Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites
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This work builds on prior work that developed a methodology for evaluating thermal stress in cemented doublets. The prior studies were limited by a paucity of actual test data, particularly from thermally tested cemented doublets. This follow-on study uses the existing methodology to estimate stresses in cemented doublets that have been tested for a temperature range from –40°C to 85°C and establishes safe stress levels using actual data. We also discuss limitations and concerns that we need to address to improve our understanding of cemented doublet failure.
CMB-S4—the next-generation ground-based cosmic microwave background (CMB) experiment—is set to significantly advance the sensitivity of CMB measurements and enhance our understanding of the origin and evolution of the universe. Among the science cases pursued with CMB-S4, the quest for detecting primordial gravitational waves is a central driver of the experimental design. This work details the development of a forecasting framework that includes a power-spectrum-based semianalytic projection tool, targeted explicitly toward optimizing constraints on the tensor-to-scalar ratio, r, in the presence of Galactic foregrounds and gravitational lensing of the CMB. This framework is unique in its direct use of information from the achieved performance of current Stage 2–3 CMB experiments to robustly forecast the science reach of upcoming CMB-polarization endeavors. The methodology allows for rapid iteration over experimental configurations and offers a flexible way to optimize the design of future experiments, given a desired scientific goal. To form a closed-loop process, we couple this semianalytic tool with map-based validation studies, which allow for the injection of additional complexity and verification of our forecasts with several independent analysis methods. We document multiple rounds of forecasts for CMB-S4 using this process and the resulting establishment of the current reference design of the primordial gravitational-wave component of the Stage-4 experiment, optimized to achieve our science goals of detecting primordial gravitational waves for r > 0.003 at greater than 5σ, or in the absence of a detection, of reaching an upper limit of r < 0.001 at 95% CL.
This work presents a new technique for observing the solid–liquid phase transformations in complex diesel fuel blends and diesel surrogates under high-pressure conditions intended to simulate those occurring in vehicle fuel injectors. A high-pressure apparatus based on a visual identification of freezing and thawing has been designed and built to monitor phase behavior and determine the crystallization temperature of complex fuels to predict wax precipitation. The proposed methodology was validated using pure substances—n-hexadecane (C16H34), cyclohexane (C6H12), and a binary cyclohexane/n-hexadecane mixture—all of which have been well-characterized previously. The crystallization temperatures of these compounds were measured from atmospheric pressure to 400 MPa for temperatures varying from 290 to 363 K and compared to those reported in the literature. The standard error of the estimated temperatures, based on a given pressure, between the experimental data obtained in this work was compared to data in the literature from Domanska et al. This methodology is being extended to investigate the properties of more complex fuel mixtures.
smol is a Python implementation of the Cluster Expansion Method and extensions of this methodology; which is used to fit applied lattice models from first principle calculations for subsequent use in Monte Carlo simulations for computing thermodynamic and statistical properties of atomic configuration. smol has a several notable advantages over other similar software packages. The first being its Python implementation which makes it easy to use even for users with little software and coding skills. Despite being implemented in Python, essential Monte Carlo routines are implemented in Cython such that performance is not compromised and is competitive even to similar software implemented in C/C++. Furthermore, the package has specific functionality for handling complex ionic materials (such as cathodes and electrolytes) that is not readily available in other packages. Lastly, the software has a flexible and modular design with the intention of making it fast and efficient to develop and extend the methodology.
