Systems and methods of detecting molecules bound with magnetic particles

Abstract

A method for detecting the presence of a molecule in a biological sample with a Polymerase Chain Reaction (PCR) detection system, including applying a trained machine learning correction matrix to obtained PCR signals from a plurality of channels, the matrix trained with PCR training data to correct signal cross-talk between all of the plurality channels. The training includes applying a loss function representing differences in cross-talk corrected PCR data respective to the plurality of channels. Determining the presence or lack of presence of a target molecule in the biological sample is based on determining whether the corrected PCR signals represent positive or negative signals.

Description

SYSTEMS AND METHODS OF DETECTING MOLECULES BOUND WITH MAGNETIC PARTICLES CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to U. S. Provisional Patent Application No. 63 / 790314, filed April 17, 2025, the entire contents of which is herein incorporated by reference.FIELD

[0002] This application relates to the area of magnetic nanoparticle binding and sensing, particularly in the field of biomedical diagnostics.BACKGROUND

[0003] In recent years, magnetic nanoparticles (MNPs) have been used for molecule detection in various fields such as biosensing, environmental monitoring, and medical diagnostics. As their name suggests, MNPs possess magnetic properties, and they can be manipulated using external magnetic fields. In addition, MNPs can be functionalized to bind or attach with target molecules (e.g., to form complexes) and allow selective detection of the target molecules.

[0004] Some existing methods for detecting molecules from tested samples face the issues of failing to detect at low analyte concentration and / or from nonspecific binding or misplacement of analytes away from detection-sensitive / specific locations. To detect at single molecule level, some sensing systems have bioactive detection areas made down to several hundred nanometers.

[0005] Challenges are faced in discerning between targeted molecules bound with MNPs and MNPs that may be non-specifically bound or otherwise located in areas that cause a magnetic sensor to signal their presence, and thus incorrectly signal the presence of a target molecule.

[0006] When using such systems, sensor components incorporating millions of bioactive surfaces and sensors, in particular, may be exposed to assays and extraneous sample materials that non-specifically bind or position the MNPs around bioactive surfaces, and interfere with accurate detection of target molecules.

[0007] Therefore, there is a need for improvements in detecting target molecules in systems that rely on specific MNP binding.SUMMARY

[0008] A magnetic sensing device is configured to detect target biomolecules of samples by identifying the presence magnetic nanoparticles (MNPs) attached to the target molecules, and to distinguish them from the presence of MNPs that are not so attached. In some embodiments, a magnetic sensing device includes a patterned surface of bioactive surface areas proximate to magnetic sensors (e.g., magnetic tunnel junctions (MTJs)) and configured to selectively isolate and tether particular types of complexes including both the target biomolecules and MNPs.

[0009] After introduction of a sample under test and particular detection agents (e.g., assays) to the patterned surface, including MNPs and binding elements, the particular types of complexes can form and become attached / tethered to the bioactive surface areas. A first set of signals is then obtained from the magnetic sensors, which will indicate tire presence (or lack) of MNPs in a sensor’s proximity.

[0010] A modulation agent is then introduced to the patterned surface, which is configured to modulate the length of a binding element connecting MNPs of the particular types of complexes to the bioactive surface. As a result, the distance between MNPs of bound complexes will modulate (shorten or lengthen) with respect to the bioactive surface and respective magnetic sensor.

[0011] A second set of signals is then obtained from the magnetic sensors, which can indicate a change in distance of detected MNPs relative to the bioactive surface and respective magnetic sensor. Based on an indication of the change (or lack of change) in distance, the presence of a target biomolecule is determined.

[0012] In some embodiments, the binding elements that are modulated include tethers that form bonds between the bioactive surface (e.g., silicon dioxide) and the remaining portion the particular types of complexes, including target molecules and MNPs.

[0013] In some embodiments, the modulated binding elements include single stranded DNA (ssDNA) and the modulation element is selected to compress or collapse the ssDNA. The modulation agent may include magnesium salt (Mg++), for example. In some embodiments, the concentration is about 1 millimolar (mM) or more.

[0014] In some embodiments, the modulation agent comprises an electric field applied to an aqueous medium within which the ssDNA tethers are immersed (e.g.,saline). In some embodiments, the electric field applied comprises a voltage between about.1 and,2 Vnm-1 for a time period of about 20 nanoseconds or more.|0015] In some embodiments, the modulated binding elements include polyethylene glycol (PEG) linkers. A modulation agent may include a PEG antibody (anti-PEG) that collapses or compresses the backbone of the PEG linker. The PEG linker may be a long-chain PEG and can have a molecular weight of around 1000 grams per mole (g / mol).

