# Patent

## Title
Trenched sample assembly for detection of analytes with electromagnetic read-write heads

## Abstract

Described are embodiments of an invention for a sample assembly with trenches for detection of analytes with electromagnetic read heads. The sample assembly includes an outer layer with at least one sample trench. The sample trench includes a first set of antibodies that are bonded on a first surface of a base layer. Target antigens are bonded with the first set of antibodies, and a second set of antibodies are bonded to the target antigens. Further, the sample trench includes nanoparticles that are bonded to the second set of antibodies. A head module includes a write head for magnetizing nanoparticles and a read sensor for detecting the magnetized nanoparticles, and thus, the target antigens. The sample trench constrains the biological sample, and thus the target antigen, during the preparation and subsequent analysis of the biological sample. Accordingly, the target antigen is aligned with read elements of a head module such that the target antigen is reliably and accurately detected. Further, to ensure reliable and accurate detection, the outer layer is formed with a low friction material allowing the read head to remain in contact with the upper surface of the outer layer during the process of detection.

## Background
CROSS-REFERENCES TO RELATED APPLICATIONS
The present application is related to cofiled, copending and coassigned U.S. patent application Ser. No. 12/888,388 entitled “DETECTION OF ANALYTES VIA NANOPARTICLE-LABELED SUBSTANCES WITH ELECTROMAGNETIC READ-WRITE HEADS”, Ser. No. 12/888,394 entitled “READ-AFTER-WRITE DETECTION OF ANALYTES VIA NANOPARTICLE-LABELED SUBSTANCES”, U.S. patent application Ser. No. 12/888,403 entitled “A SERVO CONTROL CIRCUIT FOR DETECTING ANALYTES VIA NANOPARTICLE-LABELED SUBSTANCES WITH ELECTROMAGNETIC READ-WRITE HEADS”, and U.S. patent application Ser. No. 12/888,408 entitled “A CIRCUIT FOR DETECTING ANALYTES VIA NANOPARTICLE-LABELED SUBSTANCES WITH ELECTROMAGNETIC READ-WRITE HEADS,” all of which were filed on Sep. 22, 2010 and are hereby incorporated by reference.
FIELD OF THE INVENTION
The present invention relates to analytical devices and processes, and more particularly, to devices and processes that incorporate electromagnetic write-heads and magneto-resistive read-sensors to detect target antigens.
BACKGROUND OF THE INVENTION
It is known that antibodies bind with antigens as part of the human disease defense system. Presently, antigens are detected by such techniques as immunofluorescence, immunoperoxidase, or enzyme-linked immunosorbent assay (ELISA), each of which then employs a microscope for visual detection of the target antigen. It is desirable to exploit the use of magnetic signaling technology to automate the detection of analytes, such as antigens, and to further apply this technology to the detection of any biological matter.
SUMMARY OF THE INVENTION
Described are embodiments of an invention for a sample assembly with trenches for detection of analytes with electromagnetic read heads. The sample assembly includes an outer layer with at least one sample trench. The sample trench includes a first set of antibodies that are bonded on a first surface of a base layer. Target antigens are bonded with the first set of antibodies, and a second set of antibodies are bonded to the target antigens. Further, the sample trench includes nanoparticles that are bonded to the second set of antibodies. A head module includes a write head for magnetizing nanoparticles and a read sensor for detecting the magnetized nanoparticles, and thus, the target antigens. The sample trench constrains the biological sample, and thus the target antigen, during the preparation and subsequent analysis of the biological sample. Accordingly, the target antigen is aligned with read elements of a head module such that the target antigen is reliably and accurately detected. Further, to ensure reliable and accurate detection, the outer layer is formed with a low friction material allowing the read head to remain in contact with the upper surface of the outer layer during the process of detection.
For example, a method of forming a sample assembly of a biological sample having target antigens includes forming at least one sample trench within an outer layer, such that the sample trench has a bottom surface. Further, a base layer is formed and a first set of antibodies are bonded on a first surface of the base layer within the sample trench. The sample trench having the first set of bonded antibodies is exposed to a biological sample having target antigens. The target antigens bond with the first set of antibodies within the sample trench. A second set of antibodies are bonded to nanoparticles. In one embodiment the first and second set of antibodies are biologically identical. Further, the target antigens within the sample trench are exposed to the second set of antibodies that are bonded with the nanoparticles. The second set of antibodies bond with the target antigens within the sample trench.
In one embodiment, the method includes forming a plurality of magnetic servo alignment marks on the sample assembly. The method of forming the plurality of magnetic servo alignment marks includes forming at least one servo alignment trench in the outer layer parallel to the sample trench. Further, the step of forming the plurality of magnetic servo alignment marks includes filling the servo alignment trench with tape ink, curing the tape ink and forming the plurality of magnetic servo alignment marks in the cured tape ink.
In one embodiment, the method includes magnetizing the nanoparticles. Further, the nanoparticles are magnetized by a write head. In one embodiment, the base layer is formed on the bottom surface of the sample trench. In another embodiment, the outer layer is formed on the base layer and the base layer is exposed by the bottom surface of the sample trench.
In one embodiment the outer layer is selected from the group consisting of diamond-like-carbon, polytetrafluoroethylene, aluminum oxide, and polyamides. The first set of antibodies are bonded to the target antigen with a bonding material selected from the group consisting of amide, self-assembled-monolayers (SAMS), alkoxysilane, organic functional trialkoxysilane, and thiol containing surface modifiers.
In an embodiment of detecting target antigens in a biological sample on a sample assembly, the method includes forming at least one sample trench within an outer layer, such that the sample trench has a bottom surface. Further, a base layer is formed and a first set of antibodies are bonded on a first surface of the base layer within the sample trench. The sample trench having the first set of bonded antibodies is exposed to a biological sample having target antigens. The target antigens bond with the first set of antibodies within the sample trench. A second set of antibodies are bonded to nanoparticles. In one embodiment, the first and second set of antibodies are biologically identical. Further, the target antigens within the sample trench are exposed to the second set of antibodies that are bonded with the nanoparticles. The second set of antibodies bond with the target antigens within the sample trench. A head module is swept over the sample assembly. The head module includes at least one magneto-resistive read sensor to detect the target antigens.
In an embodiment of a sample assembly including a biological sample having a target antigen, the sample assembly includes an outer layer having at least one sample trench. The sample trench has a bottom surface. The sample assembly also includes a base layer. The sample trench includes a first set of antibodies bonded on a first surface of the base layer. The sample trench further includes target antigens which are bonded with the first set of antibodies. Further the sample trench includes a second set of antibodies which are bonded to the target antigens and nanoparticles bonded to the second set of antibodies. The first and second set of antibodies are biologically identical.
For a fuller understanding of the present invention, reference should be made to the following detailed description taken in conjunction with the accompanying drawings.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a top view of a sample assembly, not drawn to scale, in accordance with an embodiment of the invention;
FIG. 2A is a cross-sectional view of a portion of a sample assembly, not drawn to scale, including a sample trench in accordance with an embodiment of the invention;
FIG. 2B is a cross-sectional view of a portion of a sample assembly, not drawn to scale, including a sample trench in accordance with another embodiment of the invention;
FIG. 2C is a cross-sectional view of sample assembly, not drawn to scale, including sample trenches and an alignment trench in accordance with an embodiment of the invention;
FIG. 3 is a cross-sectional view of a portion of a sample assembly, not drawn to scale, including a biological sample in accordance with an embodiment of the invention;
FIG. 4 is a flow chart illustrating steps of an analytic process in accordance with an embodiment of the invention;
FIG. 5 is a flow chart illustrating additional steps of an analytic process in accordance with an embodiment of the invention;
FIG. 6 illustrates control circuitry for the X-axis and Y-axis motion of the head module in an embodiment of the invention; and
FIG. 7 illustrates read and write circuitry in an embodiment of the invention.



