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At least 829 records · Page 46

Stationary stability for evolutionary dynamics in finite populations

Here, we demonstrate a vast expansion of the theory of evolutionary stability to finite populations with mutation, connecting the theory of the stationary distribution of the Moran process with the Lyapunov theory of evolutionary stability. We define the notion of stationary stability for the Moran process with mutation and generalizations, as well as a generalized notion of evolutionary stability that includes mutation called an incentive stable state (ISS) candidate. For sufficiently large populations, extrema of the stationary distribution are ISS candidates and we give a family of Lyapunov quantities that are locally minimized at the stationary extrema and at ISS candidates. In various examples, including for the Moran andWright–Fisher processes, we show that the local maxima of the stationary distribution capture the traditionally-defined evolutionarily stable states. The classical stability theory of the replicator dynamic is recovered in the large population limit. Finally we include descriptions of possible extensions to populations of variable size and populations evolving on graphs.

60 APPLIED LIFE SCIENCES↗

Structural evaluation of candidate space shuttle thermal protection systems

The characteristics and development of a lightweight reusable thermal protection system for the space shuttle are discussed. The test articles consisted of metallic substrates with upper surfaces covered with all-silica, reusable, surface insulation material. The material is processed in the form of tiles. The external surfaces of the tiles are provided with a coating system which consists of a borosilicate coating with a silicon carbide emittance agent and impregnation with a hydrophobic agent. The finished tiles are attached to the metal substrate by adhesive bonding. Charts and graphs of the properties of the material are provided.

Burns, A. B.↗

Computer-aided system design

A technique has been developed for combining features of a systems architecture design and assessment tool and a software development tool. This technique reduces simulation development time and expands simulation detail. The Architecture Design and Assessment System (ADAS), developed at the Research Triangle Institute, is a set of computer-assisted engineering tools for the design and analysis of computer systems. The ADAS system is based on directed graph concepts and supports the synthesis and analysis of software algorithms mapped to candidate hardware implementations. Greater simulation detail is provided by the ADAS functional simulator. With the functional simulator, programs written in either Ada or C can be used to provide a detailed description of graph nodes. A Computer-Aided Software Engineering tool developed at the Charles Stark Draper Laboratory (CSDL CASE) automatically generates Ada or C code from engineering block diagram specifications designed with an interactive graphical interface. A technique to use the tools together has been developed, which further automates the design process.

Walker, Carrie K.↗

Image segmentation by hierarchial agglomeration of polygons using ecological statistics

A method for rapid hierarchical image segmentation based on perceptually driven contour completion and scene statistics is disclosed. The method begins with an initial fine-scale segmentation of an image, such as obtained by perceptual completion of partial contours into polygonal regions using region-contour correspondences established by Delaunay triangulation of edge pixels as implemented in VISTA. The resulting polygons are analyzed with respect to their size and color/intensity distributions and the structural properties of their boundaries. Statistical estimates of granularity of size, similarity of color, texture, and saliency of intervening boundaries are computed and formulated into logical (Boolean) predicates. The combined satisfiability of these Boolean predicates by a pair of adjacent polygons at a given segmentation level qualifies them for merging into a larger polygon representing a coarser, larger-scale feature of the pixel image and collectively obtains the next level of polygonal segments in a hierarchy of fine-to-coarse segmentations. The iterative application of this process precipitates textured regions as polygons with highly convolved boundaries and helps distinguish them from objects which typically have more regular boundaries. The method yields a multiscale decomposition of an image into constituent features that enjoy a hierarchical relationship with features at finer and coarser scales. This provides a traversable graph structure from which feature content and context in terms of other features can be derived, aiding in automated image understanding tasks. The method disclosed is highly efficient and can be used to decompose and analyze large images.

