Notice of Pre-AIA or AIA Status The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA. Priority This application 17/836,250 claims priority from JP2021 -148849 filed on 09/13/2021 . Information Disclosure Statement The information disclosure statements (IDS) submitted on 06/09/2022, 02/15/2023, 04/25/2023, 06/18/2025 and 10/06/2025 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements have been considered by the examiner. Status of Claims Claims 1-10 are pending. Claims 1-10 are rejected. Claim Rejections - 35 USC § 101 35 U.S.C. 101 reads as follows: Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title. Claims 1-10 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite: (a) mathematical concepts, (e.g., mathematical relationships, formulas or equations, mathematical calculations); and (b) mental processes, i.e., concepts performed in the human mind, (e.g., observation, evaluation, judgement, opinion). Subject matter eligibility evaluation in accordance with MPEP 2106: Eligibility Step 1: Claims 1-8 are directed towards a method (process) for outputting the structure of a plurality of amino acids based on the answer to a combinatorial optimization problem. Claim 9 is directed to a method (process) for outputting the structure of a plurality of amino acids based on the answer to a combinatorial optimization problem. Claim 10 is directed to a device (apparatus) for the purpose of running a search for a combinatorial optimization problem and outputting the structure of a plurality of amino acids. [Step 1: YES] Eligibility Step 2A : First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in Prong Two whether the recited judicial exception is integrated into a practical application of that exception. Eligibility Step 2A Prong One: In determining whether a claim is directed to a judicial exception, examination is performed that analyzes whether the claim recites a judicial exception, i.e., whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim. Independent c laim 1 recites the following steps which fall within the mental process and/or mathematical concepts groupings of abstract ideas: Searching for, as an answer of a combinatorial optimization problem, a first arrangement of a plurality of amino acids included in a medium molecule based on a value of a first cost arithmetic expression that does not make distinction between a L-form and a D-form of the plurality of amino acids (i.e., mental processes and mathematical concepts); Searching for, as the answer of the combinatorial optimization problem, a second arrangement of the plurality of amino acids based on a value of a second cost arithmetic expression that makes distinction between the L-form and the D- form of the plurality of amino acids by setting the first arrangement as an initial arrangement of searching (i.e., mental processes and mathematical concepts); Dependent claims 2-8 further recite the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas, as noted below. Dependent claim 2 further recites the following steps which fall within the mental process and/or mathematical concepts groupings of abstract ideas: searching for a third arrangement of the plurality of amino acids by changing a coefficient of a certain constraint term among a plurality of constraint terms that constrains an arrangement of the plurality of amino acids ( i.e., mental processes and mathematical concepts); Dependent claim 3 further recites the following steps which fall within the mental process and/or mathematical concepts groupings of abstract ideas: wherein the searching for the third arrangement includes searching for the third arrangement by lowering the coefficient of the certain constraint term (i.e., mental processes and mathematical concepts). Dependent claim 4 further recites the following steps which fall within the mental process and/or mathematical concepts groupings of abstract ideas: wherein the plurality of constraint terms includes constraint terms that ensure that each of the plurality of amino acids included in the medium molecule exists at only one place in a lattice space (i.e., mental processes and mathematical concepts). Dependent claim 5 further recites the following steps which fall within the mental process and/or mathematical concepts groupings of abstract ideas: wherein the plurality of constraint terms includes constraint terms that ensure that each of the plurality of amino acids included in the medium molecule does not exist at a same lattice point (i.e., mental processes and mathematical concepts). Dependent claim 6 further recites the following steps which fall within the mental process and/or mathematical concepts groupings of abstract ideas: wherein the plurality of constraint terms includes constraint terms that ensure that amino acids of the plurality of amino acids included in the medium molecule are interlinked in a certain sequence (i.e., mental processes and mathematical concepts). Dependent claim 7 further recites the following steps which fall within the mental process and/or mathematical