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Optimizing Oil Production in Oleaginous Yeast by Cell-Wide Measurements and Genome-Based Models (Final Report)
The work funded under this DOE genomics grant focused on characterizing, modifying and developing genetic engineering tools for the then very promising but under-characterized oleaginous yeast Yarrowia lipolytica. To-date, all biodiesel production facilities rely on vegetable oils and animal fats as feedstocks, which are very limited. Nature, on the other hand, is very well equipped for making carbohydrates, which are very plentiful throughout the world and rather well distributed in various forms. While numerous (biochemical and thermochemical) technologies exist presently for carbohydrate conversion to alcohols, there is none available for the cost-efficient production of lipids from carbohydrate feedstocks. Such a technology would have wide-ranging implications in land use, renewable resource utilization and production of transportation fuels with minimal carbon footprint. The global research objectives of this award were to develop tools for cell-wide measurement of metabolites and lipids that, along with transcriptional data, will allow the construction of genome-scale metabolic models, as well as models of transcriptional regulation, that will guide the further metabolic engineering of Yarrowia lipolytica. To achieve these goals, a very strong international and diverse team consisting of research groups at MIT, UCLA, PNNL and Chalmers University was put together, whose specific goals, achievements and breakthroughs are included in this report.
Spatio-temporal Estimates of Disease Transmission Parameters for COVID-19 with a Fully-Coupled, County-Level Model of the United States
Sandia National Laboratories has developed a capability to estimate parameters of epidemiological models from case reporting data to support responses to the COVID-19 pandemic. A differentiating feature of this work is the ability to simultaneously estimate county-specific disease transmission parameters in a nation-wide model that considers mobility between counties. The approach is focused on estimating parameters in a stochastic SEIR model that considers mobility between model patches (i.e., counties) as well as additional infectious compartments. The inference engine developed by Sandia includes (1) reconstruction and (2) transmission parameter inference. Reconstruction involves estimating current population counts within each of the compartments in a modified SEIR model from reported case data. Reconstruction produces input for the inference formulations, and it provides initial conditions that can be used in other modeling and planning efforts. Inference involves the solution of a large-scale optimization problem to estimate the time profiles for the transmission parameters in each county. These provide quantification of changes in the transmission parameter over time (e.g., due to impact of intervention strategies). This capability has been implemented in a Python-based software package, epi_inference, that makes extensive use of Pyomo [5] and IPOPT [10] to formulate and solve the inference formulations.
MSD CoP Webinar: "Generative agents: A new frontier for representing human actors and their behavior in MSD models"
Context: This webinar was hosted by the MultiSector Dynamics Community of Practice (MSD CoP; https://multisectordynamics.org). Talk #1: Behavioral Generative Agents for Energy Operations Presenter: Dr. Cong Chen (Thayer School of Engineering, Dartmouth College) Abstract: Accurately modeling consumer behavior in energy operations remains challenging due to inherent uncertainties, behavioral complexities, and limited empirical data. This talk introduces a novel approach leveraging generative agents--artificial agents powered by large language models--to realistically simulate customer decision-making in dynamic energy operations. Talk #2: Simulating multiple human perspectives in socio-ecological systems using large language models Presenter: Dr. Yongchao Zeng (Institute of Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU) of the Karlsruhe Institute of Technology in Germany) Abstract: Understanding socio-ecological systems requires insights from diverse stakeholder perspectives. This talk describes a novel simulation system called HoPeS (Human-oriented Perspective Shifting). HoPeS enables model users to not only explore simulated socio-ecological systems (SESs) from a third-person observer's perspective but also take any of the simulated stakeholder roles, like playing an RPG game. By shifting multiple perspectives, model users can reflect and integrate the situated knowledge learned through the participatory simulation, approximating a more holistic and less biased understanding of SESs. Moderators: Jim Yoon (MSD CoP Human Systems Modeling Working Group Co-Chair); Stefano Galelli (MSD CoP Using AI to Enhance MSD Research Working Group Co-Chair); Patrick M. Reed (MSD CoP Facilitation Team) This webinar was held on: November 13th, 2025 from 12-1 PM EST.
