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DOE OSTI2025

Understanding the dynamic nature of plant lipid anabolic and catabolic metabolism is key to sustainable oilseed engineering

Plant-derived oils are essential sources of reduced carbon and various fatty acid (FA) structures for food, biofuels, and the oleochemical industry. Despite extensive efforts, engineering mainstream oilseed crops to produce high levels of industrially valuable unusual FAs (UFAs) remains challenging. This review synthesizes recent advances in the understanding of lipid metabolic networks, emphasizing how species-specific regulation of FA synthesis, activation, and delivery influences triacylglycerol (TAG) assembly to govern the efficiency of UFA accumulation. Key insights reveal that acyl flux through anabolic and catabolic branches of lipid metabolism is tightly controlled by enzyme substrate selectivities, diacylglycerol (DAG) pool compartmentalization, and metabolic context, including lipid remodeling and degradation pathways. Engineering success is often constrained by incompatibilities between UFA biosynthetic enzymes and endogenous host metabolism, leading to flux imbalances, futile cycles, and undesired phenotypes. We highlight emerging strategies to overcome these barriers, such as the use of UFA-selective acyltransferases, coordinated manipulation of DAG source pools, suppression of competing endogenous enzymes, and exploitation of TAG remodeling mechanisms. This integrated synthesis provides a conceptual framework for logic-based engineering of oilseeds with enhanced UFA content by offering new avenues for sustainable biomanufacturing of valuable lipids.

acyltransferase specificity↗

DOE OSTI2018

Know your enemy, embrace your friend: using omics to understand how plants respond differently to pathogenic and mutualistic microorganisms

Summary Microorganisms, or ‘microbes’, have formed intimate associations with plants throughout the length of their evolutionary history. In extant plant systems microbes still remain an integral part of the ecological landscape, impacting plant health, productivity and long‐term fitness. Therefore, to properly understand the genetic wiring of plants, we must first determine what perception systems plants have evolved to parse beneficial from commensal from pathogenic microbes. In this review, we consider some of the most recent advances in how plants respond at the molecular level to different microbial lifestyles. Further, we cover some of the means by which microbes are able to manipulate plant signaling pathways through altered destructiveness and nutrient sinks, as well as the use of effector proteins and micro‐ RNA s (mi RNA s). We conclude by highlighting some of the major questions still to be answered in the field of plant‐microbe research, and suggest some of the key areas that are in greatest need of further research investment. The results of these proposed studies will have impacts in a wide range of plant research disciplines and will, ultimately, translate into stronger agronomic crops and forestry stock, with immune perception and response systems bred to foster beneficial microbial symbioses while repudiating pathogenic symbioses.

Plett, Jonathan M.↗

DOE OSTI2020

Progress on Understanding Rayleigh–Taylor Flow and Mixing Using Synergy Between Simulation, Modeling, and Experiment

Simultaneous advances in numerical methods and computing, theoretical techniques, and experimental diagnostics have all led independently to better understanding of Rayleigh–Taylor (RT) instability, turbulence, and mixing. In particular, experiments have provided significant motivation for many simulation and modeling studies, as well as validation data. Numerical simulations have also provided data that is not currently measurable or very difficult to measure accurately in RT unstable flows. Thus, simulations have also motivated new measurements in this class of buoyancy-driven flows. This overview discusses simulation and modeling studies synergistic with experiments and examples of how experiments have motivated simulations and models of RT instability, flow, and mixing. First, a brief summary of measured experimental and calculated simulation quantities, of experimental approaches, and of issues and challenges in the simulation and modeling of RT experiments is presented. Implicit large-eddy, direct numerical, and large-eddy simulations validated using RT experimental data are then discussed. This is followed by a discussion of modeling using analytical, modal, buoyancy–drag, and turbulent transport models of RT mixing experiments. The discussion will focus on three-dimensional RT mixing arising from multimode perturbations. Finally, this focused review concludes with a perspective on future simulation, modeling, and experimental directions for further research. Research in simulation and modeling of RT unstable flows, coupled with experiments, has made significant progress over the past several decades. This overview serves as an opportunity to both discuss progress and to stimulate future research on simulation and modeling of this unique class of hydrodynamically unstable turbulent flows.

