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At least 145 records · Page 8

Navigating the Expansive Landscapes of Soft Materials: A User Guide for High-Throughput Workflows

Synthetic polymers are highly customizable with tailored structures and functionality, yet this versatility generates challenges in the design of advanced materials due to the size and complexity of the design space. Thus, exploration and optimization of polymer properties using combinatorial libraries has become increasingly common, which requires careful selection of synthetic strategies, characterization techniques, and rapid processing workflows to obtain fundamental principles from these large data sets. Herein, we provide guidelines for strategic design of macromolecule libraries and workflows to efficiently navigate these high-dimensional design spaces. We describe synthetic methods for multiple library sizes and structures as well as characterization methods to rapidly generate data sets, including tools that can be adapted from biological workflows. We further highlight relevant insights from statistics and machine learning to aid in data featurization, representation, and analysis. This Perspective acts as a “user guide” for researchers interested in leveraging high-throughput screening toward the design of multifunctional polymers and predictive modeling of structure–property relationships in soft materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Topological vulnerability of power grids to disasters: Bounds, adversarial attacks and reinforcement

Natural disasters like hurricanes, floods or earthquakes can damage power grid devices and create cascading blackouts and islands. The nature of failure propagation and extent of damage, among other factors, is dependent on the structural features of the grid, that are distinct from that of random networks. This paper analyzes the structural vulnerability of real power grids to impending disasters and presents intuitive graphical metrics to quantify the extent of topological damage. We develop two improved graph eigen-value based bounds on the grid vulnerability. Further we study adversarial attacks aimed at weakening the grid’s structural robustness and present three combinatorial algorithms to determine the optimal topological attack. Simulations on power grid networks and comparison with existing work show the improvements of the proposed measures and attack schemes.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Relaxed Multibang Regularization for the Combinatorial Integral Approximation

Multibang regularization and combinatorial integral approximation decompositions are two actively researched techniques for integer optimal control. In this work, we consider a class of polyhedral functions that arise particularly as convex lower envelopes of multibang regularizers and show that they have beneficial properties with respect to regularization of relaxations of integer optimal control problems. We extend the algorithmic framework of the combinatorial integral approximation such that a subsequence of the computed discrete-valued controls converges to the infimum of the regularized integer control problem.

97 MATHEMATICS AND COMPUTING↗

Discovery of Peptidomimetic Ligands of EED as Allosteric Inhibitors of PRC2

The function of EED within polycomb repressive complex 2 (PRC2) is mediated by a complex network of protein–protein interactions. Allosteric activation of PRC2 by binding of methylated proteins to the embryonic ectoderm development (EED) aromatic cage is essential for full catalytic activity, but details of this regulation are not fully understood. EED’s recognition of the product of PRC2 activity, histone H3 lysine 27 trimethylation (H3K27me3), stimulates PRC2 methyltransferase activity at adjacent nucleosomes leading to H3K27me3 propagation and, ultimately, gene repression. By coupling combinatorial chemistry and structure-based design, we optimized a low-affinity methylated jumonji, AT-rich interactive domain 2 (Jarid2) peptide to a smaller, more potent peptidomimetic ligand (K d = 1.14 ± 0.14 μM) of the aromatic cage of EED. Our strategy illustrates the effectiveness of applying combinatorial chemistry to achieve both ligand potency and property optimization. Furthermore, the resulting ligands, UNC5114 and UNC5115, demonstrate that targeted disruption of EED’s reader function can lead to allosteric inhibition of PRC2 catalytic activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multi-objective optimization of PWR core design using NSGA-II in RAVEN’s optimization framework

Designing an PWR loading pattern is a combinatorial problem challenging to solve by brute force or traditional methods due to the sheer amount of possible combination, and constraints. Nature-inspired algorithms, such as the genetic algorithm, have demonstrated the potential to tackle this problem. The goal of this work was to improve and demonstrate the capabilities for constrained, multi-objective optimization (MOO) of loading patterns using NSGA-II in RAVEN’s optimization framework.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system

Designing an optimal microbial cell factory often requires overexpression, knock-down, and knock-out of multiple gene targets. Unfortunately, such rewiring of cellular metabolism is often carried out sequentially and with low throughput. Here, we report a combinatorial metabolic engineering strategy based on an orthogonal tri-functional CRISPR system that combines transcriptional activation, transcriptional interference, and gene deletion (CRISPR-AID) in the yeast Saccharomyces cerevisiae . This strategy enables perturbation of the metabolic and regulatory networks in a modular, parallel, and high-throughput manner. We show that the application of CRISPR-AID not only to increase the production of β-carotene by 3-fold in a single step, but also to achieve 2.5-fold improvement in the display of an endoglucanase on the yeast surface by optimizing multiple metabolic engineering targets in a combinatorial manner.

