Abstract: A method of fabricating an addressable array of biopolymer probes on a substrate according to a target array pattern using a deposition apparatus, and a deposition apparatus which can execute the method and computer program products for the apparatus. The deposition apparatus which, when operated according to a target drive pattern based on nominal operating parameters of the apparatus, provides the probes on the substrate in the target array pattern. The method includes examining at least one operating parameter for an error from a nominal value which error will result in use of the target drive pattern producing a discrepancy between the target array pattern and an actual array pattern deposited. When an error is detected deriving, based on the error, a corrected drive pattern different from the target drive pattern such that use of the corrected drive pattern results in a reduced discrepancy between the target and actual array patterns.

Abstract: A method of fabricating an addressable array of chemical probes at respective feature locations on a substrate surface. The method may use a deposition apparatus with a substrate unit which includes the substrate and with a drop deposition unit which includes a drop deposition head. Such an apparatus when operated according to a target drive pattern based on nominal operating parameters of the apparatus provides the probes on the substrate surface in the target array pattern. The method may include depositing at least one drop from the head unit onto the substrate surface. A fiducial on the substrate unit is optionally viewed from a sensor. A deposited drop on the substrate surface is viewed from a sensor. An actual position of the viewed deposited drop may be determined relative to a fiducial on the substrate unit, based on the views of the fiducial and deposited drop. An error is determined based on any difference between the actual and target positions.

Abstract: An improved method is provided for conducting chemical or biochemical reactions on a substrate surface in which the reactions take place in an enclosed chamber between components of a fluid and molecular moieties present on an interior surface of the chamber, wherein the improvement involves mixing the fluid during the reactions and maximizing contact between the fluid's components and the entirety of the reactive interior surface by (a) applying centrifugal force to the chamber and simultaneously (b) rotating the chamber about an axis thereof. The improved method is particularly advantageous in the context of a hybridization assay in which molecular components within a sample fluid hybridize to surface-bound molecular probes (e.g., as may be present in a spatially defined and physically addressable array) within a hybridization chamber, and wherein process and device parameters (e.g., sample volume, chamber volume, temperature, number of parts and materials, and the like) are critical.

Abstract: Methods, apparatus, and computer program, for use in fabricating a chemical array. The method may use an apparatus which includes a head system, a transport system, and a processor. The head system has multiple groups of drop dispensers which move in unison, each group having multiple dispensers. The transport system can move the head system with respect to a substrate with different dispensers of the groups following respective paths. The processor can dispense droplets from dispensers during operation of the transport system, in a pattern along a selected path for each group so as to form the array. The method includes identifying an error in one or more dispensers. When a dispenser of a first group is in error, then a second dispenser of each group is moved along the selected path for its group while dispensing droplets from at least the second dispenser of the first group in at least part of the pattern for the selected path of the first group.

Abstract: A process of constructing an array of chemical moieties having the following steps: forming multiple discrete physical entities (tiles) from a substantially planar material having one or more species of chemical moiety attached thereto; and picking and placing the entities (tiles) stably on a support at spatially distinct ascertainable locations to form an array of chemical moieties. The formed array includes at least two species of chemical moiety and preferably from about 50 to about 1000 species. The claimed invention includes an array formed by this process.

Abstract: A method, apparatus and computer program product, for fabricating an array of biopolymers on a substrate. The method uses a biopolymer or biomonomer fluid and a drop dispenser having a chamber into which the fluid is loaded and an orifice communicating with the chamber from which the fluid is dispensed. The method includes, when the chamber is loaded, applying a prime pressure to the fluid which varies over a range sufficient to move fluid within the drop dispenser but insufficient to cause fluid to be dispensed from the orifice. Drops are dispensed from the dispenser to the substrate so as to form the array.

Abstract: A method of reading an array of moieties such as polynucleotides (for example, DNA) on at least a portion of a surface of a transparent slide which is opposite a first portion on the opposing surface, which array has been previously exposed to a sample. The method may include mounting the slide on a slide holder and retaining the slide thereon in a mounted position in which the holder does not contact the previously exposed array. The holder is then inserted into an array reader and the array read. A holder and slides which can be used in the method are also provided.

Abstract: A method of interrogating an addressable array having a plurality of different chemical features. The method may include simultaneously illuminating different regions of the array with light of different intensities (which, for example, can, but need not be, also of a same waveband). Light emitted from the different regions in response to the illuminating (which light, for example, can, but need not be, of a same waveband) may be simultaneously detected with different detectors. An apparatus, addressable array unit, and related methods are further provided.

Abstract: Liquids are transferred from a plurality of wells or depots having openings arranged in a selected format to one or more receptacles, by displacing liquid contained in each well so that a convex meniscus swells from the opening, and contacting the receptacle with the swollen meniscus to draw a portion of the liquid into the receptacle. According to the invention, the liquid transfer is effected directly from the depot to the corresponding receptacle without contact between depots and receptacles, and without interposition of any transfer device between depots and receptacles.

