DETAILED ACTION
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 .
Applicant's amendments and remarks, filed, 12/14/2025, are acknowledged. Rejections and/or objections not reiterated from previous office actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Status of Claims
Claims 7, 8, 21, 32, and 37 are under examination.
Claims 1-6, 9-12, 22-25, 33-36, 38-41 are withdrawn.
Claims 8, 13-20, 26-32 are cancelled.
Priority
Applicant’s claim for the benefit of foreign priority under 35 U.S.C. 119(a)-(d) to Japanese Patent Application No. 2021-031234, filed on February 26, 2021, is acknowledged. Receipt of the certified priority document has been received. However, a translation of said papers has not been made of record in accordance with 37 CFR 1.55. See MPEP § 201.15. In addition, Applicant is reminded that a foreign priority claim has NO EFFECT on the effective filing date of a U.S. application. The filing date of the foreign priority document is not the effective filing date of the U.S. application. MPEP §§ 201.13 III. and 706.02 V. Thus, the one-year bar of 35 U.S.C. § 102(b) dates from the effective U.S. filing date and not from the foreign filing date. This means that a reference with a publication or patent date less than a year before the priority date but more than a year before the effective U.S. filing date, is a reference under 35 U.S.C. § 102(b). This also applies when the claimed invention had been into a public use or on sale in this country more than one year prior to the effective U.S. filing date. 35 U.S.C. § 119(a). Accordingly, the effective filing date for the instant application is 01/18/2022.
Objections
The amendment to the specification is acceptable. Accordingly, the objection to the disclosure because it contains an embedded hyperlink and/or other form of browser-executable code is withdrawn.
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.
The following rejection is necessitated by amendment.
Claims 7, 8, 21, 32, and 37 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and ‘as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355).
Guidance Step 1: Under the broadest reasonable interpretation, the claimed invention (claims 7, 21, 37 being representative) is directed to a method/system of computing membrane permeability. Therefore, the claims fall into one of the four statutory categories. [Step 1: YES]
A. Guidance Step 2A, Prong 1
The Revised Guidance instructs us first to determine whether any judicial exception to patent eligibility is recited in the claim. The Revised Guidance identifies three judicially-excepted groupings identified by the courts as abstract ideas: (1) mathematical concepts, (2) certain methods of organizing human behavior such as fundamental economic practices, and (3) mental processes. In this case, the following steps encompass an abstract idea:
execute a simulation simulating dynamics of a peptide permeating through a first solvent region in a cell, a membrane region of said cell, and a second solvent region of said cell,
obtain simulation results of said simulation:
compute, using said obtained simulation results, a free energy G(z) of the peptide for each reaction coordinate z of a plurality of reaction coordinates, each expressing a position of the peptide in a region including the first solvent region…;
compute for each of the plurality of reaction coordinates z a difference AG(z) between a minimum value Gmin from among a plurality of free energies G(z) of the peptide, each computed for the respective reaction coordinates z and a respective free energy G(z)…;
compute a value R(z) expressing a local resistance of the peptide at the reaction coordinate z based on the difference AG(z) computed for the respective reaction coordinates z and based on the local diffusion coefficient D(z);
compute a predicted value of membrane permeability of the peptide, permeating from said first solvent region adjacent to one side of the membrane region, through said membrane region, to said second solvent region adjacent to another side of the membrane region, based on the value R(z) expressing the local resistance computed for each of the plurality of reaction coordinates z.
Mental Processes
Regarding claim(s) 7, 21, 37, under the BRI, the claimed steps clearly encompass manipulating data and performing calculations. In addition, the specification describes computational and/or algorithmic methods for achieving the claimed functions [see at least pages 15-28]. As such, the specification provides sufficient evidence that the claims are directed to an abstract idea since the specific descriptions provided for accomplishing these tasks include only data reception and analysis, which may be performed in the human mind via normal processes of observation and evaluation. For these reasons, the above step falls within the mental process groupings of abstract ideas. See MPEP 2106.04(a)(2), subsection III. [Step 2A, Prong 1: YES].
Mathematical Concept
In addition, these claims also require computing various parameters, e.g. predicted values, free energies, local resistance. In addition, the specification describes specific equations for achieving the claimed functions [see at least pages 27-28]. As such, these steps require mathematical concepts and/or mathematical calculations. See MPEP 2106.04(a)(2). Therefore, when read in light of applicant’s own specification, the claims are directed to a mathematical concept. See MPEP 2106.04 and 2106.05(II).
B. Guidance Step 2A, Prong 2
This part of the eligibility analysis evaluates whether the claim includes any additional steps/elements that integrate the recited judicial exception into a practical application of the exception. In this case, the additional steps/elements that are not part of the abstract idea are as follows: memory and processor;
With regards to the claimed processor and memory, these limitations are recited at high level of generality and read on a generic computer. Accordingly, these features are merely being used as tools to perform generic computer functions or the abstract idea, and therefore amount to no more than mere instructions to apply the exception using a generic computer. See MPEP 2106.05(f). Even when viewed in combination, these additional elements do not integrate the recited judicial exception into a practical application. [Step 2A, Prong 2: NO].
C. Guidance Step 2B:
This part of the eligibility analysis evaluates whether the claim as a whole amount to significantly more than the recited exception i.e., whether any additional element, or combination of additional elements, adds an inventive concept to the claim. See MPEP 2106.05.
As discussed above, the claim does not recite any additional steps/elements that amount to significantly more than the judicial exception. Moreover, a review of the specification [see at least page 37 and Figures 1, 5] teaches routine and conventional computer elements for performing the claimed invention and there is no evidence to suggest applicant has inventive some type of new hardware. Accordingly, there is nothing inventive with regards to the claimed memory and processing hardware. The courts have also explained that the use of generic computer elements do not alone transform an otherwise abstract idea into patent-eligible subject matter. See DDR Holdings (Fed. Cir. 2014). Thus, the independent claim(s) as a whole do not amount to significantly more than the exception itself. Therefore, the claim(s) is/are not patent eligible. [Step 2B: NO].