concepts groupings of abstract ideas: wherein the plurality of constraint terms includes constraint terms that ensure that unlinked amino acids of the plurality of amino acids contained in the medium molecule do not exist in adjacent lattices (i.e., mental processes and mathematical concepts). Dependent claim 8 further recites the following steps which fall within the mental process and/or mathematical concepts groupings of abstract ideas: wherein the outputting the third arrangement includes when the third arrangement found by the search in which the coefficient of the constraint terms is lowered at a k+1-th time is same as the third arrangement found by the search in which the coefficient of the constraint terms is lowered at a k- th time, outputting the third arrangement found by the search in which the coefficient of the constraint terms is lowered at the k- th time, the k being any integer (i.e., mental processes and mathematical concepts). Independent claim 9 recites the following steps which fall within the mental process and/or mathematical concepts groupings of abstract ideas: searching for, as an answer of a combinatorial optimization problem, a first arrangement of a plurality of amino acids included in a medium molecule based on a value of a first cost arithmetic expression that does not make distinction between a L-form and a D-form of the plurality of amino acids (i.e., mental processes and mathematical concepts); searching for, as the answer of the combinatorial optimization problem, a second arrangement of the plurality of amino acids based on a value of a second cost arithmetic expression that makes distinction between the L-form and the D- form of the plurality of amino acids by setting the first arrangement as an initial arrangement of searching (i.e., mental processes and mathematical concepts); Independent claim 10 recites the following steps which fall within the mental process and/or mathematical concepts groupings of abstract ideas: search for, as an answer of a combinatorial optimization problem, a first arrangement of a plurality of amino acids included in a medium molecule based on a value of a first cost arithmetic expression that does not make distinction between a L-form and a D-form of the plurality of amino acids (i.e., mental processes and mathematical concepts); search for, as the answer of the combinatorial optimization problem, a second arrangement of the plurality of amino acids based on a value of a second cost arithmetic expression that makes distinction between the L-form and the D- form of the plurality of amino acids by setting the first arrangement as an initial arrangement of searching (i.e., mental processes and mathematical concepts); The abstract ideas recited in the claims are evaluated under the broadest reasonable interpretation (BRI) of the claim limitations when read in light of and consistent with the specification. As noted in the foregoing section, the claims are determined to contain limitations that can practically be performed in the human mind with the aid of a pencil and paper, and therefore recite judicial exceptions from the mental process grouping of abstract ideas. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind. Therefore, claims 1-10 recite an abstract idea. [Step 2A Prong One: YES] Eligibility Step 2A Prong Two: In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that when examined as a whole integrates the judicial exception(s) into a practical application (MPEP 2106.04(d)). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)(III)). The judicial exceptions identified in Eligibility Step 2A Prong One are not integrated into a practical application because of the reasons noted below. Dependent claims 3-7 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception. The additional element in independent claim 1 i s: Outputting the second arrangement The additional element in dependent claim 2 is: outputting the third arrangement when the third arrangement is different from the second arrangement The additional element in independent claim 9 is: Outputting the second arrangement The additional element in independent claim 10 is: Outputting the second arrangement The additional element of outputting the second arrangement (claims 1, 9, 10) and outputting the third arrangement when the third arrangement is different from the second arrangement (claim 2) merely invoke a computer as a tool (see MPEP 2106.05(a)). Thus, the additionally recited elements merely invoke a computer as a tool, and/or amount to insignificant extra-solution data gathering activity, and as such, when all limitations in claims 1-5 have been considered as a whole , the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application, and therefore claims 1 -5 are directed to an abstract idea (MPEP 2106.04(d)). [Step 2A Prong Two: NO] Eligibility Step 2B : Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are probed for a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they amount to significantly more than the judicial exception (MPEP 2106.05A i -vi). The claims do not include any additional elements that are sufficient to amount to significantly more than the judicial exception(s) because of the reasons noted below. Dependent claims 3-7 do not recite any elements in addition to the judicial exception(s). The additional elements recited in independent claim 1, 9 and 10 and dependent claim 2 and 5 are identified above, and carried over from Step 2A : Prong Two along with their conclusions for analysis at Step 2B . Any additional element or combination of elements that was considered to be insignificant extra-solution activity at Step 2A : Prong Two was re-evaluated at Step 2B , because if such re-evaluation finds that the element is unconventional or otherwise more than what is well-understood, routine, conventional activity in the field, this finding may indicate that the additional element is no longer considered to be insignificant; and all additional elements and combination of elements were evaluated to determine whether any additional elements or combination of elements are other than what is well-understood, routine, conventional activity in the field, or simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, per MPEP 2106.05(d). The additional element of outputting the second arrangement (claims 1, 9, 10) and outputting the third arrangement when the third arrangement is different from the second arrangement (claim 2) merely invokes a computer as a tool and does not improve the technology of a generic computer (see MPEP 2106.05(a)). Therefore, when taken alone, all additional elements in claims 1-10 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as a combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 1-10 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s) (MPEP 2106.05(II)). [Step 2B : NO] Claim Rejections - 35 USC § 102 In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status. The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action: A person shall be entitled to a patent unless – (a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention. Claims 1-10 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wassenaar et al. ( Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models Tsjerk A. Wassenaar, Kristyna Pluhackova , Rainer A. Böckmann , Siewert J. Marrink , and D. Peter Tieleman Journal of Chemical Theory and Computation 2014 10 (2), 676-690 DOI: 10.1021/ ct400617g ) Regarding the limitations of independent claim 1 , independent claim 9, independent claim 10, a non-transitory computer-readable storage medium storing a search program that causes at least one computer to execute a process, the process comprising (claim 1) , a search method for a computer to execute a process comprising (claim 9) , a search device comprising: one or more memories and one or more processors coupled to the one or more memories and the one or more processors configured to (claim 10) , Wassenaar et al. teaches a computer program run on an Intel Xeon 5160 "Woodcrest" chip, using four cores, running at 3.0 GHz. (pg. 680) Regarding the limitations of independent claim 1 , independent claim 9, independent claim 10 , searching for, as an answer of a combinatorial optimization problem, a first arrangement of a plurality of amino acids included in a medium molecule based on a value of a first cost arithmetic expression that does not make distinction between a L-form and a D-form of the plurality of amino acids , Wassenaar et al. teaches a peptide with 20 amino acids (i.e. a medium molecule) for which an arrangement is searched as an answer of a combinatorial optimization problem (i.e. energy minimization ) based on a cost function (i.e. MARTINI energy force field terms ), which cannot distinguish a L-form and D-form of amino acids (i.e. a single backbone bead in MARTINI) (pg. 682) . Regarding the limitations of independent claim 1 , independent claim 9, independent claim 10 , searching for, as the answer of the combinatorial optimization problem, a second arrangement of the plurality of amino acids based on a value of a second cost arithmetic expression that makes distinction between the L-form and the D- form of the plurality of amino acids by setting the first arrangement as an initial arrangement of searching , Wassenaar et al. teaches the CHARMM36 system (Figure 5, p. 684 and description thereof, p682 ) that allows allow placement of a particle cis, trans, out, or chiral with respect to a set of particles, as shown in Figure 1 (p. 678). The first stage is the generation of an atomistic starting structure from coarse-grained coordinates, which is followed by the second stage, consisting of the relaxation of the atomistic structure (p. 676). Examiner’s reasoning is minimization (corresponding to searching for a second arrangement etc. with an all-atom energy function, i.e. CHARMM36 ) is performed after back mapping (corresponding to the feature "setting the first arrangement as an initial arrangement"). CHARMM36 is able to give an energy difference for L and D-forms of amino-acid, since