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Artificial intelligence tools for enzyme engineering and metabolic engineering

Enzyme engineering and metabolic engineering drive innovation in energy biotechnology. In recent years, artificial intelligence (AI) has supported successful applications in designing effective enzymes and productive microbial cell factories. This review summarizes recent advances in enzyme redesign using protein language models, de novo enzyme design with generative models, and AI tools for engineering metabolism and related cellular phenotypes. Across these areas, AI models are shifting from single modality inputs to integrated representations of protein function, metabolic pathways, and cell states. We emphasize that unifying the diverse data representations across scales will be necessary for advancements in energy biotechnology.

Volk, Michael [Univ. of Illinois at Urbana-Champai

Do Research Software Engineers and Software Engineering Researchers Speak the Same Language?

Anecdotal evidence suggests that research software engineers (RSEs) and software engineering researchers (SERs) often use different terminologies for similar concepts, creating communication challenges. To better understand these divergences, we have started investigating how software engineering fundamentals from the SER community are interpreted within the RSE community, identifying aligned concepts, knowledge gaps, and areas for potential adaptation. In conclusion, our preliminary findings reveal opportunities for mutual learning and collaboration, and our systematic methodology for terminology mapping provides a foundation for a crowdsourced extension and validation in the future.

Kehrer, Timo [Univ. of Bern (Switzerland)] (ORCID:

Virtual Engineering: Python framework for engineering process design

Virtual Engineering (VE) is a Python software framework designed to accelerate the research and development of engineering processes that are fundamentally defined by multiple unit operations executed in series. VE supports a wide variety of different multi-physics models and integrates them to simulate a complete end-to-end process. To automate the execution of this model sequence, VE provides (i) a robust method to communicate between models, (ii) a high-level, user-friendly interface to set model parameters and enable optimization, and (iii) an overall model-agnostic approach that allows new computational units to be swapped in and out of workflows. Although the VE framework was developed to support the biochemical conversion of biomass to fuel, we have designed each component to easily accommodate new domains and unit models.

09 BIOMASS FUELS

Engineering Services in a Mission Critical Environment: Engineering Services - Science and Technology Operations’ Infrastructure Support at Los Alamos National Laboratory

As an engineering team within a facilities-driven organization, Engineering Services – Science and Technology Operations (ES-STO), supports Los Alamos National Laboratory (LANL), playing a pivotal role in the U.S. nuclear stockpile mission. This report outlines ES-STO’s contributions through the installation of crucial systems such as HVAC units, compressors, and scientific specialty equipment, as well as providing expert consultation to optimize laboratory operations. ES-STO’s goal is to ensure that LANL's infrastructure and research facilities are aligned with mission-critical needs, supporting both operational efficiency and safety in the nuclear stockpile management and maintenance. This report discusses the installation processes, ongoing consultations, and the significant impact of our efforts on national security objectives.

42 ENGINEERING

Development of Engine Valve Materials for Next Generation Higher Efficiency Engines

The growing demand to increase the performance and efficiency of light-, medium-, and heavy-duty engines continues to drive increases in combustion intensities and cylinder pressures, which result in higher exhaust gas temperatures. Thus, there is a critical need for new materials that can meet the performance and cost targets for components such as exhaust valves which are exposed to these higher exhaust gas temperatures. Oak Ridge National Laboratory (ORNL) has developed several lower-cost, high-strength alloys that have the potential to be adopted into intake and/or exhaust valves in the next generation, high-efficiency engines and other high temperature applications. These alloys are covered by two issued patents.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI

Development of Engine Valve Materials for Next Generation Higher Efficiency Engines