59 BASIC BIOLOGICAL SCIENCES↗

Optimizing thermal stability and mechanical behavior in segregation-engineered nanocrystalline Al–Ni–Ce alloys: A combinatorial study

The deliberate use of solute enrichment at grain boundaries, otherwise known as segregation engineering, is a promising approach to tailor the properties of interface-dominated materials such as nanocrystalline alloys. Here, the ensuing chemical and structural evolution at grain boundaries can give rise to thermal stability and excellent mechanical properties, but the interplay between enrichment, phase decomposition, grain growth, and mechanical behavior exists in a vast composition and processing space. In this study, a combinatorial synthesis and rapid characterization approach was applied to segregation-engineered nanocrystalline Al–Ni–Ce alloys to assess the evolution of microstructure and resulting mechanical behavior as functions of alloying content and annealing conditions. In addition to the identification of alloys and processing conditions that give rise to exceptional thermal stability, strength retention, and homogeneous plastic flow, we construct combined thermal stability and deformation mechanism maps that demarcate several important regimes of behavior.

36 MATERIALS SCIENCE↗

HyperSpace

Machine learning (ML) models often contain numerous hyperparameters, free parameters that must be set before the models can be trained. As the number of model hyperparameters increases, their optimization becomes significantly more challenging as we face a combinatorial increase in potential model configurations. Similarly, there is an increased chance that our models’ hyperparameters interact in complex ways. HyperSpace allows a user to optimize complex machine learning algorithms based on their hyperparameters. HyperSpace works by parallelizing parameter search spaces, running Bayesian model based optimization (SMBO) over each of these spaces in parallel. It was designed to be as minimally invasive as possible such that very little change to existing code will be needed to get a user started.

Ramanathan, Arvind↗

Nearly optimal quantum control: an analytical approach

We propose here nearly optimal control strategies for changing the states of a quantum system. We argue that quantum control optimization can be studied analytically within some protocol families that depend on a small set of parameters for optimization. This optimization strategy can be preferred in practice because it is physically transparent and does not lead to combinatorial complexity in multistate problems. Finally, as a demonstration, we design optimized control protocols that achieve switching between orthogonal states of a naturally biased quantum two-level system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Parallel algorithms for finding connected components using linear algebra

Finding connected components is one of the most widely used operations on a graph. Optimal serial algorithms for the problem have been known for half a century, and many competing parallel algorithms have been proposed over the last several decades under various different models of parallel computation. This paper presents a class of parallel connected-component algorithms designed using linear-algebraic primitives. These algorithms are based on a PRAM algorithm by Shiloach and Vishkin and can be designed using standard GraphBLAS operations. Here, we demonstrate two algorithms of this class, one named LACC for Linear Algebraic Connected Components, and the other named FastSV which can be regarded as LACC’s simplification. With the support of the highly-scalable Combinatorial BLAS library, LACC and FastSV outperform the previous state-of-the-art algorithm by a factor of up to 12x for small to medium scale graphs. For large graphs with more than 50B edges, LACC and FastSV scale to 4K nodes (262K cores) of a Cray XC40 supercomputer and outperform previous algorithms by a significant margin. This remarkable performance is accomplished by (1) exploiting sparsity that was not present in the original PRAM algorithm formulation, (2) using high-performance primitives of Combinatorial BLAS, and (3) identifying hot spots and optimizing them away by exploiting algorithmic insights.

97 MATHEMATICS AND COMPUTING↗

High-throughput printing of combinatorial materials from aerosols

The development of new materials and their compositional and microstructural optimization are essential in regard to next-generation technologies such as clean energy and environmental sustainability. However, materials discovery and optimization have been a frustratingly slow process. The Edisonian trial-and-error process is time consuming and resource inefficient, particularly when contrasted with vast materials design spaces 1 . Whereas traditional combinatorial deposition methods can generate material libraries 2,3 , these suffer from limited material options and inability to leverage major breakthroughs in nanomaterial synthesis. Here we report a high-throughput combinatorial printing method capable of fabricating materials with compositional gradients at microscale spatial resolution. In situ mixing and printing in the aerosol phase allows instantaneous tuning of the mixing ratio of a broad range of materials on the fly, which is an important feature unobtainable in conventional multimaterials printing using feedstocks in liquid–liquid or solid–solid phases 4–6 . We demonstrate a variety of high-throughput printing strategies and applications in combinatorial doping, functional grading and chemical reaction, enabling materials exploration of doped chalcogenides and compositionally graded materials with gradient properties. The ability to combine the top-down design freedom of additive manufacturing with bottom-up control over local material compositions promises the development of compositionally complex materials inaccessible via conventional manufacturing approaches.