DETAILED DESCRIPTION OF THE INVENTION
The present invention is described in exemplary embodiments in the following description with reference to the Figures, in which like numbers represent the same or similar elements. While the invention is described in terms of the best mode for achieving the invention's objectives, it will be appreciated by those skilled in the art that variations may be accomplished in view of these teachings without deviating from the spirit or scope of the invention.
Described are embodiments of an invention for a sample assembly with trenches for detection of analytes with electromagnetic read heads. The sample assembly includes an outer layer with at least one sample trench. The sample trench includes a first set of antibodies that are bonded on a first surface of a base layer. Target antigens are bonded with the first set of antibodies, and a second set of antibodies are bonded to the target antigens. Further, the sample trench includes nanoparticles that are bonded to the second set of antibodies. A head module includes a write head for magnetizing nanoparticles and a read sensor for detecting the magnetized nanoparticles, and thus, the target antigens. The sample trench constrains the biological sample, and thus the target antigen, during the preparation and subsequent analysis of the biological sample. Accordingly, the target antigen is aligned with read elements of a head module such that the target antigen is reliably and accurately detected. Further, to ensure reliable and accurate detection, the outer layer is formed with a low friction material allowing the read head to remain in contact with the upper surface of the outer layer during the process of detection.
FIG. 1 is a top view of a sample assembly 100, not drawn to scale, in accordance an embodiment of the invention. The sample assembly 100 includes a substrate 199. The substrate 199 may comprise, without limitations, a Peltier hard-substrate, a glass substrate, a polyethylene terephthalate (PET, which is commonly known by the trade name of MylarTM) substrate, a flexible-substrate, or other materials having similar properties. The term “substrate” refers to any supporting structure, including, but not limited to, the substrates described above. Further, the substrate may include of more than one layer of material.
An outer layer 253 is formed over substrate 199. Deposition techniques utilized herein include, but are not limited to, photolithography, silk-screening, and other similar processes. The outer layer may comprise diamond-like-carbon (DLC), polytetrafluoroethylene, aluminum oxide, polyamides, or other low-friction materials known in the art. The outer layer 253 may be formed to a thickness of between 0.2 to 60 microns. The outer layer 253 includes sample trenches 180. The process of forming the sample trenches 180 is described with respect to FIGS. 2A and 2B.
One embodiment of forming sample trenches 180 is illustrated in FIG. 2A. In this embodiment, a base layer 252 is formed on substrate 199. Base layer 252 may comprise nonmagnetic materials such as gold, silicon, or SiO2, or other materials having similar magnetic properties, without limitation. An outer layer 253 is then formed on base layer 252. Outer layer 253 has an upper surface 254. A plurality of sample trenches 180 are formed within outer layer 253. Sample trenches 180 may be formed by known methods in the art including laser milling, x-ray milling, or photolithographically. Sample trenches 180 may be formed to have a depth of between 0.2 to 60 microns. It should be understood by one of ordinary skill in the art that, while only one sample trench is shown, a plurality of sample trenches 180 may be formed within the outer layer 253 with the same method described herein. Each sample trench 180 is formed having a bottom surface 255. In one embodiment, the bottom surface of the trench exposes base layer 252.
Another embodiment of forming sample trenches 180 is described with respect to FIG. 2B. In this embodiment, outer layer 253 is formed on substrate 199. The outer layer 253 has an upper surface 254. A plurality of sample trenches 180 are formed within outer layer 253. Sample trenches 180 may be formed by known methods in the art including laser milling, x-ray milling, or photolithographically. Sample trenches may be formed to have a depth of between 0.2 to 60 microns. It should be understood by one of ordinary skill in the art that, while only one sample trench is shown, a plurality of sample trenches 180 may be formed within the outer layer 253 with the same methods described herein. Each sample trench 180 is formed having a bottom surface 255. Base layer 252 is formed within each sample trench 180 and on the bottom surface 255 of each sample trench 180. Base layer 252 may comprise nonmagnetic materials such as gold, silicon, or SiO2, or other materials having similar magnetic properties, without limitations. As shown in FIG. 2B, the base layer 252 only partially fills sample trenches 180. There are many embodiments in which base layer 252 may be formed to only partially fill sample trenches 180. For example, in one embodiment, base layer 252 may be formed conformally over the outer layer 253 and within sample trenches 180. Base layer may then be removed by etching or planarization techniques known in the art. Alternatively, the base layer 252 may be selectively deposited by known methods in the art. The described embodiment of forming a base layer 252 only within the sample trench 180 is particularly advantageous in embodiments in which expensive materials are utilized, such as gold since much less material is required to form the base layer 252.
As shown in FIG. 1, eight sample trenches 180 may be formed to correspond to the head module 104 of the IBM® TS1130 writing with eight write elements 106 and reading with eight read sensors 108 simultaneously, as further explained below. The sample trenches 180 are parallel to each other and extend along the Y-axis.
In one embodiment, as shown in FIGS. 1 and 2C, the outer layer 253 further includes at least one servo alignment track 194 with a plurality of magnetic servo alignment marks 193. The servo alignment track 194 is parallel with the sample trenches 180 and extends along the Y-axis. The servo alignment track 194 may be a servo alignment trench 194 with a plurality of magnetic servo alignment marks 193. FIG. 2C shows a cross section of substrate 199 along the X-axis illustrating an embodiment in which an alignment trench 194 is formed within outer layer 253. For simplicity of illustration, base layer 252 is not illustrated in FIG. 2C. Alignment trench 194 may be formed in the same manner as described for forming sample trenches 180 shown in FIGS. 2A and 2B. In one embodiment, alignment trench 194 is formed simultaneously with the formation of sample trenches 180. Specifically, alignment trench 194 may be formed by known methods in the art including laser milling, x-ray milling, or photolithographically. Alignment trench 194 may have a depth of between 0.2 to 60 microns. It should be understood by one of ordinary skill in the art that, while only one alignment trench 194 is shown, a plurality of alignment trenches 194 may be formed within the outer layer 253 as described herein. For example, alignment trenches 194 could be formed between each of the sample trenches 180.
In this embodiment, sample trenches 180 are masked and the servo alignment trench 194 is filled with tape ink. The tape ink, which contains magnetic recording particles in a polymer matrix, is cured by methods known in the art. Magnetic encoded servo alignment marks 193 are subsequently encoded in the cured tape ink.
In another embodiment, magnetic encoded servo alignment marks 193 are encoded on a piece of magnetic tape which is adhered to outer layer 253. Further, the magnetic encoded servo alignment marks 193 may be encoded by the manufacturer of substrate 199 on the magnetic tape. Magnetic encoded servo alignment marks 193 may be in the form of timing based servo marks as taught by U.S. Pat. No. 7,639,448 and entitled “Differential Timing Based Servo Pattern for Magnetic-Based Storage Media,” which is hereby incorporated by reference in its entirety. Servo alignment marks 193 are read by read sensor 106 and used to keep the write elements 108 and read sensors 106 in alignment with sample trenches 180 along the X-axis while the head module 104 moves relative to sample trenches 180 along the Y-axis.
