the sensors  316 , the bottom surface of optical elements  410  have four (4) pre-selected analyte-specific receptors patterns spaced from each other but there may be more or less patterns as described with respect to  FIG. 1A  above. Details of one non-limiting and exemplary method of depositing these preselected patterns on a substrate is disclosed in U.S. Pat. No. 6,981,445 issued to Cracauer et al. on Jan. 3, 2006 entitled: Method And Apparatus For Micro-Contact Printing, which is incorporated herein in its entirety by reference. 
     Prior to operation, the sensors  316  are inserted into the sensor station  19  stations in the optical subsystem  460  and a clamp  554  shown in  FIG. 13  is closed which includes an interlock system to ensure the laser beam is not turned on until the interlock system is engaged. 
     Optical Subsystem 
     As seen in  FIG. 8 , the optical subsystem  460  ( FIG. 7 ) is comprised of the main structure assembly  461 , the latch side assembly  462 , and the clamp side assembly  463 .  FIG. 9  shows an exploded view of the main structure assembly  461  which is comprised of the frame assembly  464  and the block assembly  465 . The frame assembly  464  is comprised of two supports  466 , one connected to each end of prism bed  467 . The prism bed  467 , made of machined and anodized aluminum, is the main component in the optical subsystem  460  responsible for positioning the sensor  316  (not shown) in the optical path. The prism bed  467  contains four sensor receiving structures  468  (but could be configured to include more or less), each capable of accepting one sensor  316 . 
     The sensor receiving structures  468 , essentially identical to one another, match the form fit of the patterned prism  400  and provides contact surfaces  474  and  476  shown in  FIG. 10  which is a cross-sectional schematic showing the relationship between the patterned prism  400  and the sensor receiving structures  468  contained within the prism bed  467 . Feature  474  is an essentially planar element of the sensor receiving structures  468  to which feature  478 , an essentially planar element of the optical element  410  registers. This registration establishes one axis of optical alignment between the optical element  410  of the patterned prism  400  and the prism bed  467 . Additionally this registration is the primary location of heat transfer between the prism bed  467  and the sensors  316 . Features  476  are essentially planar elements of the sensor receiving structures  468  to which features  480 , an essentially planar element of the patterned prism  400 , register. This registration establishes lateral alignment of the optical element  410  to the prism bed  467 . Additionally this registration is a secondary location of heat transfer between the prism bed  467  and the sensors  316 . 
     This configuration advantageously provides precise positional locationing of the optical element  410  relative to prism bed  467  at a location in closest proximity to the relevant optical surfaces of optical element  410 . This registration therefore provides the necessary optical alignment between the sensor  316  and the prism bed  467  while at the same time providing the necessary thermal control at a location close to the patterns and fluid channel in the sensor  316 . Since both thermal drift and optical misalignment may cause a rapid degradation of signal integrity this configuration is highly advantageous. 
     The prism bed  467 , thereby the sensor(s)  316 , as they are in thermal contact, may be temperature controlled in the range from about 4 to about 40 deg Celsius as an example. 
     Referring to  FIG. 11A  through  FIG. 11D  the optics block  500  is the structural component, made of machined and anodized aluminum, which holds the laser-head  502 , at least one diffraction signal detector  504 , and optionally a reflected main beam detector  506  in a fixed reference relative to each other. The laser-head  502  houses a red laser diode (not shown) whose emission is a laser beam  508  co-linear with the centroid of the outer shell of laser-head  502 , thus allowing for the alignment of the laser beam  508  with respect to the optics block  500  to be determined by the mechanical precision of the machined bore  510  relative to optical block mounting bores  514  and  516 , where the two bores  514  receive the signal detectors  504 , and bore  516  receives the reflected main detector  506 . Additionally, the precision of the fit between the laser head  508  and the bore  510  facilitates the establishment of a stable thermal relationship between the laser head  508  and the optics block  500 . The unitary structure of the block  500  facilitates highly precise machined relationships without secondary assembly tolerances affecting the precision of the optical alignment. Additionally, this unitary construction minimizes the affects of thermal expansion and contraction on the optical alignment of all optical elements within the block assembly  465 . It will be understood that the laser head may house a variety of laser diodes of appropriate wavelength and power and may house additional optical conditioning elements to shape and direct the beam. 