Discovering Physically Meaningful Structures from Climate Extreme Data
The original proposal described an interdisciplinary team spanning UC San Diego (lead), Columbia University, and UC Irvine, with Columbia investigators including Pierre Gentine, Elias Bareinboim, and Marcus van Lier-Walqui. The proposal further specified a leadership structure in which Columbia co-investigators contributed across the three aims, with Co-PI Gentine serving as a point of contact with science teams and with responsibilities distributed across aims.
Evaluating the limitations of Bayesian metabolic control analysis
Bayesian Metabolic Control Analysis (BMCA) is a promising framework for inferring metabolic control coefficients in data-limited scenarios, combining Bayesian inference with linear-logarithmic (lin-log) rate laws. These metabolic control coefficients quantify how changes in enzyme activities affect steady-state fluxes and metabolite concentrations across a metabolic network. However, its predictive accuracy and limitations remain underexplored. This study systematically evaluates BMCA’s ability to infer elasticity values, flux control coefficients (FCC), and concentration control coefficients (CCC) under varying data availability conditions using three synthetic metabolic network models. We demonstrate that BMCA predictions are highly dependent on the inclusion of flux and enzyme concentration data, with the omission of these datasets leading to severe inaccuracies. In our synthetic, enzyme-perturbation datasets, external metabolite concentrations had minimal impact and, in some cases, their exclusion improved predictions; when external-nutrient perturbations were introduced and those concentrations were observed, gains were at most modest. Additionally, we find that posterior estimation with both ADVI and HMC can underestimate large-magnitude elasticities in our synthetic settings, with ADVI showing somewhat higher variance under strong up-regulation; thus, recovering |elasticity| ≳ 1.5 remains challenging regardless of the inference engine. ADVI also fails to accurately infer allosteric interactions, even when regulatory effects are strong. While BMCA maintains reasonable accuracy in partially recovering the rankings of the highest FCC values, its estimates of absolute values remain constrained by prior assumptions and data limitations. Our findings reveal the BMCA algorithm’s strengths and weaknesses, providing guidance on its application in metabolic engineering, and highlighting the need for methodological refinements to enhance its predictive capabilities.
Application of an automated machine learning-genetic algorithm (AutoML-GA) coupled with computational fluid dynamics simulations for rapid engine design optimization
In recent years, the use of machine learning-based surrogate models for computational fluid dynamics (CFD) simulations has emerged as a promising technique for reducing the computational cost associated with engine design optimization. However, such methods still suffer from drawbacks. One main disadvantage is that the default machine learning (ML) hyperparameters are often severely suboptimal for a given problem. This has often been addressed by manually trying out different hyperparameter settings, but this solution is ineffective in case of a high-dimensional hyperparameter space. Besides this problem, the amount of data needed for training is also not known a priori. In response to these issues that need to be addressed, the present work describes and validates an automated active learning approach, AutoML-GA, for surrogate-based optimization of internal combustion engines. In this approach, a Bayesian optimization technique is used to find the best machine learning hyperparameters based on an initial dataset obtained from a small number of CFD simulations. Subsequently, a genetic algorithm is employed to locate the design optimum on the ML surrogate surface. In the vicinity of the design optimum, the solution is refined by repeatedly running CFD simulations at the projected optima and adding the newly obtained data to the training dataset. It is demonstrated that AutoML-GA leads to a better optimum with a lower number of CFD simulations, compared to the use of default hyperparameters. The proposed framework offers the advantage of being a more hands-off approach that can be readily utilized by researchers and engineers in industry who do not have extensive machine learning expertise.
A Power Application Developer’s Guide to the Common Information Model: An Introduction for Power Systems Engineers and Application Developers – CIM17v40
A key issue in creating the next generation of energy management system (EMS) and advanced distribution management system (ADMS) platforms will be the ability to represent and exchange power system network model data in a consistent manner. To this end, the Common Information Model (CIM) stands out as the only standardized vocabulary (or ontology) for defining power system network models and asset data in a comprehensive, consistent manner across the generation-transmission-distribution boundary. The CIM is freely available to use and extend. The CIM is maintained by the UCAiug (informally known as the CIM User’s Group) under an Apache 2.0 license. The CIM Users Group collaborates with the IEC and other standards communities for the development of technical and informative specifications. Although portions of the information model are referred to by the corresponding IEC standards naming, it is not necessary to purchase any of the IEC standards to use the CIM information model. This document provides a roadmap for power system engineers and application developers not familiar with semantic modeling to start using the CIM for modeling, simulation, optimization, and development of advanced power applications. The key classes needed for defining power system topology and equipment are explained systematically. Key focus areas include modeling of lines, transformers, generators, switching equipment, loads, and distributed energy resources (DERs).
