Patents by Inventor Daniel Branton
Daniel Branton has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Publication number: 20070262050Abstract: The invention provides a method for forming a patterned material layer on a structure, by condensing a vapor to a solid condensate layer on a surface of the structure and then localized removal of selected regions of the condensate layer by directing a beam of energy at the selected regions. The structure can then be processed, with at least a portion of the patterned solid condensate layer on the structure surface, and then the solid condensate layer removed. Further there can be stimulated localized reaction between the solid condensate layer and the structure by directing a beam of energy at at least one selected region of the condensate layer.Type: ApplicationFiled: December 9, 2004Publication date: November 15, 2007Inventors: Jene Golovchenko, Gavin King, Gregor Schurmann, Daniel Branton
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Patent number: 7258838Abstract: A solid state nanopore device including two or more materials and a method for fabricating the same. The device includes a solid state insulating membrane having an exposed surface, a conductive material disposed on at least a portion of the exposed surface of the solid state membrane, and a nanopore penetrating an area of the conductive material and at least a portion of the solid state membrane. During fabrication a conductive material is applied on a portion of a solid state membrane surface, and a nanopore of a first diameter is formed. When the surface is exposed to an ion beam, material from the membrane and conductive material flows to reduce the diameter of the nanopore. A method for evaluating a polymer molecule using the solid state nanopore device is also described. The device is contacted with the polymer molecule and the molecule is passed through the nanopore, allowing each monomer of the polymer molecule to be monitored.Type: GrantFiled: February 14, 2003Date of Patent: August 21, 2007Assignee: President and Fellows of Harvard CollegeInventors: Jiali Li, Derek M. Stein, Gregor M. Schurmann, Gavin M. King, Jene Golovchenko, Daniel Branton, Michael Aziz
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Publication number: 20070172386Abstract: A solid state nanopore device including two or more materials and a method for fabricating the same. The device includes a solid state insulating membrane having an exposed surface, a conductive material disposed on at least a portion of the exposed surface of the solid state membrane, and a nanopore penetrating an area of the conductive material and at least a portion of the solid state membrane. During fabrication a conductive material is applied on a portion of a solid state membrane surface, and a nanopore of a first diameter is formed. When the surface is exposed to an ion beam, material from the membrane and conductive material flows to reduce the diameter of the nanopore. A method for evaluating a polymer molecule using the solid state nanopore device is also described. The device is contacted with the polymer molecule and the molecule is passed through the nanopore, allowing each monomer of the polymer molecule to be monitored.Type: ApplicationFiled: February 14, 2003Publication date: July 26, 2007Inventors: Jiali Li, Derek Stein, Gregor Schurmann, Gavin King, Jene Golovchenko, Daniel Branton, Michael Aziz
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Patent number: 7238485Abstract: Systems and methods for analysis of polymers, e.g., polynucleotides, are provided. The systems are capable of analyzing a polymer at a specified rate. One such analysis system includes a structure having a nanopore aperture and a molecular motor, e.g., a polymerase, adjacent the nanopore aperture.Type: GrantFiled: March 23, 2005Date of Patent: July 3, 2007Assignees: President and Fellows of Harvard College, Regents of the University of California, Agilent Technologies, Inc.Inventors: Mark Akeson, Daniel Branton, David W. Deamer, Jeffrey R. Sampson
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Publication number: 20070128357Abstract: The invention provides a method for forming a patterned material layer on a structure, by condensing a vapor to a solid condensate layer on a surface of the structure and then localized removal of selected regions of the condensate layer by directing a beam of energy at the selected regions, exposing the structure at the selected regions. A material layer is then deposited on top of the solid condensate layer and the exposed structure at the selected regions. Then the solid condensate layer and regions of the material layer that were deposited on the solid condensate layer are removed, leaving a patterned material layer on the structure.Type: ApplicationFiled: December 9, 2004Publication date: June 7, 2007Inventors: Daniel Branton, Jene Golovchenko, Gavin King, Warren MoberlyChan, Gregor Schurmann
