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At least 487 records · Page 27

Native Chemical Ligation of Peptoid Oligomers

Bioorganic chemists are inspired by natural biopolymers to design peptidomimetic oligomers that can exhibit sequence-structure-function relationships. Biomimetic polymers can be synthesized to incorporate a specific sequence of nonbiological monomer units using a variety of iterative solution-phase or solid-phase reaction schemes. These protocols generally provide access to a vast diversity of oligomeric compounds but are limited with respect to their ability to attain protein-like chain lengths. This constraint can preclude access to sequence-defined synthetic macromolecules with sufficient sizes required to exhibit tertiary structure and other protein-mimetic attributes. In contrast, peptide chemists have overcome this limitation by developing convergent synthetic methods, such as native chemical ligation, to join individual, smaller peptide chains together to make larger peptides or full proteins. A similar convergent approach is needed to establish efficient synthetic routes to non-natural sequence-defined macromolecules. Herein, we adapt the peptide native chemical ligation method to peptoid oligomers, demonstrating how short chains can be conjoined to create sequence-defined peptoid macromolecules. Nanosheet-forming peptoid polymers with distinct surface loop display domains were generated by sequential ligation of several discrete fragments. This method provides a reliable convergent ligation route for sequence-defined polypeptoids that results in a native amide bond joining the fragments. We envision that this strategy will be useful in synthesizing peptoid-based proteomimetics that incorporate diverse chemical features.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Adapting CLUTCH methodology to multigroup TSUNAMI-3D for eigenvalue sensitivity calculations

The sensitivity of the eigenvalue to uncertainties in nuclear data and its evaluation are important for nuclear criticality safety. TSUNAMI-3D sequences within the SCALE code system offer several options to the user community for calculating eigenvalue sensitivity coefficients with multigroup (MG) and continuous energy (CE) 3D transport capabilities. TSUNAMI-3D sequences implement the adjoint-based perturbation theory with MG KENO code, the Contributon Linked eigenvalue sensitivity/Uncertainty estimation via Track length importance CHaracterization (CLUTCH) method with CE KENO code, and the Iterated Fission Probability (IFP) method with CE KENO and Shift codes. Each method has benefits and limitations depending on the problem that is run. The work presented here aims to adapt the CLUTCH method, which enables the Contributon method's mesh-free, memory-efficient approach for calculating adjoint-weighted tallies for sensitivity calculations, to the MG TSUNAMI-3D sequence. This application would eliminate the explicit adjoint KENO calculation, as well as the memory-consuming mesh flux moment tallies required by the conventional MG TSUNAMI-3D. Smaller memory footprints in the CLUTCH methodology and relatively shorter runtimes in MG KENO transport can make MG TSUNAMI-3D a viable method for some complex problems. Moreover, this adaptation allows MG sensitivity calculations with Shift, ORNL's next-generation high-performance Monte Carlo transport code, which currently does not offer any sensitivity capabilities with MG particle transport simulations. Initial implementation of the new MG TSUNAMI-3D sequence and its preliminary results with a selected critical benchmark experiment in the Verified, Archived Library of Inputs and Data (VALID) are presented in this study.

KENO↗

Safe Reinforcement Learning for Emergency Load Shedding of Power Systems

The paradigm shift in the electric power grid necessitates a revisit of existing control methods to ensure the grid’s security and resilience. In particular, the increased uncertainties and rapidly changing operational conditions in power systems have revealed outstanding issues in terms of either speed, adaptiveness, or scalability of the existing control methods for power systems. On the other hand, the availability of massive real-time data can provide a clearer picture of what is happening in the grid. Recently, deep reinforcement learning (RL) has been regarded and adopted as a promising approach leveraging massive data for fast and adaptive grid control. However, like most existing machine learning (ML)- based control techniques, RL control usually cannot guarantee the safety of the power systems. In this paper, we introduce a novel method for safe RL-based load shedding of power systems that can enhance the safe voltage recovery of the electric power grid after experiencing faults. Numerical simulation on the IEEE 39-bus testcase is performed to demonstrate the effectiveness of the proposed safe RL emergency control, as well as its adaptive capability to faults not seen in the training.