36 MATERIALS SCIENCE↗

Selecting a Classification Ensemble and Detecting Process Drift in an Evolving Data Stream

We characterize the commercial behavior of a group of companies in a common line of business using a small ensemble of classifiers on a stream of records containing commercial activity information. This approach is able to effectively find a subset of classifiers that can be used to predict company labels with reasonable accuracy. Performance of the ensemble, its error rate under stable conditions, can be characterized using an exponentially weighted moving average (EWMA) statistic. The behavior of the EWMA statistic can be used to monitor a record stream from the commercial network and determine when significant changes have occurred. Results indicate that larger classification ensembles may not necessarily be optimal, pointing to the need to search the combinatorial classifier space in a systematic way. Results also show that current and past performance of an ensemble can be used to detect when statistically significant changes in the activity of the network have occurred. The dataset used in this work contains tens of thousands of high level commercial activity records with continuous and categorical variables and hundreds of labels, making classification challenging.

Ensemble classifiers↗

Automated scanning probe microscopy of combinatorial ferroelectric libraries: Gaussian-process-guided exploration and noise-aware experiment planning

Combinatorial materials libraries provide an efficient route for mapping composition–property relationships, but their broader impact depends on rapid, quantitative, and functionally relevant characterization. Scanning Probe Microscopy (SPM), including piezoresponse force microscopy (PFM), offers significant potential for quantitative, functionally relevant combi-library readouts. Here, we implement a fully automated SPM workflow for ferroelectric combinatorial libraries and benchmark Gaussian-process-based Bayesian optimization strategies for autonomous experiment planning. The workflow integrates automated probe motion, contact optimization, imaging, and dual amplitude resonance tracking-PFM spectroscopy, and uses scalarized spectroscopic observables to guide subsequent measurements. Stage motion, probe engagement, in-contact tuning, imaging, spectroscopy, and the choice of the next measurement location all proceed without human input. We demonstrate the approach on Sm-doped BiFeO 3 and Zn x Mg 1−x O libraries. By comparing vanilla Bayesian optimization with a measured-noise variant, we show that explicit treatment of local reproducibility can improve modeling of composition-dependent response when the measured variance is physically meaningful, but can also reduce robustness when variability is dominated by outliers or topographic artifacts. Furthermore, these results establish automated SPM as a bridge between combinatorial synthesis and quantitative functional characterization.

Liu, Yu [University of Tennessee, Knoxville, TN (U↗

Optimization-Based Azeotropic Distillation System Synthesis Using Geometric Insights

The synthesis of azeotropic distillation systems is challenging due to the existence of compartments in the residue curve map coupled with the combinatorial aspects from numerous possible system configurations. In this work, an optimization-based approach is introduced to synthesize homogeneous azeotropic distillation systems. The approach employs a network-based representation generated via a matrix method. To design the distillation columns, the modified Underwood equations are adopted, in which pseudocomponent-based compositions are used. For cases where separatrices are significantly curved, corrections via piece-wise linear functions and collinearity properties are implemented. Two examples are presented to illustrate the proposed approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Machine Learning on a Robotic Platform for the Design of Polymer–Protein Hybrids

Polymer–protein hybrids are intriguing materials that can bolster protein stability in non-native environments, thereby enhancing their utility in diverse medicinal, commercial, and industrial applications. One stabilization strategy involves designing synthetic random copolymers with compositions attuned to the protein surface, but rational design is complicated by the vast chemical and composition space. Here, a strategy is reported to design protein-stabilizing copolymers based on active machine learning, facilitated by automated material synthesis and characterization platforms. The versatility and robustness of the approach is demonstrated by the successful identification of copolymers that preserve, or even enhance, the activity of three chemically distinct enzymes following exposure to thermal denaturing conditions. Although systematic screening results in mixed success, active learning appropriately identifies unique and effective copolymer chemistries for the stabilization of each enzyme. Overall, this work broadens the capabilities to design fit-for-purpose synthetic copolymers that promote or otherwise manipulate protein activity, with extensions toward the design of robust polymer–protein hybrid materials.

36 MATERIALS SCIENCE↗

CSRI Summer Proceedings 2021

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia National Laboratories for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researches to learn about problems in computer and computational science at DOE laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, algebraic preconditioners, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, validation and verification methods, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, beyond Moore’s Law computing, exascale computing tools and application design, reduced order and multiscale modeling, parallel input/output, and theoretical computer science. The CSRI Summer Program is organized by CSRI and includes a weekly seminar series and the publication of a summer proceedings.

97 MATHEMATICS AND COMPUTING↗

CSRI Summer Proceedings 2021

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia National Laboratories for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researches to learn about problems in computer and computational science at DOE laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, algebraic preconditioners, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, validation and verification methods, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, beyond Moore’s Law computing, exascale computing tools and application design, reduced order and multiscale modeling, parallel input/output, and theoretical computer science. The CSRI Summer Program is organized by CSRI and includes a weekly seminar series and the publication of a summer proceedings.

97 MATHEMATICS AND COMPUTING↗