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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 541 records · Page 30

UnigeneFinder: An Automated Pipeline for Gene Calling From Transcriptome Assemblies Without a Reference Genome

ABSTRACT For most species, transcriptome data are much more readily available than genome data. Without a reference genome, gene calling is cumbersome and inaccurate because of the high degree of redundancy in de novo transcriptome assemblies. To simplify and increase the accuracy of de novo transcriptome assembly in the absence of a reference genome, we developed UnigeneFinder. Combining several clustering methods, UnigeneFinder substantially reduces the redundancy typical of raw transcriptome assemblies. This pipeline offers an effective solution to the problem of inflated transcript numbers, achieving a closer representation of the actual underlying genome. UnigeneFinder performs comparably or better, compared with existing tools, on plant species with varying genome complexities. UnigeneFinder is the only available transcriptome redundancy solution that fully automates the generation of primary transcript, coding region, and protein sequences, analogous to those available for high‐quality reference genomes. These features, coupled with the pipeline’s cross‐platform implementation, focus on automation, and an accessible, user‐friendly interface, make UnigeneFinder a useful tool for many downstream sequence‐based analyses in nonmodel organisms lacking a reference genome, including differential gene expression analysis, accurate ortholog identification, functional enrichments, and evolutionary analyses. UnigeneFinder also runs efficiently both on high‐performance computing (HPC) systems and personal computers, further reducing barriers to use.

Xue, Bo [Plant Resilience Institute Michigan State↗

Cumulants of multiple conserved charges and global conservation laws

We analyze the behavior of cumulants of conserved charges in a subvolume of a thermal system with exact global conservation laws by extending a recently developed subensemble acceptance method (SAM) to multiple conserved charges. Explicit expressions for all diagonal and off-diagonal cumulants up to sixth order that relate them to the grand canonical susceptibilities are obtained. The derivation is presented for an arbitrary equation of state with an arbitrary number of different conserved charges. The global conservation effects cancel out in any ratio of two second order cumulants, in any ratio of two third order cumulants, as well as in a ratio of strongly intensive measures Σ and Δ involving any two conserved charges, making all these quantities particularly suitable for theory-to-experiment comparisons in heavy-ion collisions. We also show that the same cancellation occurs in correlators of a conserved charge, like the electric charge, with any non-conserved quantity such as net proton or net kaon number. The main results of the SAM are illustrated in the framework of the hadron resonance gas model. We also elucidate how net-proton and net-Λ fluctuations are affected by conservation of electric charge and strangeness in addition to baryon number.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Transcriptional control of Clostridium autoethanogenum using CRISPRi

Gas fermentation by Clostridium autoethanogenum is a commercial process for the sustainable biomanufacturing of fuels and valuable chemicals using abundant, low-cost C1 feedstocks (CO and CO 2 ) from sources such as inedible biomass, unsorted and nonrecyclable municipal solid waste, and industrial emissions. Efforts toward pathway engineering and elucidation of gene function in this microbe have been limited by a lack of genetic tools to control gene expression and arduous genome engineering methods. To increase the pace of progress, here we developed an inducible CRISPR interference (CRISPRi) system for C. autoethanogenum and applied that system toward transcriptional repression of genes with ostensibly crucial functions in metabolism.

59 BASIC BIOLOGICAL SCIENCES↗

Asymptotic preserving methods for fluid electron-fluid models in the large magnetic field limit with mathematically guaranteed properties (Final Report)

The current manuscript is a final report on the activities carried out under the Project LDRD-CIS #226834. In scientific terms, the work reported in this manuscript is a continuation of the efforts started with Project LDRD-express #223796 with final report of activities SAND2021-11481, see [83]. In this section we briefly explain what pre-existing developments motivated the current body of work and provide an overview of the activities developed with the funds provided. The overarching goal of the current project LDRD-CIS #226834 and the previous project LDRD-express #223796 is the development of numerical methods with mathematically guaranteed properties in order to solve the Euler-Maxwell system of plasma physics and generalizations thereof. Even though Project #223796 laid out general foundations of space and time discretization of Euler-Maxwell system, overall, it was focused on the development of numerical schemes for purely electrostatic fluid-plasma models. In particular, the project developed a family of schemes with mathematically guaranteed robustness in order to solve the Euler-Poisson model. This model is an asymptotic limit where only electrostatic response of the plasma is considered. Its primary feature is the presence of a non-local force, the electrostatic force, which introduces effects with infinite speed propagation into the problem. Even though instantaneous propagation of perturbations may be considered nonphysical, there are plenty of physical regimes of technical interest where such an approximation is perfectly valid.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Examination of Genetic Control Elements in the Phototrophic Firmicute Heliomicrobium modesticaldum