The growing demand to increase the performance and efficiency of light-, medium-, and heavy-duty engines continues to drive increases in combustion intensities and cylinder pressures, which result in higher exhaust gas temperatures. Thus, there is a critical need for new materials that can meet the performance and cost targets for components such as exhaust valves which are exposed to these higher exhaust gas temperatures. Oak Ridge National Laboratory (ORNL) has developed several lower-cost, high-strength alloys that have the potential to be adopted into intake and/or exhaust valves in the next generation, high-efficiency engines and other high temperature applications. These alloys are covered by two issued patents: 1. G. Muralidharan, U. S. Patent No. 9,605,565 B2, “Low-cost Fe--Ni--Cr alloys for high temperature valve applications,” March 28, 2017. 2. G. Muralidharan, U. S. Patent 9,752, 468 B2, “Low-Cost, High-Strength Fe-Ni-Cr Alloys for High Temperature Exhaust Valve Applications, Issued Sep. 5, 2017. The overall scope of this CRADA project was for Oak Ridge National Laboratory to collaborate with Tenneco Powertrain to: 1) better define the properties required for intake and/or exhaust valves for next generation vehicles, 2) fabricate industrial scale heats of alloys down-selected from existing patents, 3) generate critical high temperature property data that will help evaluate the suitability of these new alloys for high temperature intake and/or exhaust valves, and finally to 4) fabricate and evaluate the performance of prototype intake/and or exhaust valves.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI

Data for Multisite Field Evaluation of Oil Accumulation and Agronomic Performance in Grain and Sweet Sorghums Engineered for Lipid Hyperaccumulation

Oil sorghum (OS) has been developed by engineering grain (TX430) and sweet (Ramada) genetic backgrounds to accumulate triacylglycerols (TAG) in vegetative tissues as an energy-dense feedstock for sustainable aviation fuel (SAF) and other biofuels. This study evaluated two TX430 OS lines (TxHO-2, TxHO-3) and two Ramada OS lines (RmHO-1, RmHO-2) alongside wild-type (WT) lines in NE and IL over 2 years (2023–2024) to quantify genotype × environment effects on agronomic performance and TAG accumulation. Across four environments, TX430 OS lines showed average TAG concentrations of 15.0 g kg−1 in leaves and 12.8 g kg−1 in stems, approximately 19-fold higher than WT. Ramada OS lines accumulated 26.1 g kg−1 in leaves and 12.3 g kg−1 in stems, approximately 25-fold and 13-fold increases over WT, respectively. OS lines in TX430 exhibited an 18% reduction in biomass (8.4 vs. 9.9 Mg ha−1 for WT), while Ramada OS lines had similar WT biomass (18.3 vs. 19.9 Mg ha−1 for WT). Among TX430 OS lines, TxHO-2 achieved the highest TAG yield (190 kg ha−1), while RmHO-1 led the Ramada lines (335 kg ha−1) due to higher biomass and similar TAG concentration. Enhanced TAG accumulation increased N, P, and K removal in TX430 lines but not in Ramada lines. Structural carbohydrate and ash concentration were unaffected. Overall, results confirm vegetative lipid accumulation as a viable strategy for high-biomass sorghum, supporting its potential as a dual-purpose feedstock for SAF. Future work should focus on minimizing biomass yield penalties and improving nutrient use efficiency in oil sorghum systems.

Agronomy

Design and Demonstration of a NH3-Fueled Two-Stroke Uniflow Engine for Greenhouse Gas Reduction

The maritime shipping industry is growing increasingly interested in both low and non-carbon-containing fuels to meet future greenhouse gas emission targets. Specifically of interest is ammonia, as it has a relatively high volumetric energy density compared to other future fuels, such as hydrogen, making it more economical to transport. The robust engine architecture of low-speed two-stroke marine engines makes them an ideal candidate for ammonia fuel, overcoming many of the issues surrounding its poor ignitability and low flame speed. If emissions and fueling system challenges can be addressed, retrofits of current low-speed two-stroke dual-fuel engines represent a viable pathway for bringing ammonia engines to market. This study explores these technical hurdles by describing the design, analysis, and experimental validation of a single cylinder research engine converted to operate on ammonia fuel. The engine is a reduced-scale uniflow two-stroke marine engine with two previous hardware configurations available – diesel and high-pressure CNG dual-fuel. A concept study was used to evaluate possible ammonia-fueled engine architectures and the associated tradeoffs and design considerations. With the chosen architecture, low-pressure dual fuel, 1D and 3D analysis tools were used to inform hardware selection and to determine hardware configurations which minimized ammonia-slip. In addition to these considerations the hardware and engine configuration were designed to provide a versatile and robust testing platform. This includes options to test both gaseous and liquid ammonia injection, as well as a wide range of performance parameters such as AFR, swirl, valve timing, SOI, and many others. Design constraints imposed by the existing engine hardware necessitated an iterative loop between design and analysis toolsets, ultimately converging on a final design for the ammonia-conversion hardware. The engine was rebuilt with the new hardware and evaluated in an engine test cell. A new control strategy developed and flashed onto a prototyping electronic control unit allowed for full control over all engine parameters. An initial calibration was developed, providing test data for validation of the engine 1D and 3D models. The impact of the design choices on engine operability and the ability to meet program targets is discussed as well as opportunities for further optimization of the ammonia-conversion hardware, informed by the validated models.