reinforcement learning, emergency control, power g↗

Advances in Kriging-Based Autonomous X-Ray Scattering Experiments

Autonomous experimentation is an emerging paradigm for scientific discovery, wherein measurement instruments are augmented with decision-making algorithms, allowing them to autonomously explore parameter spaces of interest. We have recently demonstrated a generalized approach to autonomous experimental control, based on generating a surrogate model to interpolate experimental data, and a corresponding uncertainty model, which are computed using a Gaussian process regression known as ordinary Kriging (OK). We demonstrated the successful application of this method to exploring materials science problems using x-ray scattering measurements at a synchrotron beamline. Here, we report several improvements to this methodology that overcome limitations of traditional Kriging methods. The variogram underlying OK is global and thus insensitive to local data variation. We augment the Kriging variance with model-based measures, for instance providing local sensitivity by including the gradient of the surrogate model. As with most statistical regression methods, OK minimizes the number of measurements required to achieve a particular model quality. However, in practice this may not be the most stringent experimental constraint; e.g. the goal may instead be to minimize experiment duration or material usage. We define an adaptive cost function, allowing the autonomous method to balance information gain against measured experimental cost. We provide synthetic and experimental demonstrations, validating that this improved algorithm yields more efficient autonomous data collection.

36 MATERIALS SCIENCE↗

Comparison of Rotor Wake Identification and Characterization Methods for the Analysis of Wake Dynamics and Evolution

Optimal wind power plant design requires understanding of wind turbine wake physics and validation of engineering wake models under wake-controlled operating conditions. In this work, we have developed and investigated several different wake identification and characterization methods for analyzing wake evolution and dynamics. The accuracy and robustness of these methods, based on Gaussian function fitting and adaptive contour identification, have been assessed by application to a large-eddy simulation data set. A new contour-based method based on downstream momentum deficit has been considered. Uncertainties arising from wake-identification errors result in characterizations of the wake expansion, recovery, and meandering motion that differ by 19% of the rotor area, 4% of the freestream, and 15% rotor diameter, respectively.

17 WIND ENERGY↗

Differentiable Multiphysics Codes: A Breakthrough Technology for Simulation and Computing

This document summarizes the findings of a strategic planning exercise commissioned by the Weapons Simulation and Computing, Computational Physics (WSC/CP) program at the Lawrence Livermore National Laboratory (LLNL) in FY24. During the year, the committee met with multiple stakeholder communities to gather input, opinions, suggestions and concerns which have been incorporated throughout this document. The key findings from this exercise are summarized: • The development of multiphysics modelling and simulation (mod/sim) codes and software technologies, their deployment on exascale compute platforms, and their broad adoption across the NNSA is a major success of the Advanced Simulation and Computing (ASC) program and the Exascale Computing Project (ECP). Sustained investment in these core technologies is essential. • Today’s state of the art involves running ensembles of O(100K) simulations to perform uncertainty quantification (UQ) and design studies using multiple statistical methods such as Bayesian optimization to understand sensitivities of our models and explore parameterized design spaces. Even with exascale computing, we are practically limited to O(10) parameters in these studies since the number of simulations required to sample the space scales exponentially with the number of design parameters. • The data from these simulation ensembles is increasingly being used to train machine learned (ML) surrogates (or reduced order models, ROMs) which can then be used for optimization or real time design exploration. However, the trained surrogates are still limited in the number of parameters they can represent due to the sampling limitations previously noted. • Augmenting our suite of integrated multiphysics simulation codes, both current and emerging, with the ability to compute gradients (solution derivatives) of arbitrary simulation outputs with respect to (some or all) simulation inputs would be a breakthrough technology, opening the door to a new era of efficient and automated inverse design based on verified and validated mod/sim capabilities. • This capability, which we refer to as differentiable multiphysics codes (DMCs), would revolutionize both UQ and optimization studies by breaking the curse of dimensionality that presently limits our “gradient-free” ensemble based computing approach. A similar breakthrough occurred in the AI/ML community once the ability to compute gradients of arbitrary loss functions using back-propagation became commonplace. Gradient information from the multiphysics codes can also be used to dramatically improve the efficiency and scale of training of ML/ROM surrogates for rapid assessments. • Achieving this in our suite of codes will be a grand challenge, similar to the amount of effort that was required to transition from CPU to GPU computing. It will require buy-in from the entire WSC/CP program and beyond, including all integrated codes, physics and engineering models, third-party library dependencies and performance portability abstractions. It will also require investment in research and development of numerical methods for computing adjoints of coupled physics across multiple adaptively refined moving meshes and of stochastic (Monte Carlo) and mesh free (SPH) methods. • New software and numerical techniques, largely pioneered by the AI/ML community, make this feasible. Chief among these is automatic differentiation (AD), the ability to employ AD at point-wise locations in a physics calculation (instead of traditional black-box approaches) and the ability to perform “back-propagation in time” (or reverse mode AD) for non-linear partial differential equations (PDEs). Fundamentally, the conclusion of this strategic planning exercise is that the time is right to undertake a large scale effort in WSC, centered on the existing integrated codes, to continue the natural evolution of mod/sim in the age of AI/ML. Instead of attempting to replace mod/sim with purely data driven AI/ML models, we believe the key to success is to integrate AI/ML by building on top of the decades of hard-won knowledge and the verified/validated multiphysics modelling capability that is the hallmark of the ASC program.

