# US 2019/0318803 A1 · Reduction of surface nucleotide hybridization by optimizing a biosensor sensing surface area > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2019/0318803 A1 - Document ID: US20190318803A1 - Status: Published application - Kind: A1 - Application number: 16/454,203 - Filed: 2019-06-27 - Published: 2019-10-17 - Earliest claimed: 2016-06-03 - Assignees: International Business Machines Corporation - Applicants: International Business Machines Corporation - Inventors: Robert L. Bruce; Payel Das; HsinYu Tsai; Sufi Zafar - Web page: https://patentgrep.com/patent/US20190318803A1 ## CPC - G16B 25/00: ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression - C12Q 1/6837: using probe arrays or probe chips (C12Q1/6874 takes precedence) - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES ## Abstract A method, computer program product, and system for identifying a surface area size of a biosensing structure, for use in a bionsensor device, based on a plurality of nucleotides structures under test. A first set of properties are determined comprising: reaction coordinate values, and potential of mean force (PMF) values, for the plurality of nucleotide structures based on a first set of testing conditions comprising a first surface area material, a first surface area pattern, and a first surface area size. A second set of properties is determined comprising reaction coordinate values, and PMF values, for the plurality of nucleotide structures based on a second set of testing conditions comprising a second surface area material, a second surface area pattern, a second surface area size, or a combination thereof and a target population of nucleotide structures among the plurality of nucleotide structures are identified. ## Claims ### Claim 1 A method comprising: determining first and second sets of properties comprising reaction coordinate values and potential of mean force (PMF) values for first and second pluralities of nucleotide structures based on respective first and second sets of testing conditions comprising respective first and second surface area material, respective first and second surface area patterns, and respective first and second surface area sizes of a biosensing structure; and identifying a target population of nucleotide structures among the plurality of nucleotide structures, the target population comprising nucleotide structures whose PMF values in the second set of properties are less than corresponding PMF values in the first set of properties. ### Claim 2 (depends on 1) The method of claim 1, further comprising: determining a third set of properties comprising reaction coordinate values, and PMF values, for at least the target population of nucleotide structures, based on a third set of testing conditions comprising a third surface area material, a third surface area pattern, a third surface area size, or a combination thereof; and identifying which of the second and third sets of properties have the greatest difference compared to the first set of properties. ### Claim 3 (depends on 1) The method of claim 1, wherein the first set of testing conditions comprises: the first surface area material comprising gold, silicon oxide, or both; and the first surface area pattern comprises one or more of a sheet and a plurality of dots, wherein the first surface area size for the sheet is the area of the sheet, and the surface area size for the plurality of dots is the area of the top surfaces of the dots. ### Claim 4 (depends on 2) The method of claim 2 wherein the third surface area material is the same as the second surface area material, and the third surface area pattern is different from the second surface area pattern. ### Claim 5 (depends on 2) The method of claim 2, wherein the third surface area material is different from the second surface area material and the third surface area pattern is the same as the second surface area pattern. ### Claim 6 (depends on 2) The method of claim 2, wherein the third surface area material is the same as the second surface area material, the third surface area pattern is the same as the second surface area pattern, and the third surface area size is different from the second surface area size ### Claim 7 (depends on 2) The method of claim 2, wherein the second and third sets of properties have the greatest difference compared to the first set of properties further comprises one or more of: the second and third sets of properties having the largest area of PMF values below the PMF values of the first set of properties; the second and third sets of properties with the largest negative slope; the second and third sets of properties with the greatest delta value compared to the first set of properties; and the second and third sets of properties with the lowest absolute PMF value. ### Claim 8 (depends on 7) The method of claim 7, wherein the lowest absolute PMF value is within a range constrained by a first and second threshold, the first threshold being based on one or more of: a probe length value and a max probe energy value; and the second threshold is based on one or more of: the determined reaction coordinate value and a repulsive surface PMF value. ### Claim 9 (depends on 1) The method of claim 1, further comprising: generating a graphical representation based on the identified target population of nucleotide structures among the plurality of nucleotide structures; presenting the graphical representation to a user; and receiving from the user, a selection of a surface area value based on the generated graphical representation. ### Claim 10 A computer program product for identifying a surface area size of a biosensing structure, for use in a bionsensor device, based on a plurality of nucleotides structures under test, the computer program product comprising: one or more computer-readable storage media and program instructions stored on