Still further, in one embodiment the alignment marks 193 may be non-magnetic marks. For example, the alignment marks may be lithographed, silk-screened or ink-jet printed, and read with an optical laser.
The sample trenches 180 include a biological sample having a target antigen. Sample trenches 180 act to constrain the biological sample, and thus the target antigen 210, during the preparation and subsequent analysis of the biological sample, as discussed below. For example, the sample trenches 180 prevent the biological sample from being rinsed away during a rinse step. Further, the sample trenches 180 allow the biological sample and the target antigen to be constrained to an area that is aligned with read elements 108, such that detection of target antigen 210 is reliably and accurately detected.
The preparation of the biological sample with target antigens 210 within the sample trench 180 is discussed further with respect to FIGS. 3 and 4. FIG. 3 illustrates preparation of biological sample including the target antigen 210 on sample assembly 100. FIG. 4 illustrates the steps of preparing sample assembly 100 and detecting the target antigens 210. For simplicity of explanation, FIG. 3 shows the embodiment in which the base layer 252 is formed within the sample trench 180 and a single sample trench 180. However, it should be understood that the base layer may be formed by any of the methods described herein and a plurality of sample trenches 180 may be formed. As discussed above, an outer layer 253 is formed on substrate 199. In step 402, at least one sample trench 180 is formed in outer layer 253. Base layer 252 is formed on the bottom surface 255 of the sample trench 180.
In step 404, antibodies 208A are bonded within sample trenches 180 to the first surface of base layer 252. The antibodies 208A may be bonded within the sample trenches to the base layer 252 via bonds 206A such as amide, self-assembled-monolayers (SAMS), alkoxysilane, organic functional trialkoxysilane, thiol bonds, or the like. It is important to note that the material of base layer 252 facilitates the bonding of antibody 208A within sample trench 180.
In one embodiment, it is preferred that bond 206A is applied only to the first surface of base layer 252. In one example, the bonding comprises first coating base layer 252 with amide, self-assembled-monolayers (SAMS), alkoxysilane, or thiol and then placing a solution of antibodies 208A on substrate 199 and gently rocking substrate 199 for a period of time, up to six hours. Amide refers to organic compounds that include the functional group including an acyl group, with the chemical notation C═O, linked to a nitrogen (N) atom. A SAM is an organized layer of amphiphilic molecules in which one end of the molecule, the “head group,” shows a special affinity for gold, silicon, or SiO2, such as that utilized in base layer 252. At the terminal end, the opposite end of the SAM from the “head group” is a functional group. In one embodiment, the first set of antibodies 208A are attached to this functional group in step 404. Lastly, a thiol is a compound that includes the functional group composed of a sulfur atom and a hydrogen atom (—SH). Being the sulfur analog of an alcohol group (—OH), this functional group is referred to either as a thiol group or a mercaptan group.
There are generally five known isotopes (types) of antibodies 208A and 208B for mammals. In FIG. 3, the Y-shape of antibodies 208A and 208B are that of monomer antibodies. There are three isotopes of monomer antibodies: IgD, IgE, and IgG, where the prefix Ig is the symbol for Immunoglobulin, and these monomer antibodies each have one unit of Ig. There is only one isotope of a dimer antibody, IgA, which has two Ig units. Finally, there is only one isotope of pentamer antibody, IgM, which has five Ig units. These antibodies are further described in copending and coassigned U.S. patent application Ser. No. 12/888,388 entitled “DETECTION OF ANALYTES VIA NANOPARTICLE-LABELED SUBSTANCES WITH ELECTROMAGNETIC READ-WRITE HEADS”, which is incorporated herein by reference. The analytical process described herein may be used in human medicine, veterinarian medicine, and, as well as to other biological analyses.
In one embodiment, step 404 may include a step of rinsing substrate 199 with water or another rinsing agent to remove any antibodies 208A that are not bonded within sample trenches 180. In all rinsing steps discussed herein a surfactant may be added to the water or rinsing agent to reduce surface tension. In one example, the surfactant may include a detergent solution.
In step 406, antibodies 208A bonded within sample trench 180 are exposed to a biological sample including target antigens 210. In one example, this is accomplished by placing a blood sample or other biological sample on substrate 199. As shown in FIG. 3, the target antigens 210 bond to monomer antibodies 208A at antigen receptors 209A. The antigen receptors 209A are diagrammatically shown to be at the v-shaped end of antibodies 208A. As shown, each monomer antibody 208A has two antigen receptors 209A. Step 406 may include the repetitive rocking of substrate 199 to facilitate bonding of the target antigens 210 with antibodies 208A at antigen receptors 209A. For example the substrate is gently rocked for up to six hours. Further, step 406 may include a step of rinsing substrate 199 with water or another rinsing agent to remove antigens 210 not bonded to antibodies 208A
Target antigens 210 may comprise cancer cells, viruses, or bacteria. In one embodiment, the target antigens 210 are viruses such as Human Papilloma Virus (HPV) which is known to lead to cancer. It is important to note that the antibodies 208A utilized in step 404 are specifically chosen based on the targeted antigens 210 utilized in step 406.
In step 408, a second set of antibodies 208B are bonded with nanoparticles 212. It is important to note that the first set of antibodies 208A and the second set of antibodies 208B are biologically identical, as both bond to the same target antigen 210. In one embodiment, the second set of antibodies 208B are bonded with nanoparticles 212 in parallel with steps 404 and 406. In other embodiments, the second set of antibodies 208B may be bonded with nanoparticles 212 before or after steps 404 and 406. The nanoparticles 212 include a magnetic inner core 216 and a outer shell 214. Magnetic inner cores 216 may comprise hard magnetic materials with high coercivity, such as Fe2O3, CrO2, and Barium Ferrite BaFe. For example, magnetic inner cores 216 may comprise iron oxide based nanoparticle materials, including M Fe2O4 (where M may be Co, Ni, Cu, Zn, Cr, Ti, Ba, or Mg) nanomaterials, and iron oxide coated nanoparticle materials or other structures with similar functionality.
In one embodiment, step 408 further includes preparing the nanoparticles 212 prior to bonding the nanoparticles 212 to antibodies 208A. The preparation of nanoparticles 212 is described in FIG. 5. Magnetized nanoparticles are prone to agglomerate and form lumps. Therefore, in step 502 the magnetic inner cores 216 of nanoparticles 212 are demagnetized. In one embodiment, the magnetic inner cores 216 of nanoparticles 212 are heated above their Curie temperature to demagnetize the inner cores 216. The heated magnetic inner cores 216 are allowed to cool. The step of demagnetization keeps the inner cores 216 of nanoparticles 212 as individual particles.
In another embodiment, the step of demagnetizing the inner cores 216 of nanoparticles may be omitted. The process of manufacturing the inner cores 216 of nanoparticles may include a step of high temperature sintering. Thus, the manufacturing process of the nanoparticles 212 may demagnetize the inner cores 216. The formation of nanoparticles is taught without limitation by U.S. Pat. No. 6,962,685, entitled “Synthesis of Magnetite Nanoparticles and the Process of Forming,” which is hereby incorporated by reference in its entirety.