[0016] The binding elements can be adapted with functional ends for binding them to the bioactive surface areas and other elements of the particular complexes. For example, a silane head may be incorporated into a binding element and used for tethering complexes with an SiO2surface. A biotin-based functional end may be used, for example, to covalently bind a linker with another molecule, such as an antibody molecule.

[0017] In some embodiments, the particular types of complexes can include capture antibodies and detection antibodies (e.g., as part of assays), wherein the antibodies are selected to attach to target analytes, and further attach with the binding elements and MNPs to form the complexes that selectively attach to the bioactive surface areas.

[0018] In some embodiments, the magnetic sensor includes a magnetic tunnel junction (MTJ) sensor configured to generate signals representing a change in a magnetic field around and magnetoresistance of the sensor, the sensor signals responsive to and indicative of the relative proximity of an MNP. The generated signals are obtained (both before and after introduction of a modulation agent) and analyzed to determine the presence and relative proximity of a MNP before and after introduction of the modulation agent, and thereby used to determine whether the MNP is attached to a target biomolecule.BRIEF DESCRIPTION OF THE DRAWINGS

[0019] Objects, features, and advantages of the disclosure will be readily apparent from the following description of certain embodiments taken in conjunction with the accompanying drawings in which:

[0020] FIG. 1A is an illustrative cross-sectional view of a magnetic sensing device with a target analyte and MNP captured in a nanowell proximite to a magnetic sensor according to some embodiments.

[0021] FIG. IB is an illustrative cross-sectional view of a patterned surface including an array of bioactive surface areas and magnetic sensors according to some embodiments.

[0022] FIG. 2A is an illustrative cross-sectional view of an MNP complex selectively bound to a bioactive surface area proximate a magnetic sensor according to some embodiments.

[0023] FIG. 2B is a chart of resistance changes measured from signals of a magnetic tunnel junction (MTJ) responsive to different proximities of an MNP.

[0024] FIG. 3 is an illustrative perspective view of a magnetic sensing device with a microfluidic chamber according to some embodiments.

[0025] FIG. 4A is an illustrative cross-sectional view of an MNP complex bound to a bioactive surface with a ssDNA tether according to some embodiments.

[0026] FIG. 4B is an illustrative cross-sectional view of the MNP complex of FIG. 4A after introduction of a magnesium salt.

[0027] FIG. 5 is a flow diagram of a method for detecting the presence of a target molecule by modulating the length of an MNP complex.

[0028] FIG. 6A is an illustrative cross-sectional view of an MNP complex bound with a PEG tether to a bioactive surface area of a magnetic sensor according to some embodiments.

[0029] FIG. 6B is an illustrative cross-sectional view of the MNP complex of FIG.6 A after introducti on of an anti -PEG agent.

[0030] FIG. 7 is an illustrative diagram of a computer sy stem such as utilized in some embodiments.DETAILED DESCRIPTION

[0031] Devices, systems, and methods include use of magnetic sensing elements and bioactive surface areas to detect the presence of biomolecules w ith the assistance of selectively bound nanoparticles (MNPs). MNPs, along with other detection agents (e.g., in assays), are used to form complexes with target biomolecules and selectively bind to the bioactive areas where they can be detected by the sensing elements. Modulation agents are further utilized to assist w ith differentiating betw een MNP complexes bound or not bound with target molecules by selectively modulating (or not modulating) the length of bound or unbound complexes. The modulation causes adetectable difference in distance between the bound MNPs and a respective sensing element.|0001] FIG. 1A is an illustrative cross-sectional view of a magnetic sensing device with a target analyte and MNP captured in a nanowell proximate to a magnetic sensor according to some embodiments. A magnetic sensing device 100 includes a bioactive layer 110 and substantially inert layer 120, within which nanowells 150 are formed for isolating MNPs 140 proximate to a magnetic sensor 130 configured for detecting MNPs.