36 MATERIALS SCIENCE↗

Optimal structure and parameter learning of Ising models

Reconstruction of the structure and parameters of an Ising model from binary samples is a problem of practical importance in a variety of disciplines, ranging from statistical physics and computational biology to image processing and machine learning. The focus of the research community shifted toward developing universal reconstruction algorithms that are both computationally efficient and require the minimal amount of expensive data. Here, we introduce a new method, interaction screening, which accurately estimates model parameters using local optimization problems. The algorithm provably achieves perfect graph structure recovery with an information-theoretically optimal number of samples, notably in the low-temperature regime, which is known to be the hardest for learning. Here, the efficacy of interaction screening is assessed through extensive numerical tests on synthetic Ising models of various topologies with different types of interactions, as well as on real data produced by a D-Wave quantum computer. Finally, this study shows that the interaction screening method is an exact, tractable, and optimal technique that universally solves the inverse Ising problem.

97 MATHEMATICS AND COMPUTING↗

Computer-aided operations engineering with integrated models of systems and operations

CONFIG 3 is a prototype software tool that supports integrated conceptual design evaluation from early in the product life cycle, by supporting isolated or integrated modeling, simulation, and analysis of the function, structure, behavior, failures and operation of system designs. Integration and reuse of models is supported in an object-oriented environment providing capabilities for graph analysis and discrete event simulation. Integration is supported among diverse modeling approaches (component view, configuration or flow path view, and procedure view) and diverse simulation and analysis approaches. Support is provided for integrated engineering in diverse design domains, including mechanical and electro-mechanical systems, distributed computer systems, and chemical processing and transport systems. CONFIG supports abstracted qualitative and symbolic modeling, for early conceptual design. System models are component structure models with operating modes, with embedded time-related behavior models. CONFIG supports failure modeling and modeling of state or configuration changes that result in dynamic changes in dependencies among components. Operations and procedure models are activity structure models that interact with system models. CONFIG is designed to support evaluation of system operability, diagnosability and fault tolerance, and analysis of the development of system effects of problems over time, including faults, failures, and procedural or environmental difficulties.

Malin, Jane T.↗

An automated target species selection method for dynamic adaptive chemistry simulations

The relative importance index (RII) approach for determining appropriate target species for dynamic adaptive chemistry (DAC) simulations using the directed relation graph with error propagation (DRGEP) method is developed. The adequacy and effectiveness of this RII method is validated for two fuels: n-heptane and isopentanol, representatives of a ground transportation fuel component and bio-alcohol, respectively. The conventional method of DRGEP target species selection involves picking an unchanging (static) set of target species based on the combustion processes of interest; however, these static target species may not remain important throughout the entire combustion simulation, adversely affecting the accuracy of the method. In particular, this behavior may significantly reduce the accuracy of the DRGEP-based DAC approach in complex multidimensional simulations where the encountered combustion conditions cannot be known a priori with high certainty. Moreover, testing multiple sets of static target species to ensure the accuracy of the method is generally computationally prohibitive. Instead, the RII method determines appropriate DRGEP target species solely from the local thermo-chemical state of the simulation, ensuring that accuracy will be maintained. Further, the RII method reduces the expertise required of users to select DRGEP target species sets appropriate to the combustion phenomena under consideration. Constant volume autoignition simulations run over a wide range of initial conditions using detailed reaction mechanisms for n-heptane and isopentanol show that the RII method is able to maintain accuracy even when traditional static target species sets fail, and are even more accurate than expert-selected target species sets. Additionally, the accuracy and efficiency of the RII method are compared to those of static target species sets in single-cell engine simulations under homogeneous charge compression ignition conditions. For simulations using more stringent DRGEP thresholds, the RII method performs similarly to that of the static target species sets. With a larger DRGEP threshold, the RII method is significantly more accurate than the static target species sets without imposing significant computational overhead. Moreover, the applicability of the RII method to a DRG-based DAC scheme is discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis

Counterfactual inference is a useful tool for comparing outcomes of interventions on complex systems. It requires us to represent the system in form of a structural causal model, complete with a causal diagram, probabilistic assumptions on exogenous variables, and functional assignments. Specifying such models can be extremely difficult in practice. The process requires substantial domain expertise, and does not scale easily to large systems, multiple systems, or novel system modifications. At the same time, many application domains, such as molecular biology, are rich in structured causal knowledge that is qualitative in nature. This manuscript proposes a general approach for querying a causal knowledge graph with a causal question and converting the qualitative result into a quantitative structural causal model that can learn from data to answer the question. Here, we demonstrate the feasibility, accuracy and versatility of this approach using two case studies in systems biology. The first demonstrates the appropriateness of the underlying assumptions and the accuracy of the results. The second demonstrates the versatility of the approach by querying a knowledge base for the molecular determinants of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced cytokine storm and performing counterfactual inference to predict the causal effect of medical countermeasures for severely ill COVID-19 patients.

60 APPLIED LIFE SCIENCES↗

Generative Design for Resilience of Interdependent Network Systems

Abstract Interconnected complex systems usually undergo disruptions due to internal uncertainties and external negative impacts such as those caused by harsh operating environments or regional natural disaster events. To maintain the operation of interconnected network systems under both internal and external challenges, design for resilience research has been conducted from both enhancing the reliability of the system through better designs and improving the failure recovery capabilities. As for enhancing the designs, challenges have arisen for designing a robust system due to the increasing scale of modern systems and the complicated underlying physical constraints. To tackle these challenges and design a resilient system efficiently, this study presents a generative design method that utilizes graph learning algorithms. The generative design framework contains a performance estimator and a candidate design generator. The generator can intelligently mine good properties from existing systems and output new designs that meet predefined performance criteria while the estimator can efficiently predict the performance of the generated design for a fast iterative learning process. Case studies results based on synthetic supply chain networks and power systems from the IEEE dataset have illustrated the applicability of the developed method for designing resilient interdependent network systems.

Engineering↗

Application of Modified Meshgraphnets for Subsurface Prediction during CO2 Sequestration

In the face of the increasingly dire consequences of anthropogenic climate change, capturing and storing carbon dioxide is paramount. However, several impediments exist to the safe and effective subsurface storage of CO2, such as cost of transport, identification of suitable sites for subsurface storage, and assessment of long-term risk from storage in subsurface aquifers. Accurate subsurface modeling is necessary to ensure that CO2 storage is both safe and effective. Still, such modeling has traditionally required either substantial time and computational power (numerical simulation) or a substantial amount of pre-existing data for training (machine learning models). Additionally, these models lack flexibility in dealing with both changes in discretization of the input data and generalizability beyond the data on which they are trained. In order to address these issues, this research applies graph neural networks (GNNs) to predict subsurface saturation and pressure during CO₂ injection in a model of the Illinois Basin-Decatur Project (IBDP). GNNs provide a flexible, intuitive method for representing and manipulating complex unstructured data, which is often found in many practical domain problems such as fluid flow and subsurface characterization. These unstructured grids are easily represented in GNNs by representing spatially-localized features such as permeability, porosity, saturation, and pressure as nodes in a graph and relationships between these properties as edges connecting these nodes. This research applies a specific GNN model called MeshGraphNets (MGN) to model the change in CO2 saturation and pressure over a 50-month time period (36 months of injection, 14 months post-injection). The MGN model leverages a message passing process that allows the network to learn both the spatial and temporal dynamics of this system simultaneously. Additionally, training on a limited dataset (64 realizations, 20 time points each) resulted in a high degree of accuracy in saturation prediction both within the same timeframe as the training (20 months, 0.039 average RMSE) and when projecting out to the end of injection (36 months, 0.053 average RMSE). Temporal predictions such as those generated by MGNs and other similar models are prone to accumulated error over time; in order to address this, a multi-step rollout (MSR) training process was applied to calculate training loss. This method mimics the forward prediction during inference by “rolling out” multiple time points in a single training step using the previous prediction as input to the MGN model. By calculating the loss several time steps forward from the current prediction, the model is forced to find a more stable state over time. Application of MSR to the MGN model resulted in an average 15% reduction in inference error over time during forward prediction. This study showcases the immense potential of GNNs as a game-changing methodology for predicting pressure and saturation evolution in CCS projects, ultimately paving the way for more sustainable and effective carbon storage solutions. Presentation prepared for the 2024 AiChE Annual Meeting, October 27 to November 1 2024, San Diego, CA.