Heliomicrobium modesticaldum has been used as a model organism for the Heliobacteria, the only phototrophic family in the Firmicutes. It is a moderately thermophilic anoxygenic phototrophic bacterium that is capable of fermentative growth in the dark. The genetic manipulation of H. modesticaldum is still in its infancy. Methods to introduce genes through the use of exogenous plasmids and to delete genes from the chromosome through the use of the native CRISPR/Cas system have been developed in the last several years. To expand our genetic toolkit, it was necessary to control gene expression. In this study, we analyzed constitutive and inducible promoters developed for clostridia for their use in H. modesticaldum and further tested two reporters, adhB and lacZ, as indicators of promoter strength. Alcohol dehydrogenase (AdhB) was unsuitable as a reporter in this species due to high endogenous activity and/or low activity of the reporter, but a thermostable LacZ worked well as a reporter. A set of constitutive promoters previously reported to work in Clostridium thermocellum was found to be reliable for controlling the expression of the lacZ reporter gene in H. modesticaldum at a range of activities spanning an order of magnitude. An anhydrotetracycline-inducible promoter was created by inserting tetO operators into a strong constitutive promoter, but it was not fully repressible. The implementation of a xylose-inducible promoter resulted in complete repression of β-gal in the absence of xylose, and reliable expression tunable through the concentration of xylose added to the culture.

59 BASIC BIOLOGICAL SCIENCES↗

Hepatic transcriptome analyses of juvenile white bass ( Morone chrysops ) when fed diets where fish meal is partially or totally replaced by alternative protein sources

White bass (Morone chrysops) are a popular sportfish throughout the southern United States, and one parent of the commercially-successful hybrid striped bass (M. chrysops male x M. saxatilis female). Currently, white bass are cultured using diets formulated for other carnivorous fish, such as largemouth bass (Micropterus salmoides) or hybrid striped bass and contain a significant percentage of marine fish meal. Since there are no studies regarding the utilization of alternative proteins in this species, we evaluated the global gene expression of white bass fed diets in which fish meal was partially or totally replaced by various combinations of soybean meal, poultry by-product meal, canola meal, soy protein concentrate, wheat gluten, or a commercial protein blend (Pro Cision™). Six isonitrogenous (40% protein), isolipidic (11%), and isocaloric (17.1 kJ/g) diets were formulated to meet the known nutrient and energy requirements of largemouth bass and hybrid striped bass using nutrient availability data for most of the dietary ingredients. One of the test diets consisted exclusively of plant protein sources. Juvenile white bass (40.2 g initial weight) were stocked into a flow-through aquaculture system (three tanks/diet; 10 fish/tank) and fed the test diets twice daily to satiation for 60 days. RNA sequencing and bioinformatic analyses revealed significant differentially expressed genes between all test diets when compared to fish meal control. A total of 1,260 differentially expressed genes were identified, with major ontology relating to cell cycle and metabolic processes as well as immune gene functions. This data will be useful as a resource for future refinements to moronid diet formulation, as marine fish meal becomes limiting and plant ingredients are increasingly added as a reliable protein source

59 BASIC BIOLOGICAL SCIENCES↗

Dynamics of photosynthetic light harvesting systems interacting with N-photon Fock states

Here, we develop a method to simulate the excitonic dynamics of realistic photosynthetic light harvesting systems, including non-Markovian coupling to phonon degrees of freedom, under excitation by N-photon Fock state pulses. This method combines the input–output and the hierarchical equations of motion formalisms into a double hierarchy of density matrix equations. We show analytically that under weak field excitation relevant to natural photosynthesis conditions, an N-photon Fock state input and a corresponding coherent state input give rise to equal density matrices in the excited manifold. However, an N-photon Fock state input induces no off-diagonal coherence between the ground and excited subspaces, in contrast with the coherences created by a coherent state input. We derive expressions for the probability to absorb a single Fock state photon with or without the influence of phonons. For short pulses (or, equivalently, wide bandwidth pulses), we show that the absorption probability has a universal behavior that depends only upon a system-dependent effective energy spread parameter Δ and an exciton–light coupling constant Γ. This holds for a broad range of chromophore systems and for a variety of pulse shapes. We also analyze the absorption probability in the opposite long pulse (narrow bandwidth) regime. We then derive an expression for the long time emission rate in the presence of phonons and use it to study the difference between collective vs independent emission. Finally, we present a numerical simulation for the LHCII monomer (14-mer) system under single photon excitation that illustrates the use of the double hierarchy equations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Semantic Interoperability to Enable Smart, Grid-Interactive Efficient Buildings