97 MATHEMATICS AND COMPUTING↗

A projection method for particle resampling

Particle discretizations of partial differential equations are advantageous for high-dimensional kinetic models in phase-space due to their better scalability than continuum approaches with respect to dimension. Complex processes collectively referred to as particle noise hamper long time simulations with particle methods. One approach to address this problem is particle mesh adaptivity, or remapping, known as particle resampling and remeshing. Here, this work introduces a resampling method that projects particles to and from a (finite element) function space. The method is simple, using standard sparse linear algebra and finite element techniques, and it preserves all moments up to the order of a polynomial represented exactly by the continuum function space. It is distinguished from most other mesh-based methods in that new particle positions and number are decoupled from the mesh, allowing particle and continuum meshes to be adapted relatively independently. While this work is developed with structured particle and continuum phase-space grids on 1X + 1V Vlasov-Poisson models of Landau damping and two-stream instability, the method is well-suited to unstructured grids. Stable long time dynamics are demonstrated up to time T = 500. Reproducibility artifacts and data are publicly available.

Kinetic methods↗

Adaptive anomaly detection for identifying attacks in cyber-physical systems: A systematic literature review

Modern cyberattacks in cyber-physical systems (CPS) rapidly evolve and cannot be deterred effectively with most current methods, which focus on characterizing past threats. Adaptive anomaly detection (AAD) is among the most promising techniques to detect evolving cyberattacks, with an emphasis on fast data processing and model adaptation. AAD has been researched extensively; however, to the best of our knowledge, our work is the first systematic literature review (SLR) on current research in this field. We present a comprehensive SLR, gathering 397 relevant papers and systematically analyzing 65 of them (47 research and 18 survey papers) on AAD in CPS from 2013 to November 2023. We introduce a novel taxonomy considering attack types, CPS application, learning paradigm, data management, and algorithms. Our findings show that most studies addressed either model adaptation or data processing, but rarely both simultaneously. This indicates a research gap in fully adaptive solutions. We also categorize algorithms, datasets, and attack characteristics, and summarize strengths and weaknesses across the literature. Our review provides a structured and accessible reference for researchers and practitioners, offering insights into key trends and highlighting limitations in current approaches. Finally, we outline several future research directions, including the need for integrated real-time processing and adaptive learning, explainability, and uncertainty quantification in AAD for CPS.