42 ENGINEERING↗

DOE OSTI2022

Understanding the Elastic, Plastic, and Damage Features in Fracturing of Self-reinforced Thermoplastic Composites via Non-destructive Digital Imaging Correlation

This work demonstrated the utilization of non-destructive Digital Imaging Correlation (DIC) method to characterize the elastic, plastic, and damage features during the Mode I intra-laminar fracturing process of self-reinforced thermoplastic composites by using a self-reinforced polypropylene (PP) composite as an example. The DIC results clearly showed the development of huge plastic zone (PZ) and non-negligible Fracture Process Zone (FPZ) in front of the notch tip during the fracturing process, and the geometries and sizes of the foregoing zones at the peak load were further quantified. Such an interesting fracturing behavior of self-reinforced thermoplastic composites is way different from brittle materials (e.g., glass, acrylic, etc.), ductile materials (e.g., aluminum, steel, etc.), and even quasi-brittle materials (e.g., concrete, nanoparticle-reinforced composites, tough ceramics, wood, cement, carbon/glass fiber-reinforced polymers, etc.). Thus, understanding the elastic, plastic, and damage features is the first step before better characterizing the material fracture properties of self-reinforced thermoplastic composites through new analytical methods and computational modeling. These efforts are of utmost importance for wide applications of self-reinforced thermoplastic composites in various engineering fields in the future.

Lightweight Composites, Self-reinforced Thermoplas↗

DOE OSTI2023

Understanding the transient large amplitude oscillatory shear behavior of yield stress fluids

A full understanding of the sequence of processes exhibited by yield stress fluids under large amplitude oscillatory shearing is developed using multiple experimental and analytical approaches. A novel component rate Lissajous curve, where the rates at which strain is acquired unrecoverably and recoverably are plotted against each other, is introduced and its utility is demonstrated by application to the analytical responses of four simple viscoelastic models. Using the component rate space, yielding and unyielding are identified by changes in the way strain is acquired, from recoverably to unrecoverably and back again. The behaviors are investigated by comparing the experimental results with predictions from the elastic Bingham model that is constructed using the Oldroyd–Prager formalism and the recently proposed continuous model by Kamani, Donley, and Rogers in which yielding is enhanced by rapid acquisition of elastic strain. The physical interpretation gained from the transient large amplitude oscillatory shear (LAOS) data is compared to the results from the analytical sequence of physical processes framework and a novel time-resolved Pipkin space. The component rate figures, therefore, provide an independent test of the interpretations of the sequence of physical processes analysis that can also be applied to other LAOS analysis frameworks. Each of these methods, the component rates, the sequence of physical processes analysis, and the time-resolved Pipkin diagrams, unambigiously identifies the same material physics, showing that yield stress fluids go through a sequence of physical processes that includes elastic deformation, gradual yielding, plastic flow, and gradual unyielding.

Kamani, Krutarth M. (ORCID:0000000338975420)↗

DOE OSTI2019

Understanding and eliminating the detrimental effect of thiamine deficiency on the oleaginous yeast Yarrowia lipolytica

Thiamine is a vitamin that functions as a cofactor for key enzymes in carbon and energy metabolism for all living cells. While most plants, fungi and bacteria can synthesize thiamine de novo , the oleaginous yeast, Yarrowia lipolytica , cannot. In this paper, we used proteomics together with physiological characterization to understand key metabolic processes influenced and regulated by thiamine availability and identified the genetic basis of thiamine auxotrophy in Y. lipolytica . Specifically, we found thiamine depletion results in decreased protein abundance of the lipid biosynthesis pathways and energy metabolism (i.e., ATP synthase), attributing to the negligible growth and poor sugar assimilation observed in our study. Using comparative genomics, we identified the missing 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase (THI13) in the de novo thiamine biosynthesis of Y. lipolytica , and discovered an exceptional promoter, P3, that exhibits strong activation or tight repression by low and high thiamine concentrations, respectively. Capitalizing on the strength of our thiamine-regulated promoter (P3) to express the missing gene from Saccharomyces cerevisiae (scTHI13), we engineered the thiamine-prototrophic Y. lipolytica . By comparing this engineered strain to the wildtype, we unveiled the tight relationship linking thiamine availability to lipid biosynthesis and demonstrated enhanced lipid production with thiamine supplementation in the engineered thiamine-prototrophic Y. lipolytica .

