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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 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Solvation-guided inhibition of manganese dissolution of lithium- and manganese- rich cathode via cyclic carbonate molecular engineering

Lithium and manganese-rich (LMR) layered oxides represent a leading class of high-energy cathode materials, but their practical realization is fundamentally limited by severe manganese (Mn) dissolution, a process that triggers structural degradation and rapid capacity fade. While mitigation efforts have predominantly focused on interfacial engineering, the intrinsic contribution of bulk electrolyte solvation to this degradation pathway remains largely unexplored, primarily due to the difficulty of deconvolving its effects from concurrent cathode-electrolyte interphase (CEI) formation. Here, we report an experimental design to isolate the role of solvation. We systematically varied the electrolyte solvent solvation power by substituting the strongly coordinating ethylene carbonate (EC) with its weaker coordinating fluorinated derivatives, fluoroethylene carbonate (FEC) and trans-4,5-Difluoro-1,3-dioxolan-2-one (DFEC), while maintaining a consistent interfacial chemistry. Remarkably, the electrolyte formulated with the weakest solvent, DFEC, exhibits superior cycling stability, suppressing Mn dissolution by up to 63% relative to the conventional EC-based system. Post-mortem analysis unequivocally attributes this performance enhancement to the preservation of the LMR cathode's structural integrity, a direct consequence of mitigated Mn dissolution. This work provides conclusive evidence that modulating bulk electrolyte solvation is a potent and direct strategy for stabilizing LMR cathodes, establishing a vital design principle for next-generation battery systems.

25 ENERGY STORAGE↗
DOE OSTI2024

Transforming Cyber Education thru Open to All Accessible Pathways

Boise State University’s (BSU) Cyber Operations and Resilience CORe program was intentionally designed so that any student, especially non-traditional and non-technical students, with an interest in cybersecurity could have an education and training pathway to enter the cyber workforce. The CORe curriculum focuses on teaching students how to design, apply, and improve cybersecurity through the interaction of people, processes, and technology. CORe is a stackable curriculum with elective credit hours and options for various academic and industry certificates and certifications that enable students to customize their unique career pathway. The CORe program guides students to think about the system being managed, the risks presented, and the dynamic intersection of system elements when considering how to incorporate resilience frameworks in achieving a resilient system. By developing systems thinking, the students gain an understanding of the interdependencies interacting with the operational system. Further, the CORe program encourages students to integrate cybersecurity knowledge with models and frameworks found in other academic disciplines through a unifying systems approach. CORe is designed around the realities of today’s broad cyber landscape: that breaches will occur in any system over time and proactive design of resilience into systems to detect, respond, and recover in a timely and orderly manner is critical. Students are taught to think holistically about cybersecurity focusing on all system elements. CORe is not a traditional cybersecurity degree. CORe is distinguished by the non-traditional engineering, computer science approach to cybersecurity education with the singular focus on infusing resilience operations and transdisciplinary systems thinking principles throughout the curriculum.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2018

Tunable stacking fault energies by tailoring local chemical order in CrCoNi medium-entropy alloys

High-entropy alloys (HEAs) are an intriguing new class of metallic materials due to their unique mechanical behavior. Achieving a detailed understanding of structure–property relationships in these materials has been challenged by the compositional disorder that underlies their unique mechanical behavior. Accordingly, in this work, we employ first-principles calculations to investigate the nature of local chemical order and establish its relationship to the intrinsic and extrinsic stacking fault energy (SFE) in CrCoNi medium-entropy solid-solution alloys, whose combination of strength, ductility, and toughness properties approaches the best on record. We find that the average intrinsic and extrinsic SFE are both highly tunable, with values ranging from –43 to 30 mJ•m –2 and from –28 to 66 mJ•m –2 , respectively, as the degree of local chemical order increases. The state of local ordering also strongly correlates with the energy difference between the face-centered cubic ( fcc ) and hexagonal close-packed ( hcp ) phases, which affects the occurrence of transformation-induced plasticity. Here, this theoretical study demonstrates that chemical short-range order is thermodynamically favored in HEAs and can be tuned to affect the mechanical behavior of these alloys. It thus addresses the pressing need to establish robust processing–structure–property relationships to guide the science-based design of new HEAs with targeted mechanical behavior.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Gluon distributions and their applications to Ioffe-time distributions