Holcomb, Paul↗

CONFIG: Integrated engineering of systems and their operation

This article discusses CONFIG 3, a prototype software tool that supports integrated conceptual design evaluation from early in the product life cycle, by supporting isolated or integrated modeling, simulation, and analysis of the function, structure, behavior, failures and operations of system designs. Integration and reuse of models is supported in an object-oriented environment providing capabilities for graph analysis and discrete event simulation. CONFIG supports integration among diverse modeling approaches (component view, configuration or flow path view, and procedure view) and diverse simulation and analysis approaches. CONFIG is designed to support integrated engineering in diverse design domains, including mechanical and electro-mechanical systems, distributed computer systems, and chemical processing and transport systems.

Malin, Jane T.↗

Coating Development for GRCop-84 Liners for Reusable Launch Vehicles Aided by Modeling Studies

The design of the next generation of reusable launch vehicles calls for using GRCop-84 copper alloy liners based on a composition invented at the NASA Glenn Research Center. Despite its considerable advantage over other copper alloys, it is expected that GRCop-84 will suffer from environmental degradation depending on the type of rocket fuels used and on thermomechanical fatigue. Applying protective coatings on GRCop-84 substrates can minimize or eliminate many of these problems and extend the operational life of the combustion liner. This could increase component reliability, shorten depot maintenance turnaround times, and lower operating costs. Therefore, Glenn is actively pursuing the development of advanced coatings technology for GRCop-84 liners. Technology is being developed in four major areas: (1) new metallic coating compositions, (2) application techniques, (3) test methods, and (4) life prediction design methodology using finite element analysis. The role of finite element analysis in guiding the coating effort is discussed in this report. Thermal analyses were performed at Glenn for different combinations of top- and bondcoat compositions to determine the temperature variation across the coated cross section with the thickness of the top coat. These calculations were conducted for simulated LH2/LO2 booster engine conditions assuming that the bond coat had a constant thickness of 50 m. The preceding graphs show the predicted temperatures at the outer surface of the top coat (hot wall), at the top-coat/bond-coat interface, at the bond-coat/GRCop-84 interface, and at the GRCop-84 cold wall as a function of top-coat thickness for Cu- 26(wt%)Cr top coat (top graph), Ni-17(wt%)Cr-6%Al-0.5%Y top coat and Cu-26%Cr bond coat, and NiAl top coat and Ni bond coat. In all cases, the temperature of the top coat at the hot wall increased with increasing top-coat thickness and with corresponding decreases in the temperatures at the two interfaces and the cold wall. These temperatures are not acutely sensitive to the thermal conductivity of the top coat when it exceeds 25 and 50 W/m/K for low and high heat flux engines. This observation is significant for two reasons. First, several different top-coat compositions can be evaluated as potential protective coatings without loss in the heat-transfer efficiency of the coated system. Second, materials with thermal conductivities less than the critical values of 25 or 50 W/m/K are more likely to act as thermal barrier coatings. The deposition of overlay coatings on GRCop-84 substrates results in the development of residual stresses. The presence of these residual stresses influences the probability of coating spallation, the thermal cycling life, and the fatigue properties of the coated substrate during use. Since it is important to understand how these stresses develop during the vacuum-plasma-spraying coating deposition process, the nature and magnitudes of the cool-down residual stresses were calculated and compared with experimentally determined values across the coated cross section of a disk specimen. The calculations were conducted assuming that the specimen cools down to room temperature from vacuum plasma-spraying temperatures of either 250 or 650 C. The effects of coating the substrate with and without grit blasting were also theoretically examined. The final graph compares the predicted and the experimental results for a GRCop-84 disk coated with about a 50- m-thick Ni bond coat and a 75- to 100- m NiAl top coat, where the curves for NASA-2 assume the presence of a prior residual stress generated by grit blasting under conditions similar to the experimental situation. The predicted cool-down in-plane stresses were compressive in both the NiAl top coat and the Ni bond coat. They were also compressive in the substrate to a depth of about 0.25 mm from the Ni/GRCop-84 interface when the vacuum-plasma-spraying temperature was low. However, using a higher plasma spraying temperaturs likely to leave the substrate under a small tensile stress to counter the compressive stresses in the bond and top coats because of the relaxation of residual stresses generated in the substrate during the grit blasting of its surface prior to spraying. These results suggest that the NiAl and Ni coatings are unlikely to spall after spraying as confirmed by the microstructural observations shown in the following photomicrograph of an as-sprayed specimen. Finally, it is noted that the calculated and experimental results are not in complete agreement, which indicates that both the experimental and modeling techniques need further refinement.