This paper presents a novel approach for modeling liquid wall ablation in liquid wall-protected inertial fusion energy (IFE) chambers. These systems are promising candidates for the implementation of fusion technology, yet significant gaps remain in understanding the underlying physical processes and their implications for design. Following target ignition, a portion of the fusion energy is released as x-rays, which deposit their energy into an array of liquid jets, leading to partial vaporization. Accurately modeling this heat deposition and vaporization process remains challenging due to the complex geometries typical of (pre-conceptual) IFE chamber designs. Furthermore, the subsequent expansion of vaporized material into the chamber’s vacuum environment poses difficulties for conventional CFD methods based on continuum assumptions, which can lead to significant inaccuracies. To address some aspects of these challenges, this work introduces a ray-tracing-based methodology to map the spatial distribution of ablated material in liquid wall-protected systems. In addition, a vacuum-tracking scheme is developed to extend the applicability of an OpenFOAM-based solver to gas dynamics in rarefied environments. The proposed approach has been verified through numerical benchmarks and applied to a practical case involving the HYLIFE-II (High Yield Lithium Injection Fusion Energy) chamber. The methodology advances the modeling capabilities for liquid wall-protected IFE systems and provides valuable tools to support their design and optimization.
One of the main goals of the Thermal/Epithermal eXperiments (TEX) project is to use existing Nuclear Criticality Safety Program (NCSP) assets to create critical experiment plutonium and uranium test beds for materials important to criticality safety that have insufficient benchmark evaluations. The plutonium test bed experiments were completed in 2018 and are published in the 2020 edition of the International Criticality Safety Benchmark Evaluation Project (ICSBEP) Handbook. The uranium test bed assemblies were completed in 2023 and accepted in the 2024 edition of the ICSBEP Handbook. The Nuclear Criticality Safety (NCS) group at Y-12 National Security Complex has identified programmatic need for validation cases for uranium electrorefining operations at Y-12. The electrorefining operation credits lithium enriched in 6 Li in addition to 35 Cl as absorbers in the design criticality safety evaluation for precluding criticality under upset conditions in the large and geometrically unfavorable electro-refiner. There is, however, inadequate experimental validation for the 6 Li absorbers. As an extension of the TEX uranium test bed, TEX-Cl critical experiments were performed with sodium chloride salt to address the 35 Cl thermal absorption as well as other validation needs at Los Alamos National Laboratory (LANL). These experiments were completed in 2024 and accepted into the 2025 ICSBEP Handbook. To continue the methodology used in TEX-Cl, TEX-Li aims to accomplish the same. The overall design of both experiments was to use commercially available, high purity, salts with polyethylene moderator and HEU plates to configure a critical assembly. Three experiments are planned for TEX-Li using encapsulated lithium carbonate (Li 2 CO 3 ), with natural 6 Li abundance. For all experiments, the highly enriched uranium (HEU) Jemima plates will be used as fissile material. Multiple layers will be stacked together with encapsulated Li 2 CO 3 alternated with polyethylene in standard configurations. Standard stacking was found to be optimal in matching the different sensitivity profiles provided by the Y-12 models. Three configurations are proposed with varying polyethylene moderation and a constant 1/4” absorber thickness. The first uses 11 layers of 5/4” polyethylene, the second uses 9 layers of 3/4” polyethylene, and the third uses 10 layers of 1/2” polyethylene. Calculations showed that some alternative forms of lithium-based materials provided slightly less-optimal sensitivity profiles when compared to lithium carbonate but come with other drawbacks. These alternatives included lithium aluminate (LiAlO 2 ), Aluminum-2050 alloy, Aluminum-8090, Aluminum-2095, lithium hydride (LiH), and lithium fluoride (LiF). Lithium aluminate and aluminum-2050 provided comparable sensitivity profiles when compared to lithium carbonate and can be used instead if lithium carbonate cannot be readily procured. After a broad material study, lithium carbonate outperformed any alternative material with a balance in affordability and workability. The assessment of experimental uncertainties of the non-absorber and absorber components was predicted to be 0.00089 and 0.00093 Δk eff , respectively. The largest uncertainties may be reduced with precision dimensional inspection of the components. Many of the parts and equipment for IER 575 have already been fabricated or procured for previous projects and therefore do not contribute significantly to the overall cost of this experiment. This includes the Jemima plates and Comet critical assembly machine, which are existing NCSP assets, as well as the aluminum platen and polyethylene reflector rings, which were fabricated and authorized for the TEX experiment involving HEU with polyethylene. Lithium carbonate containers will be procured by LANL and will be filled by LLNL. The total material costs for TEX-Li experiments are estimated to be on the order of $\$$47,400. Precision inspection, including dimensional, mass, density, and impurity, is recommended for all components for an estimated cost of $\$$12,000.