Adaptation↗

Learning with Adaptive Conservativeness for Distributionally Robust Optimization: Incentive Design for Voltage Regulation: Preprint

Information asymmetry between the Distribution System Operator (DSO) and Distributed Energy Resource Aggregators (DERAs) obstructs designing effective incentives for voltage regulation. To capture this effect, we employ a Stackelberg game-theoretic framework, where the DSO seeks to overcome the information asymmetry and refine its incentive strategies by learning from DERA behavior over multiple iterations. We introduce a model-based online learning algorithm for the DSO, aimed at inferring the relationship between incentives and DERA responses. Given the uncertain nature of these responses, we also propose a distributionally robust incentive design model to control the probability of voltage regulation failure and then reformulate it into a convex problem. This model allows the DSO to periodically revise distribution assumptions on uncertain parameters in the decision model of the DERA. Finally, we present a gradient-based method that permits the DSO to adaptively modify its conservativeness level, measured by the size of a Wasserstein metric-based ambiguity set, according to historical voltage regulation performance. The effectiveness of our proposed method is demonstrated through numerical experiments.

distribution system operator↗

Bridging the Gap between Cosmological Simulations with Graph Neural Networks and Domain Adaptation

Deep learning models have been shown to outperform methods that rely on summary statistics, like the power spectrum, in extracting information from complex cosmological data sets. However, due to differences in the subgrid physics implementation and numerical approximations across different simulation suites, models trained on data from one cosmological simulation show a drop in performance when tested on another. Similarly, models trained on any of the simulations would also likely experience a drop in performance when applied to observational data. Training on data from two different suites of the CAMELS hydrodynamic cosmological simulations, we examine the generalization capabilities of Domain Adaptive Graph Neural Networks (DA-GNNs). By utilizing GNNs, we capitalize on their capacity to capture structured scale-free cosmological information from galaxy distributions. Moreover, by including unsupervised domain adaptation via Maximum Mean Discrepancy (MMD), we enable our models to extract domain-invariant features. We demonstrate that DA-GNN achieves higher accuracy and robustness on cross dataset tasks (up to 28% better relative error and up to almost an order of magnitude better χ 2 ). Using data visualizations, we show the effects of domain adaptation on proper latent space data alignment. This shows that DA-GNNs are a promising method for extracting domain-independent cosmological information, a vital step toward robust deep learning for real cosmic survey data.

97 MATHEMATICS AND COMPUTING↗

Estimating Sparse Direct Effects in Multivariate Regression With the Spike-and-Slab LASSO

The multivariate regression interpretation of the Gaussian chain graph model simultaneously parametrizes (i) the direct effects of p predictors on q outcomes and (ii) the residual partial covariances between pairs of outcomes. We introduce a new method for fitting sparse versions of these models with spike-and-slab LASSO (SSL) priors. We develop an Expectation Conditional Maximization algorithm to obtain sparse estimates of the p × q matrix of direct effects and the q × q residual precision matrix. Our algorithm iteratively solves a sequence of penalized maximum likelihood problems with self-adaptive penalties that gradually filter out negligible regression coefficients and partial covariances. Because it adaptively penalizes individual model parameters, our method is seen to outperform fixed-penalty competitors on simulated data. We establish the posterior contraction rate for our model, buttressing our method’s excellent empirical performance with strong theoretical guarantees. Using our method, we estimated the direct effects of diet and residence type on the composition of the gut microbiome of elderly adults.

EM algorithm↗

Adaptive cold-load pickup considerations in 2-stage microgrid unit commitment for enhancing microgrid resilience

In an extended main grid outage spanning multiple days, load shedding serves as a critical mechanism for islanded microgrids to maintain essential power and energy reserves that are indispensable for fulfilling reliability and resiliency mandates. However, using load shedding for such purposes leads to increasing occurrence of cold load pickup (CLPU) events. Here, this study presents an innovative adaptive CLPU model that introduces a method for determining and incorporating parameters related to CLPU power and energy requirements into a two-stage microgrid unit commitment (MGUC) algorithm. In contrast to the traditional fixed-CLPU-curve approach, this model calculates CLPU duration, power, and energy demands by considering outage durations and ambient temperature variations within the MGUC process. By integrating the adaptive CLPU model into the MGUC problem formulation, it allows for the optimal allocation of energy resources throughout the entire scheduling horizon to fulfill the CLPU requirements when scheduling multiple CLPU events. The performance of the enhanced MGUC algorithm considering CLPU needs is assessed using actual load and photovoltaic (PV) data. Simulation results demonstrate significant improvements in dispatch optimality evaluated by the amount of load served, customer comfort, energy storage operation, and adherence to energy schedules. These enhancements collectively contribute to reliable and resilient microgrid operation.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Electronic structure theory on modeling short-range noncovalent interactions between amino acids