[0002] Operation of device 100 is arranged with materials / processes that facilitate selective / specific formation of complexes of target biomolecules 170 attached to MNPs 140 and bioactive layer 110. Detection of MNPs 140 ("‘reporter molecules”) by sensor 130 thereby indicates the presence of biomolecules 170 from a sample under test introduced to surfaces of l ayers 110 and 120,

[0003] Antibodies 175 (“capture antibodies”) are configured / introduced to selectively attach with target biomolecules 170 such as to form a sandwich immunoassay.Capture antibodies 175 are configured to selectively bind with the surface of bioactive layer 110, thereby attaching target biomolecules 170 to layer 110.

[0004] Antibodies 145 (“detection antibodies”) are configured to selectively bind with target biomolecules 170 and configured to attach with MNPs 140 with linkers 135. Complexes 125 of antibodies 145 and 175, target biomolecules 170, and MNPs 140 thereby attach to bioactive layer 110 proximate to sensor 130, Target biomolecules 170 may be target antigens, for example, while antibodies 145 and 175 are selected based on their known reactivity with target biomolecules 170.

[0032] FIG. IB is an illustrative cross-sectional view of a patterned surface including an array of bioactive surface areas and magnetic sensors according to some embodiments. Device 100 includes a patterned surface 105 with a plurality of nanowells 150 and magnetic sensors (e.g., sensors 130), integrated within a CMOS chip 155 used for circuitry' that powers magnetic sensors and through which signals are transmitted representing the presence of target MNPs (e.g., as part of a complex 125) proximate to the sensors as further described herein.

[0033] FIG. 2A is an illustrative cross-sectional view of an MNP complex selectively bound to a bioactive surface area 210 proximate a magnetic sensor according to some embodiments, A complex 125 includes an MNP 140, the presence of which can be detected with use of a magnetic sensor 200. A distance 230 represents a proximity ofMNP 140 to sensor 200, and in response to changes in distance 230 between MNP 140 and sensor 200, a level of magnetoresistance changes in sensor 200.10034] FIG. 2B is a chart of resistance changes measured from signals of a magnetic tunnel junction (MTJ) responsive to different proximities of an MNP. A MNP and a MTJ were configured and arranged at different distances from each other, and levels of changes in magnetoresistance in the MTJ were respectively measured. Changes in distances of around 10 nm created measurable and detectable differences in resistance within the sensor.

[0005] FIG. 3 is an illustrative perspecti ve view of a magnetic sensing device with a microfluidic chamber according to some embodiments. A MNP sensing device 300 includes a microfluidic chamber 310 configured to introduce and flow test materials (e.g., samples, MNPs, reagents) over a patterned surface and magnetic sensor array 340 including surfaces / layers and sensors such as further described herein. An inflow 320 receives the test materials, which are further directed toward and over the magnetic sensor array 340, where detection of MNPs and target molecules occurs. Magnetic sensor array 340 can include a plurality (e.g., grid) of nanowells (e.g., nanowells 150 of FIGs. 1 and 1B).

[0006] Magnetic sensing device 300 is configured with electronics for providing power to magnetic sensor array 340, processing / propagating magnetic signals and control signals, and / or facilitating suction / pressure applied to materials with device 300. Signals include those received in response to changes in magnetic fields around the sensors and indicative of the presence of MNPs, and may subsequently be directed to a computing device for further processing and storage of data.

[0007] Materials that may be passed through the device include solutions of MNPs, linkers, antibodies, surfactants, tethers, and modulation agents such as further described herein for isolation and detection of target molecules bound with MNPs. After materials are introduced to the device through inflow 320 and microfluidic chamber 310, they may flow through or be removed from chamber 310 via outflow 330. Flow may be assisted with pumping, suction, and / or passive force mechanisms.

[0008] In some embodiments, device 300 includes electrodes 350A and 350B for applying an electric field across the patterned surface upon which detection agents (e.g., tethers) bind. Such as further described herein, application of an electric field can be used to modulate the distance of MNPs of target complexes from the patternedsurface and magnetic sensor array 340, and to thereby detect the presence of target molecules.|0035] FIG. 4A is an illustrative cross-sectional view of an MNP complex 425 bound to a bioactive surface 410 with a single stranded DNA (ssDNA) tether 460 according to some embodiments. Hie ssDNA tether 460 is adapted to bind with capture antibodies 475 and to modulate the distance of MNPs 440 of target-bound / captured complexes 425 with respect to bioactive surface 410 and a proximate magnetic sensor 430.

