DETAILED ACTION
Applicant's response, filed 15 August 2025, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 .
Status of the Claims
Claims 1 and 5-17 are pending.
Claims 2-4 and 18-20 are cancelled.
Claims 1 and 5-17 are rejected.
Priority
The effective filing date of the claimed invention is 18 August 2021.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 19 April 2022 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Claim Objections
The objections to the claims are withdrawn in view of the amendments to the claims, filed 18 August 2025.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that use the word “means” or
“step” or equivalent but are nonetheless not being interpreted under 35 U.S.C. 112(f) or pre -AIA
35 U.S.C. 112, sixth paragraph because the claim limitation recites sufficient structure, materials, or acts to entirely perform the recited function. In claims 1 and 5-7, “configured to” is the generic placeholder for “means for” and is coupled with functional language. Claims 1 and 5-7 recite sufficient structure to perform the functional language as disclosed in these claim limitations.
Such claim limitations are:
“a microbial efficiency-matrix stabilization (MEMS) ecosystem model configured to receive” in claim 1;
“the ecosystem model is configured to create… and divide” in claim 5;
“the ecosystem model is configured to divide” in claim 6;
“the ecosystem model is configured to run” in claim 7.
Because these claim limitations are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, they are not being interpreted to cover only the corresponding structure, material, or acts described in the specification as performing the claimed function, and equivalents thereof.
If applicant intends to have these limitations interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitations to remove the structure, materials, or acts that performs the claimed function; or (2) present a sufficient showing that the claim limitations do not recite sufficient structure, materials, or acts to perform the claimed function.
Response to Arguments
Regarding 35 USC § 112(b): Applicant’s arguments (see page 5, Section: Rejections under 35 U.S.C. § 112), filed 19 August 2025, with respect to claims 18-19 have been fully considered and are persuasive. The rejection of claims 18-19 under 35 USC § 112(b) has been withdrawn in view of the cancellation of the claims, filed 19 August 2025.
Regarding 35 USC § 112(d): Applicant’s arguments (see pages 5-6, Section: Rejections under 35 U.S.C. § 112), filed 19 August 2025, with respect to claim 14 have been fully considered and are not persuasive. After further reconsideration of claim 14, the rejection under 35 USC § 112(d) has been withdrawn.
Regarding 35 USC § 101: Applicant’s arguments (see pages 6-7, Section: Rejections under 35 U.S.C. § 101), filed 19 August 2025, with respect to claims 1-20 have been fully considered but are not persuasive. The rejection of the claims under 35 USC § 101 has been maintained.
The Applicant asserts “that the subject matter of claims 1 and 5-20 constitutes mental processes such that these claims are drawn to an abstract idea. Notably, the Office Action did not make these assertions with respect to the subject matter of claims 2-4, seemingly acknowledging that these claims were not drawn to a judicial exception.”
The Examiner asserts that the additional elements of the inputs comprise input files, parameter data, an operation schedule, net primary productivity (NPP) data, and weather data; the input files comprise a control file, a site file, and a weather file; and the parameter data comprises base parameters, plant parameters, and site parameters; are not improvements to computer functionality itself, and therefore do not integrate the recited judicial exceptions into a practical application. 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)).
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 the additional elements of the inputs comprise input files, parameter data, an operation schedule, net primary productivity (NPP) data, and weather data; the input files comprise a control file, a site file, and a weather file; and the parameter data comprises base parameters, plant parameters, and site parameters; are conventional.
Evidence for the conventionality is shown by Achat et al. (Biogeochemistry, 2016, Vol. 131, pp. 173-202). Achat et al. reviews future challenges in coupled C–N–P cycle models for terrestrial ecosystems under global change: a review (Title); and reviews the processes that are included in ecosystem models, but focus on coupled C–N–P cycle models. Achat et al. highlights important plant adjustments to climate change, elevated atmospheric CO2, and/or nutrient limitations that are currently not—or only partially—incorporated in ecosystem models by reviewing experimental studies and compiling data (Abstract).