     Two linear rails  518  link the prism bed rail reference surface  520  to the block rail reference surfaces  512  thereby establishing a reference between the block assembly  465  and the sensors  316 . These two linear rails  518  provide the mechanical reference between the block assembly  465  and the frame assembly  464  and allow longitudinal motion with respect to sensor  316  enabling presentation of each analyte-receptor patterns  412  on each sensor  316  to the laser beam  508  and transmission of the diffraction beams  522  and the reflected main beam  524  to diffraction signal detectors  504  and reflected beam detector  506 , respectively. Linear rails  518  must be of adequate precision to satisfy the required optical alignment tolerances. Components of the required precision (15 to 25 micron true position) are readily commercially available at reasonable cost. However, the disclosed embodiment describing the linear rails  518  as the linkage between the block assembly  465  and the frame assembly  461  are merely exemplary, and it should be understood that this linkage may be embodied as a vee-groove and vee-feature linkage, a dovetail slot and dovetail feature linkage, integral bearing configurations, and the like. 
     In this embodiment at least one diffraction beam  522 , and optionally at least one additional diffraction beam  522 , and optionally a reflected beam  524  are monitored by pre-amplified photodiode optical detectors  504  and  506  respectively. The detectors  504  and  506  are constructed using industry standard outer housing dimensions. The precision of the relative position of the detection surface to the housing, and the precision of the housing dimensions are such that detectors  504  and  506  may be placed into bores  514  and  516  without the need for alignment or adjustment thus increasing reliability and reducing cost. This configuration also thermally couples the detectors  504  and  506  to the optics block  500 . In order to stabilize the electronics and to minimize the affects of thermal gradients induced by changes in the ambient temperature of the operating environment, the temperature of the optics block  500  is controlled to a fixed temperature above ambient. Various other types of optical detectors may be used, for example, CCDs, PMTs, and the like. The microprocessor controller is configured to compare the diffracted light signals captured by optical detector  504  and the reflected light signals captured by the second optical detector  505  for purposes of calibration. 
     Referring again to  FIG. 9  a stepper motor  530  generates the force required for the longitudinal motion of the block assembly  465  by rotating ball screw  532  to which it is coupled and which is essentially axially static relative to the frame assembly  464 . The nut  534  is mounted to the block assembly  465  and translates the rotational motion of the ball screw  532  into linear motion of the block assembly  465  in the longitudinal direction with respect to the prism bed  467 . A home switch  536  and a limit switch  538  provide a positional reference and travel limit, respectively, for the block assembly  465  that feedback to the logic control system under the control of the microprocessor. Thus, in this embodiment the structure containing the detectors  504  and  506  and the laser head  502  moves with respect to a static structure holding the sensors  316 . This is the preferred embodiment as it enables the tubing  320  and  330  ( FIG. 4 ) leading to the sensors  316  to remain essentially stationary. This is beneficial as it avoids undesired movement of fluids within the sensors  316  which may be present in an alternative configuration whereby the structure holding the sensors  316  moves with respect to a static structure containing the detectors  504  and  506  and the laser head  502 . This fluid movement may result from inertial forces as the sensors  316  and the fluids therein experience forces due to acceleration and volumetric changes in the tubing  320  and  330  as it flexes. Notwithstanding these possible drawbacks, this alternative configuration could also be employed. 
     The overall structure of the optical subsystem  460  facilitates a precise and robust alignment of optical elements while allowing for a single source (laser) and a single detector to address multiple analyte-receptor patterns  412 . The use of a single source and detector reduces the need for compensating for variability inherent with multiple sources and detectors, in a cost effective manner. Alternative means could be used to accomplish this single source and detector relationship. Examples are beam splitters, fiber optic conduits, micro-mirror arrays and the like. These solutions bear additional complications in either required alignments at assembly, additional high precisions components, additional high tolerance machining steps and increased sensitivity to induced temporary or permanent misalignment of the optical path resulting from impact or vibration. Notwithstanding these drawbacks, the aforementioned embodiments may be employed. 
     Referring to  FIG. 8  the clamp side assembly  463  and the latch side assembly  462  are mounted to the main structure assembly  461 , and apply a force to the upper surface  319  of the upper lid  402  which transfers to the patterned prism  400  ensuring that it is properly seated in the sensor receiving structures  468 , and provide means to prevent the operator from gaining exposure to laser radiation levels beyond acceptable limits by means of a mechanical interlock. 
     Referring to  FIG. 13B , there is a position at one extent of the travel of the block assembly  465  where the laser beam  508  is blocked by a feature  550  on the clamp side assembly  463  before it can encounter the sensors  316 , and this position is referred to as the safe position  FIG. 13B . While the block assembly  465  is in the safe position as shown in  FIG. 13B  the clamps  554  can be freely opened  557  and closed  555 . 