[0036] Capture antibodies 475 are adapted to selectively bind with target analytes 470 and tethers 460, while detection antibodies 445 are adapted to selectively bind with the target analytes 470 and MNPs 440, thereby selectively attaching complexes of MNPs 440 and target analytes 470 to bioactive surface 410 with ssDNA tethers 460 and capture antibodies 475. Magnetic sensor 430 proximate to bioactive surface 410 provides responsive signals indicating a presence of the MNP 440 (e.g., based on changes in magnetic fields and / magnetoresistance as illustrated in FIG. 3) and its relative proximity represented by distance 450A.

[0037] FIG. 4B is an illustrative cross-sectional view of the MNP complex 425 of FIG. 4A after introduction of a magnesium salt (e.g., MgSO4 / Mg++) and / or electric field to. With the introduction of and response to magnesium salt, tether 460 coils and decreases the distance between attached MNP complex 425 and bioactive surface 410. A closer distance / proximity 450B between MNP 440 and sensor 430 is represented by corresponding signals from sensor 430. An MNP that may have been non-selectively attached or proximate sensor 430 should not modulate in proximity commensurate to that of complex 425, Thereby, a magnetic signal representing such a non-selectively present MNP would not indicate the presence of a target analyte.

[0038] FIG. 5 is a flow diagram of a method for detecting the presence of a target molecule by modulating the length of an MNP complex. At block 510, sample materials and reagents, including MNPs, are introduced to surfaces of a magnetic sensing device (e.g., of FIGs.l A-1B, 2A, 3, and 4A-4B). Reagents may include elements for forming complexes used to detect target analytes (e.g., MNPs, capture / detection antibodies, tethers). In some embodiments, a sensing device is provided with surfaces pre-coated with some sensing agents (e.g., tethers, antibodies, anti-fouling coatings). For example, a device (e.g,, device 100, 300) may bepreconfigured with capture antibodies (antibodies 175 and 475 tethered with tethers 160 and 460 to bioactive surfaces 110 and 410 of FIGs, 1 and 4).10039] Analytes included (or not) in a patient sample are introduced to the device so as to permit attachment at block with capture antibodies bound to bioactive surfaces and configured to bind with analytes. In some embodiments, after an opportunity for analytes to be bound with capture antibodies (first incubation), the surfaces of the device may be rinsed so as to remove certain extraneous elements (e.g., of unbound non-target portions of the patient sample). After the wash / rinse, MNPs (e.g., 140, 440) are introduced, including with or attached with detection antibodies (e.g., 145, 445).10040] At block 520, detection antibody -bound MNPs are provided time to bind with analytes to form target complexes bound to bioactive surfaces (incubation). After the incubation, the surfaces may then be washed (again).

[0041] At block 530, a first reading from magnetic sensors is obtained. Signals representing changes in magnetic fields and / or magnetoresistance may provide an indication of the presence of an MNP and its relative proximity to the sensor (e.g., as shown in FIG. 2B). At block 540, a modulation agent (e.g., Mg++ salt, electric field, anti-PEG) is introduced in order to modulate the distance of complexes bound with a target analyte and bioactive surface (e.g., complex 125, 425).

[0042] At block 550, after introduction of the modulation agent, a second set of signals from magnetic sensors is obtained. At block 560, the second set of measurements is then analyzed to determine differences (if any) with the first set of measurements. At block 570, based on the analysis, a determination is made about whether the relati ve position of MNPs proximate respective sensors has been modulated to reflect a presence of a target-bound complex (125, 425 of FIGs. 1 and 4). For example, a predetermined threshold or range of signal measurement differences may be used, depending on the particular type of tether and / or modulation agent utilized. Pre-testing data may be used to establish the threshold or range.

[0043] FIG, 6A is an illustrative cross-sectional view of an MNP complex 620 bound with a PEG tether 660 to a bioactive surface area 610 of a magnetic sensor 630 according to some embodiments. FIG. 6B is an illustrative cross-sectional view of the MNP complex 620 of FIG. 7A after introduction of anti-PEG agent 665. In some embodiments, target-bound complexes 620 include use of PEG tether 660 to bindcomplexes 620 to bioactive surfaces 610 and PEG antibody (anti-PEG) molecules 665 to modulate MNP 640 distance with a magnetic sensor.10044] In some embodiments, the PEG tether or linker is a long -chain PEG and has a molecular weight of about 1000 g / mol. The PEG tether may have a length of about 10 nm or more and a base (coiled) height of about 3 nm or more and an expanded (uncoiled) height of an additional 5 nm or more (e.g., corresponding to length of anti- PEG molecule) upon application of an anti-PEG. Particular PEGs include those marketed under the names PEG40K, PEG20K, PEG5K, PEG12, for example. Anti-PEGs, particularly those that bind with and ‘"open” the backbone of a PEG structure, include commercially available products from Genscript including, for example, THE™ PEG Antibody, mAb, Mouse.