Stochastic modeling and statistical calibration with model error and scarce data
This paper introduces a procedure to assess the predictive accuracy of stochastic models subject to model error and sparse data. Model error is introduced as uncertainty on the coefficients of appropriate polynomial chaos expansions (PCE). The error associated with finite sample size allows us to conceive of these coefficients as statistics of the data that we describe as random variables whose influence on output quantities of interest is evaluated through the extended polynomial chaos expansion (EPCE). A Bayesian data assimilation scheme is introduced to update these expansions by considering the resulting nested chaos expansion as a hierarchical probabilistic model. Stochastic models of quantities of interest (QoI) are thus constructed and efficiently evaluated. Here, the Metropolis–Hastings Markov chain Monte Carlo procedure is used to sample the posterior. Two illustrative analytical and numerical problems are used to demonstrate the proposed approach.
Soot Formation and Ignition Characteristics of Ethanol/Gasoline Blends in a Rapid Compression Machine
With the ever-increasing demand for sustainable energy, alcohol fuels have garnered interest for use in heavy duty engines. The significant infrastructure for ethanol production and blending of ethanol with gasoline make these fuels/fuel blends desirable candidates. However, development of heavy duty engine technology that is capable of burning alcohol fuels while retaining the advantages of traditional diesel combustion requires an improved understanding of the soot formation for these fuels under conditions relevant to mixing-controlled combustion. This work uses an extinction diagnostic to study the sooting tendency of ethanol and gasoline/ethanol blends ranging from E10 to E98 during ignition in a homogeneous environment. Experiments were conducted in a rapid compression machine (RCM) for compressed conditions of 20 ± 1 bar and an approximately constant temperature (± 10K) which was unique for each fuel. For a given soot volume fraction, a linear relationship was observed between ethanol content and the equivalence ratio in which that soot volume fraction was formed. Accounting for the oxygenated nature of ethanol, E85 and E98 fuels produced similar amounts of soot at a given Φ ox, , suggesting other factors outside of fuel oxygen content, such as fuel morphology, impact soot formation. Ignition delay data is reported for compressed pressures of 20 ± 1 bar and compressed temperatures ranging from 633 – 670 K for E10 and 771 – 789 K for E98. Varying pressures for E10 and E98 at conditions producing similar soot volume fractions demonstrated a linear dependence of soot formation on pressure, regardless of if the pressure considered was at top dead center or peak combustion pressure. Furthermore, the data gleaned from this work will be used to select soot models and chemical kinetic mechanisms for RCM simulations to ultimately model heavy duty engine technology with the studied fuels.
Rotating Detonation Combustion for Gas Turbines: Modeling and System Synthesis to Exceed 65% Efficiency Goal (Phase II)
As of May 2019, all RDE test hardware and test operations were completed for this program. Over 700 hot fire tests were conducted at 4 facilities with 7 RDE assemblies, with the data available for future analysis. In particular, measured static and dynamic pressure and computational fluid dynamics (CFD) provided basis for pressure gain combustion (PGC) analysis of the Engineering Scale RDE. It was demonstrated via measurements and CFD that a carefully designed diffuser can recover some total pressure of the highly oscillatory RDE exhaust. In general, the isolator/injector is largest contributor of pressure losses; however a low loss design was demonstrated that improves significantly on previous natural-gas/air RDEs. Also, a tailored injector and mixing technique was demonstrated that allowed NG-air RDE operation with overall equivalence ratio of less than 0.6. CFD models by AR, the UofM and Purdue University were extensively used throughout the program to refine diffuser design for improved pressure recovery, to simulate injection and mixing, to estimate turbine interaction, to estimate combustor pressure gain anchored with test data and to provide input to other design and analytical tasks. CFD analyses were completed for many of the configurations tested at Purdue with the 13.4” RDE including the shark fin and low area ratio isolators. Results were compared favorably to available hot fire test particle image velocimetry (PIV) measurements and wave speeds. The results of these CFD analyses suggest a modest pressure gain of 33% with a sufficiently low area ratio isolator. A thermodynamic power plant system model was set up which utilizes an RDE combustor. The performance of the RDE combustor module was scaled based on measurements from the Engineering Scale RDE tests with low loss injector and tailored fuel flow. This combined model indicates potential for significant plant efficiency improvement. The successful tailored fuel injection test result with lower than .6 equivalence ratio has implication that a power plant can use a RDE combustor configuration where all the air flows through the combustion zone thereby not requiring a bypass mixer. In this configuration, the results of the natural gas combined cycle (NGCC) plant system indicate net efficiency of 66.4%.