While short-range noncovalent interactions (NCIs) are proving to be of importance in many chemical and biological systems, these atypical bindings happen within the so-called van der Waals envelope and pose an enormous challenge for current computational methods. We introduce SNCIAA, a database of 723 benchmark interaction energies of short-range noncovalent interactions between neutral/charged amino acids originated from protein x-ray crystal structures at the “gold standard” coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory with a mean absolute binding uncertainty less than 0.1 kcal/mol. Subsequently, a systematic assessment of commonly used computational methods, such as the second-order Møller−Plesset theory (MP2), density functional theory (DFT), symmetry-adapted perturbation theory (SAPT), composite electronic-structure methods, semiempirical approaches, and the physical-based potentials with machine learning (IPML) on SNCIAA is carried out. It is shown that the inclusion of dispersion corrections is essential even though these dimers are dominated by electrostatics, such as hydrogen bondings and salt bridges. Overall, MP2, ωB97M-V, and B3LYP+D4 turned out to be the most reliable methods for the description of short-range NCIs even in strongly attractive/repulsive complexes. SAPT is also recommended in describing short-range NCIs only if the δMP2 correction has been included. The good performance of IPML for dimers at close-equilibrium and long-range conditions is not transferable to the short-range. We expect that SNCIAA will assist the development/improvement/validation of computational methods, such as DFT, force-fields, and ML models, in describing NCIs across entire potential energy surfaces (short-, intermediate-, and long-range NCIs) on the same footing.

Chemistry↗

Traffic Signal Optimization by Integrating Reinforcement Learning and Digital Twins

Machine learning (ML) methods, especially reinforcement learning (RL), have been widely considered for traffic signal optimization in intelligent transportation systems. Most of these ML methods are centralized, lacking in scalability and adaptability in large traffic networks. Further, it is challenging to train such ML models due to the lack of training platforms and/or the cost of deploying and training in a real traffic networks. This paper presents an approach for the integration of decentralized graph-based multi-agent reinforcement learning (DGMARL) with a Digital Twin (DT) to optimize traffic signals for the reduction of traffic congestion and network-wide fuel consumption related to stopping. Specifically, the DGMARL agents learn traffic state patterns and make decisions regarding traffic signal control with assistance from a Digital Twin module, which simulates and replicates the traffic behaviors of a real traffic network. The proposed approach was evaluated using PTV-Vissim [1], a microscopic traffic simulation platform. PTV-Vissim is also the simulation engine of the DT, enabling emulation and optimization of the traffic signals on the MLK Smart Corridor in Chattanooga, Tennessee. Compared to an actuated signal control baseline approach, experiment results show that Eco_PI, a developed performance measure capturing the impact of stops on fuel consumption, was reduced by 44.27% in a 24-hour and an average of 29.88% in a PM-peak-hour scenario.

Multi-Agent Reinforcement Learning, Digital Twin, ↗

Verification of Adaptive Protection in Hardware in the Loop for Coordination with Solar Variability

As inverter-based resources continue to be installed at all levels of the electric grid, the fixed protection schemes used at the distribution level will continue to be stressed until they no longer ensure the protection of the grid. Adaptive protection has been proposed as a solution with the ability to update the protection schemes in near real-time to ensure reliability and increase the resilience of the grid. However, weather variability poses a significant challenge to the ability of these methods to keep the selectivity and reliability of these schemes coordinated. If the ramp rates, due to solar variability, of the inverter-based resources change faster than the adaptive protection can issue new settings, the protection system could be uncoordinated, with the wrong device responding to a system fault. The proposed adaptive protection method ensures that due to solar variability, communication, and protection calculation latency, it can issu e coordinated protection settings promptly, in one minute or less. The hardware-in-the-loop results show the protection settings being issued and maintaining system coordination in under a minute.