Abstract: A method, apparatus and computer program product, for fabricating an array of biopolymers on a substrate. The method uses a biopolymer or biomonomer fluid and a drop dispenser having a chamber into which the fluid is loaded and an orifice communicating with the chamber from which the fluid is dispensed. The method includes, when the chamber is loaded, applying a prime pressure to the fluid which varies over a range sufficient to move fluid within the drop dispenser but insufficient to cause fluid to be dispensed from the orifice. Drops are dispensed from the dispenser to the substrate so as to form the array.

Abstract: A septum penetrable by a member and which maintains a seal following member penetration in an axial direction and withdrawal. The septum includes a first layer of resilient material having first and second opposed surfaces, and a second layer extending across the first surface of the first layer and which is in radial tension. A third layer under tension may extend across the second surface. Septum assemblies and methods of fabricating the septa are also provided.

Abstract: A method, apparatus, and computer program, for fabricating multiple arrays arranged successively in a first direction on a substrate and each having multiple feature sets arranged successively in the first direction within the array. The method uses a head system having multiple successive sets of dispensers. In the method, the head system is advanced in the first direction over the substrate while dispensing drop sets for each array from dispenser sets so as to form the arrays. In one aspect, drop sets are dispensed in an order the reverse of that from which the dispenser sets pass over a given location on the substrate as the head system advances in the first direction. In this case, each dispenser set deposits a drop set at a distance ahead of a drop set deposited by a preceding dispenser set which is less than the distance to the successive drop dispenser set which deposits the next drop set.

Abstract: A method of fabricating an array with multiple sets of neighboring features. In the method, for each of multiple sets of neighboring features, at least one set of drops is deposited from a corresponding same pulse jet dispenser onto a substrate so as to form the array with the sets formed from drops deposited by respective different dispensers. Apparatus and computer program products which can execute a method of the invention, are also provided.

Abstract: Apparatus and method for scanning a surface. An optical system generates a light beam to illuminate a surface. A carrier supports the surface for reciprocating motion with respect to the light beam to form one axis of a raster. A propulsion system moves the carrier at a substantially constant speed and a position sensor provides an output signal representing the surface position with respect to the light beam. A control system responsive to the output signal modulates a sample period reciprocally to carrier speed to achieve substantially constant scan length per sample and to control data acquisition timing.

Abstract: The system includes a confocal optical system to illuminate an object at an intended detection plane and to focus light from the object onto a pinhole. An opaque obstacle is disposed within the confocal optical system, the obstacle selected to suppress light originating outside the intended detection plane from passing through the pinhole. It is preferred that the obstacle size and location be selected to achieve a desired level of suppression. A design goal is a 100-fold reduction in background with a 10% or less loss of signal.

Abstract: A method of fabricating a biopolymer array, and an apparatus which can execute the method, droplets of fluid carrying the biopolymer or a biomonomer are deposited onto a front side of a transparent substrate. Light is directed through the substrate from the front side, back through a substrate back side and a first set of deposited droplets on the first side to an image sensor. The substrate may be mounted by means of a chuck with parallel channels, and a scanning operation of a droplet dispensing head, light source, and sensor conducted in unison in the direction of the channels.

Abstract: A method, and apparatus and computer program products for executing the method. The method includes obtaining a set of multiple images of a target feature location on an array of multiple features, each image of the set representing the target feature location following deposition of a corresponding sub-set of multiple droplets for that feature. An overlay composite may be generated from the image set. The overlay composite may be used as a quality control tool, or in interrogating the array or processing results of the interrogation.

Abstract: A microfluidic pumping apparatus and method using the apparatus. The apparatus may include a first pulse jet and working fluid in the pulse jet such that the first pulse jet, in response to activation by a set of electrical pulses, moves corresponding pulses of fluid from a first to an second side of the first pulse jet. A chamber with an opening is in pressure communication and with the first side of the first pulse jet such that activation of the first pulse jet causes a reduced pressure at the opening. The method comprising contacting the opening with a fluid and activating the first pulse jet so as to draw a sample fluid through the opening into the chamber. A second pulse jet, oppositely oriented from the first, may be provided to discharge loaded sample fluid.

Abstract: A method and apparatus is provided for mixing a film of fluid, particularly a film of chemical, biochemical, or biological fluids undergoing a reaction. The apparatus comprises a means for nucleating a bubble using a discrete heat source, such as a resistor, and moving the bubble in the fluid by creating a temperature gradient, thereby mixing the fluid.

Abstract: A method of evaluating for the presence of a target polynucleotide in a sample, using an addressable array of multiple polynucleotide probes linked to a substrate. The sample is exposed to the array and a set of polynucleotide target probes, such that target polynucleotide which may be present will bind to a predetermined feature of the array through multiple target probes of the set by forming at respective target regions on a target molecule, simultaneous hybrids with anti-target regions of the multiple target probes. A binding pattern on the array is observed and the presence of the target polynucleotide evaluated based on the observed binding pattern. Kits using such arrays, and methods for selecting target probes are further provided.