Achat et al. shows incorporating N and P cycles in ecosystem models is required to specifically simulate the effects of N and P fertilization and atmospheric deposition as well as the role of N2-fixing plants; first, in addition to climate change, management factors, especially fertilization, contribute to greater ecosystem productivity and C accumulation potential (Noormets et al. 2015) by alleviating N and/or P limitations (Elser et al. 2007); second, the deposition of reactive N, which represented about 100 Tg-N year-1 in 1995 (Galloway et al. 2004), can also protect terrestrial (and also aquatic) ecosystems from N limitations (Meunier et al. 2016; Sardans et al. 2016) (pg. 175, col. 1, para. 2).
Achat et al. further shows inputs of both N and P into the ecosystem can include atmospheric deposition and fertilization. Ecosystem models also include biological N2 fixation and P weathering, which are N- and P-specific processes, respectively. Biological N2-fixation (N-specific process) is performed by N2-fixing symbionts in roots of legumes and several other groups of plants (i.e. symbiotic N2-fixation; Vitousek et al. 2002; Augusto et al. 2013) and free-living micro-organisms in soils (i.e. asymbiotic N2-fixation; Reed et al. 2011). Although the flux of symbiotic fixation was found greater than the flux of asymbiotic fixation (Galloway et al. 2004; Herridge et al. 2008; Reed et al. 2011), both processes can be represented in C–N models (e.g. Esser et al. 2011) and also C–N–P models (Table 1). Depending on the C–N model, biological N2 fixation is estimated empirically as a function of climate (e.g. Yang et al. 2009) or proportionally to plant productivity (NPP; Thornton et al. 2007). In some C–N–P models (e.g. Karam et al. 2013; Yang et al. 2014; Zhu et al. 2016), N2 fixation is also estimated depending on plant species or proportionally to NPP (Table 1) (pg. 179, col. 2, paras. 2-3).
Achat et al. further shows in the C–N–P models reviewed here, sorption/desorption reactions are generally described using Langmuir-type isotherms, assuming that equilibrium is reached at each time step. For instance, ‘‘labile’’ and ‘‘sorbed/secondary mineral’’ inorganic P are assumed to be in equilibrium at each one month time step in CENTURY (Metherell et al. 1993) or one day time step in CASA-CNP and JSBACH-CNP (Wang et al. 2010; Goll et al. 2012). In CLM-CNP (Yang et al. 2014), the phosphate ions in the soil solution and ‘‘labile’’ inorganic P are assumed to be in equilibrium at each 30-min time step (pg. 179, col. 1, para. 4).
Achat et al. further shows 182 published studies that developed or applied coupled C-nutrient cycle models for terrestrial ecosystems (see list of models in Table S2 and references in Supplementary Material) (pg. 175, col. 2, para. 4). Achat et al. further shows more than 70 ecosystem or earth system models that include C–N interactions, with the aim of assessing management or environment effects on ecosystems (Table S2). But a small number of these models also include interactions with the P cycle. The main C–N–P models Achat et al. analyzed are listed in Table 1; other models that include the P cycle (Liu et al. 1991; Verburg and Johnson 2001; Smaill et al. 2011; Table S2) are simpler or more empirical in terms of C–N–P interactions.The ISI Web of Science database was also used to identify experimental studies on key processes, particularly plant adjustments to nutrient limitations (e.g. exudation of phosphatases and carboxylates) (pg. 176, col. 1, para. 2).
Furthermore, all additional elements in claims 1 and 5-17 have been evaluated individually and in combination, and are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exceptions (MPEP 2106.05(II)).
Regarding 35 USC § 102: Applicant’s arguments (see page 7, Section: Rejections under 35 U.S.C. § 102), filed 19 August 2025, with respect to claims 18-20 have been fully considered and are persuasive in view of the cancellation of the claims. The rejection of claims 18-20 under 35 USC § 102 has been withdrawn in view of the cancellation of the claims, filed 19 August 2025.
Regarding 35 USC § 103: Applicant’s arguments (see pages 7-8, Section: Rejections under 35 U.S.C. § 103), filed 19 August 2025, with respect to claims 1-17 have been fully considered but are not persuasive. The rejection of claims 1 and 5-17 under 35 USC § 103 has been maintained.