[0045] Prior to introduction of an anti-PEG agent, the distance between MNP 640 and sensor 630 is illustrated by 650A and measured with use of signals from sensor 630, After introduction of anti-PEG agent 665, anti-PEG molecules attach to PEG tethers 660 and cause the tether backbone to stretch open or uncoil. After opening of the tethers 660, the distance of MNP 640 from sensor 630 increases as illustrated at 650B. Further signals from sensor 630 reflect the increased distance 650B of MNP 640 and thereby the presence of a complex-bound analyte 670.

[0046] Computer systems may be utilized for assisting in performing the methods described herein, such as for controlling and powering the described magnetic sensing devices, receiving, transmitting, and processing data from the magnetic sensing devices, controlling inflow and / or outflow of samples and detection agents to and from the devices, and controlling the manufacturing processes. The computer systems may utilize any suitable number of subsystems. Examples of such subsystems are shown in FIG. 7 in computer system 10,

[0047] In some embodiments, a computer system includes a single computer apparatus, where the subsystems can be the components of the computer apparatus. In other embodiments, a computer system can include multiple computer apparatuses, each being a subsystem, with internal components. A computer system can include desktop and laptop computers, tablets, mobile phones and other mobile devices. In some embodiments, a cloud infrastructure (e.g., Amazon Web Services), a graphical processing unit (GPU), etc., can be used to implement the disclosed techniques.

[0001] The subsystems shown in FIG. 7 are interconnected via a system bus 75. Additional subsystems such as a printer 74, keyboard 78, storage device(s) 79,monitor 76, which is coupled to display adapter 82, and others are shown. Peripherals and input / output (I / O) devices, which couple to I / O controller 71, can be connected to the computer system by any number of means known in the art such as input / output (I / O) port 77 (e.g., USB, FireWire*’). For example, I / O port 77 or external interface 81 (e.g. Ethernet, Wi-Fi, etc.) can be used to connect computer system 10 to a wide area network such as the Internet, a mouse input device, or a scanner. The interconnection via system bus 75 allows the central processor 73 to communicate with each subsystem and to control the execution of a plurality of instructions from system memory 72 or the storage device(s) 79 (e.g., a fixed disk, such as a hard drive, or optical disk), as well as the exchange of information between subsystems. The system memory 72 and / or the storage device(s) 79 may embody a computer readable medium. Another subsystem is a data collection device 85, such as a camera, microphone, accelerometer, and the like. Any of the data mentioned herein can be output from one component to another component and can be output to the user.

[0048] A computer system can include a plurality of tire same components or subsystems, e.g., connected together by external interface 81 or by an internal interface. In some embodiments, computer systems, subsystem, or apparatuses can communicate over a network. In such instances, one computer can be considered a client and another computer a server, where each can be part of a same computer system. A client and a server can each include multiple systems, subsystems, or components.

[0049] Aspects of embodiments can be implemented in the form of control logic using hardware (e.g. an application specific integrated circuit or field programmable gate array) and / or using computer software with a generally programmable processor in a modular or integrated manner. As used herein, a processor includes a single-core processor, multi-core processor on a same integrated chip, or multiple processing units on a single circuit board or networked. Based on the disclosure and teachings provided herein, a person of ordinary skill in the art w ill know and appreciate other ways and / or methods to implement embodiments of the present invention using hardware and a combination of hardware and software.

[0050] Machine learning models utilized herein, such as for analyzing magnetic sensor data for determining the presence of MNPs and attached molecules, may include one or more of a Naive Bayes (NB) model, a logistic regression (LR) model, a random forest (RF) model, a support vector machine (SVM) model, an artificialneural network model, a multilayer perceptron (MLP) model, a convolutional neural network (CNN), a Large Language model (LLM), and / or other machine learning or deep leaning models, etc. The machine learning models can be updated / trained using a supervised learning technique, an unsupervised learning technique, etc.