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Patent number: 7189503Abstract: The invention relates to a method for detecting a double-stranded region in a nucleic acid by (1) providing two separate, adjacent pools of a medium and a interface between the two pools, the interface having a channel so dimensioned as to allow sequential monomer-by-monomer passage of a single-stranded nucleic acid, but not of a double-stranded nucleic acid, from one pool to the other pool; (2) placing a nucleic acid polymer in one of the two pools; and (3) taking measurements as each of the nucleotide monomers of the single-stranded nucleic acid polymer passes through the channel so as to differentiate between nucleotide monomers that are hybridized to another nucleotide monomer before entering the channel and nucleotide monomers that are not hybridized to another nucleotide monomer before entering the channel.Type: GrantFiled: December 18, 2003Date of Patent: March 13, 2007Assignees: President and Fellows of Harvard College, Regents of the University of CaliforniaInventors: Mark Akeson, Daniel Branton, George Church, David W. Deamer
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Publication number: 20060063171Abstract: Systems and methods for analysis of polymers, e.g., polynucleotides, are provided. The systems are capable of analyzing a polymer at a specified rate. One such analysis system includes a structure having a nanopore aperture and a molecular motor, e.g., a polymerase, adjacent the nanopore aperture.Type: ApplicationFiled: March 23, 2005Publication date: March 23, 2006Inventors: Mark Akeson, Daniel Branton, David Deamer, Jeffrey Sampson
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Publication number: 20050241933Abstract: The invention provides a method for molecular analysis. In the method, sidewalls are formed extending through a structure between two structure surfaces, to define an aperture. A layer of material is deposited on the aperture sidewalls and the two structure surfaces. The aperture with the deposited material layer is then configured in a liquid solution with a gradient in a chemical potential, between the two structure surfaces defining the aperture, that is sufficient to cause molecular translocation through the aperture.Type: ApplicationFiled: December 17, 2004Publication date: November 3, 2005Applicant: President and Fellows of Harvard CollegeInventors: Daniel Branton, Roy Gordon, Peng Chen, Toshiyuki Mitsui, Damon Farmer, Jene Golovchenko
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Publication number: 20050053961Abstract: The invention relates to a method for detecting a double-stranded region in a nucleic acid by (1) providing two separate, adjacent pools of a medium and a interface between the two pools, the interface having a channel so dimensioned as to allow sequential monomer-by-monomer passage of a single-stranded nucleic acid, but not of a double-stranded nucleic acid, from one pool to the other pool; (2) placing a nucleic acid polymer in one of the two pools; and (3) taking measurements as each of the nucleotide monomers of the single-stranded nucleic acid polymer passes through the channel so as to differentiate between nucleotide monomers that are hybridized to another nucleotide monomer before entering the channel and nucleotide monomers that are not hybridized to another nucleotide monomer before entering the channel.Type: ApplicationFiled: December 18, 2003Publication date: March 10, 2005Inventors: Mark Akeson, Daniel Branton, Geroge Church, David Deamer
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Publication number: 20040229386Abstract: A method for controlling a gap in an electrically conducting solid state structure provided with a gap. The structure is exposed to a fabrication process environment conditions of which are selected to alter an extent of the gap. During exposure of the structure to the process environment, a voltage bias is applied across the gap. Electron tunneling current across the gap is measured during the process environment exposure and the process environment is controlled during process environment exposure based on tunneling current measurement. A method for controlling the gap between electrically conducting electrodes provided on a support structure. Each electrode has an electrode tip separated from other electrode tips by a gap. The electrodes are exposed to a flux of ions causing transport of material of the electrodes to corresponding electrode tips, locally adding material of the electrodes to electrode tips in the gap.Type: ApplicationFiled: January 29, 2004Publication date: November 18, 2004Applicant: President and Fellows of Harvard CollegeInventors: Jene A. Golovchenko, Gregor M. Schurmann, Gavin M. King, Daniel Branton