The Applicant asserts “Regarding claim 1 for example, it specifies that the inputs "comprise input files, parameter data, an operation schedule, net primary productivity (NPP) data, and weather data" where "the input files comprise a control file, a site file, and a weather file" and "the parameter data comprises base parameters, plant parameters, and site parameters." Similarly, independent claim 1 requires an input file that includes a site file and parameter data that includes site parameters. The Office Action cites Table 1 of Hartman for teaching these aspects of claim 1, but fails to identify how Table 1 teaches both an input file that includes a site file and parameter data that includes site parameters. Similarly, Table 1 only appears to teach the use of site parameters and is silent with respect to an input file that includes a site file.”
Regarding claim 1, the Examiner asserts that Hartman et al. teaches the DayCent environment (Figure 1) consists of the DayCent model, a number of (inputs) parameter files, a schedule file, a weather file, and many output files (pg. 12, para. 2); the DayCent model simulates the long-term dynamics of Carbon (C), Nitrogen (N), Phosphorus (P), and Sulfur (S) for different Plant-Soil Systems (pg. 67, para. 1). Hartman et al. further teaches DayCent simulates exchanges of carbon, nutrients, and trace gases among the atmosphere, soil, and plants as well as events and management practices such as fire, plant harvest, grazing, cultivation, irrigation, and organic matter or fertilizer additions (pg. 11, para. 3; pg. 21, Section 3.1. Introduction). Hartman et al. further teaches the DayCent environment (Figure 1) consists of the DayCent model, a number of parameter files, a schedule file, a weather file, and many output files (pg. 12, para. 2; and Figure 1); it is important to verify that SOC levels appear reasonable because SOC integrates many processes in the model (e.g., NPP, decomposition) (pg. 65, para. 2). Hartman et al. further teaches input files (control and site files) and parameter data including base parameters, plant parameters, and site parameters (pg. 15-17, Table 1).
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 and 5-17 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).
Following the flowchart in MPEP 2106:
Eligibility Step 1
Claims 1-14 are directed to a computer system (machine or manufacture) comprising multiple inputs and an ecosystem model for generating information of carbon and nitrogen dynamics in soil, plants, and the atmosphere; claims 15-17 are directed to methods (processes) of using an ecosystem model; and claims 18-20 are directed to an ecosystem model (machine or manufacture). Therefore, these claims are encompassed by the categories of statutory subject matter, and thus, satisfy the subject matter eligibility requirements under step 1.
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 claim 1 recites a mental process of considering data and a mathematical concept of a system comprising a microbial efficiency-matrix stabilization (MEMS) ecosystem model.
Independent claim 15 recites a mental process of considering data and a mathematical concept of creating a soil profile and dividing the soil profile into continuous soil horizons in a model input file, with user-defined depths for each horizon; and a mental process of considering data and a mathematical concept of running a plurality of simulations with submodels using the MEMS ecosystem model with the inputs and divided soil profile.
Dependent claim 5 further recites a mental process of considering data and a mathematical concept wherein the ecosystem model is configured to create a one dimension soil profile and divide the one-dimension soil profile into continuous soil horizons in a model input file, with user-defined depths for each horizon.
Dependent claim 6 further recites a mental process of considering data and a mathematical concept wherein the ecosystem model is configured to, while executing a model simulation, divide the soil horizons into thinner layers to solve partial differential equations.
Dependent claim 7 further recites a mental process of considering data and a mathematical concept wherein the ecosystem model is configured to run simulations in accordance with submodels.
Dependent claim 8 further recites a mental process of considering data and a mathematical concept wherein the submodels comprise algorithms respectively directed to an atmosphere submodel, a plant submodel, a soil surface submodel, and a soil submodel.
Dependent claim 9 further recites a mental process of considering data and a mathematical concept wherein the atmosphere submodel comprises weather, evapotranspiration (ET) demand, and N deposition.
Dependent claim 10 further recites a mental process of considering data and a mathematical concept wherein the plant submodel comprises aboveground biomass, belowground biomass, and exudate.
Dependent claim 11 further recites a mental process of considering data and a mathematical concept wherein the soil surface submodel comprises litter and surface temperature.
Dependent claim 12 further recites a mental process of considering data and a mathematical concept wherein the soil submodel comprises soil layer, soil water, soil temperature, soil minerals, nitrate, ammonium, and soil organic matter (SOM) pools.