it represents chirality accurately.) and outputting the second arrangement ( e.g. Fig 5, p684 ). Regarding the limitation of d ependent c laim 2 , t he additional feature of searching for a third arrangement of the plurality of amino acids by changing a coefficient of a certain constraint term among a plurality of constraint terms that constrains an arrangement of the plurality of amino acids; and outputting the third arrangement when the third arrangement is different from the second arrangement , Wassenaar et al. teaches simulated annealing simulations of the back mapped system, which includes changing the constraint of the simulation temperature (a constraint term) (fig. 5, p. 684). Regarding the limitation of d ependent c laim 3, the searching for the third arrangement includes searching for the third arrangement by lowering the coefficient of the certain constraint term , Wassenaar et al. teaches simulated annealing simulations of the back mapped system, which includes changing the constraint of the simulation temperature (a constraint term) (fig. 5, p. 684). Regarding the limitation of d ependent c laim 4 , the plurality of constraint terms includes constraint terms that ensure that each of the plurality of amino acids included in the medium molecule exists at only one place in a lattice space , Wassenaar et al. teaches e lectrostatic interactions were calculated using particle-mesh Ewald (PME) summation. This is because all atom force-field based simulations, e.g. with CHARMM36 , have only one representation of each amino acid. Thus, being at more than one place in a lattice space as, e.g., defined by the grid used for the PME approach for the electrostatic interactions in the simulations, is an intrinsic property of the topology in Wassenaar et al . (p . 681) Regarding the limitation of d ependent c laim 5 , t he plurality of constraint terms includes constraint terms that ensure that each of the plurality of amino acids included in the medium molecule does not exist at a same lattice point , Wassenaar et al. teaches that Electrostatic interactions were calculated using particle-mesh Ewald (PME) summation". The reason therefor is that the non-bonded interactions in the all-atom simulations in Wassenaar et al. are treated via the PME approach, which is solved on a grid, i.e. lattice. This applies a constraint, namely the electrostatic repulsion term, which prevents two atoms to be in the same spot on the grid because the repulsion approaches infinity in such a case (p. 681) . Regarding the limitation of d ependent c laim 6 , t he plurality of constraint terms includes constraint terms that ensure that amino acids of the plurality of amino acids included in the medium molecule are interlinked in a certain sequence , Wassenaar et al. achieves t his by the bonded terms of the applied force-field (p. 682, " CHARMM 36 system ). Regarding the limitation of d ependent c laim 7 , t he plurality of constraint terms includes constraint terms that ensure that unlinked amino acids of the plurality of amino acids contained in the medium molecule do not exist in adjacent lattices , Wassenaar et al. teaches e lectrostatic interactions were calculated using particle mesh Ewald (PME) summation . Non-bonded interactions in all-atom simulations are treated via the PME approach, which is solved on a grid, i.e. lattice. This applies a constraint, namely the electrostatic repulsion term, which prevents two atoms to be in adjacent spots on the grid (typical grid spacing for PME being 0.01 nm) because the repulsion approaches infinity in such a case (p. 681). Regarding the limitation of d ependent c laim 8 , t he outputting the third arrangement includes when the third arrangement found by the search in which the coefficient of the constraint terms is lowered at a k+1-th time is same as the third arrangement found by the search in which the coefficient of the constraint terms is lowered at a k- th time, outputting the third arrangement found by the search in which the coefficient of the constraint terms is lowered at the k- th time, the k being any integer , Wassenaar et al. has output according to a general convergence criterion with discrete time setup, which is anticipated by inter alia the minimizations or the last part of the simulated annealing procedure given ( Figure 5, p.684 and the description thereof) . Therefore claims 1-10 are anticipated . Conclusion Any inquiry concerning this communication or earlier communications from the examiner should be directed to FILLIN "Examiner name" \* MERGEFORMAT Connor Beveridge whose telephone number is FILLIN "Phone number" \* MERGEFORMAT 571-272-2099 . The examiner can normally be reached FILLIN "Work Schedule?" \* MERGEFORMAT Monday - Thursday 9 am - 5 pm . Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, FILLIN "SPE Name?" \* MERGEFORMAT Karlheinz Skowronek can be reached at FILLIN "SPE Phone?" \* MERGEFORMAT 571-272-9047 . The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. 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