Abstract: Disclosed herein are systems for detecting molecules. In some embodiments, a system includes a multiplexer, a read amplifier coupled to the multiplexer, a digitizer coupled to the read amplifier, a first nanopore, a first sense electrode situated on a first side of the first nanopore, a first counter electrode situated on a second side of the first nanopore, a first shield at least partially surrounding the first sense electrode and coupled to the multiplexer, a first shield driver coupled to the first shield, drive circuitry coupled to the first sense electrode, and control logic coupled to the drive circuitry, the multiplexer, and to the digitizer. In some embodiments, the control logic is configured to control the drive circuitry and/or the multiplexer to select the first sense electrode and/or the first counter electrode, and obtain a digitized signal from the digitizer, the digitized signal representing a current through the first nanopore.

Abstract: A device may include a fluid region. A device may also include a magnetochemical sensor for detecting magnetic particles in the fluid region, wherein the magnetochemical sensor comprises: a first ferromagnetic layer, a second ferromagnetic layer, and a spacer layer situated between and coupled to the first ferromagnetic layer and the second ferromagnetic layer. A device may further include a current-carrying structure for drawing the magnetic particles in the fluid region toward the magnetochemical sensor, wherein: the current-carrying structure consists of a single, undivided structure, and the current-carrying structure is configured to carry a current in at least one direction that is substantially parallel to an in-plane axis or a longitudinal axis of the magnetochemical sensor. The magnetochemical sensor may be one of a plurality of magnetochemical sensors in a sensor array.

Abstract: Disclosed herein are devices, systems, and methods that can improve the SNR of nanopore measurements by mitigating the effect of parasitic capacitance between the sense electrode and the counter electrode. In some embodiments, a feedback circuit is used to inject a charge into the sense electrode to at least partially cancel the parasitic capacitance between the sense electrode and the counter electrode. In some embodiments, bootstrapping of a signal from the amplifier output or from the sense electrode is used to inject a charge on the counter electrode to substantially cancel the parasitic capacitance.

Abstract: Disclosed herein are systems and devices for detecting molecules. In some embodiments, a system for detecting molecules comprises an amplifier and a nanopore unit, wherein the nanopore unit comprises a nanopore, a sense electrode, a counter electrode, and a shield situated between the sense electrode and the counter electrode and coupled to an output of the amplifier. The shield may be recessed from a hole in the nanopore. A system or device may include an array of nanopore units that may share some components, such as a read amplifier, a digitizer, drive circuitry, control logic, and/or a multiplexer.

Abstract: Disclosed herein are improved methods and systems for sequencing nucleic acid that exploit the temperature-dependence of the emitted intensity of fluorescent dyes. The temperature of the sequencing reaction is adjusted during each sequencing cycle, and the emission, or lack of emission, of light meeting or exceeding a threshold by the fluorescent dyes at different temperatures, or within different temperature ranges, is used to detect the fluorescent labels of the incorporated dNTPs and thereby sequence the nucleic acid. The disclosed methods enable a determination of the dNTP incorporated at any given site with a reasonable number of chemistry steps without the complex optics necessary for prior-art systems.

Abstract: Disclosed herein are devices, systems, and methods for controlling a translocation speed of a molecule through a nanopore. In some embodiments, a speed-control device comprises at least one fluid-retaining surface, a fluid region, a field-responsive fluid coupled to the fluid-retaining surface and situated in the fluid region. In some embodiments, a system comprises the nanopore, the speed-control device, and a field generator for generating a magnetic or electric field across the fluid region. The viscosity of the field-responsive fluid is dependent on a magnitude of the magnetic or electric field across the fluid region and can be controlled by changing a magnitude of the magnetic or electric field across the fluid region.