Dependent claim 16 further recites a mental process of considering data and a mathematical concept wherein the submodels comprise algorithms respectively directed to an atmosphere submodel, a plant submodel, a soil surface submodel, and a soil submodel, wherein the atmosphere submodel comprises weather, evapotranspiration (ET) demand, and N deposition, wherein the plant submodel comprises aboveground biomass, belowground biomass, and exudate, wherein the soil surface submodel comprises litter and surface temperature, and wherein the soil submodel comprises soil layer, soil water, soil temperature, soil minerals, nitrate, ammonium, and soil organic matter (SOM) pools.
Dependent claim 17 further recites a mental process of considering data and a mathematical concept of dividing the soil horizons into thinner layers to solve partial differential equations.
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, and are determined to be directed to the analysis of data that in the simplest embodiments are mental processes that are not too complex to be performed in the human mind with the aid of a pencil and paper. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas (e.g., “while executing model simulation… to solve partial differential equations” at [0042] in the Specification) are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind.
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)). 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.
The additional elements in independent claim 1 include:
a system, comprising: a plurality of inputs; …and a plurality of outputs comprising the generated information;
the inputs comprise input files, parameter data, an operation schedule, net primary productivity (NPP) data, and weather data;
the input files comprise a control file, a site file, and a weather file;
the parameter data comprises base parameters, plant parameters, and site parameters.
The additional elements in independent claim 15 include:
receiving a plurality of inputs at a microbial efficiency-matrix stabilization (MEMS) ecosystem model,
the inputs comprise weather data, soil properties, plant characteristics, input files, parameter data, an operation schedule, net primary productivity data (NPP) and management practices;
producing outputs from the simulations with submodels, on a daily time step or a subdaily time step; and
providing the outputs to a display device or a storage device
the input files comprise a control file, a site file, and a weather file;
the parameter data comprises base parameters, plant parameters, and site parameters.
The additional elements in dependent claims 13-14 include:
the outputs are produced on a daily time step or a subdaily time step (claim 13);
a storage device to store the outputs in output files (claim 14);
The judicial exceptions noted above are not integrated into a practical application because the additional elements of
a system, comprising: a plurality of inputs; …and a plurality of outputs comprising the generated information; the inputs comprise input files, parameter data, an operation schedule, net primary productivity (NPP) data, and weather data; the input files comprise a control file, a site file, and a weather file; the parameter data comprises base parameters, plant parameters, and site parameters in independent claim 1;
receiving a plurality of inputs at a microbial efficiency-matrix stabilization (MEMS) ecosystem model; the inputs comprise weather data, soil properties, plant characteristics, input files, parameter data, an operation schedule, net primary productivity data (NPP) and management practices; producing outputs from the simulations with submodels, on a daily time step or a subdaily time step; providing the outputs to a display device or a storage device; the input files comprise a control file, a site file, and a weather file; the parameter data comprises base parameters, plant parameters, and site parameters.in independent claim 15;
outputs are produced on a daily time step or a subdaily time step in dependent claim 13; and
a storage device to store the outputs in output files in dependent claim 14;
are not improvements to computer functionality itself, or an improvement to any other technology or technical field, and therefore do not integrate the recited judicial exceptions into a practical application (see MPEP at 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes).
The judicial exceptions noted above are not integrated into a practical application because the additional elements are not improvements to computer functionality itself, and therefore do not integrate the recited judicial exceptions into a practical application.
All limitations in claims 1 and 5-17 have been considered as a whole, and are deemed to not recite any additional elements that would integrate a judicial exception into a practical application (MPEP 2106.04(d)).
Eligibility Step 2B
Because the claim recites an abstract idea, and does not integrate that abstract idea into a practical application, the claim is 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 the additional elements of a system, comprising multiple inputs and outputs in independent claim 1; a storage device to store the outputs in output files in dependent claim 14; receiving input; producing output; and providing output to a display or storage device in independent claim 15; inputs comprise input files, and parameter data in independent claim 1; outputs produced on a daily time step or a subdaily time step in dependent claim 13; are conventional (see MPEP at 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes).
The additional elements of inputs comprise an operation schedule, net primary productivity (NPP) data, and weather data; input files comprise a control file, a site file, and a weather file; and parameter data comprises base parameters, plant parameters, and site parameters in independent claims 1 and 15; the inputs comprise weather data, soil properties, plant characteristics, input files, parameter data, an operation schedule, net primary productivity data (NPP) and management practices in independent claim 15; and outputs are produced on a daily time step or a subdaily time step in dependent claim 13 and independent claim 15; are conventional.
