Abstract: In a method for forming nanopores, two opposing surfaces of a membrane are exposed to an electrically conducting liquid environment. A nanopore nucleation voltage pulse, having a first nucleation pulse amplitude and duration, is applied between the two membrane surfaces, through the liquid environment. After applying the nanopore nucleation voltage pulse, the electrical conductance of the membrane is measured and compared to a first prespecified electrical conductance. Then at least one additional nanopore nucleation voltage pulse is applied between the two membrane surfaces, through the liquid environment, if the measured electrical conductance is no greater than the first prespecified electrical conductance.

Abstract: The invention relates to a method for characterizing a target polynucleic acid by providing a surface containing a channel of a dimension sufficient to allow sequential monomer-by-monomer passage of a single-stranded polynucleic acid, but not of a double-stranded polynucleic acid; providing a source of hybridized target polynucleic acid at the surface; inducing passage of the target polynucleic acid through the channel, whereby the target polynucleic acid undergoes base pair separation (melts) prior to its passage; and making one or more measurements over time as the target polynucleic acid moves relative to the channel yielding data suitable to determine a monomer-dependent characteristic of the target polynucleic acid.

Abstract: The invention relates to a method for characterizing a target polynucleic acid by providing a surface containing a channel of a dimension sufficient to allow sequential monomer-by-monomer passage of a single-stranded polynucleic acid, but not of a double-stranded polynucleic acid; providing a source of hybridized target polynucleic acid at the surface; inducing passage of the target polynucleic acid through the channel, whereby the target polynucleic acid undergoes base pair separation (melts) prior to its passage; and making one or more measurements over time as the target polynucleic acid moves relative to the channel yielding data suitable to determine a monomer-dependent characteristic of the target polynucleic acid.

Abstract: There is provided a nanopore system including a nanopore in a solid state membrane. A first reservoir is in fluidic connection with the nanopore, the first reservoir being configured to provide, to the nanopore, nucleic acid molecules in an electrolytic solution. A second reservoir is in fluidic connection with the nanopore, with the nanopore membrane separating the first and second reservoirs. A pressure source is connected to the first reservoir to apply an external pressure to the first reservoir to cause nanopore translocation of nucleic acid molecules in the solution in the first reservoir. A voltage source is connected between the second and first reservoirs, across the nanopore, with a voltage bias polarity that applies an electric field counter to the externally applied pressure. Force of the externally applied pressure is greater than force of the electric field during nanopore translocation by the nucleic acid molecules.

Abstract: There is provided a nanopore system including a nanopore in a support structure. A first reservoir is in fluidic connection with the nanopore and a second reservoir is in fluidic connection with the nanopore. The support structure separates the first and second reservoirs. A pressure source is connected to one of the first and second reservoirs to apply an external pressure to one of the first and second reservoirs. A voltage source is connected between the first and second reservoirs to apply a voltage bias between the first and second reservoirs, across the nanopore. This system enables a method for analysis of species in solution, wherein there is provided to the nanopore a fluidic solution that includes a species for translocation through the nanopore, with an external pressure applied to the species in fluidic solution and a voltage bias applied across the nanopore.

Abstract: The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. The methods employ a nanopore which the polymer, e.g., a nucleic acid, traverses. As the polymer traverses the nanopore, measurements of transport properties of the nanopore yield data on the conformation of the polymer.

Abstract: In a method for forming nanopores, two opposing surfaces of a membrane are exposed to an electrically conducting liquid environment. A nanopore nucleation voltage pulse, having a first nucleation pulse amplitude and duration, is applied between the two membrane surfaces, through the liquid environment. After applying the nanopore nucleation voltage pulse, the electrical conductance of the membrane is measured and compared to a first prespecified electrical conductance. Then at least one additional nanopore nucleation voltage pulse is applied between the two membrane surfaces, through the liquid environment, if the measured electrical conductance is no greater than the first prespecified electrical conductance.

Abstract: In a method for imaging a solid state substrate, a vapor is condensed to an amorphous solid water condensate layer on a surface of a solid state substrate. Then an image of at least a portion of the substrate surface is produced by scanning an electron beam along the substrate surface through the water condensate layer. The water condensate layer integrity is maintained during electron beam scanning to prevent electron-beam contamination from reaching the substrate during electron beam scanning. Then one or more regions of the layer can be locally removed by directing an electron beam at the regions. A material layer can be deposited on top of the water condensate layer and any substrate surface exposed at the one or more regions, and the water condensate layer and regions of the material layer on top of the layer can be removed, leaving a patterned material layer on the substrate.

Abstract: Suspended nanotubes are used to capture and ionize neutral chemical units, such as individual atoms, molecules, and condensates, with excellent efficiency and sensitivity. Applying a voltage to the nanotube(s) (with respect to a grounding surface) creates an attractive potential between a polarizable neutral chemical unit and the nanotube that varies as 1/r2, where r is the unit's distance from the nanotube. An atom approaching the nanotube with a sub-threshold angular momentum is captured by the potential and eventually spirals towards the nanotube. The atom ionizes as in comes into close proximity with a sidewall of the nanotube, creating an ion whose polarity matches the polarity of the electric potential of the nanotube. Repulsive forces eject the ion, which can be detected more easily than a neutral chemical unit. Suspended nanotubes can be used to detect small numbers of neutral chemical units (e.g., single atoms) for applications in sensing and interferometry.

