Nano computing device and method of operating nano computing device

A nano computing device, comprising:

• a plurality of molecular inputs;
• a plurality of nanoparticle memories configured to store the plurality of molecular inputs;
• wherein each nanoparticle memory of the plurality of nanoparticle memories comprises a nanoparticle functionalized with a plurality of single-stranded DNA domains configured to hybridize with an input DNA representing a logic “0” or logic “1”, the input DNA modifying an exposed single-stranded region of the nanoparticle memory so as to define its storage state;
• a plurality of instruction molecules programmed for performing a logic operation;
• a plurality of nanoparticle reporters configured to determine an output;
• wherein each nanoparticle reporter of the plurality of nanoparticle reporters comprises a nanoparticle functionalized with a plurality of reporter-binding DNA domains configured to bind a nanoparticle floater through multivalent hybridization with a report DNA strand having a hybridization domain of lower melting temperature than trap DNA, such that assembly of the nanoparticle floater to the nanoparticle reporter produces a detectable optical scattering change representing a logic output;
• and
• a plurality of nanoparticle floaters bound to the plurality of nanoparticle memory or the plurality of nanoparticle reporters based on the molecular inputs and the instruction molecules;
• wherein each nanoparticle floater of the plurality of nanoparticle floaters comprises a mobile nanoparticle possessing at least two distinct hybridization domains, including (i) a trap-binding domain configured to hybridize to a memory-specific trap DNA corresponding to the storage state of the nanoparticle memory, and (ii) a reporter-binding domain configured to hybridize to a report DNA for assembly to the nanoparticle reporter, the nanoparticle floater being freely diffusible on a supported lipid bilayer until selectively captured by trap DNA or report DNA;
• wherein:
• each of the plurality of nanoparticle floaters is selectively bound to the nanoparticle memory over the nanoparticle reporter due to a competition wherein a first reaction rate between the nanoparticle memory and the nanoparticle floater by a first instruction molecule among the instruction molecules is faster than a second reaction rate between the nanoparticle reporter and the nanoparticle floater by a second instruction molecule among the instruction molecules;
• wherein the first reaction rate comprises a diffusion-limited hybridization of a trap DNA having a hybridization domain length of about 14 nucleotides and a melting temperature above about 40° C., resulting in rapid nanoparticle memory-nanoparticle floater assembly;
• and wherein the second reaction rate comprises a slower, kinetically delayed assembly via a report DNA having a hybridization domain of about 8 nucleotides and a melting temperature below about 20° C., such that reporter assembly requires multivalent interactions and proceeds only after a trap-DNA-mediated reaction window has elapsed.

A nano computing device, comprising:

• an input layer including a plurality of nanoparticle memories;
• wherein each nanoparticle memory of the plurality of nanoparticle memories comprises a nanoparticle functionalized with a plurality of single-stranded DNA domains configured to hybridize with an input DNA representing a logic “0” or logic “1”, the input DNA modifying an exposed single-stranded region of the nanoparticle memory so as to define its storage state;
• a hidden layer including a plurality of nanoparticle floaters;
• wherein each nanoparticle floater of the plurality of nanoparticle floaters comprises a mobile nanoparticle possessing at least two distinct hybridization domains, including (i) a trap-binding domain configured to hybridize to a memory-specific trap DNA corresponding to the storage state of the nanoparticle memory, and (ii) a reporter-binding domain configured to hybridize to a report DNA for assembly to the nanoparticle reporter, the nanoparticle floater being freely diffusible on a supported lipid bilayer until selectively captured by trap DNA or report DNA;
• and
• an output layer including a plurality of nanoparticle reporters;
• wherein each nanoparticle reporter of the plurality of nanoparticle reporters comprises a nanoparticle functionalized with a plurality of reporter-binding DNA domains configured to bind a nanoparticle floater through multivalent hybridization with a report DNA strand having a hybridization domain of lower melting temperature than trap DNA, such that assembly of the nanoparticle floater to the nanoparticle reporter produces a detectable optical scattering change representing a logic output;
• wherein the nano computing device is programmed with a nanoparticle neural network including a plurality of instruction molecules corresponding to weights between the input layer and the hidden layer and between the hidden layer and the output layer;
• and
• wherein:
• each of the plurality of nanoparticle floaters is selectively bound to the nanoparticle memory over the nanoparticle reporter due to a competition wherein a first reaction rate between the nanoparticle memory and the nanoparticle floater by a first instruction molecule among the plurality of instruction molecules is faster than a second reaction rate between the nanoparticle reporter and the nanoparticle floater by a second instruction molecule among the plurality of instruction molecules;
• wherein the first reaction rate comprises a diffusion-limited hybridization of a trap DNA having a hybridization domain length of about 14 nucleotides and a melting temperature above about 40° C., resulting in rapid nanoparticle memory-nanoparticle floater assembly;
• and wherein the second reaction rate comprises a slower, kinetically delayed assembly via a report DNA having a hybridization domain of about 8 nucleotides and a melting temperature below about 20° C., such that reporter assembly requires multivalent interactions and proceeds only after the trap-DNA-mediated reaction window has elapsed.