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Patent number: 6783643Abstract: A solid state structure having a surface is provided and exposed to a flux, F, of incident ions under conditions that are selected based on: ∂ ∂ t ⁢ C ⁡ ( r , t ) = F ⁢ ⁢ Y 1 + D ⁢ ∇ 2 ⁢ C - C τ trap - F ⁢ ⁢ C ⁢ ⁢ &sigmType: GrantFiled: June 27, 2002Date of Patent: August 31, 2004Assignee: President and Fellows of Harvard CollegeInventors: Jene A. Golovchenko, Daniel Branton, Michael J. Aziz, Jiali Li, Derek M. Stein, Ciaran J. McMullan
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Patent number: 6746594Abstract: Single-channel thin film devices and methods for using the same are provided. The subject devices comprise cis and trans chambers connected by an electrical communication means. At the cis end of the electrical communication means is a horizontal conical aperture sealed with a thin film that includes a single nanopore or channel. The devices further include a means for applying an electric field between the cis and trans chambers. The subject devices find use in applications in which the ionic current through a nanopore or channel is monitored, where such applications include the characterization of naturally occurring ion channels, the characterization of polymeric compounds, and the like.Type: GrantFiled: June 8, 2001Date of Patent: June 8, 2004Assignees: The Regents of the University of California, President and Fellows of Harvard CollegeInventors: Mark A. Akeson, David W. Deamer, Daniel Branton
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Patent number: 6673615Abstract: The invention relates to a method for detecting a double-stranded region in a nucleic acid by (1) providing two separate, adjacent pools of a medium and a interface between the two pools, the interface having a channel so dimensioned as to allow sequential monomer-by-monomer passage of a single-stranded nucleic acid, but not of a double-stranded nucleic acid, from one pool to the other pool; (2) placing a nucleic acid polymer in one of the two pools; and (3) taking measurements as each of the nucleotide monomers of the single-stranded nucleic acid polymer passes through the channel so as to differentiate between nucleotide monomers that are hybridized to another nucleotide monomer before entering the channel and nucleotide monomers that are not hybridized to another nucleotide monomer before entering the channel.Type: GrantFiled: February 20, 2002Date of Patent: January 6, 2004Assignee: President and Fellows of Harvard CollegeInventors: Timothy J. Denison, Alexis Sauer, Jene Golovchenko, Amit Meller, Eric Brandin, Daniel Branton
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Patent number: 6627067Abstract: A method for evaluating a polymer molecule including linearly connected monomer residues includes providing a polymer molecule in a liquid, contacting the liquid with an insulating solid-state membrane having a detector capable of detecting polymer molecule characteristics, and causing the polymer molecule to traverse a limited region of the solid-state membrane so that monomers of the polymer molecule traverse the limit region in sequential order, whereby the polymer molecule interacts linearly with the detector and data suitable to determine polymer molecule characteristics are obtained. The limited region may be defined by a nanometer-sized aperture in the membrane.Type: GrantFiled: June 22, 2000Date of Patent: September 30, 2003Assignee: President and Fellows of Harvard CollegeInventors: Daniel Branton, Jene A. Golovchenko, Timothy J. Denison
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Publication number: 20030104428Abstract: To probe the characteristics of a target nucleic acid molecule or a population of target nucleic acid molecules, a local cross-sectional area, local charge, or local chemistry of a molecule is modified. The modified nucleic acid is contacted with a substrate that includes a detector that is responsive to the modification in the local cross-sectional area, local charge, or local chemistry of the nucleic acid molecule. The modified nucleic acid molecule traverses a defined and preferably molecular dimensioned volume on the substrate so that nucleotides of the modified nucleic acid molecule interact with the detector in sequential order, whereby data correlating with the cross-sectional area, local charge, or local chemistry of the nucleic acid molecule are obtained. The nucleic acid molecule may be modified in a number of locations along the molecule's length.Type: ApplicationFiled: June 21, 2002Publication date: June 5, 2003Applicant: President and Fellows of Harvard CollegeInventors: Daniel Branton, Stephen S. Laderman, Zohar Yakhini, Jeffrey R. Sampson, Hui Wang