We investigate unpolarized and polarized gluon distributions and their applications to the Ioffe-time distributions, which are related to lattice QCD calculations of parton distribution functions. Guided by the counting rules based on the perturbative QCD at large momentum fraction x and the color coherence of gluon couplings at small x, we parametrize gluon distributions in the helicity basis. By fitting the unpolarized gluon distribution, the inferred polarized gluon distribution from our parametrization agrees with the one from global analysis. A simultaneous fit to both unpolarized and polarized gluon distributions is also performed to explore the model uncertainty. The agreement with the global analysis supports the (1 - x) power suppression of the helicity-antialigned distribution relative to the helicity-aligned distribution. The corresponding Ioffe-time distributions and their asymptotic expansions are calculated from the gluon distributions. Our results of the Ioffe-time distributions can provide guidance to the extrapolation of lattice QCD data to the region lacking precise gluonic matrix elements. Therefore, they can help regulate the ill-posed inverse problem associated with extracting the gluon distributions from discrete data from first-principle calculations, which are available in a limited range of the nucleon momentum and the spatial separation between the gluonic currents. Given various limitations in obtaining lattice QCD data at large Ioffe time, phenomenological approaches can provide important complementary information to extract the gluon distributions in the entire momentum fraction region, especially at small x. The possibility of investigating higher-twist effects and other systematic uncertainties in the contemporary first-principle calculations of parton distributions from phenomenologically well-determined Ioffe-time distributions in the large Ioffe-time region is also discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS2009

Spaceflight Systems Training: A Comparison and Contrasting of Techniques for Training Ground Operators and Onboard Crewmembers

When developing techniques and products for instruction on manned spaceflight systems, training organizations are often faced with two very different customers: ground operators and onboard crewmembers. Frequently, instructional development focuses on one of these customers with the assumption that the other s needs will be met by default. Experience teaches us that differing approaches are required when developing training tailored to the specific needs of each customer. As a rule, ground operators require focused instruction on specific areas of expertise. Their knowledge should be of the details of the hardware, software, and operational techniques associated with that system. They often benefit from historical knowledge of how their system has operated over its lifetime. Since several different ground operators may be interfacing with the same system, each individual operator must understand the agreed-to principles by which that system will be run. In contrast, onboard crewmembers require a more broad, hands-on awareness of their operational environment. Their training should be developed with an understanding of the physical environment in which they live and work and the day-to-day tasks they are most likely to perform. Rarely do they require a deep understanding of the details of a system; it is often sufficient to teach them just enough to maintain situational awareness and perform basic tasks associated with maintenance and operation of onboard systems. Crewmembers may also develop unique onboard operational techniques that differ from preceding crews. They should be taught what flexibility they have in systems operations and how their specific habits can be communicated to ground support personnel. This paper will explore the techniques that can be employed when developing training for these unique customers. We will explore the history of International Space Station training development and how past efforts can guide us in creating training for users of future manned spaceflight efforts.

Balmain, Clinton↗
DOE OSTI2018

Deciphering microbial interactions in synthetic human gut microbiome communities

The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model-guided framework to predict higher-dimensional consortia from time-resolved measurements of lower-order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi-species community dynamics, as opposed to higher-order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history-dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human-associated intestinal species and illuminated design principles of microbial communities.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Accelerated screening of functional atomic impurities in halide perovskites using high-throughput computations and machine learning

The pressing need for novel materials that can serve rising demands in solar cell and optoelectronic technologies makes the nexus of halide perovskites, high-throughput computations, and machine learning, very promising. Ever increasing amounts of data on the structure, fundamental properties, and device performance of halide perovskites provide opportunities for learning chemical rules and design principles that make these materials attractive, and applying them across wide chemical spaces. In this work, we show that impurity properties of halide perovskites computed using density functional theory (DFT) can be combined with machine learning (ML) to deliver predictive models and quick identification of optoelectronically active impurity atoms. Our computation lead to the largest reported dataset of the formation energies and charge transition levels of Pb-site impurities in methylammonium lead halide (MAPbX 3 ) perovskites. Descriptors are defined to uniquely represent any impurity atom in any MAPbX 3 compound and mapped to the computed impurity properties using regression techniques such as Gaussian process regression, neural networks, and random forests. We use the best optimized predictive models to make predictions for hundreds of impurities across 9 MAPbX 3 compounds and create lists of dominating impurities, that is, impurities that can shift the equilibrium Fermi level in the perovskite as determined by native point defects. Finally, this accelerated screening powered by computations and machine learning can guide the identification of problematic impurities that may cause undesired recombination of charge carriers, as well as impurities that can be deliberately introduced to tune the perovskite conductivity and resulting photovoltaic absorption.