Kaul, Brian [ORNL] (ORCID:0000000184813620)

Experimental study of airpath electrification in an opposed-piston two stroke (OP2S) engine architecture

The opposed-piston two stroke (OP2S) engine shows potential as an alternative engine architecture to the conventional four stroke engine due to its high-power density, thermal efficiency, and versatile airpath management system. Since the pistons of a two-stroke engine do not pump the air into and out of the cylinder like in a four-stroke engine, the selection of the air induction devices and airpath actuators becomes critical to optimize engine performance. Both the pumping losses and the in-cylinder combustion process can be affected by the scavenging process in a two-stroke engine. Therefore, this study compares two different airpath configurations for the same family of OP2S engines and investigates performance metrics like scavenging control, pumping work, net indicated and brake efficiencies, and engine-out emissions associated with each airpath. Data was collected on a 3.2 L, two-cylinder OP2S engine with an electrically assisted turbocharger (EAT) and a 4.9 L displacement, three-cylinder engine with a variable geometry turbocharger (VGT) and a supercharger. The experiments consisted of speed and load sweeps for both engines at the same operating conditions to compare scavenge control in both architectures. For the three-cylinder layout, the SE sweep range was much higher, and the intake pressure could be independently varied with air flowrate, thus providing more flexibility for scavenging control. The supercharger and the VGT usage was optimized based on its efficiency map and thus, this layout had lower pumping losses compared to the EAT. The two-cylinder engine had a higher overall SE as compared to the three-cylinder engine, but the intake pressure and air flowrate could not be decoupled, leading to over scavenging and increased short circuiting of fresh charge into the exhaust.

Bhatt, Ankur [Clemson University, Clemson, SC, USA

Recovery of Natural Gas Equipment Emissions into Gas Compression Engines for the Reduction of Potential Greenhouse Gas Emissions

Since the turn of the millennium, the United States (U.S.) oil and natural gas (ONG) industry has nearly doubled its natural gas production rate. As a result, the ONG industry has recently come under increasing scrutiny for its contributions to greenhouse gas (GHG) emissions. Consequently, various solutions to this problem have been proposed and formulated to reduce the impacts of GHG emissions on the environment. West Virginia University (WVU) have found it important to research the impacts of recovering vented gas streams into prime-mover engines. The U.S. Department of Energy (DOE) and National Energy Technology Laboratory (NETL) have granted WVU funding to research and develop a “Methane Mitigator” (M2) - a “Scalable Vent Mitigation Strategy to Simultaneously Reduce Methane Emissions and Fuel Consumption from the Compression Industry.” One of the main areas of interest for this research was the collection of emissions from natural gas equipment into a Caterpillar G3508J natural gas compression engine. The parameters being analyzed from the engine were brake-specific emissions and power output. The emissions sources considered for this research were pneumatic controllers (PCs), reciprocating compressor vents, and the engine’s open crankcase breather. The compressor vent and PC emissions were simulated using a mass flow controller (MFC) and flowed into the engine using two separate methods: (1) directly into the air intake, and (2) through a retrofitted closed crankcase ventilation system (CCV), serving as a buffer volume. The crankcase emissions were quantified without the CCV, and the impact on exhaust emissions from circulating the crankcase gases into the intake was measured. The simulated compressor vent and PC flows from the MFC had limited effect on the steady state operation of the engine and resulting performance. When the simulated flows were fed directly into the engine’s air intake, the changes within the engine’s continuous performance and emission parameters were larger but lasted for shorter durations. Conversely, when the simulated flows were fed into the CCV before entering the air intake, the changes in the engine’s performance and emission parameters were less pronounced for continuous analysis but lasted for longer durations. In either case, the continuous emission changes in both emissions and performance varied in size depending on the test scenario being run, but the cycle average changes in emissions and performance showed little impact overall compared to the engine’s baseline operation. As a result, the inclusion of a CCV shows a decrease in baseline carbon dioxide equivalent (CO2-eq.) engine emissions (from combined exhaust and open crankcase) of almost 4%. Likewise, the CCV inclusion reduced baseline total methane (CH4) from combined exhaust and open crankcase by upwards of 16%. These atmospheric emissions only decreased further with the inclusions of collected PC and compressor vent flows. The resulting changes in time-averaged rated exhaust behavior (or lack thereof) prove that the proposed M2 system could likely be deployed at sites with modern lean-burn natural gas engines as a viable option for reducing and eliminating potential GHG sources that would have otherwise been unutilized as energy sources.