[0051] Any of the software components or functions described in this application may be implemented as software code to be executed by a processor using any suitable computer language such as, for example, Java, C, C++, C#, Objective-C, Swift, or scripting language such as Perl or Python using, for example, conventional or object- oriented techniques. The software code may be stored as a series of instructions or commands on a computer readable medium for storage and / or transmission. A suitable non-transitory computer readable medium can include random access memory (RAM), a read only memory (ROM), a magnetic medium such as a harddrive or a floppy disk, or an optical medium such as a compact disk (CD) or DVD (digital versatile disk), flash memory, and the like. The computer readable medium may be any combination of such storage or transmission devices.

[0052] Such programs and / or data may also be encoded and transmitted using carrier signals adapted for transmission via wired, optical, and / or wireless networks conforming to a variety of protocols, including the Internet. As such, a computer readable medium may be created using a data signal encoded with such programs. Computer readable media encoded with the program code may be packaged with a compatible device or provided separately from other devices (e.g., via Internet download). Any such computer readable medium may reside on or within a single computer product (e.g. a hard drive, a CD, or an entire computer system), and may be present on or within different computer products within a system or network. A computer system may include a monitor, printer, or other suitable display for providing any of the results mentioned herein to a user.

[0053] Any of the methods described herein may be at least partially performed with a computer system including one or more processors, which can be configured to perform the steps. Thus, embodiments can be directed to computer systems configured to perform elements of the steps of any of the methods described herein, potentially with different components performing a respective steps or a respective group of steps. Steps of methods herein can be performed at a same time or in a different order. Additionally, portions of these steps may be used with portions of other steps from other methods. Also, all or portions of a step may be optional.Additionally, any of the steps of any of the methods can be performed with modules, units, circuits, or other means for performing these steps.10054] The specific details of particular embodiments may be combined in any suitable manner without departing from the spirit and scope of embodiments of the invention. However, other embodiments of the invention may be directed to specific embodiments relating to each individual aspect, or specific combinations of these individual aspects.

[0055] The above description of example embodiments of the invention has been presented for the purposes of illustration and description. It is not intended to be exhaustive or to limit the invention to the precise form described, and many modifications and variations are possible in light of the teaching above.

[0056] A recitation of "a", "an" or "the" is intended to mean "one or more" unless specifically indicated to the contrary. The use of “or” is intended to mean an “inclusive or,” and not an “exclusive or” unless specifically indicated to the contrary. Reference to a “first” component does not necessarily require that a second component be provided. Moreover reference to a “first” or a “second” component does not limit the referenced component to a particular location unless expressly stated.

[0057] All patents, patent applications, publications, and descriptions mentioned herein are incorporated by reference in their entirety for all purposes. None is admitted to be prior art.

Claims

CLAIMS1. A method for detection of molecules using a magnetic sensor, the method comprising:obtaining a magnetic sensing device with a patterned surface comprising bioactive surface areas proximate to respective magnetic sensors and configured to selectively isolate and tether particular types of complexes of target biomolecules and magnetic nanoparticles to the bioactive surface areas;introducing a biological sample and one or more detection agents of MNPs and binding elements to the magnetic sensing device for forming the particular types of complexes;receiving first signals from a respective magnetic sensor of the magnetic sensing device, the signals representing a change in a magnetic field strength or direction proximate to the respective sensor;introducing a modulation agent configured to modulate a length of a binding element of the binding elements introduced to tire magnetic sensing device;receiving second signals from the respective magnetic sensor representing a change in a magnetic field strength or direction proximate to the sensor;detecting, based on the first and second signals, a change in relative proximity of one of the MNPs to the respective magnetic sensor;based on the detected change in relative proximity of the MNP, determining a presence of a target biomolecule of the biological sample specifically bound to one of the particular types of complexes.

2. The method of claim 1 wherein the magnetic sensor comprises a magnetic tunnel junction (MTJ) configured and arranged to measure a magnetoresistance based on tire presence and proximity of the MNPs to the magnetic sensor.

3. The method of claim 1 wherein the particular types of binding elements comprise single stranded DNA (ssDNA) tethers configured to bind with the bioactive surface areas.

4. The method of claim 3 wherein the modulation agent comprises a magnesium salt (Mg++) selected to compress or collapse the ssDNA.

5. The method of claim 3 wherein the modulation agent comprises an electric field applied to an aqueous medium within which the ssDNA tethers are immersed.