36 MATERIALS SCIENCE↗
NASA NTRS2012

Optimal Routing and Control of Multiple Agents Moving in a Transportation Network and Subject to an Arrival Schedule and Separation Constraints

We address the problem of navigating a set of moving agents, e.g. automated guided vehicles, through a transportation network so as to bring each agent to its destination at a specified time. Each pair of agents is required to be separated by a minimal distance, generally agent-dependent, at all times. The speed range, initial position, required destination, and required time of arrival at destination for each agent are assumed provided. The movement of each agent is governed by a controlled differential equation (state equation). The problem consists in choosing for each agent a path and a control strategy so as to meet the constraints and reach the destination at the required time. This problem arises in various fields of transportation, including Air Traffic Management and train coordination, and in robotics. The main contribution of the paper is a model that allows to recast this problem as a decoupled collection of problems in classical optimal control and is easily generalized to the case when inertia cannot be neglected. Some qualitative insight into solution behavior is obtained using the Pontryagin Maximum Principle. Sample numerical solutions are computed using a numerical optimal control solver.

Sadovsky, A. V.↗
DOE OSTI2024

A Framework Using Applied Process Analysis Methods to Assess Water Security in the Vu Gia–Thu Bon River Basin, Vietnam

The Vu Gia–Thu Bon (VG–TB) river basin is facing numerous challenges to water security, particularly in light of the increasing impacts of climate change. These challenges, including salinity intrusion, shifts in rainfall patterns, and reduced water supply in downstream areas, are of great concern. This study comprehensively assessed the current state of water security in the basin using robust statistical analysis methods such as the Process Analysis Method (PAM), SMART principle, and Analytic Hierarchy Process (AHP). This resulted in the development of a comprehensive assessment framework for water security in the VG–TB river basin. This framework identified five key dimensions, with basin development activities (0.32), the ability to meet water needs (0.24), and natural disaster resilience (0.19) being the most crucial and water resource potential being the least crucial (0.11) according to the AHP methodology. The latter also highlighted 15 indicators, four of which are particularly influential, including waste resources (0.54), flood (0.53), water storage capacity (0.45), and basin governance (0.42). Furthermore, 28 variables with high weight factors were identified. This framework aligns with the UN-Water water security definition and addresses the global water sustainability criteria outlined in Sustainable Development Goal 6 (SDG6). It enables the computation of a comprehensive Water Security Index (WSI) for specific regions, providing a strong foundation for decision-making and policy formulation. It aims to enhance water security in the context of climate change and support sustainable basin development, thereby guiding future research and policy decisions in water resource management.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Regional suitability of heating tower heat pumps based on technical and economic performance maps

The heating tower heat pump (HTHP) technology is evolving rapidly due to its high performance in summer and frost-free characteristic in winter. However, lacking comprehensive comparisons between the HTHP and conventional methods, such as air-source heat pump (ASHP), and chiller and boiler, greatly limits its applications. To address this problem, this paper carries out technological and economic performance analyses of the three systems in 353 locations over China by the processes of building load calculation, system sizing, annual simulation, performance comparison, and demonstration. Energy saving principle and potential of the HTHP are presented and explained. Based on that, economic performance comparison is conducted by considering the energy conversion efficiency and prices. The results show that the HTHP has advantage over the ASHP in most locations in China. The improvement in annual coefficient of performance (COP) is about 10% to 20%. For the locations in southwest China like Chongqing, the improvement is also less than 10% due to the large regeneration penalization in winter and small difference between dry-bulb and wet-bulb temperature in summer. The annual COP of the HTHP is 10% to 23% higher than that of the chiller and boiler in hot summer and cold winter zone, and cold zone. However, the HTHP shows no advantage over the chiller and boiler in severe cold zone because of the low efficiency of heat pump in winter, neither in hot summer and warm winter zone due to the small heating load. Based on the results, technical and economic performance maps are developed to guide the application of the HTHP in different climate regions.

heating tower heat pump, air-source heat pump, chi↗
DOE OSTI2022

Exploring the Origin of Anionic Redox Activity in Super Li-Rich Iron Oxide-Based High-Energy-Density Cathode Materials