       FIG. 14  A shows the assembled latch side assembly  462  and additionally, as seen in the  FIG. 14B , an exploded view of the latch side assembly  462 , optical sensors  560  within the latch side assembly  462  monitor if the clamps  554  are in the closed  555  position. The logic control system under the microprocessor computer control will not instruct the stepper motor  530  to move the block assembly  465  out of the safe position  FIG. 13B  unless all of the clamps  554  are closed  555  position. Furthermore, once the clamps  554  are all closed  555  position, and the stepper motor  530  has moved the block assembly  465  out of the safe position  FIG. 13B  a mechanical interlock prevents the operator from moving the clamps  554  to the open  557  position. Should the clamps  554  become opened  557  while the block assembly  465  is not in the safe position  FIG. 13A , power to the laser head  502  is cut, thereby turning off the laser beam  508 . Once the block assembly  465  returns to the safe position  FIG. 13B  power to the laser head  502  is restored, thereby restoring 
     Referring to  FIG. 15  a schematic view of the optical element  410  of the patterned prism  400  shown in transverse cross-section, in order to ensure that the instrument  10  operates in total-internal-reflection given the material of which the optical element  410  and the analyte-receptor pattern  412  are composed, the angle made between the incident laser beam  508  and the vector  570  normal to the patterned surface  572  of the optical element  410  which is referred to as the critical angle is a function of the indices of refraction of the material of which the optical element  410  is comprised and the material used to generate the analyte receptor pattern  412  on the patterned surface  572 . In this embodiment the critical angle is 65 degrees thus the angle between the incident laser beam  508  and the patterned surface  572  is 25 degrees. Thus to maximize coupling of the incident laser-beam  508  power into the analyte-receptor pattern  412 , the optical element  410  is comprised of a triangular prism such that the incident optical surface  574  forms a right angle  576  with the incident laser-beam  508 . Thus the angle between the optical surface  572  and the incident face  574  must equal 25 degrees. 
     It has been determined that the performance of the instrument  10  is optimal when the lines of the analyte-receptor pattern  412  are rotated at an angle of 45 deg relative to the longitudinal axis of the sensor  316 . In this orientation the signal-to-noise ratio is maximized. While this angle is advantageous other angles may be used effectively. 
     Alternative means of precisely identifying the location of the analyte-receptor pattern array  411  ( FIG. 1 ) on each patterned prism  400  have been implemented. These means are dependent on the interrogation of the sensor  316  by the laser beam  508 , the precision and repeatability of the array  411 , and precision and repeatability of the stepper motor  530  and lead screw  532  and nut  534 . Scanning longitudinally across the array  411  produces a distinctive pattern of high and low signal intensity when signal is plotted against position. The signal values may be analyzed and compared to the theoretical pattern generated by a sensor scan. The scanned pattern is then matched in software to the theoretical pattern and locational references in the system software are adjusted accordingly. This adjustment produces an essentially exact map of the analyte-receptor pattern  412  locations relative to the optical subsystem  460  without the need for a home sensor or other means of mechanical alignment. Since this alignment references the analyte-receptor patterns  412  and the optical path directly, no intervening variabilities in optical subsystem  460  construction which impact the axis of scan are relevant, nor are any variabilities in sensor fabrication resulting in minor alignment errors of the array  411  to the patterned prism  400  relevant. The matching of the expected signal pattern to the actual pattern measured by the instrument  10  is accomplished by a simple lowest-quartile-filter, thus establishing the location of the expected regions of low signal between the analyte-receptor patterns  412 . This pattern is then cross correlated to the expected pattern and the locational references in the appropriate software files are adjusted for the individual sensors  316 . Other means of detecting the analyte-receptor patterns  412  and subsequent correlation to the file locations are possible. For example Fourier transform techniques could be employed to match a portion of one entire scan or a portion thereof to the expected scan. Examination of a single analyte-receptor pattern  412  or any number of analyte-receptor patterns  412  either in whole or part could provide adequate information to allow registration of the array  411  to the optical subsystem  460 . 