03 NATURAL GAS

Catalytic enhancement in the performance of the microscopic two-stroke heat engine

Here we consider a model of heat engine operating in the microscopic regime: the two-stroke engine. It produces work and exchanges heat in two discrete strokes that are separated in time. The working body of the engine consists of two d-level systems initialized in thermal states at two distinct temperatures. Additionally, an auxiliary nonequilibrium system called catalyst may be incorporated with the working body of the engine, provided the state of the catalyst remains unchanged after the completion of a thermodynamic cycle. This ensures that the work produced by the engine arises solely from the temperature difference. Upon establishing the rigorous thermodynamic framework, we characterize twofold improvement stemming from the inclusion of a catalyst. Firstly, we prove that in the noncatalytic scenario, the optimal efficiency of the two-stroke heat engine with a working body composed of two-level systems is given by the Otto efficiency, which can be surpassed by incorporating a catalyst with the working body. Secondly, we show that incorporating a catalyst allows the engine to operate in frequency and temperature regimes that are not accessible for noncatalytic two-stroke engines. We conclude with a general conjecture about the advantage brought by a catalyst: including the catalyst with the working body always allows to improve efficiency over the noncatalytic scenario for any microscopic two-stroke heat engines. We prove this conjecture for two-stroke engines where the working body is composed of two d-level systems initialized in thermal states at two distinct temperatures, as long as the final joint state leading to optimal efficiency in the noncatalytic scenario is not a product state, or at least one of the d-level system is not thermal.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC

Fuel Property Effects on Stochastic Preignition Events During Engine Load Transitions

Stochastic preignition (SPI) is an abnormal combustion phenomenon that can cause catastrophic engine damage. There have been several proposed mechanisms of SPI, where a uniform source is still not certain, however, SPI tendencies have been shown to be influenced by engine operating conditions, oil composition, engine age, and fuel chemical and physical properties. Laboratory research and testing for SPI propensity is challenging given the stochastic nature of events, as well as the potential for significant degradation of the engine platform and measuring equipment over time. Thus, SPI specific experiments are generally conducted under either sustained or cyclic patterning of steady-state operating conditions to avoid the influence of transient engine boundary conditions on test parameters of interest (e.g. oil additive package, fuel properties, engine speed/load, etc.). In this work a cyclically varying SPI test sequence involves a 5 min engine warmup period at a low engine load of around 4 bar gross indicated mean effective pressure (IMEPg), followed by a transition to high load (~20 bar IMEPg) at a constant 2000 rev/min engine speed for a total of 25 min. This individual test sequence load schedule is then sequentially repeated 10 times to generate significant statistical data for analysis. This work examines the influence of fuel chemical and physical properties on SPI tendency during the unsteady portion of the 10-cycle sequence (the first 5 min of the high load operation in each sequence of the loading cycle) which has been discarded from previous analyses due to the uncertainty in engine operating and thermal boundary conditions. Results from this analysis suggest an increasing trend in the ratio of SPI events during the unsteady test period relative to the steady test period with increasing fuel Reid Vapor Pressure (RVP), implying differences in uncontrolled ignition source terms, possibly from, fuel wall interactions and retention during the load transition phase of the test.