Achieving a widespread transition to grid-interactive, efficient buildings (GEBs) depends critically on there being sufficient interoperability among connected building systems. While many critical elements already exist at the technical interoperability level (TCP/IP, BACnet, etc.), a lack of interoperability in the semantic level hinders streamlined integration of interdependent applications. Semantics refers to expressing information about “things” in a way that can be consistently understood by applications. Key components of formalized semantics include identifying what a “thing” is (its “type”), defining general information about that “thing” (its characteristics or properties), and defining the appropriate relationships of that “thing” to other “things” (its function or role in a larger system). Although this might seem initially trivial, the success of smart building applications is highly dependent on maintaining consistent self-descriptive notions of the “things”. Without semantic interoperability, it is technically difficult, labor-intensive, and cost-prohibitive to enable three key objectives of GEBs: optimizing performance, automatically identifying and diagnosing faults, and delivering grid services. Industry, academia, and standards bodies have invested effort in developing information models to facilitate semantic interoperability, however, they have not been widely adopted across the U.S. commercial building portfolio. This paper will present a pathway to drive semantic interoperability through a three-pronged approach to be led by the DOE Building Technologies Office in partnership with NIST and multiple national laboratories comprising: 1) industry engagement and coordination across existing efforts; 2) a semantic interoperability standard that empowers building owners to identify and require interoperable attributes when procuring equipment and applications; 3) tools to assist in implementation and a test framework to verify compliance of products with semantic interoperability specifications. This approach is designed to accelerate the timeline for adoption of semantic interoperability specifications. The intent is to reduce soft costs associated with implementing advanced controls, fault detection and diagnostics, and other smart building technologies and use cases as a necessary step in achieving an energy efficient smart grid future.

Bergmann, Harry↗

Semantic Interoperability to Enable Smart, Grid-Interactive Efficient Buildings

Achieving a widespread transition to grid-interactive, efficient buildings (GEBs) depends critically on there being sufficient interoperability among connected building systems. While many critical elements already exist at the technical interoperability level (TCP/IP, BACnet, etc.), a lack of interoperability in the semantic level hinders streamlined integration of interdependent applications. Semantics refers to expressing information about “things” in a way that can be consistently understood by applications. Key components of formalized semantics include identifying what a “thing” is (its “type”), defining general information about that “thing” (its characteristics or properties), and defining the appropriate relationships of that “thing” to other “things” (its function or role in a larger system). Although this might seem initially trivial, the success of smart building applications is highly dependent on maintaining consistent self-descriptive notions of the “things”. Without semantic interoperability, it is technically difficult, labor-intensive, and cost-prohibitive to enable three key objectives of GEBs: optimizing performance, automatically identifying and diagnosing faults, and delivering grid services. Industry, academia, and standards bodies have invested effort in developing information models to facilitate semantic interoperability, however, they have not been widely adopted across the U.S. commercial building portfolio. This paper will present a pathway to drive semantic interoperability through a three-pronged approach to be led by the DOE Building Technologies Office in partnership with NIST and multiple national laboratories comprising: 1) industry engagement and coordination across existing efforts; 2) a semantic interoperability standard that empowers building owners to identify and require interoperable attributes when procuring equipment and applications; 3) tools to assist in implementation and a test framework to verify compliance of products with semantic interoperability specifications. This approach is designed to accelerate the timeline for adoption of semantic interoperability specifications. The intent is to reduce soft costs associated with implementing advanced controls, fault detection and diagnostics, and other smart building technologies and use cases as a necessary step in achieving an energy efficient smart grid future.

