Systems and methods for genome mapping

A method of molecular mapping, the method comprising:

• loading a sample of molecules from a reservoir into a nanofluidic channel, the reservoir and the nanofluidic channel being defined within a semiconductor substrate;
• trapping the sample of molecules in the nanofluidic channel at least in part with an electrophoretic force generated by a plurality of electrodes in electrical communication with the nanofluidic channel;
• and
• detecting a fluorescence emission from at least one molecule in the sample of molecules using at least one avalanche photodiode fabricated in the semiconductor substrate and disposed within a distance from the nanofluidic channel that is less than a wavelength of the fluorescence emission.

A system for molecular mapping, the system comprising:

• a semiconductor substrate defining a reservoir to receive a sample of molecules and a nanofluidic channel having a width substantially equal to or less than 100 nm and in fluid communication with the reservoir;
• a plurality of electrodes, disposed on the semiconductor substrate in electrical communication with the nanofluidic channel, to electrophoretically trap the sample of molecules in the nanofluidic channel;
• and
• at least one avalanche photodiode, fabricated in the semiconductor substrate and disposed within 800 nm of the nanofluidic channel, to detect fluorescence emission from at least one molecule in the sample of molecules, wherein:
• the at least one avalanche photodiode comprises a p-doped region and an n-doped region and configured to receive the fluorescence emission along a direction substantially parallel to an interface between the p-doped region and the n-doped region, and
• the at least one avalanche photodiode is configured to detect the fluorescence emission with a resolution below a diffraction limit of the fluorescence emission.