Summers, Adam↗

Leveraging data mining, active learning, and domain adaptation for efficient discovery of advanced oxygen evolution electrocatalysts

Developing advanced catalysts for acidic oxygen evolution reaction (OER) is crucial for sustainable hydrogen production. This study presents a multistage machine learning (ML) approach to streamline the discovery and optimization of complex multimetallic catalysts. Our method integrates data mining, active learning, and domain adaptation throughout the materials discovery process. Unlike traditional trial-and-error methods, this approach systematically narrows the exploration space using domain knowledge with minimized reliance on subjective intuition. Then, the active learning module efficiently refines element composition and synthesis conditions through iterative experimental feedback. The process culminated in the discovery of a promising Ru-Mn-Ca-Pr oxide catalyst. Our workflow also enhances theoretical simulations with domain adaptation strategy, providing deeper mechanistic insights aligned with experimental findings. By leveraging diverse data sources and multiple ML strategies, we demonstrate an efficient pathway for electrocatalyst discovery and optimization. This comprehensive, data-driven approach represents a paradigm shift and potentially benchmark in electrocatalysts research.

Science & Technology - Other Topics↗

Modeling, analysis, and optimization of complex nuclear processes and facilities via computational methods: The HALEU process case study

Improving and adapting industrial systems to timely meet changing programmatic and market demands is an important goal to achieve, including when operating and maintaining complex nuclear processes and facilities. However, changes to these complex systems are costly, particularly when they are already in place and bounded to stringent requirements and constraints such as when handling radioactive material and contaminated equipment. These conditions often exist when treating spent nuclear fuel remotely within shielded nuclear radiation chambers, commonly referred as hot cells, to condition nuclear material and/or fabricate products for utilization in other nuclear enterprises such as in the manufacture of advanced nuclear fuel. The illustrative case considered here is the production of high assay low enriched uranium (HALEU) products supporting the deployment of advanced nuclear reactors. For the HALEU program, resources invested were and are being systematically analyzed so that these investments are maximized in a facility that is nearly 60 years old. A methodology that has effectively enabled optimized and improvements in the Spent Fuel Treatment (SFT) program, and consequently the HALEU program, involves discrete event simulation as addressed in this article. Here, the quantification of multiple productivity metrics, including material processing rates, cycle times, bottlenecks, number of material transfers as well as equipment, workstation, and material handling utilization, has resulted in a myriad of diverse discoveries and data-informed decisions regarding process layout and constituent, labor levels and schedules, selection of new process units, storage needs, and other critical process configurations. This article describes such a computational capability being applied for decision-making, illustrates its application to an actual process and program, provides illustrative results, and argues how computational methods for the modeling, analysis, and optimization of complex processes and facilities does lead to informed decisions derived from data and not only from intuition.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Temporal multi-omic analysis uncovers sex-biased molecular programs underlying skeletal muscle adaptation to endurance training

Background. Exercise training is known to benefit health and reduce disease risk. While adaptations in skeletal muscles are fundamental to many of the health benefits of exercise training, the common and sex-specific molecular regulators that mediate these adaptations remain to be fully elucidated. Methods. To this end, we leveraged skeletal muscle multi-omics data generated by the Molecular Transducers of Physical Activity Consortium (MoTrPAC), where 6 month-old male and female rats endurance trained for 1, 2, 4, or 8 weeks. Our objective was to identify shared and sex-specific multi-omic molecular responses to endurance training in skeletal muscle, and relate them to phenotypic adaptations. Results. We identified largely sexually-conserved transcriptomic and proteomic enrichments in the gastrocnemius, which correlated with skeletal muscle responses from a published exercise study in humans. We uncovered sex-consistent post-translational modifications, including decreased oxidation of MYH2 and deacetylation of the ß-oxidation enzyme HADHA. Pathway enrichment analyses revealed sex-specific remodeling across the acetylome, redox proteome, and phosphoproteome; females decreased mitochondrial protein oxidation and increased mitochondrial cristae proteins, indicative of enhanced redox buffering and mitochondrial efficiency. Despite observed decreases in the oxidation of key mitochondrial proteins, females displayed increases in the oxidation of proteins involved in glucose catabolism relative to males after 8 weeks of training, suggestive of sex-biased subcellular reactive oxygen species generation. Conclusions. This work shows a large portion of the adaptive response to endurance training in skeletal muscle is shared between females and males, while there are distinct and nuanced sex-specific adaptations that are evident, particularly at the level of post-translational regulation.

Many, Gina M.↗