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Understanding Hepatitis B Virus Dynamics and the Antiviral Effect of Interferon Alpha Treatment in Humanized Chimeric Mice

Whereas the mode of action of lamivudine (LAM) against hepatitis B virus (HBV) is well established, the inhibition mechanism(s) of interferon alpha (IFN-α) is less completely defined. To advance our understanding, we, for this study, mathematically modeled HBV kinetics during 14-day pegylated IFN-α-2a (pegIFN), LAM, or pegIFN-plus-LAM (pegIFN+LAM) treatment of 39 chronically HBV-infected humanized uPA/SCID chimeric mice. Serum HBV DNA and intracellular HBV DNA were measured frequently. We developed a multicompartmental mathematical model and simultaneously fit it to the serum and intracellular HBV DNA data. Unexpectedly, even in the absence of an adaptive immune response, a biphasic decline in serum HBV DNA and intracellular HBV DNA was observed in response to all treatments. Kinetic analysis and modeling indicate that the first phase represents inhibition of intracellular HBV DNA synthesis and secretion, which was similar under all treatments with an overall mean efficacy of 98%. In contrast, there were distinct differences in HBV decline during the second phase, which was accounted for in the model by a time-dependent inhibition of intracellular HBV DNA synthesis, with the steepest decline observed during pegIFN+LAM treatment (1.28/day) and the slowest (0.1/day) during pegIFN monotherapy. Reminiscent of observations in patients treated with pegIFN and/or LAM, a biphasic HBV decline was observed in treated humanized mice in the absence of an adaptive immune response. Interestingly, combination treatment did not increase the initial inhibition of HBV production but rather enhanced second-phase decline, providing insight into the dynamics of HBV treatment response and the mode of action of IFN-α against HBV.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

A roadmap to understanding and anticipating microbial gene transfer in soil communities

Engineered microbes are being programmed using synthetic DNA for applications in soil to overcome global challenges related to climate change, energy, food security, and pollution. However, we cannot yet predict gene transfer processes in soil to assess the frequency of unintentional transfer of engineered DNA to environmental microbes when applying synthetic biology technologies at scale. This challenge exists because of the complex and heterogeneous characteristics of soils, which contribute to the fitness and transport of cells and the exchange of genetic material within communities. Here, we describe knowledge gaps about gene transfer across soil microbiomes. Here, we propose strategies to improve our understanding of gene transfer across soil communities, highlight the need to benchmark the performance of biocontainment measures in situ, and discuss responsibly engaging community stakeholders. We highlight opportunities to address knowledge gaps, such as creating a set of soil standards for studying gene transfer across diverse soil types and measuring gene transfer host range across microbiomes using emerging technologies. By comparing gene transfer rates, host range, and persistence of engineered microbes across different soils, we posit that community-scale, environment-specific models can be built that anticipate biotechnology risks. Such studies will enable the design of safer biotechnologies that allow us to realize the benefits of synthetic biology and mitigate risks associated with the release of such technologies.

bioccontainment↗

DOE OSTI2020

Recent Progress to Understand and Improve Zeolite Stability in the Aqueous Medium

The work reviewed here attempts to summarize the growing literature on zeolite stability in hot liquid water. This required to first establish the nature, structure and interactions of the active sites in Brønsted and Lewis acidic microporous materials in the presence of liquid water. This understanding was then transferred to zeolite stability and catalyst deactivation. While early results correctly established Si–O–Si hydrolysis as the dominant pathway compared to the Si–O–Al hydrolysis observed in steaming, it also focused extensively on the positive role of framework and extra-framework Al in stabilizing zeolites. However, stability was instead found to more directly correlate with the number of internal structural defects and intraporous water concentration. Stabilization protocols for Brønsted acidic zeolites are described in detail. In the case of Lewis acidic zeolites, their inherent hydrophobic behavior (Si/M >100) makes them more resistant towards water, however, issues such as reversible carbonaceous species formation as well as irreversible metal leaching and fouling remain. Finally, we summarize the most important factors in designing robust and efficient zeolite catalysts made to withstand hot liquid water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Building hypotheses to understand the synergistic effects of heat and pollution exposure in a changing climate

The increasing intensity, frequency, and duration of extreme weather events due to climate change poses a broad range of health risks, and the synergistic effects of extreme temperature co-occurring with other hazardous exposures such as air pollution may result in higher risks of all-cause mortality and cardiovascular and respiratory morbidity than exposure to either event alone. There are a number of hypothesized mechanisms for this interaction effect, including increased susceptibility to heat effects on chronic conditions affected by air pollution exposure, exacerbation of pollution effects due to temperature-induced stress, and shared pathophysiological pathways (e.g., systemic inflammation), but specific physiological mechanisms are not well understood. In this editorial, the authors discuss this aspect of a recently published study examining ambient formaldehyde combined with high temperature exposure and respiratory disease admissions among children. Here, the observation that the health effects of pollutants such as formaldehyde are amplified following periods of high temperature can help inform risk warning systems even without knowledge of the underlying physiological mechanisms, but a deeper biological understanding of the interaction effects of heat and ambient air pollution may better inform interventions. This is even more important in view of increases in both extreme temperature and pollution events tied to climate change.