Abstract: A system includes at least one waveguide with optical interaction portions that represent a sequence of reference symbols based on the order of the optical interaction portions in the at least one waveguide. At least one light source sends photons of one or more predetermined wavelengths into the at least one waveguide representing a string of query symbols. A detector detects photons received from the at least one waveguide that result from optical interactions between photons sent into the at least one waveguide and one or more corresponding optical interaction portions with an interaction between photons and an optical interaction portion indicating a match between a query symbol and a reference symbol. An analyzer determines one or more respective relative locations of the one or more corresponding optical interaction portions indicating one or more relative locations of the string of query symbols in the reference sequence.

Abstract: A system includes at least one waveguide with optical interaction portions that represent a sequence of reference symbols based on the order of the optical interaction portions in the at least one waveguide. At least one light source sends photons of one or more predetermined wavelengths into the at least one waveguide representing a string of query symbols. A detector detects photons received from the at least one waveguide that result from optical interactions between photons sent into the at least one waveguide and one or more corresponding optical interaction portions with an interaction between photons and an optical interaction portion indicating a match between a query symbol and a reference symbol. An analyzer determines one or more respective relative locations of the one or more corresponding optical interaction portions indicating one or more relative locations of the string of query symbols in the reference sequence.

Abstract: Example systems, read channels, and methods provide bit value detection from an encoded data signal using a neural network soft information detector. The neural network detector determines a set of probabilities for possible states of a data symbol from the encoded data signal. A soft output detector uses the set of probabilities for possible states of the data symbol to determine a set of bit probabilities that are iteratively exchanged as extrinsic information with an iterative decoder for making decoding decisions. The iterative decoder outputs decoded bit values for a data unit that includes the data symbol.

Abstract: Disclosed herein are devices, systems, and methods can improve the signal-to-noise ratio of measurements made in biological applications. In some embodiments, an amplifier circuit that comprises a three-terminal device is situated in a configuration (e.g., a common-base or similar configuration) that allows the circuit to detect current through a nanopore while providing feedback to the sense electrode to reduce parasitic capacitance between the sense electrode and the counter electrode. The amplifier circuit may include, for example, a bi-polar junction transistor (BJT), a diamond transistor, a CMOS transistor, an operational transconductance amplifier, a voltage-controlled current source, a transconductor, a macro transistor, and/or a second-generation current conveyor (CCII+).

Abstract: Disclosed herein are methods and apparatuses for sequencing nucleic acids using a detection device, the detection device comprising a plurality of spin torque oscillators (STOs) and at least one fluidic channel. In some embodiments of a method, a nucleotide precursor is labeled with a magnetic nanoparticle (MNP), and the labeled nucleotide precursor is added to the fluidic channel of the detection device. It is determined whether at least one of the plurality of STOs is generating a signal. Based at least in part on the determination of whether the at least one of the plurality of STOs is generating the signal, it is determined whether the labeled nucleotide precursor has been detected.

Abstract: Disclosed herein are devices for molecule detection and methods for using detection devices for molecule detection, such as nucleic acid sequencing. In some embodiments, a detection device comprises one or more pole pieces, one or more sensors, each of the one or more sensors coupled to at least one of the one or more pole pieces, and detection circuitry coupled to the one or more sensors. The detection circuitry is configured to detect a characteristic of each of the one or more sensors, the characteristic indicating presence or absence of one or more magnetic nanoparticles (MNPs) coupled to at least one of a plurality of molecules to be detected, and at least one of the one or more pole pieces is operable to draw the one or more MNPs toward at least one of the one or more sensors.

Abstract: This disclosure relates to secure optical communication links. In particular, this disclosure relates to data storage devices, random access memories, host interfaces, and network layers that comprise a secure optical communication link. A data storage device comprises an optical data port to connect to an optical communication link external to the data storage device and a non-volatile storage medium to store user content data received over the optical communication link. A controller controls access to the user content data stored on the non-volatile storage medium. A cryptography engine uses a cryptographic key to perform cryptographic operations on data sent and received through the optical data port. An optical key distribution device coupled to the optical data port performs quantum key distribution over the optical communication link to provide the cryptographic key to the cryptography engine.