Raj, Sai V.↗

On the integration of molecular dynamics, data science, and experiments for studying solvent effects on catalysis

Computational workflows that combine molecular dynamics (MD) simulations and emerging data-centric (DC) methods can accelerate the screening and analysis of solvent systems experimentally and computationally. Here, MD simulations provide atomic positions and velocities of reactant, solvent, and catalyst materials that can be manipulated into data representations that in turn can be used by DC techniques to conduct predictive modeling, feature extraction, and experimental design. For liquid-phase catalytic applications, emerging DC techniques such as Convolutional and Graph Neural Networks (CNN/GNN), Topological Data Analysis (TDA), and Active Learning (AL) can leverage MD and experimental data to quickly predict solvent effects on reaction outcomes. For instance, in recent studies, 3D solvent environments obtained with MD have been exploited by CNNs to predict experimental reaction rates for homogeneous acid-catalyzed lignocellulosic processes. In this perspective, we discuss basic principles of DC methods and how these can be combined with MD to enable high-throughput screening of solvent selection for diverse catalysis applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Adsorbate chemical environment-based machine learning framework for heterogeneous catalysis

Abstract Heterogeneous catalytic reactions are influenced by a subtle interplay of atomic-scale factors, ranging from the catalysts’ local morphology to the presence of high adsorbate coverages. Describing such phenomena via computational models requires generation and analysis of a large space of atomic configurations. To address this challenge, we present Adsorbate Chemical Environment-based Graph Convolution Neural Network (ACE-GCN), a screening workflow that accounts for atomistic configurations comprising diverse adsorbates, binding locations, coordination environments, and substrate morphologies. Using this workflow, we develop catalyst surface models for two illustrative systems: (i) NO adsorbed on a Pt 3 Sn(111) alloy surface, of interest for nitrate electroreduction processes, where high adsorbate coverages combined with low symmetry of the alloy substrate produce a large configurational space, and (ii) OH* adsorbed on a stepped Pt(221) facet, of relevance to the Oxygen Reduction Reaction, where configurational complexity results from the presence of irregular crystal surfaces, high adsorbate coverages, and directionally-dependent adsorbate-adsorbate interactions. In both cases, the ACE-GCN model, trained on a fraction (~10%) of the total DFT-relaxed configurations, successfully describes trends in the relative stabilities of unrelaxed atomic configurations sampled from a large configurational space. This approach is expected to accelerate development of rigorous descriptions of catalyst surfaces under in-situ conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

cuTS: Scaling Subgraph Isomorphism on Distributed Multi-GPUSystems Using Trie Based Data Structure

Subgraph isomorphism is a pattern-matching algorithm widely used in many domains such as chem-informatics, bioinformatics, databases, and social network analysis. It is computationally expensive and is a proven NP-hard problem. The massive parallelism offered by the GPU hardware is well suited for solving the subgraph isomorphism. However, current GPU implementations are far from the achievable performance. Moreover, the enormous memory requirement of current approaches limits the problem size that can be handled. This work analyzes the fundamental challenges associated with processing the subgraph isomorphism on GPUs and develops an efficient GPU hardware-aware implementation. We also develop a new GPU-friendly trie-based data structure to drastically reduce the intermediate storage space requirement. Hence, our approach runs larger benchmarks than the competitors. We also develop the first distributed sub-graph isomorphism algorithm for GPUs. Our experimental evaluation section demonstrates the efficacy of our approach by comparing the execution time and number of cases that we can handle against the state-of-the-art GPU implementations.