In this article, the development of nanoporous metals and metallic composites through dealloying processes presents significant opportunities in materials engineering. However, designing multicomponent precursor alloys and establishing corresponding processing methods that yield predictable compositions and nanostructures remain a complex challenge. This article explores how machine learning (ML)-augmented computational and experimental methodologies can tackle these challenges by predicting precursor alloy compositions, final nanoporous structures, and mechanical properties, while integrating ML-enabled autonomous experimentation for material design and quantification. We highlight recent advancements in applying ML to nanostructured materials design via dealloying and discuss how techniques from other nanomaterial designs can be adapted for improved control over morphological and compositional outcomes in nanoporous and nanocomposite materials. Furthermore, we explore the role of ML in autonomous synchrotron x-ray experimentation, enabling real-time feedback between modeling and experimental setups. ML-driven approaches to microstructure characterization and mechanical property prediction are also examined, with a focus on modeling and advanced imaging techniques such as three-dimensional nanotomography. Finally, this article outlines future directions for ML-enhanced materials science, emphasizing the exploration of high-dimensional parameter spaces and the incorporation of materials kinetics into processing and property evaluation, ultimately advancing the design of nanoporous structures and materials science.
An in-depth comprehension of the changing impact of mode choice influencing factors is essential in planning for behavior-adaptive mode shift policies. This study developed a framework to investigate a method of evaluation of the changes in mode choice using a small participation pool. A field application in Pima County, Arizona was developed to test the developed framework to evaluate the impact of a real transit experience. Twenty-two participants were recruited and repeated measurements were taken before and after their transit trip. The results revealed that people are less susceptible to their mental biases after a transit trip and consider more objective elements such as walking time. The developed framework resulted in successful evaluation methods that are reproducible for other application study designs. Thus, the results further present that low participant recruitment in application-based field studies can be accomplished using this developed methodology, for other regions and studies.
The Westinghouse Lead-cooled Fast Reactor (LFR) is a medium-size, passively safe, economic, Gen-IV nuclear reactor. An important effort within the Westinghouse LFR program is the development of the safety analysis methodology, which comprises computer code development, model development, and experimental testing. A key initial task associated with the development of the safety analysis methodology is the identification of processes and phenomena that affect the plant's capability to meet selected safety performance indicators. This is accomplished through the development of a Phenomena Identification and Ranking Table (PIRT) for selected accident scenarios which, for this specific PIRT effort, included selected postulated design basis accidents and hypothetical beyond design basis accidents in LFRs. This paper describes the role of PIRT in the development of the Westinghouse LFR safety analysis methodology and the process used in the PIRT development. Specifically, the Westinghouse LFR PIRT assessed importance of pertinent phenomena and identified gaps in their knowledge-base by evaluating current modeling capabilities and data available for validation. The ultimate goal was to provide guidance on computer code development and validation efforts and to prioritize testing to support LFR design and licensing. The key phenomena and processes that are deemed highly important for the safety performance indicators, but for which the state of knowledge is low, are presented. The testing program and analyses development are planned to address significant phenomena in the PIRT.