Super alkali-rich materials (alkali:transition metal ratio of ≥2:1), such as Li 5 FeO 4 , exhibit the potential to realize anionic redox upon deep delithiation. Li 5 FeO 4 was shown to undergo reversible cycling between Li 4 FeO 3.5 and Li 3 FeO 3.5 with combined cation/anion redox, a remarkable capacity of 189 mAh/g, and no O 2 release. However, the impact of phase transformations on the reaction thermodynamics and the correlation between the structural changes and reaction reversibility remain unclear. In this study, we use first-principles calculations to examine the delithiation and (re)lithiation reactions of Li 5 FeO 4 . We show that the experimentally observed charge and discharge processes go through non-equilibrium pathways. Upon delithiation, the compound undergoes a phase transformation from Li 5 FeO 4 , with tetrahedrally coordinated (T d ) Fe ions, to a delithiated disordered rocksalt structure, with octahedral (O h ) Fe ions. Fe-ion migration has an asymmetric kinetic barrier that makes T d → O h migration facile, whereas the reverse process has a much larger barrier, explaining the difficulties in reaction reversibility. We further elucidate the transition metal and O redox sequences during the charge cycle and identify the complex electrochemistry associated with the dual participation of cationic redox (Fe 3+ /Fe 4+ ) and anionic redox (O 2– /O – /O o ). Armed with this knowledge, we conduct high-throughput screening of known alkali-rich transition metal oxides by evaluating their potential to enable reversible anionic redox, with multiple candidates proposed for further experimental trials. Furthermore, our work provides a useful guide for the further development of super alkali-rich anionic-redox-active electrodes for high-energy-density batteries.

25 ENERGY STORAGE↗
DOE OSTI2018

Steam Reforming Process for Treating Radioactive Waste - 18172

In 2005 the THOR steam reforming fluidized-bed reactor (FBR) technology was selected by the DOE for treatment of sodium-bearing waste (SBW) at the INL. During commissioning a number of equipment reliability and process control challenges were encountered preventing the start of radiological operations. To address these challenges the team adopted a phased systematic mechanistic approach, underpinned by scientific principles and supported by some of the world's leading experts in FBR technology. The Phase 1 effort broadly addressed the entire plant and associated modifications. Phase 2 focused on the most critical issues associated with the denitration and mineralization reformer (DMR) vessel: specifically, mitigation of wall scale (mineral deposits) that formed on the inside of the DMR; mitigation of friable agglomerates (sand-castles) that caused operational instabilities; repair of damaged lower fluidizing gas distributor (ring header), and resolution of auger-grinder (A/G) reliability issues. Basic chemistry and fluidization, as well as operational issues were evaluated using engineering analysis, modeling, bench-scale, pilot scale, and full-scale runs to validate the resolutions. The bench scale testing revealed the need to ensure at least a 5 vol% concentration of CO{sub 2} in the fluidizing gas to minimize undesirable reaction intermediates that could form in less fluidized regions of the bed. Engineering analysis and modeling results pointed to the need to redesign the fluidizing gas distributor to overcome fluidization problems. Chemistry evaluations guided efforts to minimize the deposition of wall-scale. The process modifications were confirmed on the pilot level and are being validated in the full-scale unit (Phase 3). (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Fluxionality of Subnano Clusters Reshapes the Activity Volcano of Electrocatalysis

The Sabatier activity volcano provides intuitive guide for catalyst design, but also imposes fundamental limitations on the composition and maximal activity of catalysts. Here we show that the ORR activity volcano is shifted and reshaped by the potential-dependent fluxionality of subnano cluster catalysts. Fluxionality causes the typically under-binding Ag/Au to gain optimal activity in the cluster form, and surpass Pt/Pd. Furthermore, isomerization of clusters as a function of the potential breaks linear scaling relationships, enabling surpassing the volcano “apex” relative to the bulk. The effect is likely general for fluxional cluster catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1999