Abstract: Disclosed herein is a detection device comprising sensors with spin torque oscillators (STOs), at least one fluidic channel configured to receive molecules to be detected, and detection circuitry coupled to the sensors. At least some of the molecules to be detected are labeled by magnetic nanoparticles (MNPs). The presence of one or more MNPs in the vicinity of a STO subjected to a bias current changes the oscillation frequency of the STO. The sensors are encapsulated by a material, such as an insulator, separating the sensors from the at least one fluidic channel. A surface of the material provides binding sites for the molecules to be detected. The detection circuitry is configured to detect changes in the oscillation frequencies of the sensors in response to presence or absence of one or more MNPs coupled to one or more binding sites associated with the sensors.

Abstract: Disclosed herein are devices, systems, and methods that can improve the SNR of nanopore measurements by mitigating the effect of parasitic capacitance between the sense electrode and the counter electrode. In some embodiments, a feedback circuit is used to inject a charge into the sense electrode to at least partially cancel the parasitic capacitance between the sense electrode and the counter electrode. In some embodiments, bootstrapping of a signal from the amplifier output or from the sense electrode is used to inject a charge on the counter electrode to substantially cancel the parasitic capacitance.

Abstract: Disclosed herein are systems and devices for detecting molecules. In some embodiments, a system for detecting molecules comprises an amplifier and a nanopore unit, wherein the nanopore unit comprises a nanopore, a sense electrode, a counter electrode, and a shield situated between the sense electrode and the counter electrode and coupled to an output of the amplifier. The shield may be recessed from a hole in the nanopore. A system or device may include an array of nanopore units that may share some components, such as a read amplifier, a digitizer, drive circuitry, control logic, and/or a multiplexer.

Abstract: Disclosed herein are detection devices and methods of making them. A detection device comprises a fluid region, a magnetochemical sensor for detecting magnetic particles, and an electrode coupled to the magnetochemical sensor, the electrode for reading the magnetochemical sensor. A surface of a reactive layer situated on the electrode is functionalized to attract the magnetic particles within the fluid region, and/or an area of the fluid region that is not situated over the electrode is functionalized to repel the magnetic particles. The same mask used to pattern the electrode can be used to pattern the reactive layer to ensure alignment with the electrode. Another detection device embeds the reactive layer in the sensor stack and exposes a surface of it via a trench. The exposed surface can be functionalized to attract magnetic particles toward the magnetochemical sensor.

Abstract: Disclosed herein are molecular storage systems and methods of reading molecules that include integrity markers. A molecular storage system may comprise read hardware configured to read molecules storing data, and at least one processor coupled to the read hardware. The processor is configured to determine whether a molecule being read by the read hardware includes an expected integrity marker, and, in response to a determination that the molecule being read by the read hardware does not include the expected integrity marker, instruct the read hardware to abandon a read operation associated with the molecule being read by the read hardware. The partial readback can be placed in a buffer and used in an assembly process only if an intact molecule is not available.

Abstract: Disclosed herein are detection methods that use magnetic nanoparticles (MNPs) to allow molecules to be identified. Embodiments of this disclosure include methods of using magnetic sensors (e.g., magnetoresistive sensors) to detect temperature-dependent magnetic fields (or changes in magnetic fields) emitted by MNPs, and, specifically to distinguish between the presence and absence of magnetic fields emitted, or not emitted, by MNPs at different temperatures selected to take advantage of knowledge of how the MNPs' magnetic properties change with temperature. Embodiments disclosed herein may be used for nucleic acid sequencing, such as deoxyribonucleic acid (DNA) sequencing.

Abstract: Disclosed herein are devices, systems, and methods for controlling a translocation speed of a molecule through a nanopore. In some embodiments, a speed-control device comprises at least one fluid-retaining surface, a fluid region, a field-responsive fluid coupled to the fluid-retaining surface and situated in the fluid region. In some embodiments, a system comprises the nanopore, the speed-control device, and a field generator for generating a magnetic or electric field across the fluid region. The viscosity of the field-responsive fluid is dependent on a magnitude of the magnetic or electric field across the fluid region and can be controlled by changing a magnitude of the magnetic or electric field across the fluid region.