Evidence for the conventionality is shown by Achat et al. (Biogeochemistry, 2016, Vol. 131, pp. 173-202). Achat et al. reviews future challenges in coupled C–N–P cycle models for terrestrial ecosystems under global change: a review (Title); and reviews the processes that are included in ecosystem models, but focus on coupled C–N–P cycle models. Achat et al. highlights important plant adjustments to climate change, elevated atmospheric CO2, and/or nutrient limitations that are currently not—or only partially—incorporated in ecosystem models by reviewing experimental studies and compiling data (Abstract).
Achat et al. shows incorporating N and P cycles in ecosystem models is required to specifically simulate the effects of N and P fertilization and atmospheric deposition as well as the role of N2-fixing plants; first, in addition to climate change, management factors, especially fertilization, contribute to greater ecosystem productivity and C accumulation potential (Noormets et al. 2015) by alleviating N and/or P limitations (Elser et al. 2007); second, the deposition of reactive N, which represented about 100 Tg-N year-1 in 1995 (Galloway et al. 2004), can also protect terrestrial (and also aquatic) ecosystems from N limitations (Meunier et al. 2016; Sardans et al. 2016) (pg. 175, col. 1, para. 2).
Achat et al. further shows inputs of both N and P into the ecosystem can include atmospheric deposition and fertilization. Ecosystem models also include biological N2 fixation and P weathering, which are N- and P-specific processes, respectively. Biological N2-fixation (N-specific process) is performed by N2-fixing symbionts in roots of legumes and several other groups of plants (i.e. symbiotic N2-fixation; Vitousek et al. 2002; Augusto et al. 2013) and free-living micro-organisms in soils (i.e. asymbiotic N2-fixation; Reed et al. 2011). Although the flux of symbiotic fixation was found greater than the flux of asymbiotic fixation (Galloway et al. 2004; Herridge et al. 2008; Reed et al. 2011), both processes can be represented in C–N models (e.g. Esser et al. 2011) and also C–N–P models (Table 1). Depending on the C–N model, biological N2 fixation is estimated empirically as a function of climate (e.g. Yang et al. 2009) or proportionally to plant productivity (NPP; Thornton et al. 2007). In some C–N–P models (e.g. Karam et al. 2013; Yang et al. 2014; Zhu et al. 2016), N2 fixation is also estimated depending on plant species or proportionally to NPP (Table 1) (pg. 179, col. 2, paras. 2-3).
Achat et al. further shows in the C–N–P models reviewed here, sorption/desorption reactions are generally described using Langmuir-type isotherms, assuming that equilibrium is reached at each time step. For instance, ‘‘labile’’ and ‘‘sorbed/secondary mineral’’ inorganic P are assumed to be in equilibrium at each one month time step in CENTURY (Metherell et al. 1993) or one day time step in CASA-CNP and JSBACH-CNP (Wang et al. 2010; Goll et al. 2012). In CLM-CNP (Yang et al. 2014), the phosphate ions in the soil solution and ‘‘labile’’ inorganic P are assumed to be in equilibrium at each 30-min time step (pg. 179, col. 1, para. 4).
Achat et al. further shows 182 published studies that developed or applied coupled C-nutrient cycle models for terrestrial ecosystems (see list of models in Table S2 and references in Supplementary Material) (pg. 175, col. 2, para. 4). Achat et al. further shows more than 70 ecosystem or earth system models that include C–N interactions, with the aim of assessing management or environment effects on ecosystems (Table S2). But a small number of these models also include interactions with the P cycle. The main C–N–P models Achat et al. analyzed are listed in Table 1; other models that include the P cycle (Liu et al. 1991; Verburg and Johnson 2001; Smaill et al. 2011; Table S2) are simpler or more empirical in terms of C–N–P interactions.The ISI Web of Science database was also used to identify experimental studies on key processes, particularly plant adjustments to nutrient limitations (e.g. exudation of phosphatases and carboxylates) (pg. 176, col. 1, para. 2).
Furthermore, all additional elements in claims 1-20 have been evaluated individually and in combination, and are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exceptions (MPEP 2106.05(II)).