6. The method of claim 5 wherein the electric field applied comprises a voltage between about.1 and.2 Vnm-1.

7. The method of claim 1 wherein the particular types of binding elements comprise a polyethylene glycol (PEG) tether configured to bind with the bioactive surface areas and wherein the modulation agent comprises a PEG antibody (anti-PEG) selected to bind with and expand a backbone of the PEG tether.

8. The method of claim 1 wherein the patterned surface comprises:a first layer having a first surface energy configured for binding with the particular types of complexes;a second layer positioned on the first layer, the second layer having a second surface energy substantially inert to the binding elements, target molecules, and MNPs of the particular types of complexes;one or more nanowells formed within the second layer, each exposing a surface of the first layer, the nanowells configured to selectively bind the particular types of complexes to the exposed surfaces of the first layer;one or more magnetic sensors arranged from beneath the exposed surface of each of the nanowells, the magnetic sensors configured to respectively detect the presence of the target biomolecules through detection of the MNPs within the complexes.

9. The method of claim 8, wherein the first layer comprises silicon dioxide (SiO2) and the second layer comprises diamond-like carbon (DLC).

10. The method of claim 1 wherein the complexes comprise a capture antibody and detection antibody each configured to bind with the target biomolecule, the capture antibody configured to attach to the binding elements and the detection antibody configured to attach to the MNPs.

11. The method of claim 10 wherein the signals are indicative of changes in relative proximity of the MNPs of around ten nanometers or greater.

12. A magnetic sensing system for detection of molecules, the system comprising:a magnetic sensing device comprising a patterned surface with bioactive surface areas proximate to respective magnetic sensors and configured to selectively isolate and tether particular types of complexes of target biomolecules and magnetic nanoparticles to the bioactive surface areas;one or more processors programmed and configured to:control an introduction of a biological sample and one or more detection agents of MNPs and binding elements to the magnetic sensing device for forming the particular types of complexes;receive first signals from a respective magnetic sensor of the sensing device, the signals representing a change in a magnetic field strength or direction proximate to the sensor;control an introduction of a modulation agent configured to modulate a length of a binding element of the binding elements introduced to the magnetic sensing device;receive second signals from the respective magnetic sensor representing a change in a magnetic field strength or direction proximate to the sensor;detect, based on the first and second signals, a change in relative proximity of one of the MNPs to the respective magnetic sensor;based on the detected change in relative proximity of the MNP, determining the presence of a target biomolecule of the biological sample specifically bound to one of the particular types of complexes.

13. The system of claim 12 wherein the respective magnetic sensors comprise a magnetic tunnel junction (MTJ) configured and arranged to measure a magnetoresistance and / or magnetic field based on the presence and proximity of the MNPs to the respective magnetic sensor.

14. The system of claim 12 wherein the particular types of binding elements comprise single stranded DNA (ssDNA) tethers configured to bind with the bioactive surface areas and wherein the modulation agent comprises at least one of a magnesium salt (Mg++) selected to compress or collapse the ssDNA or application of an electric field selected to uncoil the ssDNA.

15. The system of claim 14 wherein the modulation agent comprises an electric field having a voltage between about.1 and.2 Vnm-1.

16. The system of claim 12 wherein the particular types of binding elements comprise a polyethylene glycol (PEG) tether configured to bind with the bioactive surface areas and wherein the modulation agent comprises a PEG antibody (anti-PEG) selected to bind with and expand a backbone of the PEG tether.

17. The system of claim 12 wherein the patterned surface comprises:a first layer having a first surface energy configured for binding with the particular types of complexes;a second layer positioned on the first layer, the second layer having a second surface energy substantially inert to the binding elements, target molecules, and MNPs of the particular types of complexes;one or more nanowells formed within the second layer, each exposing a surface of the first layer, the nanowells configured to selectively bind the particular types of complexes to the exposed surfaces of the first layer;one or more magnetic sensors arranged from beneath the exposed surface of each of the nanowells, the magnetic sensors configured to respectively detect the presence of the target biomolecules through detection of the MNPs within the complexes.

18. The system of claim 17, wherein the first layer comprises silicon dioxide (SiO2) and the second layer comprises diamond-like carbon (DLC),19. The system of claim 12 wherein the complexes comprise a capture antibody and detection antibody each configured to bind with the target biomolecule, thecapture antibody configured to attach to the binding elements and the detection antibody configured to attach to the MNPs20. The system of claim 19 wherein the signals are indicative of changes in relative proximity of the MNPs of around ten nanometers or greater.

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