Xiang, Lizhi↗

Instrumentation for gamma-ray astronomy

The current status of gamma-ray-telescope technology for ground, airborne, and space observations is surveyed and illustrated with drawings, diagrams, and graphs and tables of typical data. For the low- and medium-energy ranges, consideration is given to detectors and detector cooling systems, background-rejection methods, radiation damage, large-area detectors, gamma-ray imaging, data analysis, and the Compton-interaction region. Also discussed are the gamma-ray interaction process at high energies; multilevel automated spark-chamber gamma-ray telescopes; the Soviet Gamma-1 telescope; the EGRET instrument for the NASA Gamma-Ray Observatory; and Cerenkov, air-shower, and particle-detector instruments for the TeV and PeV ranges. Significant improvements in resolution and sensitivity are predicted for the near future.

Bertsch, David L.↗

HDBind: encoding of molecular structure with hyperdimensional binary representations

Traditional methods for identifying “hit” molecules from a large collection of potential drug-like candidates rely on biophysical theory to compute approximations to the Gibbs free energy of the binding interaction between the drug and its protein target. These approaches have a significant limitation in that they require exceptional computing capabilities for even relatively small collections of molecules. Increasingly large and complex state-of-the-art deep learning approaches have gained popularity with the promise to improve the productivity of drug design, notorious for its numerous failures. However, as deep learning models increase in their size and complexity, their acceleration at the hardware level becomes more challenging. Hyperdimensional Computing (HDC) has recently gained attention in the computer hardware community due to its algorithmic simplicity relative to deep learning approaches. The HDC learning paradigm, which represents data with high-dimension binary vectors, allows the use of low-precision binary vector arithmetic to create models of the data that can be learned without the need for the gradient-based optimization required in many conventional machine learning and deep learning methods. This algorithmic simplicity allows for acceleration in hardware that has been previously demonstrated in a range of application areas (computer vision, bioinformatics, mass spectrometery, remote sensing, edge devices, etc.). To the best of our knowledge, our work is the first to consider HDC for the task of fast and efficient screening of modern drug-like compound libraries. We also propose the first HDC graph-based encoding methods for molecular data, demonstrating consistent and substantial improvement over previous work. We compare our approaches to alternative approaches on the well-studied MoleculeNet dataset and the recently proposed LIT-PCBA dataset derived from high quality PubChem assays. We demonstrate our methods on multiple target hardware platforms, including Graphics Processing Units (GPUs) and Field Programmable Gate Arrays (FPGAs), showing at least an order of magnitude improvement in energy efficiency versus even our smallest neural network baseline model with a single hidden layer. Our work thus motivates further investigation into molecular representation learning to develop ultra-efficient pre-screening tools. We make our code publicly available at https://github.com/LLNL/hdbind.

59 BASIC BIOLOGICAL SCIENCES↗

Realization of consensus of multi-agent systems with stochastically mixed interactions

In this paper, we propose a new consensus model in which the interactions among agents stochastically switch between attraction and repulsion. Such a positive-and-negative mechanism is described by the white-noise-based coupling. Analytic criteria for the consensus and non-consensus in terms of the eigenvalues of the noise intensity matrix are derived, which provide a better understanding of the constructive roles of random interactions. Specifically, we discover a positive role of noise coupling that noise can accelerate the emergence of consensus. We find that the converging speed of the multi-agent network depends on the square of the second smallest eigenvalue of its graph Laplacian. The influence of network topologies on the consensus time is also investigated.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