Dependent Claims
Dependent claims 8, 32 have also been considered under the two-part analysis but do not include additional steps/elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons. In particular, claim 8 further limits the specificity of the abstract idea and therefore is also not patent eligible for reasons discussed above (Step 2A, prong 1). Regarding claim(s) 32, these claims a directed to non-transitory recording mediums and therefore are also not patent eligible for reasons set forth above (Step 2A, prong 2, and Step 2B). Therefore, the claim(s) is/are not patent eligible. [Step 2B: NO].
Response to Arguments
Applicant’s arguments, filed 12/14/2025, have been fully considered but are not persuasive for the following reasons.
Applicant again argues that the claims do not recite a mental process in light of the MPEP and AI-SME Update. In response, the examiner has explicitly identified the steps that recite the abstract idea and provided sufficient reasoning as to why these steps are abstract (Step 2A, prong 1 analysis above). The courts are clear that an invention directed to the “collection, manipulation, and display of data” is an abstract process. See Intellectual Ventures, 850 F.3d at 1340; see generally id. at 1340-41. Applicant is also reminded that the Office's eligibility guidance does not set limit on the size of the data or number of calculations that can or cannot be performed mentally. MPEP § 2106.04(a)(2)III. Accordingly, absent any evidence to the contrary, the examiner maintains that the claims are directed to an abstract idea.
Applicant additionally argues that the claims do not recite a mathematical concept, asserting that the claims only involved a mathematical concept. In response, as discussed above, Applicant is reminded that the grouping of “mathematical concepts” is not limited to formulas or equations, as words used in a claim operating on data to solve a problem can serve the same purpose as a formula. Claims are also evaluated in light of the specification, and a claim does not have to recite the word "calculating" in order to be considered a mathematical calculation. As set forth above (Step 2A, prong 1 analysis), the claims explicitly recite computing various parameters, e.g. predicted values, free energies, local resistance. As such, the examiner maintains that the claims do not merely “rely upon” a mathematical concept because it explicitly recites mathematical concepts and/or mathematical calculations.
Applicant argues that the claimed method recites additional elements that integrate the alleged abstract idea into a practical application. In response, this argument is not persuasive for reasons set forth above (Step 2A, prong 2 analysis). The examiner maintains that the claimed processor and memory are merely being used as tools to perform generic computer functions or the abstract idea, and therefore amount to no more than mere instructions to apply the exception using a generic computer. See MPEP 2106.05(f).
Applicant argues that the claimed prediction device and method (directed to performing dynamic simulations) provides an improvement to the technology (by reducing computational load and increasing accuracy of the prediction device). In response, applicant appears to be arguing that the abstract idea provides the “improvement”. However, it is important to note that the judicial exception alone cannot provide the improvement. See MPEP 2106.05(a). The improvement can be provided by (1) one or more additional steps/elements appended to the judicial exception; or (2) by the additional steps/elements appended to the judicial exception in combination with the recited judicial exception. See MPEP 2106.05(a). In this case, the problem is that are no additional steps/elements appended to the abstract idea that would serve to “integrate” the abstract idea into a practical application (Step 2A, prong 2) and there is no evidence to suggest the claimed invention provides an improvement to a particular machine. Similarly, the courts have also instructed that “[t]he different use of a mathematical calculation, even one that yields different or better results, does not render patent eligible subject matter.” Board Of Trustees Of Leland Stanford Junior University, 991 F.3d 1245, 1251 (Fed. Cir. 2021). Therefore, because the claims are entirely directed to an abstract idea and do not recite any steps appended to the JE that (alone or in combination) integrate the abstract idea into a practical application, the examiner maintains that the claims do not provide an improvement to the technology (under Step 2A, prong 2, or Step 2B). See MPEP 2106.04(d)(1). For at least these reasons, the rejection is maintained.
For a list of considerations when evaluating whether additional elements integrate a judicial exception into a practical application see MPEP 2106.04(d)(1) lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
Claim rejections - 35 USC § 112, 2nd Paragraph
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
The following rejection is necessitated by amendment.
Claims 7, 8, 21, 32, and 37 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention. Claims that depend directly or indirectly from claims 7 and 21 are also rejected due to said dependency.
Claims 7, 21, 37 recite “compute a local diffusion coefficient D(z) for each of the reaction coordinates z, based on a value var(z) expressing a variance of a position of a centroid of a peptide when executing umbrella sampling for each of the plurality of reaction coordinates z and based on a value Czz(t) expressing an autocorrelation of the centroid positions at a respective time t.” In this case, the phrase “when executing umbrella sampling for each of the plurality of reaction coordinates z and based on a value Czz(t) expressing an autocorrelation of the centroid positions at a respective time t” is a conditional limitation that suggests additional limitations without explicitly requiring them (e.g. performing umbrella sampling, performing an autocorrelation). However, Applicant is reminded that claim scope is not limited by “conditional” limitations that suggests or makes optional but does not require steps to be performed. See MPEP 2111.04. As a result, it is unclear what positive process limitation is intended by the claimed “when” phrase. In addition, it is unclear in what way the “computing” step is “based on a value Czz(t) expressing an autocorrelation). A review of the specification does not provide any limiting definitions that would serve to clarify. Clarification is requested via amendment.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PABLO S WHALEY whose telephone number is (571)272-4425. The examiner can normally be reached between 1pm-9pm EST.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Anita Coope can be reached at 571-270-3614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/PABLO S WHALEY/Primary Examiner, Art Unit 3619