30 DIRECT ENERGY CONVERSION↗

Semantic Interoperability to Enable Smart, Grid-Interactive Efficient Buildings

Achieving a widespread transition to grid-interactive, efficient buildings (GEBs) depends critically on there being sufficient interoperability among connected building systems. While many critical elements already exist at the technical interoperability level (TCP/IP, BACnet, etc.), a lack of interoperability in the semantic level hinders streamlined integration of interdependent applications. Semantics refers to expressing information about “things” in a way that can be consistently understood by applications. Key components of formalized semantics include identifying what a “thing” is (its “type”), defining general information about that “thing” (its characteristics or properties), and defining the appropriate relationships of that “thing” to other “things” (its function or role in a larger system). Although this might seem initially trivial, the success of smart building applications is highly dependent on maintaining consistent notions of the “things” being self-descriptive. Without semantic interoperability, it is technically difficult, labor-intensive, and cost-prohibitive to enable three key objectives of GEBs: optimizing performance, identifying faults, and delivering grid services. Industry, academia, and standards bodies have invested effort in developing information models to facilitate semantic interoperability, however, they have not been widely adopted across the U.S. commercial building portfolio. This paper will present a pathway to drive semantic interoperability through a three-pronged approach to be led by the DOE Building Technologies Office in partnership with NIST and multiple national laboratories comprising: 1) industry engagement and coordination across existing efforts; 2) a semantic interoperability standard that empowers building owners to identify and require interoperable attributes when procuring equipment and applications; 3) tools to assist in implementation and a test framework that can verify compliance of products with semantic interoperability specifications. This strategic approach is designed to accelerate the timeline for adoption of semantic interoperability standards. The intent is to reduce soft costs associated with implementing advanced controls, fault detection and diagnostics, and other smart building technologies as a necessary step in achieving an energy efficient smart grid future.

semantic interoperability, Semantic modeling, inte↗

Hydrodynamic Effects on Biofilm Development and Recombinant Protein Expression

Hydrodynamics play an important role in the rate of cell attachment and nutrient and oxygen transfer, which can affect biofilm development and the level of recombinant protein production. In the present study, the effects of different flow conditions on the development of Escherichia coli biofilms and the expression of a model recombinant protein (enhanced green fluorescent protein, eGFP) were examined. Planktonic and biofilm cells were grown at two different flow rates in a recirculating flow cell system for 7 days: 255 and 128 L h−1 (corresponding to a Reynolds number of 4600 and 2300, respectively). The fluorometric analysis showed that the specific eGFP production was higher in biofilms than in planktonic cells under both hydrodynamic conditions (3-fold higher for 255 L h−1 and 2-fold higher for 128 L h−1). In the biofilm cells, the percentage of eGFP-expressing cells was on average 52% higher at a flow rate of 255 L h−1. Furthermore, a higher plasmid copy number (PCN) was obtained for the highest flow rate for both planktonic (244 PCN/cell versus 118 PCN/cell) and biofilm cells (43 PCN/cell versus 29 PCN/cell). The results suggested that higher flow velocities promoted eGFP expression in E. coli biofilms.

Soares, Alexandra↗

A tissue‐resolved, network‐based transcriptomic framework for abiotic stress responses in sorghum

Developing climate‐resilient crops requires a detailed understanding of stress‐induced gene expression dynamics, as maladaptive responses can compromise their productivity and survival. Sorghum, a globally important cereal with exceptional tolerance to multiple abiotic stresses, provides a powerful system for investigating these dynamics. However, how stress type, tissue specificity, and temporal progression jointly shape transcriptomic responses in crops remains poorly understood. Here, we present a comparative, time‐resolved transcriptomic atlas of sorghum responses to drought, heat, and salinity stress across shoot and root tissues. Integrative analyses revealed that tissue specificity is the dominant determinant of abiotic stress‐induced gene reprogramming across all three stresses. Building on these global comparisons, we focused on heat stress, as it elicited the most coherent and pronounced transcriptional and regulatory responses, enabling deeper network‐level interrogation. Co‐expression network analysis identified tissue‐specific modules enriched for phytohormone‐responsive genes, while gene regulatory network (GRN) mapping and cistrome analyses uncovered transcription factors (TFs) controlling key hub genes within these modules. Together, this study provides a foundational transcriptomic and network‐based resource for dissecting the regulatory architecture of abiotic stress responses in sorghum and offers prioritized candidates for future functional validation and engineering of climate‐resilient crops.

abiotic stress↗

SolarAPP+ Performance Review (2022 Data)