Returning to FIG. 5, in step 504 the inner cores 216 are coated with an outer-shell 214 of nonmagnetic gold, silicon, or SiO2, to create nanoparticles 212. Antibodies 208B are bonded to nanoparticles 212 via bonds 206B, such as amide, self-assembled-monolayers (SAMS), alkoxysilane, organic functional trialkoxysilane, or thiol bonds. This bonding may be accomplished by first coating nanoparticles 212 with amide, self-assembled-monolayers (SAMS), alkoxysilane, organic functional trialkoxysilane, or thiol. It is important to note that the material used for the outer shell 214 facilitates the bonding of antibody 208A within sample trench 180. The nanoparticles 212 may be placed in a solution including the second set of antibodies 208B and gently rocking this solution for a period of time. The repetitive rocking of substrate 199 facilitates bonding of the second set of antibodies 208B with the nanoparticles 212. For example, the substrate is gently rocked for up to six hours. Further, step 408 may include a step of rinsing substrate 199 with water or another rinsing agent to remove nanoparticles 212 not bonded to antibodies 208B.
In step 410, target antigens 210 are exposed to the second set of antibodies 208B bonded to nanoparticles 212. This may be done by placing a solution of nanoparticle-labeled antibodies 208B on substrate 199. As shown in FIG. 3, the target antigens 210 bond with the antigen receptors 209B of antibodies 208B. Step 410 may include the repetitive rocking of substrate 199 to facilitate bonding of the target antigens 210 with antibodies 208B at antigen receptors 209B. For example, the substrate is gently rocked for up to six hours. Further, step 410 may include a step of rinsing substrate 199 with water or another rinsing agent to remove nanoparticles 212 not bonded to target antigens 210.
In the embodiment in which substrate 199 is a Peltier substrate, the process may include an optional step of applying a DC voltage of a first polarity to the Peltier substrate. Applying a DC voltage of a first polarity heats the surface of the substrate 199 and dries the biological sample within the sample trench 180. A DC voltage of a second and opposite polarity may be applied to Peltier substrate, to cool the surface of the substrate. In an alternate embodiment, the Peltier substrate freezes the biological sample.
Returning to FIG. 1, head module 104 includes electromagnetic write-heads 106 and magneto-resistive read-sensors 108 arranged in pairs, such that each write head 106 is paired with a read sensor 108. The write head 106 may be a thin film write element. The electromagnetic write-heads 106 first write to sample trenches 180, and then the adjacent magneto-resistive read-sensors 106 immediately reads from sample trenches 180, which is referred to as a read-after-write operation. In an exemplary embodiment of the invention, the sample assembly 100 has eight sample trenches 180 corresponding to eight bits in a byte. Accordingly, in this embodiment the head module includes eight electromagnetic write-head 106 and magnetoresistive read-sensor 108 pairs. Advantageously, this is the same number of write heads and read sensors in a typical head module used in magnetic tape drive products, such as IBM® TS1130.Therefore, in one embodiment the head module 104 may be an IBM® TS1130 head module. It should be understood, however, any number of sample trenches 180 may be used, and the number of electromagnetic write-head 106 and magneto-resistive read-sensor 108 pairs in head module 104 may be any number. The number may be in the range from one to the number of electromagnetic write-head and magneto-resistive read-sensor pairs the head module 104. For example, in an embodiment in which there are sixteen such electromagnetic write-head and magneto-resistive read-sensor pairs, such as in a head module of an IBM® 3480 tape drive, the number of sample trenches may be sixteen. In one embodiment, the number of sample trenches 180 is an integral multiple of the number of write-head 106 and read-sensor 108 pairs. Still further, in one embodiment, the write-head 106 and the read-sensor are not separate devices. Instead a single head may perform the functions of both the write-head 106 and read-sensor 108.
As mentioned above, the sample trenches 180 may have spacing from one sample trench to the adjacent sample trench along the X-axis to match the spacing from one read sensor 108 to the adjacent read sensor 108 along the X-axis. In one embodiment the spacing between one sample trench 180 and an adjacent sample trench 180 is 166.5 microns to match the read sensor to read sensor spacing of the IBM® TS1130 tape drive.
Write-heads 106 may be any write head known in the art. In one embodiment write-heads 106 comprise miniature electromagnets, with a coil sandwiched between two poles. Read-sensors 108 may be anisotropic magneto-resistive (AMR), giant magneto-resistive (GMR), or tunnel magneto-resistive (TMR) read-sensors, or other devices with similar functionality known in the art. GMR read-sensors, which are also known as spin-valve read-sensors, typically have an internal anti-parallel pinned layer for increased sensitivity. TMR read-sensors may utilize a tunnel barrier layer to augment the GMR internal structure and to provide increased sensitivity.
As shown in FIG. 1, write-head 106 may be longer along the X-axis direction than read-sensor 108. Accordingly, the active sensing portion of read-sensor 108 is smaller than write-head 106 along the X-axis. Write-head 106 is used to magnetize nanoparticle 212 for detection by read-sensor 108 as discussed below. It is advantageous for write-head to be longer in the X-direction than read-sensor 108 because it prevents read-sensor from encountering unmagnetized nanoparticles 212, and thus, registering a false-negative detection of target antigen 210.
Head module 104 is kept in linear alignment with sample trenches 180 along the X-axis by position-error-servo (PES) read-head 192, which reads magnetically encoded servo-alignment marks 193 from servo track 194 on sample assembly 100. PES read-head 192 may be, for example, an AMR, GMR, or TMR read-sensor. In the example illustrated in FIG. 1, servo-alignment marks 193 shown are Timing Based Servo (TBS) servo-alignment marks such as those used in IBM® Linear Tape Open (LTO) tape drive products (e.g., IBM® tape product models TS1120 and TS1130). U.S. Pat. No. 6,320,719, entitled “Timing Based Servo System for Magnetic Tape Systems,” is hereby incorporated by reference in its entirety for its showing of Timing Based Servo control and TBS servo-alignment marks. U.S. Pat. No. 6,282,051, entitled “Timing Based Servo System for Magnetic Tape Systems,” is hereby incorporated by reference in its entirety for showing the writing of TBS servo-alignment marks.
In step 412 of FIG. 4, the process of detecting the target antigens 210 includes sweeping head module 104 with at least one magneto-resistive read sensor 108 over the sample assembly 100. In one embodiment head module 104 is moved linearly from left to right along the +Y axis relative to a stationary sample assembly. In another embodiment, the sample assembly 100 is swept linearly from right to left along the −Y axis past a stationary head module 104. If substrate 199 is of a flexible polyethylene terephthalate material, then in one embodiment, this right-to-left motion may be performed as data read-write operations in a magnetic tape drive. The head module 104 may sample a single sample trench 180, or simultaneously sample a plurality of sample trenches 180. As an alternate embodiment, head module 104 comprises a helical-scan rotary head module, and the Y-axis of the sample trench 180 is at an angle to the substrate 199. In this embodiment the sample trenches 180 are much shorter in length such that alignment of the head module 104 with sample trenches 180 may be accomplished without alignment marks 193. In one embodiment the IBM® MSS 3850 helical-scan tape drive may be utilized to detect analytes.
In one embodiment, the head module 104 comes into physical contact with the upper surface 254 of the outer layer 253 during the sweeping step of 412. Keeping the head module 104 in physical contact with the upper surface ensures that the head module 104 is kept at a known Z-axis position and assists with alignment of head module 104 with sample trenches 180. As discussed above, the outer layer 253 may comprise diamond-like-carbon, polytetrafluoroethylene, aluminum oxide, polyamides, or other low-friction materials known in the art. Accordingly, the low friction material of the outer layer assists the head module 104 to smoothly sweep the sample trenches 180 while in physical contact with the upper surface 254 of outer layer 253, such that the target antigens of the biological sample is reliably and accurately detected.