Graph-based Compact Modeling (GCM) of CMOS transistors for efficient parameter extraction: A machine learning approach
Parameter extraction of compact transistor models is an expensive process, heavily relying on engineering knowledge and experience. To automate such a process, we propose a novel approach, Graph-based Compact Model (GCM), that integrates physical modeling and data-driven learning. GCM utilizes Graph Neural Networks (GNNs) to establish the model structure, while retaining the physicality in compact models. Here, we implement our GCM in Verilog-A to support circuit simulations. As demonstrated with an academic 7 nm FinFET PDK, the new approach automatically generates a GCM model within a minute, and achieves excellent accuracy and efficiency in SPICE.
Block Design with Common Reference Samples Enables Robust Large-Scale Label-Free Quantitative Proteome Profiling
Label-free quantitative proteomics has become an increasingly popular tool for profiling global protein abundances. However, one major weakness is the potential performance drift of the LC-MS platform over time, which in turn limits its utility for analyzing large-scale sample sets. To address this, in this work we introduce an experimental and data analysis scheme based on a block-design with common controls within each block for enabling LC-MS-based large-scale label-free quantification. In this scheme, a large number of samples (e.g., >100 samples) are analyzed in smaller, and more manageable blocks, minimizing instrument drift and variability within a block. Furthermore, each designated block also contains common controls (or reference) samples for normalization within and across blocks. We demonstrated the effectiveness of this method by profiling the proteome response of human macrophage THP-1 cells to 11 engineered nanomaterials (ENMs) at two different doses. A total of 116 samples were analyzed in six blocks, yielding an average coverage of 4500 proteins per sample. The data revealed consistent quantification of proteins across all six blocks, as shown by highly stable quantification of house-keeping proteins in all samples and high levels of quantification correlation among samples from different blocks. The data also demonstrated that label-free quantification is robust and accurate enough to quantify even very subtle abundance changes as well as large fold-changes without potential ratio compression as often encountered with isobaric labeling. Our streamlined workflow is easy to implement and can be readily adapted to other large cohort studies for reproducible label-free proteome quantification.
Recommendations for Data-in-Transit Requirements for Securing DER Communications
With the adoption of Distributed Energy Resource (DER) interoperability standards, common communication protocols are now being deployed between power system operators and DER devices. In 2018, a revision to the US interconnection and interoperability standard, Institute of Electrical and Electronics Engineers (IEEE) Std. 1547, required DER equipment to have an IEEE 2030.5, IEEE 1815, or SunSpec Modbus communication exchange interface. This change supports the future transition to secure connection and exchange of information between the DER equipment and implementing parties, such as grid operators. Adoption of standardized communication protocols and associated information models is a critical step toward interoperability between power system operators and DER, such as photovoltaic (PV) and energy storage systems. However, security requirements for these standardized communication protocols are not comprehensive, resulting in non-standard and vendor-specific implementation that may leave DER equipment susceptible to cyberattacks. This paper examines the data-in-flight security requirements for standardized DER communication protocols, per IEEE 1547-2018 revision, as it relates to device authentication, key management, and encryption. The state of the art for these security features is also explored, addressing their impact on communication and performance of low-cost single board computers, which are typical of DER devices. In conclusion, a recommendation is provided to adopt a common set of communication requirements, which are intended to achieve interoperability and implement data security over DER network pathways, while ensuring reliable, secure, and real-time information delivery.
