Abstract: Devices for sequencing linear biomolecules (e.g., DNA, RNA, polypeptides, proteins, and the like) using quantum tunneling effects, and methods of making and using such devices, are provided. A nanofabricated device can include a small gap formed by depositing a thin film between two electrodes, and subsequently removing the film using an etching process. The width of the resulting gap can correspond with the size of a linear biomolecule such that when a part of the biomolecule (e.g., a nucleobase or amino acid) is present in the gap, a change in tunneling current, voltage, or impedance can be measured and the part of the biomolecule identified. The gap dimensions can be precisely controlled at the atomic-scale by, for example, atomic layer deposition (ALD) of the sacrificial film. The device can be made using existing integrated circuit fabrication equipment and facilities, and multiple devices can be formed on a single chip.

Abstract: Devices for sequencing linear biomolecules (e.g., DNA, RNA, polypeptides, proteins, and the like) using quantum tunneling effects, and methods of making and using such devices, are provided. A nanofabricated device can include a small gap formed by depositing a thin film between two electrodes, and subsequently removing the film using an etching process. The width of the resulting gap can correspond with the size of a linear biomolecule such that when a part of the biomolecule (e.g., a nucleobase or amino acid) is present in the gap, a change in tunneling current, voltage, or impedance can be measured and the part of the biomolecule identified. The gap dimensions can be precisely controlled at the atomic-scale by, for example, atomic layer deposition (ALD) of the sacrificial film. The device can be made using existing integrated circuit fabrication equipment and facilities, and multiple devices can be formed on a single chip.

Abstract: Devices for sequencing linear biomolecules (e.g., DNA, RNA, polypeptides, proteins, and the like) using quantum tunneling effects, and methods of making and using such devices, are provided. A nanofabricated device can include a small gap formed by depositing a thin film between two electrodes, and subsequently removing the film using an etching process. The width of the resulting gap can correspond with the size of a linear biomolecule such that when a part of the biomolecule (e.g., a nucleobase or amino acid) is present in the gap, a change in tunneling current, voltage, or impedance can be measured and the part of the biomolecule identified. The gap dimensions can be precisely controlled at the atomic-scale by, for example, atomic layer deposition (ALD) of the sacrificial film. The device can be made using existing integrated circuit fabrication equipment and facilities, and multiple devices can be formed on a single chip.

Abstract: Devices for sequencing linear biomolecules (e.g., DNA, RNA, polypeptides, proteins, and the like) using quantum tunneling effects, and methods of making and using such devices, are provided. A nanofabricated device can include a small gap formed by depositing a thin film between two electrodes, and subsequently removing the film using an etching process. The width of the resulting gap can correspond with the size of a linear biomolecule such that when a part of the biomolecule (e.g., a nucleobase or amino acid) is present in the gap, a change in tunneling current, voltage, or impedance can be measured and the part of the biomolecule identified. The gap dimensions can be precisely controlled at the atomic-scale by, for example, atomic layer deposition (ALD) of the sacrificial film. The device can be made using existing integrated circuit fabrication equipment and facilities, and multiple devices can be formed on a single chip.

Abstract: Described herein are compositions and methods for the production and quantification of barcoded or unique molecular identifier (UMI)-labeled substrates. In one aspect, the substrate is a bead comprising a template oligonucleotide that is elongated by successive extension reactions to provide a bead with an oligonucleotide comprising a plurality of barcodes and conserved anchor regions. Methods are also described for quantifying the amount of template oligonucleotide loaded onto the substrate and the products of the extension reaction after each round and after the final extension.

Abstract: A method of sequencing a DNA sample is disclosed. A nanopore-based sequencing device is provided. The nanopore-based sequencing device includes a conductive layer. The device further includes a working electrode disposed above the conductive layer. The device further includes a side wall disposed above the working electrode, wherein the side wall and the working electrode form a well in which an electrolyte may be contained, and wherein at least an upper portion of the side wall comprises a hydrophobic portion formed by a fluoropolymer material. The DNA sample is sequenced using the nanopore-based sequencing device.

Abstract: Devices for sequencing linear biomolecules (e.g., DNA, RNA, polypeptides, proteins, and the like) using quantum tunneling effects, and methods of making and using such devices, are provided. A nanofabricated device can include a small gap formed by depositing a thin film between two electrodes, and subsequently removing the film using an etching process. The width of the resulting gap can correspond with the size of a linear biomolecule such that when a part of the biomolecule (e.g., a nucleobase or amino acid) is present in the gap, a change in tunneling current, voltage, or impedance can be measured and the part of the biomolecule identified. The gap dimensions can be precisely controlled at the atomic-scale by, for example, atomic layer deposition (ALD) of the sacrificial film. The device can be made using existing integrated circuit fabrication equipment and facilities, and multiple devices can be formed on a single chip.

Abstract: Embodiments of the present invention include genetically tractable industrial yeast strains and methods for their construction. In certain preferred embodiments, the genetically tractable industrial yeast strain is a Saccharomyces cerevisiae strain, such as a derivative of the K1-V1116 wine yeast strain.

Abstract: Embodiments of the present invention include methods for the production of four carbon alcohols, specifically n-butanol, by a consolidated bioprocessing approach for the conversion of cellulosic material to the desired end product. According to some embodiments, recombinant microbial host cells are provided, preferably S. cerevisiae, that are capable of converting cellulosic material to butanol and include butanol biosynthetic pathway genes and cellulase genes.