Splitter, Derek [ORNL] (ORCID:0000000174044047)

Plasma-Assisted Pre-Chamber Ignition System for Highly Dilute Stoichiometric Heavy-Duty Natural Gas Engines (Final Technical Report)

This project explored advanced ignition technologies to significantly enhance efficiency and reduce operating costs for heavy-duty natural gas engines operating at stoichiometric conditions, while meeting ultra-low NOx emission standards. The main goal was to develop and validate a plasma-assisted pre-chamber ignition system that could deliver at least a 2% increase in brake thermal efficiency (BTE) and a 4% decrease in total cost of ownership (TCO) compared to a typical multi-cylinder engine with three-way catalyst aftertreatment, ensuring compatibility with the expected 2027 EPA/CARB regulations. In the first half of the project, the research team concentrated on developing and testing plasma-assisted pre-chamber ignition using nanosecond pulsed discharges. Extensive experiments were conducted in an optically accessible rapid-compression and expansion machine, a constant-volume chamber, and an optical single-cylinder engine. Experiments were coupled with CFD simulations. The work produced unique insights into pre-chamber flame formation, jet ignition, dilution effects, and flame quenching at pressures, temperatures, and dilution levels relevant to engines. Although plasma-assisted ignition showed promise in controlled lab settings, the research also identified fundamental and practical challenges when applying this technology to real engine conditions. Midway through the project, a crucial pivot was made, guided by three key findings. First, the power electronics required for nanosecond plasma discharges were found to be too costly for commercial use, undermining the project’s cost-of-ownership goals. Second, nanosecond plasma ignition was highly sensitive to turbulent flow in the pre-chamber, resulting in lower ignition reliability than traditional spark under engine-like conditions. Third, achieving a truly diffuse low-temperature plasma at high pressures near top dead center was not possible, reducing the anticipated chemical enhancement benefits. These results collectively suggested that continuing with plasma-assisted ignition was unlikely to meet both efficiency and cost objectives. In response, the project shifted focus to a more realistic approach: enhancing traditional spark-based pre-chamber ignition with significantly less spark energy. Using insights gained earlier in the project, the team redesigned the pre-chamber to maintain high dilution tolerance and quick combustion, even with lower ignition energy. Testing confirmed that with optimized pre-chamber design and combustion timing, a lower-energy spark could reliably ignite highly diluted stoichiometric mixtures, reduce burn time, and boost thermal efficiency. Final engine testing and techno-economic analysis verified that this revised approach successfully achieved the project goals. The optimized pre-chamber ignition system provided over a 2% increase in calculated brake thermal efficiency compared to the baseline engine. Notably, the lower ignition energy and simplified hardware reduced component stress, extended maintenance intervals, and lowered the total cost of ownership. When used with stoichiometric operation and traditional three-way aftertreatment, the system remained compatible with near-zero NOx emissions targets without increasing cost or complexity in the emissions control system. In summary, although the project deviated from its initial plasma-assisted ignition idea, the work produced a more practical and commercially viable solution. The results show that precisely optimized, low-energy pre-chamber spark ignition can significantly improve efficiency and reduce overall ownership costs for heavy-duty natural gas engines. This directly aligns with DOE goals for cleaner, more efficient, and cost-effective transportation technologies.

03 NATURAL GAS

Fuel reid vapor pressure level and ethanol content on stochastic preignition, effects at steady and unsteady engine operation

The present work investigates relations between fuel Reid vapor pressure (RVP) and biofuel (ethanol) content on stochastic preignition (SPI) at both sustained steady-state engine operation and following load transients. This work stems from in-field observations that automotive original equipment manufacturers have observed consistent seasonal increases in United States customer drivability complaints and warranty claims during September and October where SPI is suspected to be responsible. The seasonal timing of these events coincides with the United States seasonal fuel property changeover initiating on September 15 each year, where fuel RVP increases. To explore potential linkage between fuel RVP and SPI the present study employs engine SPI experiments coupled with laboratory spray measurements of fuels with RVPs of 8, 12, and 16 psi in both E10 (10% ethanol) and E25 (25% ethanol) fuels. Engine results are partitioned into fuel RVP and ethanol content effects on SPI in steady-state, sustained high-load engine operation and unsteady-state low- to high-load transitions, where off-engine spray vessel patternation and tip penetration results help to elucidate the observed fuel effects on SPI. A boosted direct-injected, spark-ignition engine was fueled with three market relevant E10 and E25 fuels with RVPs of 8, 12, and 16 to characterize the interplay between winter fuels and abnormal combustion behavior. The steady-state work shows that for high-load, steady-state engine operation, SPI is directly linked to fuel retention, which was found to be dependent on fuel distillation. The unsteady-state engine operation work shows that following low-to high-load transitions, SPI can occur from a memory of fuel property effects at low-load operation. Specifically, the fuel RVP effect on fuel spray collapse at low loads was found to correlate with SPI with a more than 95% confidence interval following low- to high-engine-load transitions. Results suggest that fuel-wall impingement at low-load operation could carry over into high-load transitions and generate SPI events following low- to high-load transitions.