As discussed with respect to step 502 in FIG. 5, in some embodiments the inner core 216 of nanoparticles are demagnetized. Accordingly, in this embodiment, as part of step 412, write-head 106 writes to nanoparticles 212 to magnetize inner cores 216 of nanoparticles. Write-head 106 writes with a constant DC magnetic polarity for the duration of the sweeping step 412, such that there are no unwritten regions of sample assembly 100. In one embodiment, write-head 106 writes with magnetically-overlapping write pulses. Further in step 412, read-sensor 108 detects the freshly magnetized inner cores 216 of nanoparticles 212, and thus detects target antigens 210. Read-sensor can detect the target antigens 210 because nanoparticles 212 are bonded to antibodies 208B, which in turn are bonded to target antigens 210.
Write head 106 magnetizes inner cores 216 of nanoparticles 212 along the Y-axis, which is the longitudinal direction of recording in the tape drive industry. Read-sensor 108 magnetically detects nanoparticles 212 along the Y-axis. As a result in step 412, the nanoparticles 212 may be magnetized by write-head 106 and then immediately and magnetically detected by read-sensor 108 during a single sweep of the sample trenches 180. As discussed above, this process is referred to as a read-after-write operation. In one embodiment, the write-head 106 and read-sensor 108 are separated by a magnetic shield (not shown) to prevent cross-talk between write-head 106 and read-sensor 108 during step 412.
Alternatively, the steps of magnetizing nanoparticles 212 and the step of detecting the nanoparticles 212 may be performed separately. For example, write head 106 magnetizes inner cores 216 of nanoparticles 212 along the Y-axis of sample assembly 100. In one embodiment, write-head 106 is then turned off. Subsequently, read-sensor 108 magnetically detects nanoparticles 212 along the Y-axis. The read module sensor 108 may be swept across sample trenches 180 along the Y-axis in both the +Y and −Y directions. Accordingly, read-sensor 108 can repeatedly check for magnetized nanoparticles 212, thus ensuring that all target antigens 210 are detected.
In an embodiment in which the number of sample trenches 180 are greater than the number of write-head 106 and read-sensor 108 pairs in head module 104, the head module 104 may scan the sample trenches 180 in a serpentine fashion. The head module 104 performs a scan in the +Y direction, as head module 104 only provides read-after-write capability in the +Y direction as shown in FIG. 1. Then, a second head module (not shown) comprising a mirror image of head module 104, conducts a read-after-write operation in the −Y direction.
The coercivity of a magnetic inner core 216 may be chosen selectively depending upon the target antigen 210 to be detected. For example, nanoparticles 212 with magnetic inner cores 216 of different coercivity values may be respectively bonded to different types of antibodies 208A and 208B to detect various types of target antigens 210 on the sample assembly 100 simultaneously. Nanoparticles 212 may have different magnetic properties associated with each antigen-antibody combination. Read-sensor 108 detects the different magnetic properties of an inner core 216 based on the materials used for that inner core 216. As discussed above, magnetic inner cores 216 may comprise hard magnetic materials with high coercivity, such as Fe2O3, CrO2, and Barium Ferrite BaFe. For example, magnetic inner cores 216 may comprise iron oxide based nanoparticle materials, including M Fe2O4 (where M may be Co, Ni, Cu, Zn, Cr, Ti, Ba, or Mg) nanomaterials, and iron oxide coated nanoparticle materials or other structures with similar functionality. As a result, in step 412, read-sensor 108 may detect more than one type of target antigens 210 with a single sweep of the sample assembly 100.
FIG. 6 illustrates an embodiment of a servo control system 600 for controlling the motion of head module 104 in the X-axis and Y-axis. For simplicity, FIG. 6 illustrates sample assembly 100 including a single trench 180. In addition, FIG. 6 shows a head module 104 including a single write-head 106 and read-sensor 108 pair and a PES read head 192. However, it should be understood that the sample assembly 100 may include a plurality of trenches and the head module 104 may include a plurality of write-heads 106 and read sensors 108. PES read-head 192 reads servo-alignment marks 193 in servo track 194. Processor 602 receives position-error-servo (PES) signals from PES read-head 192. Processor 602 sends a signal to power amplifier 604 to control X-axis actuator 606 based on the PES information. In turn, the X-axis actuator 606 controls the motion of head module 104 in the X-axis direction. X-axis actuator 606 is connected to head module 104 via mechanical connector 608. Accordingly, head module 104 can be positioned to center write-head 106 and read-sensor 108 on sample trenches 180 of sample assembly 100. Processor 602 also sends signals to power amplifier 614 to control Y-axis actuator 610 for conducting a scan by head module 104 across sample assembly 100. Y-axis actuator 610 is connected to X-axis actuator via mechanical connector 612, such that head module 104 can be moved along the Y-axis in a controllable manner.
FIG. 7 illustrates one embodiment of a write and read circuitry 700 for use in writing to the sample trenches 180 (i.e, magnetizing nanoparticles 212) and reading from the sample trenches 180 (i.e, sensing and detecting the magnetized nanoparticles 212). For simplicity, FIG. 7 illustrates sample assembly 100 including a single trench 180. In addition, FIG. 7 shows a head module including a single write-head 106 and read-sensor 108 pair. However, it should be understood that the sample assembly 100 may include a plurality of trenches and the head module 104 may include a plurality of write-heads 106 and read sensors 108.
Processor 602 sends signals to power amplifier 704. Power amplifier provides power to write-head 106 for magnetizing nanoparticles 212. Processor 602 also sends signals to power amplifier 716. Power amplifier 716 powers Wheatstone bridge 706. In one embodiment, Wheatstone bridge includes read-sensor 108. Thus, read-sensor receives DC current from the Wheatstone bridge 706. Read-sensor 108 detects a resistance change during step 412 discussed above. The resistance change is based on the magnetic field provided by the magnetized inner cores 216 of nanoparticles 212. Wheatstone bridge 706 balances out the zero-magnetism resistance of read-sensor 108 such that only the change in resistance of read-sensor 108 is sent to amplifier 714. The amplifier 714 receives the change in resistance and sends the change in resistance to processor 602 through filter 718. Filter 718 filters out noise. In one embodiment, filter 718 filters out 60 Hz noise which is the type of noise that is pervasive in an office or laboratory setting in which processes of the invention may be performed.
Processor 602 includes a matched filter 730 and a table 720. Processor 602 determines if a nanoparticle 212 was detected, and thus, if a target antigen 210 has been detected. The change in resistance of read-sensor 108 is directly proportional to the magnetic field provided by nanoparticle 212. The change in resistance of read-sensor 108 is directly proportional to the magnetic field provided by nanoparticle 212.
As discussed above, the coercivity of a magnetic inner core 216 may be chosen selectively depending upon the target antigen 210 to be detected. For example, nanoparticles 212 with magnetic inner cores 216 of different coercivity values may be respectively bonded to different types of antibodies 208A and 208B to detect various types of target antigens 210 on the sample assembly 100 simultaneously. The identification of the target antigens 210 in the sample trenches 180 may be facilitated by a lookup table 720 in processor 602. In one embodiment, the lookup table 720 includes a list of (a) target antigens 210, (b) the antibodies 208A and 208B bonded with the target antigens 210, and (c) the coercivity of the inner cores 216 of nanoparticles 212 bonded to antibodies 208B.
In one embodiment of the invention a correlation calculation is performed by the write and read circuit of FIG. 7 to improve the detection accuracy of target antigens. The processor 602 performs correlation calculation C(y) shown in equation [1] between a detection signal profile g(y) read by read-sensor 108 when a nanoparticle 212 is detected and a matched filter 730.