Satellite Enveloped with STITCHED Engineering Sensors for Detection of Approaching Objects
Today as well as tomorrows spaceborne assets impact almost all areas of national and nuclear security. Spaceborne assets can not only collect and disseminate valuable data, well beyond just the visual, but also track terrestrial-based mobile assets in real-time, and active spaceborne platforms potentially pose serious risk to vulnerable earth-based systems and infrastructures. The capability to defend national spaceborne assets from attack/interference is critical for security interests. This effort supports this mission through the cost-effective preeminent detection of approaching threats to our nation’s vital resources, in order to help secure and trust these high-value assets against the threats of tomorrow. This project develops novel fabrication techniques for conformal, low-profile and lightweight leakywave antenna (LWA) detection/imaging systems, which fuses technical embroidery (TE) and laser ablation (LA) processes with LWA design. Technical embroidery is an emerging field in additive textile manufacturing where flexible materials and functionalized fabrics are created for a wide variety of uses and purposes, while laser ablation is the process of removing material from a solid surface by irradiating it with a laser beam. Here, thin, conformal antenna designs are designed, modeled and fabricated using both TE and LA, to create lightweight, flexible and conformal object detection and imaging radars. This novel development ensures our nation’s ability to field advanced lightweight and conformal technologies to protect spaceborne assets.
In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13 C and 2 H Tracers
Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are thermophilic anaerobic bacteria with complementary metabolic capabilities that utilize distinct glycolytic pathways for the conversion of cellulosic sugars to biofuels. We integrated quantitative metabolomics with 2 H and 13 C metabolic flux analysis to investigate the in vivo reversibility and thermodynamics of the central metabolic networks of these two microbes. We found that the glycolytic pathway in C. thermocellum operates remarkably close to thermodynamic equilibrium, with an overall drop in Gibbs free energy 5-fold lower than that of T. saccharolyticum or anaerobically grown Escherichia coli . The limited thermodynamic driving force of glycolysis in C. thermocellum could be attributed in large part to the small free energy of the phosphofructokinase reaction producing fructose bisphosphate. The ethanol fermentation pathway was also substantially more reversible in C. thermocellummthan in T. saccharolyticum. These observations help explain the comparatively low ethanol titers of C. thermocellum and suggest engineering interventions that can be used to increase its ethanol productivity and glycolytic rate. In addition to thermodynamic analysis, we used our isotope tracer data to reconstruct the T. saccharolyticum central metabolic network, revealing exclusive use of the Embden-Meyerhof-Parnas (EMP) pathway for glycolysis, a bifurcated tricarboxylic acid (TCA) cycle, and a sedoheptulose bisphosphate bypass active within the pentose phosphate pathway. Thermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. Here, we provide new insights into the divergent thermodynamics of the glycolytic pathways of C. thermocellum and T. saccharolyticum, two industrially relevant thermophilic bacteria whose metabolism still is not well understood. We report that while the glycolytic pathway in T. saccharolyticum is as thermodynamically favorable as that found in model organisms, such as E. coli or Saccharomyces cerevisiae , the glycolytic pathway of C. thermocellum operates near equilibrium. The use of a near-equilibrium glycolytic pathway, with potentially increased ATP yield, by this cellulolytic microbe may represent an evolutionary adaptation to growth on cellulose, but it has the drawback of being highly susceptible to product feedback inhibition. The results of this study will facilitate future engineering of high-performance strains capable of transforming cellulosic biomass to biofuels at high yields and titers.
AWSD Reactive Burn Model for the HMX‐Based High Explosive LX‐04
An Arrhenius–Wescott–Stewart–Davis (AWSD) reactive burn model is applied to describe shock initiation and detonation properties of the HMX-based high explosive LX-04. The parameters in the model are calibrated to data from multiple sources. The thermodynamic equations of state used in the model are calibrated to a combination of thermochemical calculations for HMX and LX-04 as well as experimentally-measured cylinder expansion results for LX-04. The kinetic parameters are calibrated to velocity data from gas gun experiments performed using EDC-32—a high explosive with the same chemical composition as LX-04 but different structural properties, and scaled rate stick data for PBX 9012. The AWSD model is shown to accurately describe the shock initiation and propagation of LX-04. Very good agreement is observed between the available experimental data and the AWSD model output. The presented results constitute an accurate LX-04 reactive burn model for use in engineering-scale models and simulations.