Claim Rejections - 35 USC § 103
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 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1 and 5-17 are rejected under 35 U.S.C. 103 as being unpatentable over Hartman et al. (Natural Resource Ecology Laboratory, uploaded online 2019 (date on manual May 2, 2018), Colorado State University, pp. 1-342) in view of Cotrufo et al. (Global Change Biology, 2013, pp. 988-995, cited on IDS received April 19, 2022).
Independent claim 1 is directed to a system of inputs, outputs, and a microbial efficiency-matrix stabilization (MEMS) ecosystem model that simulates the dynamics of carbon (C) and nitrogen (N) in an ecosystem comprised of soil, plants and the atmosphere.
Regarding claim 1, Hartman et al. teaches the DayCent environment (Figure 1) consists of the DayCent model, a number of (inputs) parameter files, a schedule file, a weather file, and many output files (pg. 12, para. 2); the DayCent model simulates the long-term dynamics of Carbon (C), Nitrogen (N), Phosphorus (P), and Sulfur (S) for different Plant-Soil Systems (pg. 67, para. 1). Hartman et al. further teaches DayCent simulates exchanges of carbon, nutrients, and trace gases among the atmosphere, soil, and plants as well as events and management practices such as fire, plant harvest, grazing, cultivation, irrigation, and organic matter or fertilizer additions (pg. 11, para. 3; pg. 21, Section 3.1. Introduction). Hartman et al. further teaches the DayCent environment (Figure 1) consists of the DayCent model, a number of parameter files, a schedule file, a weather file, and many output files (pg. 12, para. 2; and Figure 1); it is important to verify that SOC levels appear reasonable because SOC integrates many processes in the model (e.g., NPP, decomposition) (pg. 65, para. 2). Hartman et al. further teaches input files (control and site files) and parameter data including base parameters, plant parameters, and site parameters (pg. 15-17, Table 1).
Hartman et al. further teaches DayCent model inputs can be divided into four categories: (i) weather information, (ii) soil information, (iii) plant information, and (iv) management information. Hartman et al. further teaches the model runs using a daily time step and the major input variables for the model include: (1) daily average maximum and minimum air temperature, (2) daily precipitation, (3) lignin content of plant material, (4) plant N, P, and S content, (5) soil texture, (6) atmospheric and soil N inputs, and (7) initial soil C, N, P, and S levels (pg. 21, 3.1. Introduction). Hartman et al. further teaches the DayCent ecosystem model includes submodels for plant productivity, decomposition of dead plant material and SOM (soil organic matter), soil water and temperature dynamics, and N gas fluxes (Figure 5) (pg. 67, para. 1). Hartman et al. further teaches the soil physical submodels (Part 2, Section 2), and the soil biogeochemical submodels (Part 2, Section 3) include nitrogen (N) cycling (nitrogen submodel, pp. 94-95; and Figure 19); soil vertical water flows (water flow submodel, pg. 68; Figure 6; and soil water submodel, pg. 71); dissolved organic matter (DOM) transport (soil organic matter submodel, pg. 78; and Figure 9); plant growth and root input (plant growth submodels, pg. 113; and Figure 25); and soil temperature dynamics (soil temperature model, pp. 77-78); microbial processes in the litter layer and rhizosphere (pg. 80; and Figures 10 and 11; and pg. 22, para. 3); DOM, particulate organic matter (POM) and mineral-associated organic matter (MAOM) dynamics in the bulk soil to a user-defined depth above the bedrock (pg. 78, para. 5; and Figure 9; pg. 23, para. 2; and Figure 2).