Chambliss, Sarah [University of Texas at Austin, T↗

DOE OSTI2026

Enhancing ZFP: A Statistical Approach to Understanding and Reducing Error Bias in a Lossy Floating-Point Compression Algorithm

The amount of data generated and gathered in scientific simulations and data collection applications is continuously growing, putting mounting pressure on storage and bandwidth concerns. A means of reducing such issues is data compression; but, lossless data compression is typically ineffective when applied to floating-point data. Thus, users tend to apply a lossy data compressor, which allows for small deviations from the original data. It is essential to understand how the error from lossy compression impacts the accuracy of the data analytics. Thus, we must analyze not only the compression properties but the error as well. In this paper, we provide a statistical analysis of the error caused by ZFP compression, a state-of-the-art, lossy compression algorithm explicitly designed for floating-point data. We show that the error is indeed biased and propose simple modifications to the algorithm to neutralize the bias and further reduce the resulting error.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Understanding Portability of Automotive Workload: A Case Study with the Points-to-Image Kernel in SYCL on Heterogeneous Computing Platforms

SYCL is a promising programming model for heterogenous computing across vendors’ devices. In this paper, we study whether SYCL can be applied to an automotive workload and its portability on heterogeneous computing platforms. We explain the automotive benchmark, describe our implementations and optimizations of the benchmark, and evaluate the performance of the benchmarks using SYCL and other programming models on heterogeneous computing devices. The study also allows us to have a better understanding of portability of the benchmark across these platforms.

Jin, Zheming↗

DOE OSTI2021

Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes

Microbiomes are complex and ubiquitous networks of microorganisms whose seemingly limitless chemical transformations could be harnessed to benefit agriculture, medicine, and biotechnology. Here, the spatial and temporal changes in microbiome composition and function are influenced by a multitude of molecular and ecological factors. This complexity yields both versatility and challenges in designing synthetic microbiomes and perturbing natural microbiomes in controlled, predictable ways. In this review, we describe factors that give rise to emergent spatial and temporal microbiome properties and the meta-omics and computational modeling tools that can be used to understand microbiomes at the cellular and system levels. We also describe strategies for designing and engineering microbiomes to enhance or build novel functions. Throughout the review,we discuss key knowledge and technology gaps for elucidating the networks and deciphering key control points for microbiome engineering, and highlight examples where multiple omics and modeling approaches can be integrated to address these gaps.

42 ENGINEERING↗

DOE OSTI2020

Understanding Li-Ion Cell Internal Short Circuit and Thermal Runaway through Small, Slow and In Situ Sensing Nail Penetration

Here we report a small, slow and in situ sensing (3S) nail penetration test method to understand Li-ion cell internal short circuit (ISC) and thermal runaway. The method not only keeps conventional nail penetration's advantage of simple implementation, but also enhances its relevance to field failures and enables detailed in situ diagnosis. It was applied to 3-Ah pouch cells and revealed insights that could not be captured by conventional methods. Most interestingly, multiple in situ temperature peaks were observed during a period of over 100 s before thermal runaway. These initial peaks exceeded safety limit but the temperature rapidly decreased after each peak instead of causing immediate thermal runaway. Further investigation suggested that the initial temperature peaks occurred when nail tip reached aluminum foil current collector to form a low resistance ISC between anode and aluminum foil. The rapid temperature decrease after each peak can be attributed to sudden drop of ISC current, which can be further attributed to rupture of aluminum foil and increase of contact resistance. The findings show that 3S nail penetration test can separate processes of ISC from thermal runaway and provide details of ISC at the level of individual electrode and current collector.