     A means has been implemented in the system software to allow selection of preferential regions within each analyte-receptor pattern  412 . A variety of deviations in the analyte-receptor pattern  412  may cause signal elevations or depression in localized regions of a given analyte-receptor pattern  412 . Examples are: light scatter caused by small defects and scratches in prism  400  fabrication or during initial pattern deposition, particle contamination on any of the optical surfaces, areas of incomplete deposition of the initial analyte-receptor pattern  412 , inhomogeneities or inclusions within the bulk of the molded prism  400 . With careful processing methods, these defects are most often confined to small regions and may be systemic in nature; for example defects in the prism  400  caused by defects in the injection mold surfaces. These defects may be random in nature caused by particulate contamination and the like. In the former case, the defects could be minimized by resurfacing the tooling faces causing the defect, but this presents a costly and iterative process as new defects may arise in the normal course of processing. Also, in some cases these defects may be reflective of inclusions or grain boundaries in the metal the tool is constructed from. In the latter case, even careful controls will not eliminate all defects and in any event cannot address contamination occurring immediately prior to use. In this embodiment a scan of each sensor is conducted prior to initiation of a binding reaction. This scan gives a baseline signal intensity reading of the sensor  316  analyte-receptor pattern(s)  412 . It should be noted that this baseline scan can be replaced by or supplemented with scans taken after binding reactions have occurred. These scans have value described hereinafter. 
     A perfect sensor  316 , when scanned by the instrument  10  would in principle produce a signal output that would, when plotted against location along the axis of the scan, resemble a square wave with the peaks representing those locations where the laser beam  502  is interrogating an analyte-receptor pattern  412  and the troughs indicating areas on the patterned prism  400  that are unpatterned. The transitions between peaks and troughs are not step changes, but are rather sloped, reflecting the entry of the laser beam  502  onto the analyte-receptor pattern  412 . Once the entire beam  502  is contained within the area proscribed by the analyte-receptor pattern  412 , the theoretical signal is constant until the laser beam  502  begins to leave the analyte-receptor pattern  412  area. 
     In practice, the peak signal level is not flat or of stable value. The aforementioned defects produce areas of high or low signal values depending on the nature of the defect. These deviations in and of themselves do not in many cases eliminate the utility of any particular region of the analyte-receptor pattern  412 . Often, binding reactions still occur and the change in signal intensity is still proportional to the degree or amount of binding to surface receptors. In a limited number of cases however, productive use of a particular area is compromised by areas of signal deviation. Examples are regions where the defect causes so much scatter so as to exceed the dynamic range of the detection system. In this circumstance, subsequent binding events cannot be detected Another example is a situation where a rapid transition from a normal signal to a very high or very low signal occurs. In this case, extremely small movements (on the order of 25 microns) of the beam relative to the analyte-receptor pattern  412  can either inject noise into the signal due to vibration and the like, or in the case where multiple analyte-receptor pattern  412  are being monitored concurrently, produce offsets in the data stream due to small inaccuracies in the return of the block assembly  465  to the previously interrogated location. 
     In practice, it has been determined that interrogating regions of the laser beam  508 /analyte-receptor pattern  412  interface with a scan resolution of about 25 microns is sufficient to reveal significantly degraded interrogation regions. A number of methods to evaluate the severity of the degradation are possible. In this embodiment, a comparison of signal level on adjacent regions within analyte-receptor patterns  412  is made using system software. Consecutive comparisons of adjacent regions are made until a best group or adjacent regions may be selected. Groups may range from two to eleven regions. Three to five regions are normally sufficient. The region at the geometric center of the group is then selected as the region where all subsequent interrogations of each analyte-receptor pattern  412  is performed. Selection criteria include but are not limited to signal range withing the selected region, amplitude difference relative to the local or distributed trough signal level, amplitude difference relative to mean analyte-receptor pattern  412  or sensor  316  values at peak location, amplitude relative to detector dynamic range, and combinations of the parameters. 
     A number of techniques to select preferred interrogation regions are available and may be tailored to specific analytical requirements. For example a rudimentary case can prioritize by demanding a specific maximum deviation from mean value within a given group of regions, coupled with a secondary requirement that the absolute signal be between two specified values. This would be useful in almost all analytical cases to avoid regions of rapid signal slew, regions of high signal (indicative of high scatter) or a zone of incomplete pattern resulting in low signal. More sophisticated selection analysis might include setting bounds per the above example, but adding a restriction to closely match values for one analyte-receptor pattern  412  relative to one or more analyte-receptor patterns  412  in the same sensor  316  or on other sensors  316  either currently in use or from previously determined values. This approach has value in improving inter and intra assay repeatability and precision. Yet more sophisticated criteria may facilitate selections of regions with surface capture molecules that are matched to other analyte-receptor patterns  412  or sensors  316 , as the initial signal above the trough is indicative of total coverage. This analysis can be particularly useful when used with consecutive scans pre and post initial binding and/or dissociation events where the initial binding event is the deposition of a capture molecule and the binding event which is the subject of investigation occurs subsequent to the first binding event. Many other combinations of parameters and rankings are possible and the methods of the execution and benefits thereof will be obvious to one skilled in the appropriate art. 