Hartman et al. further teaches the soil organic matter submodel of the DayCent model is based on multiple compartments for soil organic matter; soil organic matter is simulated for the top 20-cm soil layer and is divided into three pools (active, slow, and passive) with different potential decomposition rates; both the active and the slow organic matter pools have a surface and soil component while the passive pool has only a soil component; plant material is transferred into these soil organic matter pools from above and belowground litter pools and three dead wood pools (Figure 9) (pg. 78, para. 5); the active soil fraction includes the live soil microbes and microbial products… the slow SOM fraction is made up of lignin derived plant material and stabilized microbial products (pg. 22, para. 3); above and belowground non-woody plant residues and organic animal excreta are partitioned into structural (STRUCC(*)) and metabolic (METABC(*)) pools as a function of the lignin to N ratio in the residue. Hartman et al. further teaches structural material is assumed to contain cellulose and all of the lignin whereas metabolic material is readily decomposable. Hartman et al. further teaches with increases in the ratio, more of the residue is partitioned to the structural pools which have much slower decay rates than the metabolic pools (Figure 11); the lignin fraction of the plant material does not go through the surface microbe (SOM1C(1)) or active pools (SOM1C(2)) but is assumed to go directly to the slow C pool (SOM2C) as the structural plant material decomposes; metabolic pools are decomposed primarily by bacteria while structural pools are decomposed primarily by fungi (pg. 80, para. 1; Figures 10 and 11; pg. 83; and Figure 12); in DayCent, the sand, silt, and clay fractions used by the decomposition model are computed as the weighted average sand content from all soil layers in soils.in (pg. 24, para. 1); and a fraction of the products from the decomposition of the active pool is lost as leached organic C (STREAM(5) in Figure 9) (pg. 90, para. 1).
Independent claim 15 is directed to a method for receiving inputs of weather, soil properties, plant characteristics, and management practices to a microbial efficiency-matrix stabilization (MEMS) ecosystem model; creating a soil profile and dividing the soil profile into continuous soil layers with user-defined depths; running simulations using the inputs, soil profile, and submodels of the ecosystem model; producing outputs from the simulations on a daily or subdaily time step; and providing the outputs to a display device or a storage device.
Regarding claim 15, Hartman et al. teaches a method for receiving inputs of (i) weather information, (ii) soil information, (iii) plant information, and (iv) management information to the DayCent ecosystem model (pg. 21, Section 3.1. Introduction); creating a soil profile and dividing the soil profile into continuous soil layers with user-defined depths (pg. 23, paras. 2-3; pg. 24, para. 2; Table 2; and Figure 2); running simulations using DayCent includes submodels for plant productivity, decomposition of dead plant material and SOM, soil water and temperature dynamics, and N gas fluxes (Figure 5) (pg. 67, para. 1); while running, the simulation writes monthly output variables to a binary file and daily output variables to text files (pg. 12, para. 1); the output binary files are not human readable, and the List100 program is used to extract values from the binary file and write them to a text file with a “.lis” extension; the DayCent environment must be installed on the computer to be used (pg. 12, paras. 2-3).
Dependent claims 5-6 are directed to the ecosystem model of the system of claim 1. Claim 5 further recites the ecosystem model creates a one-dimension soil profile and divides the soil profile into continuous soil layers with user-defined depths. Claim 6 further recites the ecosystem model divides the soil layers into thinner layers to solve partial differential equations.
Dependent claim 17 is directed to the methods of claim 15. Claim 17 further recites dividing the soil layers into thinner layers to solve partial differential equations.
Regarding claims 5-6 and 17, Hartman et al. teaches users specify soil horizonation (i.e., layer thickness and number of layers to bedrock or water table) (pg. 23, para. 2; and Figure 2); in order to simulate daily soil water fluxes, soil temperature distribution with depth, and nitrogen trace gas fluxes, the DayCent model requires a finer soil layer structure than the CENTURY model; DayCent defines multiple layers within a coarser CENTURY layer to allow for a finer soil layer structure in the soil water submodel, soil temperature submodel, and trace gas submodels without impacting other code that still required the coarser CENTURY soil layer structure (pg. 23, para. 4); the DayCent soil layers are defined in the soils.in parameter file (Table 2); there can be multiple DayCent soil layers within a CENTURY soil layer, but layer boundaries must coincide as illustrated; the soil thicknesses shown above are for example; actual values are defined by the user (pg. 26, para. 1; Figure 2). Hartman et al. further teaches a divided soil profile to solve partial differential equations (pp. 71-75; Section 2.2. Soil Water Movement; pg. 78, paras. 2-4).
Dependent claims 7-12 are directed to the ecosystem model of the system of claim 1. Claim 7 further recites the ecosystem model uses submodels to run simulations. Claim 8 further recites the submodels comprise algorithms for an atmosphere submodel, a plant submodel, a soil surface submodel, and a soil submodel. Claim 9 further recites the atmosphere submodel comprises weather, evapotranspiration (ET) demand, and N deposition. Claim 10 further recites the plant submodel comprises aboveground biomass, belowground biomass, and exudate. Claim 11 further recites the soil surface submodel comprises litter and surface temperature. Claim 12 further recites the soil submodel comprises soil layer, soil water, soil temperature, soil minerals, nitrate, ammonium, and soil organic matter (SOM) pools.