the one or more computer-readable storage media, the program instructions comprising: instructions to determine first and second sets of properties comprising reaction coordinate values and potential of mean force (PMF) values for first and second pluralities of nucleotide structures based on respective first and second sets of testing conditions comprising respective first and second surface area material, respective first and second surface area patterns, and respective first and second surface area sizes of a biosensing structure; and instructions to identify a target population of nucleotide structures among the plurality of nucleotide structures, the target population comprising nucleotide structures whose PMF values in the second set of properties are less than corresponding PMF values in the first set of properties. ### Claim 11 (depends on 10) The computer program product of claim 10, further comprising: instructions to determine a third set of properties comprising reaction coordinate values, and PMF values, for at least the target population of nucleotide structures, based on a third set of testing conditions comprising a third surface area material, a third surface area pattern, a third surface area size, or a combination thereof; and instructions to identify which of the second and third sets of properties have the greatest difference compared to the first set of properties. ### Claim 12 (depends on 10) The computer program product of claim 10, wherein the first set of testing conditions comprises: the first surface area material comprising gold, silicon oxide, or both; and the first surface area pattern comprises one or more of a sheet and a plurality of dots, wherein the first surface area size for the sheet is the area of the sheet, and the surface area size for the plurality of dots is the area of the top surfaces of the dots. ### Claim 13 (depends on 11) The computer program product of claim 11, wherein the third surface area material is the same as the second surface area material, and the third surface area pattern is different from the second surface area pattern. ### Claim 14 (depends on 11) The computer program product of claim 11, wherein the third surface area material is different from the second surface area material and the third surface area pattern is the same as the second surface area pattern. ### Claim 15 (depends on 11) The computer program product of claim 11, wherein the third surface area material is the same as the second surface area material, the third surface area pattern is the same as the second surface area pattern, and the third surface area size is different from the second surface area size ### Claim 16 (depends on 11) The computer program product of claim 11, wherein the second and third sets of properties have the greatest difference compared to the first set of properties further comprises one or more of: the second and third sets of properties having the largest area of PMF values below the PMF values of the first set of properties; the second and third sets of properties with the largest negative slope; the second and third sets of properties with the greatest delta value compared to the first set of properties; and the second and third sets of properties with the lowest absolute PMF value. ### Claim 17 (depends on 16) The computer program product of claim 16, wherein the lowest absolute PMF value is within a range constrained by a first and second threshold, the first threshold being based on one or more of: a probe length value and a max probe energy value; and the second threshold is based on one or more of: the determined reaction coordinate value and a repulsive surface PMF value. ### Claim 18 (depends on 10) The computer program product of claim 10, further comprising: instructions to generate a graphical representation based on the identified target population of nucleotide structures among the plurality of nucleotide structures; instructions to present the graphical representation to a user; and instructions to receive from the user, a selection of a surface area value based on the generated graphical representation. ### Claim 19 A computer system for identifying a surface area size of a biosensing structure, for use in a bionsensor device, based on a plurality of nucleotides structures under test, the computer system comprising: one or more computer processors; one or more computer-readable storage media; program instructions stored on the computer-readable storage media for execution by at least one of the one or more processors, the program instructions comprising: instructions to determine first and second sets of properties comprising reaction coordinate values and potential of mean force (PMF) values for first and second pluralities of nucleotide structures based on respective first and second sets of testing conditions comprising respective first and second surface area material, respective first and second surface area patterns, and respective first and second surface area sizes of a biosensing structure; and instructions to identify a target population of nucleotide structures among the plurality of nucleotide structures, the target population comprising nucleotide structures whose PMF values in the second set of properties are less than corresponding PMF values in the first set of properties. ### Claim 20 (depends on 19) The computer system of claim 19, further comprising: instructions to determine a third set of properties comprising reaction coordinate values, and PMF values, for at least the target population of nucleotide structures, based on a third set of testing conditions comprising a third surface area material, a third surface area pattern, a third surface area size, or a combination thereof; and instructions to identify which of the second and third sets of properties have the greatest difference compared to the first set of properties.