C(y)=∫g(η)h(η−y)dη  Equation [1]

In equation [1], η is the integration variable along the Y-axis that varies as read-sensor 108 sweeps along the Y-axis. The matched filter 730 includes an impulse response h(y) of an ideal signal profile of a detected target nanoparticle 212. Since h(y) is used repetitively, it may be calculated once and stored as matched filter 730 in processor 602.

The range of correlation C(y) is between −1 and +1, where +1 represents an ideal correlation of one hundred percent (100%), and −1 indicates no correlation. The electrical waveform g(y) of each potential detection of a nanoparticle 212 by read-sensor 108 has its correlation C(y) calculated in step 412 of FIG. 4. Processor 602 then compares this correlation C(y) against a threshold correlation value C0 before accepting the signal g(y) as a valid detection of a nanoparticle 212. This correlation removes spurious electrical noise from actual detections of nanoparticles, and thus reduces false-positive detections of target antigens 210.
In one embodiment, the results of the sweep of step 412 may be displayed to a physician or clinician to inform the physician or clinician of the presence (or absence) of target antigens 210 in the biological sample. The results may include items such as the target antigen(s) tested for, the types of antibodies used, a simple positive-detection or negative-detection indication for each antigen, the number of nanoparticles detected for each antigen to give an indication of the prevalence of the targeted antigen, and the number of rejected detections based on the correlation calculation.
The terms “certain embodiments”, “an embodiment”, “embodiment”, “embodiments”, “the embodiment”, “the embodiments”, “one or more embodiments”, “some embodiments”, and “one embodiment” mean one or more (but not all) embodiments unless expressly specified otherwise. The terms “including”, “comprising”, “having” and variations thereof mean “including but not limited to”, unless expressly specified otherwise. The enumerated listing of items does not imply that any or all of the items are mutually exclusive, unless expressly specified otherwise. The terms “a”, “an” and “the” mean “one or more”, unless expressly specified otherwise.
Devices that are in communication with each other need not be in continuous communication with each other, unless expressly specified otherwise. In addition, devices that are in communication with each other may communicate directly or indirectly through one or more intermediaries. Additionally, a description of an embodiment with several components in communication with each other does not imply that all such components are required. On the contrary a variety of optional components are described to illustrate the wide variety of possible embodiments.
Further, although process steps, method steps, algorithms or the like may be described in a sequential order, such processes, methods and algorithms may be configured to work in alternate orders. In other words, any sequence or order of steps that may be described does not necessarily indicate a requirement that the steps be performed in that order. The steps of processes described herein may be performed in any order practical. Further, some steps may be performed simultaneously, in parallel, or concurrently.
While particular embodiments of the present invention have been shown and described, it will be obvious to those skilled in the art that, based upon the teachings herein changes and modification may be made without departing form this invention and its broader aspects and, therefore, the appended claims are to encompass within their scope all such changes and modifications as are within the true spirit and scope of this invention. Furthermore, it is to be understood that the invention is solely defined by the appended claims.