     This embodiment of the system enables several means of attaching event markers related to transition points in the data set gathered during an experiment. Transition points of most relevance are events when a reagent, sample, or combination of reagents and/or samples arrive at the analyte-receptor pattern  412  or analyte-receptor patterns  412  being monitored. These transition events are of importance as they identify the precise moment a material is available to react with the analyte-receptor pattern  412 . That is, they identify the precise starting point of the interaction. In any controlled system including the current invention, the approximate time of initiation of a reaction is relatively easy to control. However, most systems have inherent latencies between the time a command is issued to execute a movement of fluids, and the time that the commanded operation is completed. Latency, when consistent and well know is not intrinsically a problem. Variable latencies however, introduce a level of uncertainty in when an event actually occurs. Sources of variability include command execution time, uncertainties in response times of active components such as pumps and valves, lags in fluid delivery resulting form compression of air within fluid circuits, and communication delays between the main control device and active system components. In many cases small deviations in timing are insignificant. 
     In cases where very rapid reactions occur or when analytical methods such as curve fitting programs are used, results are enhanced by knowledge of the true starting time to the best degree possible. One technique available for attaching an event marker used with a diffractive optic systems is the fact that all else being equal, the signal generated is dependent on the refractive index of the medium in contact with the elements of the array  411  of analyte-receptor patterns  412 . The current invention allows introduction of media of differing refractive index at any and all transition events. For example, an air bubble introduced between sequential reagents or samples will create a large spike in signal when it moves across the diffractive element because the index of refraction of air (approximately 1.0) is significantly different than the refractive index of the elements of the analyte-receptor pattern  412 , and more significantly different than that of the reagents, buffers, samples or water typically used in experiments. The refractive index of these latter components typically ranges from 1.3 to 1.6 or thereabout. The presence of this large signal increase is readily identified and marked in the data stream by simple evaluation means in either standard or customized analysis programs such as MS Excel™ and GraphPad Prism™. The transition events can thus be temporally identified relative to the rest of the data stream essentially limited only by the granularity of data acquisition. Typically in the current invention, a data acquisition granularity of 100 milli-seconds is used. Therefore the temporal uncertainty of the arrival of a reagent can be determined within approximately 100 milli-seconds plus transition time across a portion of the beam. With proper selection of fluid flow rates, this second contribution to latency is minimal. At a relatively modest flow rate of 60 micro-liters per minute for example the transition time is below 100 milli-seconds. The uncertainty in this time is perhaps half the total. 
     It should be noted that even slight refractive index changes between fluids presented to the analyte-receptor pattern  412  are detectable. In this circumstance, a step change in the signal level can be noted as the transition point rather than a sharp spike depending on the specifics of the experimental reagents and samples used. Normal refractive index differences between reagents may be sufficient to produce a distinct, highly precise transition marker with temporal accuracy similar to that described above. 
     This embodiment enables either essentially continuous monitoring of a single analyte-receptor pattern  412  or serial iterative monitoring of multiple analyte-receptor patterns  412  depending on the needs of the experiment, thus enabling high resolution, real-time data collection or lower resolution intermittent data collection or combinations thereof. 
     The present invention has utility in many categories of experiments including but not limited to kinetic analysis of binding and/or dissociation reactions, endpoint analysis, sandwich and modified sandwich assays, amplified/enzyme substrate assays, examination of buffer conditions, reagent sample concentrations, matrix effects on reactions, comparisons of binding pairs for affinity, displacement assays, etc. 
     As used herein, the terms “comprises”, “comprising”, “including” and “includes” are to be construed as being inclusive and open ended, and not exclusive. Specifically, when used in this specification including claims, the terms “comprises”, “comprising”, “including” and “includes” and variations thereof mean the specified features, steps or components are included. These terms are not to be interpreted to exclude the presence of other features, steps or components. 
     The foregoing description of the preferred embodiments of the invention has been presented to illustrate the principles of the invention and not to limit the invention to the particular embodiment illustrated. It is intended that the scope of the invention be defined by all of the embodiments encompassed within the following claims and their equivalents.