Ultrasonic Nondestructive Characterization of Adhesive Bonds

Adhesives and adhesive joints are widely used in various industrial applications to reduce weight and costs, and to increase reliability. For example, advances in aerospace technology have been made possible, in part, through the use of lightweight materials and weight-saving structural designs. Joints, in particular, have been and continue to be areas in which weight can be trimmed from an airframe through the use of novel attachment techniques. In order to save weight over traditional riveted designs, to avoid the introduction of stress concentrations associated with rivet holes, and to take full advantage of advanced composite materials, engineers and designers have been specifying an ever-increasing number of adhesively bonded joints for use on airframes. Nondestructive characterization for quality control and remaining life prediction has been a key enabling technology for the effective use of adhesive joints. Conventional linear ultrasonic techniques generally can only detect flaws (delamination, cracks, voids, etc) in the joint assembly. However, more important to structural reliability is the bond strength. Although strength, in principle, cannot be measured nondestructively, a slight change in material nonlinearity may indicate the onset of failure. Furthermore, microstructural variations due to aging or under-curing may also cause changes in the third order elastic constants, which are related to the ultrasonic nonlinear parameter of the polymer adhesive. It is therefore reasonable to anticipate a correlation between changes in the ultrasonic nonlinear acoustic parameter and the remaining bond strength. It has been observed that higher harmonics of the fundamental frequency are generated when an ultrasonic wave passes through a nonlinear material. It seems that such nonlinearity can be effectively used to characterize bond strength. Several theories have been developed to model this nonlinear effect. Based on a microscopic description of the nonlinear interface binding force, a quantitative method was presented. Recently, a comparison between the experimental and simulated results based on a similar theoretical model was presented. A through-transmission setup for water immersion mode-converted shear waves was used to analyze the ultrasonic nonlinear parameter of an adhesive bond. In addition, ultrasonic guided waves have been used to analyze adhesive or diffusion bonded joints. In this paper, the ultrasonic nonlinear parameter is used to characterize the curing state of a polymer/aluminum adhesive joint. Ultrasonic through-transmission tests were conducted on samples cured under various conditions. The magnitude of the second order harmonic was measured and the corresponding ultrasonic nonlinear parameter was evaluated. A fairly good correlation between the curing condition and the nonlinear parameter is observed. The results show that the nonlinear parameter might be used as a good indicator of the cure state for adhesive joints.

Qu, Jianmin↗
DOE OSTI2025

Depth-Resolved Lithiated Gradients in Pristine and Laser-Ablated Anodes During Fast Charging

Laser ablating 3D electrode microstructures is a technique to improve Li-ion battery fast-charge performance. This technique has been theoretically proposed and electrochemically validated previously in the literature. The fundamental principle underlying laser ablation is that the ablated features reduce Li-ion transport pathways, improving access to the electrode active material near the current collector. This, in turn, promotes more homogeneous electrode utilization. The present study seeks to directly affirm the physics attributed to laser ablation using operando high-speed synchrotron X-ray diffraction. In this study, depth-resolved graphite lithiation gradients are measured operando during high-rate (15 min) charging. The depth-resolved lithiation dynamics of both ablated and non-ablated anodes are compared. The results highlight that the laser-ablated graphite electrode has notably more homogeneous utilization as compared to the non-ablated electrode. Additionally, the ablated electrode has a significant delay in reaching the maximum graphite lithiation at the separator, indicating less propensity for lithium plating. During low rate delithiation/discharge (2 hr), the two cells' lithiation gradients converge. Notably, a calibrated physics-based electrochemical model accurately reflects experimental findings, suggesting the potential to use pseudo-4D models not only to optimize laser ablation parameters in fast-charge capable electrodes but also to guide fast charging protocols that avoid lithium plating.

25 ENERGY STORAGE↗
DOE OSTI2025

Self‐Trapped Hole Migration and Defect‐Mediated Thermal Quenching of Luminescence in α‐ and β‐Ga 2 O 3

Gallium oxide (Ga 2 O 3 ) is a promising ultrawide bandgap semiconductor for next-generation power electronics and optoelectronic devices. Here, temperature-dependent and polarization-resolved photoluminescence excitation spectroscopy data, complemented by hybrid-functional first-principles calculations, are presented, and a microscopic model is derived that explains the interplay of hole migration, defect trapping, and carrier recombination at defects underlying thermal quenching phenomena in α- and β-Ga 2 O 3 . In α-Ga 2 O 3 , the UV emission is attributed to self-trapped holes, while the blue luminescence arises from defect-related processes, including gallium split vacancies and their defect complexes. Calculations reveal an energy barrier of 88 meV for self-trapped hole migration in α-Ga 2 O 3 , consistent with activation energies from temperature-dependent photoluminescence. This enables efficient trapping by defects, enhancing blue luminescence and quenching UV emission. In β-Ga 2 O 3 , a higher migration barrier of 0.36 eV reduces the defect trapping, allowing the UV self-trapped hole emission to remain intense, with blue luminescence emerging only at elevated temperatures. These results establish a direct link between self-trapped hole migration, defect trapping, and thermal quenching of emission in both phases. The insights advance the understanding of carrier dynamics in ultrawide bandgap oxides and may guide defect engineering for high-performance functional devices.