Dependent claim 16 is directed to the methods of claim 15. Claim 16 further recites running the simulations with submodels wherein the submodels comprise algorithms for an atmosphere submodel, a plant submodel, a soil surface submodel, and a soil submodel; the atmosphere submodel comprises weather, evapotranspiration (ET) demand, and N deposition; the plant submodel comprises aboveground biomass, belowground biomass, and exudate; the soil surface submodel comprises litter and surface temperature; and the soil submodel comprises soil layer, soil water, soil temperature, soil minerals, nitrate, ammonium, and soil organic matter (SOM) pools.
Regarding claims 7-12, and 16, Hartman et al. teaches the DayCent model simulates the long-term dynamics of Carbon (C), Nitrogen (N), Phosphorus (P), and Sulfur (S) for different Plant-Soil Systems; DayCent includes submodels for plant productivity, decomposition of dead plant material and SOM, soil water and temperature dynamics, and N gas fluxes (pg. 67, para. 1). Hartman et al. further teaches the soil physical submodels (e.g. water flow submodel) includes weather, evapotranspiration (ET), and N deposition (pg. 68, para. 1; Figures 5 and 6). Hartman et al. further teaches the soil biogeochemical submodels (e.g. plant growth submodel) include aboveground biomass, belowground biomass, and exudate (pg. 113). Hartman et al. further teaches the soil physical submodels (e.g. soil temperature submodel) include litter and surface temperature (pp. 77-78). Hartman et al. further teaches the soil physical submodels (e.g. soil water submodel, soil temperature submodel) and soil biogeochemical submodels (e.g. soil organic matter submodel, nitrogen trace gas submodel) include soil layer, soil temperature (pp. 77-78), soil water (pg. 71), soil minerals, nitrate, ammonium (pp. 104-106), and soil organic matter (SOM) pools (pg. 78).
Dependent claim 13 is directed to the outputs of the system of claim 1. Claim 13 further recites the outputs are produced on a daily time step or a subdaily time step.
Regarding claim 13, Hartman et al. teaches Daily Century, or DayCent, is the daily time step version of the CENTURY model (pg. 11, para. 1; pg. 17; pg. 21).
Dependent claim 14 is directed to the system of claim 1. Claim 14 further recites a storage device to store the outputs in output files.
Regarding claim 14, Hartman et al. teaches while running, the simulation writes monthly output variables to a binary file and daily output variables to text files (pg. 12, para. 1); the output binary files are not human readable, and the List100 program is used to extract values from the binary file and write them to a text file with a “.lis” extension; the DayCent environment must be installed on the computer to be used (pg. 12, paras. 2-3).
Hartman et al. does not teach (explicitly) an ecosystem model specifically named microbial efficiency-matrix stabilization (MEMS) ecosystem model (claims 1 and 15).
Cotrufo et al. teaches (explicitly) a microbial efficiency-matrix stabilization (MEMS) ecosystem model; the MEMS framework represents the decomposition, transformation, and stabilization of OM as a continuum, with microbial substrate use efficiency and C and N allocation and soil matrix interactions being the two key processes that control the fate of litter inputs to soils (pg. 989, col. 2, para. 3).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify Hartman et al. by incorporating the microbial efficiency-matrix stabilization (MEMS) ecosystem model of Cotrufo et al. One of ordinary skill in the art would have been motivated to combine the model of Hartman et al. and Cotrufo et al. because Cotrufo et al. states that the ability of soil biogeochemical models (e.g., Century-DayCent, Roth C, etc.) to predict long-term changes in soil C and N cycling would be improved by adopting the MEMS concepts (pg. 994, col. 1, para. 1). This modification would have had a reasonable expectation of success because both Hartman et al. and Cotrufo et al. are directed to ecosystem models for simulating carbon and nitrogen dynamics in terrestrial ecosystems.
Conclusion
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/L.E.S./Examiner, Art Unit 1687
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687
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