Method and apparatus for the analysis and identification of molecules

1. A portable molecule analyzer, comprising:

(a) a sample intake configured to receive a sample; and

(b) a funnel-shaped nanopore-based sequencing chip configured to measure one or more electrical characteristics of the sample;

wherein said funnel-shaped nanopore-based sequencing chip is in fluid communication with said sample intake, said funnel-shaped nanopore-based sequencing chip comprises a funnel-shaped nanopore array wafer defining a plurality of funnel-shaped nanopores, each of said funnel-shaped nanopores comprises one pair of embedded sensing electrodes, which are located on two separate layers along the depth of each of said funnel-shaped nanopores and comprises a hole that fits exactly to the interior of each of said funnel-shaped nanopores; wherein said funnel-shaped nanopore array wafer is fabricated by ion milling through a film on a wafer using nanopantography; said film comprises two conductive layers sandwiching a dielectric layer of 1 to 3 nm in thickness; each of said funnel-shaped nanopores comprises a first opening at the wafer and a second opening at the film, wherein said first opening is larger than said second opening; said second opening has a diameter of 1 to 3 nm; wherein said two conductive layers form said pair of embedded sensing electrodes.

2. The portable molecule analyzer of claim 1 , wherein each of said plurality of funnel-shaped nanopores comprises a plurality of layers made of different materials.

3. The portable molecule analyzer of claim 1 , wherein said embedded sensing electrodes have a first electrode and a second electrode, said first and second electrodes are at the same depth along the length of each of said funnel-shaped nanopores.

4. The portable molecule analyzer of claim 1 , wherein a plurality of embedded sensing electrodes are formed within at least two layers of each of said funnel-shaped nanopores.

5. The portable molecule analyzer of claim 1 , wherein a plurality of embedded sensing electrodes are configured to detect a change in resistance, change in capacitance, change in phase, or change in current in each of said funnel-shaped nanopores.

6. The portable molecule analyzer of claim 5 , wherein said current comprises tunneling current.

7. The portable molecule analyzer of claim 1 , wherein said portable molecule analyzer further comprises a top electrode affixed to the portable molecule analyzer above each of said funnel-shaped nanopores, and a bottom electrode affixed to the portable molecule analyzer below each of said funnel-shaped nanopores, wherein each of said funnel-shaped nanopores provides a path for electrical communication between the top electrode and the bottom electrode.

8. The portable molecule analyzer of claim 7 , wherein the bottom electrode or the top electrode is in electrical communication with an integrated circuit.

9. The portable molecule analyzer of claim 8 , wherein the integrated circuit comprises a voltage biasing scheme or a current sensing circuit.

10. The portable molecule analyzer of claim 1 , wherein each nanopore is in fluid communication with one or more nanofluidic channels and one or more microfluidic channels.

11. The portable molecule analyzer of claim 10 , wherein said one or more microfluidic channels comprise guiding electrodes configured to guide a sample along the one or more microfluidic channels, or wherein said one or more nanofluidic channels comprise guiding electrodes configured to guide a sample along the one or more nanofluidic channels.

12. A method of funnel-shaped nanopore-based sequencing using the portable molecule analyzer of claim 1 , comprising:

(a) receiving measurement data from said funnel-shaped nanopore-based sequencing chip in said portable molecular analyzer, wherein the measurement data is related to one or more electrical characteristics of a sample of molecules input to the portable molecular analyzer; and

(b) performing analysis of the measurement data to identify molecules in the sample.

13. The method of claim 12 , wherein said funnel-shaped nanopore-based sequencing chip obtains the measurement data by detecting a change in resistance, change in capacitance, change in phase, or change in current in at least one of the funnel-shaped nanopores from said plurality of funnel-shaped nanopores using at least one pair of embedded sensing electrodes in at least one of the funnel-shaped nanopores.

14. The method of claim 13 , wherein said current comprises a tunneling current.

15. The method of claim 12 , wherein each of the funnel-shaped nanopores are in fluid communication with one or more nanofluidic channels and one or more microfluidic channels.

16. The method of claim 12 , wherein said funnel-shaped nanopore-based sequencing chip obtains the measurement data from at least one of the funnel-shaped nanopores from said plurality of funnel-shaped nanopores by performing voltage trapping using at least one pair of embedded sensing electrodes in said at least one of the funnel-shaped nanopores to control the speed of translocation of a molecule through at least one of the funnel-shaped nanopores.

17. The method of claim 12 , wherein said funnel-shaped nanopore-based sequencing chip obtains the measurement data during translocation of a molecule through at least one of the funnel-shaped nanopores from said plurality of funnel-shaped nanopores by applying an alternating current using at least one pair of embedded sensing electrodes in at least one of the funnel-shaped nanopores.

18. The method of claim 12 , wherein said funnel-shaped nanopore-based sequencing chip obtains the measurement data by applying a voltage potential to at least one of the funnel-shaped nanopores from said plurality of funnel-shaped nanopores using one or more electrodes external to the funnel-shaped nanopores.

19. The method of claim 12 , wherein said electrical characteristics comprises one or more of turn-on voltage, conductance and current across a molecule in the sample of molecules.