## Claims

1. A method of forming a sample assembly of a biological sample having target antigens, the method comprising:
forming a base layer on a substrate;
forming an outer layer on the base layer;
forming at least one sample trench within the outer layer using one or more of a milling technique and a lithography technique, wherein said sample trench has a bottom surface;
forming a plurality of magnetic servo alignment marks on said sample assembly;
bonding a first set of antibodies within said at least one sample trench on a first surface of said base layer;
exposing said at least one sample trench with said first set of bonded antibodies to said biological sample having said target antigens, wherein said target antigens bond with said first set of antibodies within said at least one sample trench;
bonding a second set of antibodies to nanoparticles; and
exposing said target antigens within said at least one sample trench to said second set of antibodies bonded to said nanoparticles,
wherein said second set of antibodies bond with said target antigens within said at least one sample trench.

2. The method of claim 1, further comprising applying a voltage to the substrate.

3. The method of claim 2, wherein applying the voltage to the substrate reduces a temperature of the substrate.

4. The method as recited in claim 2, wherein applying the voltage causes a temperature of the substrate to reduce to a value less than a freezing point of at least one biological sample in the sample trench.

5. The method as recited in claim 4, wherein the substrate is a Peltier substrate, and wherein the voltage is a DC voltage.

6. The method of claim 1, further comprising:
forming at least one servo alignment trench in said outer layer, parallel to said sample trench,
filling said servo alignment trench with tape ink;
curing said tape ink; and
forming said plurality of magnetic servo alignment marks in said cured tape ink.

7. The method of claim 1, further comprising:
magnetizing said nanoparticles using a write head;
aligning the write head with the at least one sample trench using a position-error-servo (PES) technique; and
detecting said magnetized nanoparticles using a read sensor.

8. The method of claim 1, wherein said outer layer comprises a compound selected from the group consisting of diamond-like-carbon, polytetrafluoroethylene, and aluminum oxide
wherein said first set of antibodies are bonded to said target antigen via a bonding material selected from the group consisting of amide, alkoxysilane, organic functional trialkoxysilane, and thiol.

9. The method of claim 1, wherein the nanoparticles comprise a plurality of nanoparticles types, each nanoparticle type being characterized by a unique coercivity value,
wherein each nanoparticle type is configured to facilitate detection a different type of target antigen on the sample assembly simultaneously.

10. The method of claim 1, wherein the at least one sample trench comprises a plurality of parallel-oriented sample trenches, each sample trench being separated from one or more adjacent sample trenches by a distance of approximately 166 microns, and
wherein the at least one sample trench is characterized by a depth in a range from about 0.2 microns to about 60 microns.

11. The method of claim 1, wherein the bonding the first set of antibodies comprises
coating the first surface of the base layer with one or compounds selected from a group consisting of: amides, alkoxysilanes, and thiols;
contacting a solution of the first set of antibodies with the first surface of the base layer; and
rocking the first surface of the base layer in contact with the solution of the first set of antibodies for a predetermined period of time less than or equal to about six hours.