In the world of ever-advancing technology, Autonomous Systems (AS) find extensive application, bolstering functionalities of critical infrastructures such as nuclear power plants. These systems, however, are increasingly becoming a target for nefarious activities, namely through inference attacks, trojan attacks, and adversarial reprogramming. This paper delves into a comprehensive exploration of machine learning (ML)-driven autonomous control systems within advanced nuclear reactor designs, revealing the vulnerabilities and proposing strategies for defense against potential cyber-attacks. Advanced cyber-attacks against critical infrastructure and the energy sector are becoming more common. With the invention of autonomous control systems (ACS) within advanced nuclear reactor designs, system designers, reactor operators, and regulators must consider cybersecurity during the design and operational phases. This article provides a cyber threat assessment of machine learning (ML)- based digital twinning (DT) technologies in the context of advanced reactor ACS. A cyber-physical testbed was created to emulate nuclear reactor digital instrumentation and controls (I&C) and act as a basis for the ACS. The ACS was designed as two plant-level DTs predicting reactor malfunctions and determining control actions and two component-level DTs responsible for classifying component states and forecasting component inputs and outputs (I/O). Two duplicate ACS designs– one using a traditional ML framework and one using an automated ML (AutoML) framework– were created and tested against cyber-attacks on training data, real-time process data, and ML model architectures to determine their respective qualitative cyber-risk in terms of likelihood and impact. Both frameworks showed similar cyber-resilience against training, real-time, and ML architecture attacks, proving that neither is inherently more secure. Recommended safeguard and security measures are posed to system designers, reactor operators, and regulators to maintain the cybersecurity of ML-based DT technologies such as ACS, prompting a holistic view of shared responsibility for maintaining cyber-secure ML-based systems. As global reliance on generation III reactors begins to be critically assessed, the evolution towards advanced reactor systems utilizing digital instrumentation and controls (I&C) becomes not merely preferable, but essential. The integration of semi and fully autonomous control systems (ACS), powered by digital I&C and machine learning (ML)-based digital twinning (DT) technologies, emerges as a potent strategy to mitigate operations and maintenance costs, thereby enhancing the economic feasibility of novel reactor designs. However, with a staggering 500% and 380% increase in cyber-attacks reported against the energy sector by the United States Department of Energy (DoE) and the European Union respectively, a surge in cyber vulnerabilities specifically targeting the nuclear industry has been 2 markedly observed. Notable incidents, such as the W32.Ramnit spyware infiltration at the Gundremmingen nuclear power plant in Germany and the Dtrack spyware intrusion at the Kudankulam nuclear power plant in India, while not directly compromising core industrial control systems (ICS), underscore a compelling necessity to fortify cybersecurity protocols in safeguarding reactor systems against increasingly adept digital adversaries. In light of this, our investigation extends beyond conventional cybersecurity parameters, diving into the intricate web of potential vulnerabilities woven into ML-based DTs and ACS in advanced reactor systems. A crafted cyber-physical testbed and preliminary ACS were devised to act as a mirror, reflecting potential configurations of advanced reactor control designs. Moreover, this study is intertwined with a scrutinization of ML models, developed either through conventional, manually tuned methodologies or via automated means through AutoML, probing into their cyber-risk profiles within operational technology (OT) environments. Expanding on this, two distinct ACS blueprints were forged – one navigating through the corridors of traditional ML and the other traversing the path of AutoML – in an effort to holistically encapsulate the considerations pivotal to ML-based DT control system design. Employing the SANS Institute Industrial Control System (ICS) Kill Chain and the MITRE ATT&CK Tactics, Techniques, and Procedures (TTP) framework, a structured analysis was conducted, launching three targeted attacks against the training dataset, real-time dataset, and ML models, therein dissecting the potential cyber-attack implications against both ML frameworks within an ACS milieu. It is essential to note that three distinct categories of attacks were conducted against both ACS configurations, each encompassing three distinct ML-based DTs, cumulating in a total of 18 varied attacks. This exploration extends into the realms of Autonomous System Inference, Trojan, and Adversarial Reprogramming Attack and Defense, unraveling vulnerabilities, and opportunities for fortified defenses against such intrusions, particularly where ML-driven technologies, and by extension, ACS, are deployed. Final recommendations, articulated through a lens of security, safeguard, and implementation considerations, are presented for both traditional and AutoML models, anchoring upon the existing knowledge landscape and ML-based DT modeling for ACS, and are offered as a beacon to guide the nuclear industry through the intricate cybersecurity challenges that lie ahead.