The Solar Automated Permit Processing Plus (SolarAPP+) platform is an online portal to facilitate and expedite rooftop solar photovoltaic (PV) permitting processes. SolarAPP+ allows PV contractors to upload system specifications, have those specifications automatically reviewed for code compliance, and receive instant approval for code-compliant systems. SolarAPP+ also provides inspection checklists to verify installation practices and adherence to approved designs. SolarAPP+ is available to authorities having jurisdiction (AHJs) at no cost. This report is part of an ongoing series of reviews of SolarAPP+ performance. Consistent with previous performance reviews, we summarize SolarAPP+ adoption trends to date and compare various metrics for PV systems permitted through SolarAPP+ versus systems permitted through conventional AHJ permitting processes. As of the end of 2022, the National Renewable Energy Laboratory (NREL) had contacted over 1,500 AHJs with significant solar permitting volume regarding SolarAPP+. Of those, 607 AHJs had at least expressed interest in the platform. 16 AHJs had begun piloting the platform and 15 of these had publicly launched the platform by the end of 2022. In 2022, 206 installers submitted 11,092 permits through the SolarAPP+ platform, including 708 permits for solar+storage systems. SolarAPP+ permits accounted for around 37% of all permits issued in participating AHJs. We compare permitting timelines through SolarAPP+ to traditional AHJ permitting processes to assess the platform's performance. Consistent with previous SolarAPP+ performance reviews, we find that permitting timelines are significantly shorter for SolarAPP+ projects. Based on median timelines, a typical SolarAPP+ project is permitted and inspected 8 business days sooner than traditional projects. We estimate that automatic SolarAPP+ permitting saved between 3,500 and 13,900 hours of AHJ staff time in 2022. Finally, we find evidence that SolarAPP+ may improve inspection outcomes, with SolarAPP+ projects failing inspections about 28% less frequently than traditional projects.

14 SOLAR ENERGY↗

Platform for Remote Deployment and Training for Enhanced Building Operation Practices (Building Re-Tuning and On-going Commissioning)

While a building’s energy usage is driven largely by its design and use, building operator behavior has a strong influence on its energy consumption. This project developed and piloted a specific, data-driven coaching methodology to help operators understand how they can adjust operations and/or affect no/low-cost repairs or upgrades to their specific building HVAC systems to reduce energy consumption. Named BuildingCoach, the operational optimization method used is based on the Building Re-tuning approach developed by the Pacific Northwest National Laboratory. A building operations analytics market has matured over the past decade, though its potential to affect energy-saving changes has not been fully realized. Training operators to understand the methods for operational optimization with the explicit approach of using building-system performance data is hypothesized to create a more effective, longer lasting result in building energy efficiency, and this strategy is the fundamental premise of this project. With the support of an Industry Advisory Board, the project succeeded in developing materials and recruiting for and delivering three pilot cohorts. Deliverables included twenty-two self-paced training modules (accessed via a Learning Management System) and a web-based platform that includes access to real-time building system data and a repository for building system documentation. The project set out to have 100 participants from 50 buildings in three pilot cohorts. In the end, there were 28 participants from 17 buildings, i.e., a significant shortfall. The first two pilot cohorts had only two buildings in each, and this was partially due to difficulties in deploying the Building Operator Coaching Solution (“the BOCS”), which is technology that extracts the data from the controls network and presents it as prescribed for coaching. In the third cohort, the project team deployed the BOCS successfully to 13 buildings, the methodology was piloted as intended, and numerous opportunities for optimization were identified. The BuildingCoach business plan charts a path to an economically sustainable effort. However, even with a licensing model captured in the final version of the business plan, the scalability is still limited to keeping less than 1,000 buildings affected by 2033. Even so, there are unexplored paths to greater scalability that are being considered. CUNY BPL is working to perpetuate and grow the use of BuildingCoach. As of this writing, about twenty buildings have either been connected or will be connected with operators coached / to be coached in the NYC municipal portfolio, twelve buildings across four campuses in NY State will use BuildingCoach, a NY upstate county wishes for six or seven buildings to participate with the support of funding from NYSERDA, and others have also expressed interest. In the decades to come, there will be an increasing percentage of large and mid-sized buildings that incorporate automated system optimization (ASO), and the building operators’ role will shift to spend more time on maintenance and monitoring. Meanwhile, programs such as BuildingCoach will play a critical role in optimizing operations. And, regardless of the emergence of ASO, operators will still need to understand how their systems operate so that they can monitor them properly. Within that context, BuildingCoach is an important step towards operators’ understanding of efficient building system operations.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Dynamical vertex approximation for many-electron systems with spontaneously broken SU(2) symmetry