09 BIOMASS FUELS

CFD modeling of near-wall combustion and unburned methane prediction in natural gas spark ignition engines

Natural gas-powered engines play a critical role in gas drilling, compression, and transmission sectors, but methane (CH 4 ) from engine combustion slip can be significant over their lifespan, contributing to atmospheric pollution and signaling reduced engine efficiency. Here, to address this challenge, computational fluid dynamics (CFD) simulations offer valuable insights into the in-cylinder combustion process, enabling the optimization of combustion strategies and engine designs to minimize unburned CH 4 slip. This study aims to evaluate and improve combustion models for simulating the combustion process and predicting unburned CH 4 concentrations in natural gas spark-ignition (SI) engines, including engines that are part of combined reformer-engine systems. Specifically, the performance of two flamelet-based combustion models—the Extended Coherent Flame Model (ECFM) and the G-equation model—was assessed using experimental engine data collected under varying excess-air ratio (λ) conditions and fuel compositions, including natural gas and syngas blends. In addition, to enhance the predictive capabilities of the G-equation model, a flame-wall interaction (FWI) sub-model was integrated into its framework. The effects of its model parameters, such as quenching and influence distance, on combustion behavior and unburned methane predictions were analyzed in detail. The ECFM tended to predict delayed combustion phasing under diluted mixture conditions, resulting in overprediction of unburned CH 4 concentrations. In contrast, the G-equation model provided reasonable predictions of combustion pressure, while representing higher the CH 4 reduction rate across the operating condition compared to experimental data. Incorporating the FWI sub-model—with the quenching distance calculated based on a pressure-dependent relation (P -0.48 ) and a fixed influence distance of 1.5 mm—further improved the G-equation model’s accuracy in predicting CH 4 reduction rates without compromising its ability to simulate the combustion process.

Combustion model

Comparison of a Full-Scale and a 1:10 Scale Low-Speed Two-Stroke Marine Engine Using Computational Fluid Dynamics

International marine shipping is a growing component of international trade; a vast majority of all the world’s goods are being transported on large ocean-going vessels. The International Maritime Organization (IMO) introduced the Energy Efficiency Design Index in 2013, a regulatory framework of associated metrics for reducing emissions of CO 2 per tonne-mile from shipping by approximately 10% each decade. Therefore, decarbonizing the maritime sector requires the development of new fuel sources. Because of the extremely large physical size of the internal combustion engines present in shipping vessels, experimental iterative development of the engine and fuel system is cost-prohibitive. Thus, the ability to perform combustion system development in a scaled platform that can be more easily operated and modeled computationally is of interest. To that end, scaling relationships are needed to translate the results from a smaller engine to a larger counterpart. Scaling studies to date have been restricted to low scaling ratios, four-stroke light-duty engines, and under-resolved computational fluid dynamic simulations that likely do not accurately capture the physics of scaling. In this work, computational models of a 1:10 scale and a full-scale two-stroke crosshead low-speed marine engine were created and validated against experiments obtained in a real 1:10 scale engine installed at Oak Ridge National Laboratory. Further, due to the large size of the full-scale engine, the model required large high-performance computing resources to be evaluated. The availability of high-performance computing resources at the Department of Energy’s Leadership Computing Facilities is an enabler of the current work. The results of the small- and large-scale engine simulations were compared to analyze the effectiveness of the appropriate scaling laws under these extreme scaling ratio conditions.

33 ADVANCED PROPULSION SYSTEMS