Abstract: Embodiments of the present invention include methods for the production of four carbon alcohols, specifically n-butanol, by a consolidated bioprocessing approach for the conversion of cellulosic material to the desired end product. According to some embodiments, recombinant microbial host cells are provided, preferably S. cerevisiae, that are capable of converting cellulosic material to butanol and include butanol biosynthetic pathway genes and cellulase genes. According to some embodiments, recombinant microbial host cells are provided, preferably S. cerevisiae, that are capable of converting hemicellulosic material to butanol and include cellulase genes, butanol biosynthetic pathway genes and at least one gene for the conversion of a pentose sugar.

Abstract: Embodiments of the present invention include methods for the production of ethanol, by a consolidated bioprocessing approach for the conversion of cellulosic material. According to some embodiments, recombinant microbial host cells are provided, preferably S. cerevisiae, that are capable of converting cellulosic material to ethanol and include cellulase genes. According to some embodiments, recombinant microbial host cells are provided, preferably S. cerevisiae, that are capable of converting hemicellulosic material to ethanol and include cellulase genes and at least one gene for the conversion of a pentose sugar.

Abstract: A protective cover (10) for an optical device, such as a spatial light modulator or an infrared detector or receiver. The cover (10) has an optically transmissive window (11), which has a coating (12) on one or both of its surfaces. The coating (12) is made from a halogenated material, which is deposited to form a chemical bond with the surface of the window (11).

Abstract: The present invention discloses methodologies for the treatment of the surface(s) of DNA processing devices so as to greatly reduce contamination with metal ions and semi-metal ions. These aforementioned surface treatments include an ammonium hydroxide and hydrogen peroxide wash, followed by a wash with EDTA which is followed by a wash with ammonium hydroxide and hydrogen peroxide. The present invention also discloses the fabrication of DNA processing devices utilizing surface(s) treated by the methods described. Such DNA processing devices include, for example, FORA, miniaturized electrophoresis and other DNA separation devices, such as miniaturized PCR reactors, and the like. Additionally, the methodologies and devices of the present invention are also applicable to the processing of nucleic acids, in general.

Abstract: The present invention discloses methodologies for the treatment of the surface(s) of DNA processing devices so as to greatly reduce DNA adsorption to the surface(s) exposed to the DNA-containing media. These aforementioned surface treatments include: (i) the deposition of thin-films of silicon-rich, silicon nitride and of hydroxyl-containing,low-temperature silicon oxide and (ii) the washing of surface with a basic, oxidative wash solution. The present invention also discloses the fabrication of DNA processing devices utilizing surface(s) treated by the methods described above. Such DNA processing devices include, for example, miniaturized electrophoresis and other DNA separation devices, miniaturized PCR reactors, and the like. The present invention further discloses methodologies for testing the degree of DNA adherence to a given surface. Additionally, the methodologies and devices of the present invention are also applicable to the processing of nucleic acids, in generally.

Abstract: This invention relates to a method and device for separating charged particles according to their diffusivities in a separation medium by means of a spatially and temporally varying electric potential. The method is particularly suited to sizing and separating DNA fragments, to generating DNA fragment length polymorphism patterns, and to sequencing DNA through the separation of DNA sequencing reaction products. The method takes advantage of the transport of charged particles subject to an electric potential that is cycled between an off-state (in which the potential is flat) and one or more on-states, in which the potential is preferably spatially periodic with a plurality of eccentrically shaped stationary potential wells. The potential wells are at constant spatial positions in the on-state. Differences in liquid-phase diffusivities lead to charged particle separation. A preferred embodiment of the device is microfabricated. A separation medium fills physically defined separation lanes in the device.

Abstract: An integrated circuit fabrication process in which residual fluorine contamination on metal surfaces after ashing is removed by exposure to an NH.sub.3 /O.sub.2 plasma.

Abstract: A method of preventing permanent deformation of deflecting metal components of micro mechanical devices, such as hinges (12) of mirror elements (10) of a digital micro mirror device. The hinges (12) are made from a memory metal capable of undergoing austenite/martensite phase transitions. If the device is operated and the hinges (12) become mechanically distorted, the hinges (12) can be heated to cause a transition to the austenite phase and a return to their original shape.

Abstract: Apparatus and methods for precise processing of thin materials in a process chamber by the use of ellipsometer monitoring is disclosed. The process includes rapidly etching a layer 42 of material covering a semiconductor device. The process includes placing the semiconductor wafer 14 into a processing chamber 10. In a typical operation, the wafer 14 will include a selected substrate 32 having a first thin layer 30 of material covering the substrate 32 and then a second layer 42 of a different material covering the first layer 30. A process such as reactive ion anisotropic etching which rapidly etches the second layer 42 is initiated and this etching is monitored in situ by an ellipsometer in combination with a controller 28 to determine the thickness of the second layer 42' which has been achieved. Once the desired amount of second layer 42 remains, the rapid etching process stops to leave a residual layer 42' such as about 250 .ANG.

Abstract: A method of preventing adhesion of contacting surfaces of micro-mechanical devices (10). Two materials are selected that are incompatible in the sense that they have at least low solid solubility and preferably, an inability to alloy. One of these materials is used as the first contacting surface (11), and the other as the second contacting surface (17).

Abstract: A method of preventing adhesion of contacting surfaces of micro-mechanical devices (10). Two materials are selected that are incompatible in the sense that they have at least low solid solubility and preferably, an inability to alloy. One of these materials is used as the first contacting surface (11), and the other as the second contacting surface (17).