Abstract: In a method of forming a nanopore in a nanometric material, a nanopore nucleation site is formed at a location that is interior to lateral edges of the nanometric material by directing a first energetic beam, selected from the group of ion beam and neutral atom beam, at the interior location for a first time duration that imposes a first beam dose which causes removal of no more than five interior atoms from the interior location to produce at the interior location a nanopore nucleation site having a plurality of edge atoms. A nanopore is then formed at the nanopore nucleation site by directing a second energetic beam, selected from the group consisting of electron beam, ion beam, and neutral atom beam, at the nanopore nucleation site with a beam energy that removes edge atoms at the nanopore nucleation site but does not remove bulk atoms from the nanometric material.

Abstract: The invention relates to a method for characterizing a target polynucleic acid by providing a surface containing a channel of a dimension sufficient to allow sequential monomer-by-monomer passage of a single-stranded polynucleic acid, but not of a double-stranded polynucleic acid; providing a source of hybridized target polynucleic acid at the surface; inducing passage of the target polynucleic acid through the channel, whereby the target polynucleic acid undergoes base pair separation (melts) prior to its passage; and making one or more measurements over time as the target polynucleic acid moves relative to the channel yielding data suitable to determine a monomer-dependent characteristic of the target polynucleic acid.

Abstract: In a method for imaging a solid state substrate, a vapor is condensed to an amorphous solid water condensate layer on a surface of a solid state substrate. Then an image of at least a portion of the substrate surface is produced by scanning an electron beam along the substrate surface through the water condensate layer. The water condensate layer integrity is maintained during electron beam scanning to prevent electron-beam contamination from reaching the substrate during electron beam scanning. Then one or more regions of the layer can be locally removed by directing an electron beam at the regions. A material layer can be deposited on top of the water condensate layer and any substrate surface exposed at the one or more regions, and the water condensate layer and regions of the material layer on top of the layer can be removed, leaving a patterned material layer on the substrate.

Abstract: The invention relates to a method for characterizing a target polynucleic acid by providing a surface containing a channel of a dimension sufficient to allow sequential monomer-by-monomer passage of a single-stranded polynucleic acid, but not of a double-stranded polynucleic acid; providing a source of hybridized target polynucleic acid at the surface; inducing passage of the target polynucleic acid through the channel, whereby the target polynucleic acid undergoes base pair separation (melts) prior to its passage; and making one or more measurements over time as the target polynucleic acid moves relative to the channel yielding data suitable to determine a monomer-dependent characteristic of the target polynucleic acid.

Abstract: In a process for fabricating a nanopore device, at least one carbon nanotube catalyst region is formed on a structure. A plurality of nanopores is formed in the structure at a distance from the catalyst region that is no greater than about an expected length for a carbon nanotube synthesized from the catalyst region. Then at least one carbon nanotube is synthesized from the catalyst region. This fabrication sequence enables the in situ synthesis of carbon nanotubes at the site of nanopores, whereby one or more nanotubes articulate one or more nanopores without requiring manual positioning of the nanotubes.

Abstract: Suspended nanotubes are used to capture and ionize neutral chemical units, such as individual atoms, molecules, and condensates, with excellent efficiency and sensitivity. Applying a voltage to the nanotube(s) (with respect to a grounding surface) creates an attractive potential between a polarizable neutral chemical unit and the nanotube that varies as 1/r2, where r is the unit's distance from the nanotube. An atom approaching the nanotube with a sub-threshold angular momentum is captured by the potential and eventually spirals towards the nanotube. The atom ionizes as in comes into close proximity with a sidewall of the nanotube, creating an ion whose polarity matches the polarity of the electric potential of the nanotube. Repulsive forces eject the ion, which can be detected more easily than a neutral chemical unit. Suspended nanotubes can be used to detect small numbers of neutral chemical units (e.g., single atoms) for applications in sensing and interferometry.

Abstract: The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. The methods employ a nanopore which the polymer, e.g., a nucleic acid, traverses. As the polymer traverses the nanopore, measurements of transport properties of the nanopore yield data on the conformation of the polymer.

Abstract: In a method for processing a nanotube, a vapor is condensed to a solid condensate layer on a surface of the nanotube and then at least one selected region of the condensate layer is locally removed by directing a beam of energy at the selected region. The nanotube can be processed with at least a portion of the solid condensate layer maintained on the nanotube surface and thereafter the solid condensate layer removed. Nanotube processing can include, e.g., depositing a material layer on an exposed nanotube surface region where the condensate layer was removed. After forming a solid condensate layer, an electron beam can be directed at a selected region along a nanotube length corresponding to a location for cutting the nanotube, to locally remove the condensate layer at the region, and an ion beam can be directed at the selected region to cut the nanotube at the selected region.

Abstract: In a molecular analysis system, there is provided a structure including a nanopore and first and second fluidic reservoirs. The two reservoirs are fluidically connected via the nanopore. A detector is connected to detect molecular species translocation of the nanopore, from one of the two fluidic reservoirs to the other of the two fluidic reservoirs. A controller is connected to generate a control signal to produce conditions at the nanopore to induce the molecular species to re-translocate the nanopore at least once after translocating the nanopore. This enables a method for molecular analysis in which a molecular species is translocated a plurality of times through a nanopore in a structure between two fluidic reservoirs separated by the structure.

Abstract: There is provided a substantially bare, self-supported single-layer graphene membrane including a nanopore extending through a thickness of the graphene membrane from a first to a second membrane surface opposite the first graphene membrane surface. A connection from the first graphene membrane surface to a first reservoir provides, at the first graphene membrane surface, a species in an ionic solution to the nanopore, and a connection from the second graphene membrane surface to a second reservoir is provided to collect the species and ionic solution after translocation of the species and ionic solution through the nanopore from the first graphene membrane surface to the second graphene membrane surface. An electrical circuit is connected on opposite sides of the nanopore to measure flow of ionic current through the nanopore in the graphene membrane.

Abstract: 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 an ion beam 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.