12. The method as recited in claim 1, wherein the nanoparticles comprise:
a magnetic inner core comprising a material selected from a group consisting of: CrO2, BaFe, and MFe2O4, wherein M is a metal selected from a group consisting of Co, Cr, Ti, Ba and Mg; and
a shell comprising a material selected from a group consisting of nonmagnetic gold, silicon and silicon dioxide.

13. The method as recited in claim 1, further comprising:
aligning one or more write elements and one or more read sensors of a head module along an X-axis of the at least one sample trench using at least some of the servo-alignment marks;
coating the first surface of the base layer with one or compounds selected from a group consisting of: amides, alkoxysilanes, and thiols;
contacting a solution of the first set of antibodies with the coated first surface of the base layer;
rocking the coated first surface of the base layer in contact with the solution of the first set of antibodies for a predetermined period of time less than or equal to about six hours; and
magnetizing said nanoparticles using a write head of the head module;
wherein the nanoparticles comprise:
a magnetic inner core comprising a material selected from a group consisting of: CrO2, BaFe, and MFe2O4, where M is a metal selected from a group consisting of Co, Cr, Ti, Ba and Mg; and
a shell comprising a material selected from a group consisting of gold, silicon and silicon dioxide; and

wherein the tape ink comprises magnetic recording particles disposed in a polymer matrix,
wherein the at least one sample trench comprises a plurality of parallel-oriented sample trenches,
wherein the outer layer comprises a compound selected from the group consisting of diamond-like-carbon, polytetrafluoroethylene, and aluminum oxide, and
wherein the first set of antibodies are bonded to said target antigen via a bonding material selected from the group consisting of amide, alkoxysilane, organic functional trialkoxysilane, and thiol.

14. A method of detecting target antigens in a biological sample using
a sample assembly having
a base layer formed above a substrate;
an outer layer formed above the base layer;
at least one sample trench formed in the outer layer using a milling technique;
a plurality of first antibodies, at least some of the first antibodies each being bound to:
at least one surface of one or more of the sample trenches; and
one of a plurality of target antigens;
a plurality of second antibodies, at least some of the second antibodies each being bound
a target antigen bound to one of the first antibodies; and
a nanoparticle,
the method comprising:
aligning a head module with said sample trench utilizing a plurality of magnetic servo alignment marks
sweeping said head module over said sample assembly, wherein said head module includes at least one magneto-resistive read sensor configured to detect target antigens via the nanoparticles; and
detecting at least one particular antigen among the plurality of target antigens.

15. The method of claim 14, wherein said step of sweeping said head module over said sample assembly includes placing said head module in contact with an upper surface of said outer layer, wherein at least one magneto-resistive read sensor in said head module detects said target antigens in said sample trench.

16. The method of claim 14, further comprising utilizing a plurality of magnetic servo alignment marks on said sample assembly to align said at least one magneto-resistive read sensor with said sample trench.

17. The method of claim 14, said head module further comprising at least one write head configured to magnetize the nanoparticles.

18. The method of claim 14, said head module further comprising: a plurality of pairs of write heads and magneto-resistive read sensors spaced apart from each adjacent pair of said write heads and said magneto-resistive read sensors by a first distance, and
said sample assembly further comprising:
a plurality of parallel sample trenches spaced apart from each adjacent sample trench by said first distance,
the method further comprising,
sampling a plurality of magnetic servo alignment marks formed in proximity to one or more of the parallel sample trenches using at least one of the magneto-resistive servo read sensors;
magnetizing said nanoparticles with at least one of the write heads; and
detecting said nanoparticles with said magneto-resistive read sensors.

19. The method of claim 18, wherein the sampling and the magnetizing are performed simultaneously in a single sweep of the head module.

20. The method of claim 14, further comprising either:
displaying a positive-detection indication for the predetermined antigen in response to detecting the predetermined antigen; or
displaying a negative-detection indication for the predetermined antigen in response to not detecting the predetermined antigen.

21. The method of claim 14, further comprising applying a DC voltage to the substrate, wherein the substrate is a Peltier substrate, and wherein applying the DC voltage to the substrate freezes one or more biological samples in the sample trench.

22. The method of claim 14, further comprising:
exposing at least partially unbound target antigens to said second set of antibodies bonded to said nanoparticles, wherein said second set of antibodies bond with at least some of said at least partially unbound target antigens;
bonding a third set of antibodies to said nanoparticles; and
exposing at least partially unbound target antigens to said third set of antibodies bonded to said nanoparticles.

23. The method of claim 14, further comprising:
forming a plurality of magnetic servo alignment marks on said sample assembly, the plurality of magnetic servo alignment marks being configured to facilitate aligning said head module with said sample trench;
placing said head module in contact with an upper surface of said outer layer;
aligning said head module with said sample trench utilizing the plurality of magnetic servo alignment marks;
detecting said target antigens in said sample trench via the nanoparticles using a magneto-resistive servo read sensor of the head module; and
identifying one or more of the target antigens in the at least one sample trench.

24. The method of claim 23, further comprising at least one of:
magnetizing at least some of the nanoparticles using a write head of the head module; and
demagnetizing at least some of the nanoparticles using the write head of the head module.

25. A method comprising:
forming an outer layer on a base layer;
forming a plurality of parallel-oriented sample trenches and alignment trenches within the outer layer;
forming a base layer in each sample trench and each alignment trench;
forming a plurality of magnetic servo-alignment marks in each alignment trench;
aligning at least one write element and at least one read sensor along an X-axis of the at least one sample trench using the servo-alignment marks:
bonding a first set of antibodies within said at least one sample trench on a first surface of the base layer;
bonding at least some of the first set of bonded antibodies to one or more target antigens;
bonding a second set of antibodies to nanoparticles; and
bonding at least some of the second set of antibodies bound to the nanoparticles to one or more target antigens bound to one of the first set of antibodies.

26. The method as recited in claim 25, further comprising at least one of:
detecting magnetized nanoparticles using a read sensor of a head module; and
demagnetizing one or more magnetized nanoparticles, and
wherein each of the detecting and the demagnetizing comprises sweeping the head module over the nanoparticles.