Synthetic design has enabled increasing power conversion efficiency advances in organic photovoltaics (OPV). One continuing knowledge gap is detailed understanding of single-material chemical (photo)stability. Many considerations are based on prior OPV-relevant donor homopolymer systems rather than the next-generation push–pull architectures. Generally, energetic offsets between the lowest occupied molecular orbital of the donor and molecular oxygen are assumed to dictate kinetics of photo-induced charge transfer to a super oxide radical. Herein we determine the ambient-induced photo-degradation pathways, presented as proposed site-specific arrow-pushing mechanisms, for five donor polymers all containing the same push unit – alkylthienyl-substituted-benzodithiophene (BDTT) – but with chemically distinct pull units. The donor-only polymer films were subject to controlled photobleaching in air as an accelerated degradation approach, coupled with simultaneous monitoring of absorptance. Sample subsets were periodically removed and analyzed with X-ray photoelectron spectroscopy, to evaluate near-surface chemical composition and oxygen additions to hetero reporter atoms on either the BDTT push unit or distinct pull unit (i.e., sulphur and nitrogen). Here, this methodology allows us to distinguish between different mechanisms of bond cleavage and formation. Overall, we find that neither polymer redox properties nor individual push or pull unit stability are sufficient to predict photo-oxidative degradation of these polymers. Rather, there is a greater dependence on the susceptibility of unique structural groups within a polymeric system. Alkyl chain oxygen addition is generally the first attack site and direct sulfur oxidation on the conjugated backbone occurs after saturation of the alkyl chain initiation sites. This work provides a standard that could be used to evaluate relative photo-oxidative (in)stability for new OPV materials quickly – prior to time-consuming device optimization – and demonstrates an effective methodology for correlating optical degradation with chemical structure alterations via spectroscopic signatures to guide synthetic design.
Robust, low-cost nonintrusive flow meters are of interest in many industries. Particularly, a reliable nonintrusive flow measurement for the diagnosis of air leaks in compressed air systems is desirable. Measurement of the air flow due to leaks in the system ensures an accurate estimation of potential cost and energy savings. This study evaluates a novel method of using thermal responses to nonintrusively measure leakage rates in compressed air lines. The method uses heat and the resulting thermal response to calculate the flow rate inside the compressed air line. Compared to the current methods for flow measurement, this method can simplify flow measurement while decreasing the sensitivity to errors when measuring flow rates. In this study, the methodology of the proposed method is explained along with the potential advantages to the design. Two approaches are evaluated: a dynamic step response and sinusoidal frequency response. Simulated tests evaluate the feasibility of the proposed methods, followed by experiments that validate the simulation results. A clear correlation between the thermal step response and the flow rate indicate viability of the proposed method in simulation. Experimental results yielded similar results, confirming the validity of the proposed method. The results of a field test in an industrial environment demonstrate the capability of the approach to other flow rate measurement techniques.
This study introduces a sophisticated data-driven framework for analyzing Electronic Health Records (EHRs) using transformer-based models to identify and disentangle overlapping treatment contexts. The framework leverages a preprocessing pipeline that transforms structured procedural codes into semantically enriched descriptive text, enabling the use of attention mechanisms to cluster medical events into treatment milestones—cohesive and distinct components of care processes. The methodology is rigorously validated using synthetic datasets derived from the MIMIC-III database, designed to simulate the heterogeneity and overlapping procedural contexts characteristic of real-world EHR scenarios. Quantitative evaluation highlights the framework’s robustness in disentangling concurrent care pathways, with attention metrics and unsupervised clustering approaches demonstrating the ability to preserve intra-context relationships while distinguishing inter-context dependencies. By addressing challenges inherent in data heterogeneity, this approach provides a foundation for uncovering complex treatment patterns, advancing clinical decision-making, and optimizing resource allocation in diverse healthcare environments.