Hajizadeh, Nima [Leibniz-Institut im Forschungsver↗
DOE OSTI2017

Mild oxidation of methane to methanol or acetic acid on supported isolated rhodium catalysts

An efficient and direct method of catalytic conversion of methane to liquid methanol and other oxygenates would be of considerable practical value. However, it remains an unsolved problem in catalysis, as typically it involves expensive or corrosive oxidants or reaction media(5-8) that are not amenable to commercialization. Although methane can be directly converted to methanol using molecular oxygen under mild conditions in the gas phase, the process is either stoichiometric (and therefore requires a water extraction step) or is too slow and low-yielding to be practical. Methane could, in principle, also be transformed through direct oxidative carbonylation to acetic acid, which is commercially obtained through methane steam reforming, methanol synthesis, and subsequent methanol carbonylation on homogeneous catalysts. However, an effective catalyst for the direct carbonylation of methane to acetic acid, which might enable the economical small-scale utilization of natural gas that is currently flared or stranded, has not yet been reported. Here we show that mononuclear rhodium species, anchored on a zeolite or titanium dioxide support suspended in aqueous solution, catalyse the direct conversion of methane to methanol and acetic acid, using oxygen and carbon monoxide under mild conditions. Here, we find that the two products form through independent pathways, which allows us to tune the conversion: three-hour-long batch-reactor tests conducted at 150 degrees Celsius, using either the zeolitesupported or the titanium-dioxide-supported catalyst, yield around 22,000 micromoles of acetic acid per gram of catalyst, or around 230 micromoles of methanol per gram of catalyst, respectively, with selectivities of 60-100 per cent. Finally, we anticipate that these unusually high activities, despite still being too low for commercial application, may guide the development of optimized catalysts and practical processes for the direct conversion of methane to methanol, acetic acid and other useful chemicals.

09 BIOMASS FUELS↗
DOE OSTI2018

Genome-Scale 13 C Fluxomics Modeling for Metabolic Engineering of Saccharomyces cerevisiae .

Synthetic biology is a rapidly developing field that pursues the application of engineering principles and development approaches to biological engineering. Synthetic biology is poised to change the way biology is practiced, and has important practical applications: for example, building genetically engineered organisms to produce biofuels, medicines, and other chemicals. Traditionally, synthetic biology has focused on manipulating a few genes (e.g., in a single pathway or genetic circuit), but its combination with systems biology holds the promise of creating new cellular architectures and constructing complex biological systems from the ground up. Enabling this merge of synthetic and systems biology will require greater predictive capability for modeling the behavior of cellular systems, and more comprehensive data sets for building and calibrating these models. The so-called "-omics" data sets can now be generated via high throughput techniques in the form of genomic, proteomic, transcriptomic, and metabolomic information on the engineered biological system. Of particular interest with respect to the engineering of microbes capable of producing biofuels and other chemicals economically and at scale are metabolomic datasets, and their insights into intracellular metabolic fluxes. Metabolic fluxes provide a rapid and easy to understand picture of how carbon and energy flow throughout the cell. Furthermore, we present a detailed guide to performing metabolic flux analysis and modeling using the open source JBEI Quantitative Metabolic Modeling (jQMM) library. This library allows the user to transform metabolomics data in the form of isotope labeling data from a 13 C labeling experiment into a determination of cellular fluxes that can be used to develop genetic engineering strategies for metabolic engineering.The jQMM library presents a complete toolbox for performing a range of different tasks of interest in metabolic engineering. Various different types of flux analysis and modeling can be performed such as flux balance analysis, 13 C metabolic flux analysis, and two-scale 13 C metabolic flux analysis (2S- 13 C MFA). 2S- 13 C MFA is a novel method that determines genome-scale fluxes without the need of every single carbon transition in the metabolic network. In addition to several other capabilities, the jQMM library can make model based predictions for how various genetic engineering strategies can be incorporated toward bioengineering goals: it can predict the effects of reaction knockouts on metabolism using both the MoMA and ROOM methodologies. In this chapter, we will illustrate the use of the jQMM library through a step-by-step demonstration of flux determination and knockout prediction in a complex eukaryotic model organism: Saccharomyces cerevisiae ( S. cerevisiae ). Included with this chapter is a digital Jupyter Notebook file that provides a computable appendix showing a self-contained example of jQMM usage, which can be changed to fit the user's specific needs. As an open source software project, users can modify and extend the code base to make improvements at will, allowing them to share their development work and contribute back to the jQMM modeling community.

-Omics data↗