We generalize the formalism of the dynamical vertex approximation (DΓA)—a diagrammatic extension of the dynamical mean-field theory (DMFT)—to treat magnetically ordered phases. To this aim, we start by concisely illustrating the many-electron formalism for performing ladder resummations of Feynman diagrams in systems with broken SU(2) symmetry associated to ferromagnetic (FM) or antiferromagnetic (AF) order. We then analyze the algorithmic simplifications introduced by taking the local approximation of the two-particle irreducible vertex functions in the Bethe-Salpeter equations, which defines the ladder implementation of DΓA for magnetic systems. The relation of this assumption with the DMFT limit of large coordination-number/high dimensions is explicitly discussed. As a last step, we derive the expression for the ladder DΓA self-energy in the FM- and AF-ordered phases of the Hubbard model. The physics emerging in the AF-ordered case is explicitly illustrated by means of approximated calculations based on a static mean-field input for DΓA equations. The results obtained capture fundamental aspects of both metallic and insulating ground states of two-dimensional antiferromagnets, providing a reliable compass for future, more extensive applications of our approach. Furthermore, possible routes to further develop diagrammatic-based treatments of magnetic phases in correlated electron systems are briefly outlined in the Conclusions.

2-dimensional systems↗

Intrinsic operators for the translationally-invariant many-body problem

Abstract The need to enforce fermionic antisymmetry in the nuclear many-body problem commonly requires use of single-particle coordinates, defined relative to some fixed origin. To obtain physical operators which nonetheless act on the nuclear many-body system in a Galilean-invariant fashion, thereby avoiding spurious center-of-mass contributions to observables, it is necessary to express these operators with respect to the translational intrinsic frame. Several commonly-encountered operators in nuclear many-body calculations, including the magnetic dipole and electric quadrupole operators (in the impulse approximation) and generators of U(3) and Sp ( 3 , R ) symmetry groups, are bilinear in the coordinates and momenta of the nucleons and, when expressed in intrinsic form, become two-body operators. To work with such operators in a second-quantized many-body calculation, it is necessary to relate three distinct forms: the defining intrinsic-frame expression, an explicitly two-body expression in terms of two-particle relative coordinates, and a decomposition into one-body and separable two-body parts. We establish the relations between these forms, for general (non-scalar and non-isoscalar) operators bilinear in coordinates and momenta.

Physics↗

Hydrothermal Liquid Recovery of Rare Earth Elements and Critical Materials

This project demonstrated the technical viability of using tunable hydrothermal liquid (HTL) solutions to recover valuable minerals from a range of source materials. The effort focused upon rare earth elements (REE) and other minerals critical to the industrial security of the United States. This effort demonstrated, for the first time, that s, supercritical water (SCW) in particular, can: Extract critical and valuable minerals from a range of matrices ranging from rock ore to biomass; The process can be used to recover a wide range of minerals; This novel extraction chemistry can be cheap, simple, and nontoxic/”green”: The chemical extraction uses water, the cheapest industrial acid (sulfuric), and simple salts (i.e. sodium sulfate). However, other acids, salts, and additives could be used as appropriate. This Laboratory Directed Research and Development (LDRD) project identified that the process is complex with many interacting factors, but the benefits are significant if the complexities can be resolved. Challenges remain in the development of this technology and are described in this report. However, the results are positive, and commercial partners have already expressed interest. In summary, a novel, green, inexpensive mineral extraction process has been developed and demonstrated in a small batch reactor system. The effort provided information for an invention disclosure, proposal to DOE, and will support future business development efforts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Probabilistic and maximum entropy modeling of chemical reaction systems: Characteristics and comparisons to mass action kinetic models

We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with standard chemical potentials, we derive and compare the free energy dissipation and the entropy production rates. We express the relation between entropy production and the chemical master equation for modeling metabolism, which unifies chemical kinetics and chemical thermodynamics. Because prediction uncertainty with respect to parameter variability is frequently a concern with mass action models utilizing rate constants, we compare and contrast the maximum entropy model, which has its own set of rate parameters, to a population of standard mass action models in which the rate constants are randomly chosen. We show that a maximum entropy model is characterized by a high probability of free energy dissipation rate and likewise entropy production rate, relative to other models. We then characterize the variability of the maximum entropy model predictions with respect to uncertainties in parameters (standard free energies of formation) and with respect to ionic strengths typically found in a cell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