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Publication number: 20030066749Abstract: A solid state structure having a surface is provided and is exposed to a flux, F, of incident ions.Type: ApplicationFiled: June 27, 2002Publication date: April 10, 2003Applicant: President and Fellows of Harvard CollegeInventors: Jene A. Golovchenko, Daniel Branton, Michael J. Aziz, Jiali Li, Derek M. Stein, Ciaran J. McMullan
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Publication number: 20030044816Abstract: The invention relates to a method for detecting a double-stranded region in a nucleic acid by (1) providing two separate, adjacent pools of a medium and a interface between the two pools, the interface having a channel so dimensioned as to allow sequential monomer-by-monomer passage of a single-stranded nucleic acid, but not of a double-stranded nucleic acid, from one pool to the other pool; (2) placing a nucleic acid polymer in one of the two pools; and (3) taking measurements as each of the nucleotide monomers of the single-stranded nucleic acid polymer passes through the channel so as to differentiate between nucleotide monomers that are hybridized to another nucleotide monomer before entering the channel and nucleotide monomers that are not hybridized to another nucleotide monomer before entering the channel.Type: ApplicationFiled: February 20, 2002Publication date: March 6, 2003Inventors: Timothy J. Denison, Alexis Sauer, Jene Golovchenko, Amit Meller, Eric Brandin, Daniel Branton
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Patent number: 6464842Abstract: There is provided controlled fabrication of a solid state structural feature on a solid state structure by exposing the structure to a fabrication process environment the conditions of which are selected to produce a prespecified feature in the structure. A physical detection species is directed toward a designated structure location during process environment exposure of the structure, and the detection species is detected in a trajectory from traversal of the designated structure location, to indicate changing physical dimensions of the prespecified feature. The fabrication process environment is then controlled in response to the physical species detection to fabricate the structural feature.Type: GrantFiled: June 22, 2000Date of Patent: October 15, 2002Assignee: President and Fellows of Harvard CollegeInventors: Jene A. Golovchenko, Daniel Branton, Derek M. Stein, Ciaran J. McMullan, Jiali Li
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Patent number: 6362002Abstract: The invention relates to a method for detecting a double-stranded region in a nucleic acid by (1) providing two separate, adjacent pools of a medium and a interface between the two pools, the interface having a channel so dimensioned as to allow sequential monomer-by-monomer passage of a single-stranded nucleic acid, but not of a double-stranded nucleic acid, from one pool to the other pool; (2) placing a nucleic acid polymer in one of the two pools; and (3) taking measurements as each of the nucleotide monomers of the single-stranded nucleic acid polymer passes through the channel so as to differentiate between nucleotide monomers that are hybridized to another nucleotide monomer before entering the channel and nucleotide monomers that are not hybridized to another nucleotide monomer before entering the channel.Type: GrantFiled: December 9, 1999Date of Patent: March 26, 2002Assignee: President and Fellows of Harvard CollegeInventors: Timothy J. Denison, Alexis Sauer, Jene Golovchenko, Amit Meller, Eric Brandin, Daniel Branton
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Patent number: 6267872Abstract: Single-channel thin film devices and methods for using the same are provided. The subject devices comprise cis and trans chambers connected by an electrical communication means. At the cis end of the electrical communication means is a horizontal conical aperture sealed with a thin film that includes a single nanopore or channel. The devices further include a means for applying an electric field between the cis and trans chambers. The subject devices find use in applications in which the ionic current through a nanopore or channel is monitored where such applications include the characterization of naturally occurring ion channels, the characterization of polymeric compounds, and the like.Type: GrantFiled: October 29, 1999Date of Patent: July 31, 2001Assignee: The Regents of the University of CaliforniaInventors: Mark A. Akeson, David W. Deamer, Daniel Branton