Doubly-fed induction generators (DFIGs) are prone to subsynchronous resonance (SSR) with series-compensated transmission lines and experiencing SSR-generated harmonics of wide-ranging magnitudes. This paper presents a large-signal impedance-based approach for the prediction of the magnitude of SSR-generated harmonics in DFIGs. Note that the large-signal impedance of a network shows variation in its impedance response with the magnitude of perturbation at its terminals. It is discovered in this paper that the impedance of a series-compen- sated transmission line starts changing with the magnitude of SSR because of the metal-oxide varistor-based protection of series capacitors in the line. The changing line impedance halts the growth of the SSR beyond a certain point, where the DFIG forms a limit-cycle mode and emits harmonics at the SSR frequency. The discovered role of the protection of series capacitors in SSR not only enables the prediction of SSR-generated harmonics but also can be used for the timely detection of an SSR event to avoid system disruption and sudden loss of bulk generation. The large- signal impedance-based prediction of SSR-generated harmonics in DFIG-based wind and hydro generators is demonstrated using numerical simulations of a 2.5-MVA, 690-V DFIG supplying to a series-compensated transmission line.
In order to accurately characterize chemical changes to the binder in plastic-bonded explosives (PBXs) it is important to develop new gel permeation chromatography (GPC) methodologies as well as update previous methods. Herein we present new and updated GPC methodology for Viton A, Kraton G, and Oxy 461. The methods developed were specifically designed for Malvern OMNISEC with a Mixed C column, but minor modifications could be made to these methods to make applicable to other instrumentation.
The field of materials design is currently experiencing a notable evolution, driven by the convergence of sophisticated computational methodologies based on first principles and data-driven modeling approaches. I will review our recent endeavors employing AI/ML to expedite first-principles simulations and mitigate traditional methods' temporal and spatial limitations. Central to our efforts is developing and utilizing ML interatomic potentials (MLPs) across a diverse spectrum of materials. We show that MLPs serve as invaluable tools for navigating the complexities of the simulations, such as understanding the behavior of MgO at extreme environments of ~1 terapascal and temperatures >10,000 Kelvin. Moreover, we show that MLPs can provide precise details of the intricate dynamics governing the oxidation processes of binary alloy systems due to the competition between surface segregation and reconstruction tendencies. In summation, advancements in MLPs open the door to fresh possibilities in material modeling and, ultimately, discovery.
This project aims to design cost-effective thermal/environmental barrier coatings (TEBC) based on high entropy rare earth disilicates to protect SiC-based ceramic matrix composites from chemical and thermal attack for better performance of components in the hot section of gas turbine engines. To accelerate the alloy design, we utilize first-principles density functional theory (DFT) together with combinatorial chemistry methodology to predict key properties including phase stability, apparent bulk coefficient of thermal expansion (ABCTE), intrinsic lattice thermal conductivity, and temperature-dependent elastic constants. Specifically, this project focuses on β-RE2Si2O7 (RE=Yb, Y, Er, Lu, La, Ce,) with β-Yb2Si2O7 and β-Y2Si2O7 as the benchmark. Our DFT calculations predict that Er1/4Lu1/4Y3/4Yb3/4Si2O7 and Er1/2Lu1/2Y1/2Yb1/2Si2O7 have ultralow lattice thermal conductivity < 0.23 W/m/K at 1500 K and a good match of average ABCTE (5.1 - 5.2×10-6 K-1) with SiC. Owing to the low cost and abundant supply of Ce and La, the A- and G-La2Si2O7/Ce2Si2O7 disilicates are also studied. Our study shows that G-phase Ce2Si2O7 has an ultralow thermal conductivity (0.26 W/m/K at 1500 K) and the apparent bulk ABCTE (≈6.9×10-6 K-1) slightly higher than SiC, demonstrating great potential as low-cost high-performance T/EBC. However, La2Si2O7 and Ce2Si2O7 undergo an A-phase to G-phase polymorphic transition at around 1470 K.