25 ENERGY STORAGE↗

DOE OSTI2021

Understanding Evolution of Lithium Trivanadate Cathodes During Cycling via Reformulated Physics-Based Models and Experiments

Degradation of lithium trivanadate ( Li x V 3 O 8 ) cathodes has been widely reported in the literature, but studies have offered little insight towards developing a detailed understanding of the evolution of the active material, and have been inconclusive as to the root cause of degradation. Here, we refit a validated physics-based model to discharge curves over the course of cycling at C/5, and use the evolution of the model parameters to track evolution of the cathode. A regularization penalty for adjusting model parameters from the validated model is introduced as a framework to identify which model parameters can explain a significant portion of the observed change in the voltage profile over the course of cycling. SEM reveals that lithium trivandate particles fracture upon cycling at C/5, consistent with the results of the parameter estimation, deactivation of lithium trivanadate and faster diffusion of lithium within the active particles. The physics-based model is then used to design modified cycling protocols which identify the phase transformation during discharge of lithium trivanadate as the driver of the particle fracture and capacity fade.

25 ENERGY STORAGE↗

DOE OSTI2022

Perspective—Electrochemistry in Understanding and Designing Electrochemical Energy Storage Systems

The number of publications in electrochemical energy storage has increased exponentially in the past decades, focusing mostly on materials science. The electrochemical process controlling the observed overall performances is often not well discussed. This article highlights the importance of understanding rate-limiting steps in the electrochemical process which change dynamically at different conditions and scales. Applying electrochemistry to identify and overcome those rate-limiting steps in the electrochemical devices is the prerequisite to discovering effective solutions and designing different batteries to further advance electrochemical energy storage systems for a broad range of various applications.

25 ENERGY STORAGE↗

DOE OSTI2024

Theoretical Understanding of Effects of Operating Modes on the Performance Durability of Solid Oxide Cells: A Comparison between Potentiostatic and Galvanostatic Operations

In solid oxide cells (SOCs), the choice between galvanostatic (constant current) and potentiostatic (constant voltage) modes does not significantly affect the performance of SOCs as long as the cell components remain unchanged and intact. However, the degradation of cell components, which leads to changes in electrochemical and physical properties of the cell, elevates the importance of the selected operating mode. This paper aims to investigate the effects of galvanostatic and potentiostatic operating modes on the evolving properties of SOCs and their subsequent influence on performance durability. Employing non-equilibrium thermodynamic analysis, a crucial approach for understanding the degradation phenomena within an active electrochemical system, this study aims to provide in-depth insights into how these operating modes affect the longevity and efficacy of SOCs. Key findings include: In cases where oxygen electrode (OE) degradation is accelerated by higher partial pressure of oxygen ( p O 2 ), operating under constant voltage electrolysis can mitigate the high p O 2 at the OE|electrolyte (OE|EL) interface. Conversely, if OE degradation occurs more rapidly under a lower p O 2 , constant current electrolysis is more effective in suppressing degradation by achieving a high p O 2 at the OE|EL interface. For degradation of the fuel electrode (FE) due to higher p O 2 , constant current electrolysis is beneficial for more stable performance, which helps maintain low p O 2 at the FE|EL interface. When FE degradation is accelerated by lower p O 2 , constant voltage electrolysis can avert low p O 2 at the FE|EL interface. In practical scenarios, more complex degradation mechanisms come into play, especially when p O 2 significantly deviates from initial conditions. Degradation in one electrode can influence p O 2 in the other electrode, a phenomenon more pronounced in potentiostatic than in galvanostatic electrolysis.

Electrochemistry↗

DOE OSTI2024

Shape Matters: Understanding the Effect of Electrode Geometry on Cell Resistance and Chemo-Mechanical Stress

Rechargeable batteries that incorporate shaped three-dimensional electrodes have been shown to have increased power and energy densities when compared to a conventional geometry, i.e. a planar cathode and anode that sandwich an electrolyte. Electrodes can be shaped to enable a higher active material loading, while keeping ion transport distances small. However, the relationship between electrical and mechanical performance of shaped electrodes remains poorly understood. Many electrode designs have been explored, where the electrodes are individually shaped or intertwined, and advances in manufacturing and shape/topology optimization have made such designs a reality. Here, we explore sinusoidal half cells and interdigitated full cells. First, we use a simple electrostatics model to understand the cell resistance as a function of shape. Here we focus on low-temperature conditions, where the electrolyte conductivity decreases relative to that of the electrode; here, LiPF 6 EC:DMC electrolyte and MnO 2 electrode are considered. Next, we use a chemo-mechanics model to examine the stress that arises due to intercalation-driven volume expansion. We show that shaped electrodes provide a significant reduction in resistance in low-temperature conditions, however, they exhibit unfavorable stress concentrations. Overall, we find that the fully interdigitated electrodes may provide the best balance with respect to this resistance-stress trade-off.

25 ENERGY STORAGE↗