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At least 271 records · Page 15

AL4GAP: Active learning workflow for generating DFT-SCAN accurate machine-learning potentials for combinatorial molten salt mixtures

Machine learning interatomic potentials have emerged as a powerful tool for bypassing the spatiotemporal limitations of ab initio simulations, but major challenges remain in their efficient parameterization. We present AL4GAP, an ensemble active learning software workflow for generating multicomposition Gaussian approximation potentials (GAP) for arbitrary molten salt mixtures. The workflow capabilities include: (1) setting up user-defined combinatorial chemical spaces of charge neutral mixtures of arbitrary molten mixtures spanning 11 cations (Li, Na, K, Rb, Cs, Mg, Ca, Sr, Ba and two heavy species, Nd, and Th) and 4 anions (F, Cl, Br, and I), (2) configurational sampling using low-cost empirical parameterizations, (3) active learning for down-selecting configurational samples for single point density functional theory calculations at the level of Strongly Constrained and Appropriately Normed (SCAN) exchange-correlation functional, and (4) Bayesian optimization for hyperparameter tuning of two-body and many-body GAP models. Here, we apply the AL4GAP workflow to showcase high throughput generation of five independent GAP models for multicomposition binary-mixture melts, each of increasing complexity with respect to charge valency and electronic structure, namely: LiCl–KCl, NaCl–CaCl 2 , KCl–NdCl 3 , CaCl 2 –NdCl 3 , and KCl–ThCl 4 . Our results indicate that GAP models can accurately predict structure for diverse molten salt mixture with density functional theory (DFT)-SCAN accuracy, capturing the intermediate range ordering characteristic of the multivalent cationic melts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Metabolic flux optimization of iterative pathways through orthogonal gene expression control: Application to the β-oxidation reversal

Balancing relative expression of pathway genes to minimize flux bottlenecks and metabolic burden is one of the key challenges in metabolic engineering. This is especially relevant for iterative pathways, such as reverse β-oxidation (rBOX) pathway, which require control of flux partition at multiple nodes to achieve efficient synthesis of target products. Here, we develop a plasmid-based inducible system for orthogonal control of gene expression (referred to as the TriO system) and demonstrate its utility in the rBOX pathway. Leveraging effortless construction of TriO vectors in a plug-and-play manner, we simultaneously explored the solution space for enzyme choice and relative expression levels. Remarkably, varying individual expression levels led to substantial change in product specificity ranging from no production to optimal performance of about 90% of the theoretical yield of the desired products. We obtained titers of 6.3 g/L butyrate, 2.2 g/L butanol and 4.0 g/L hexanoate from glycerol in E. coli, which exceed the best titers previously reported using equivalent enzyme combinations. Since a similar system behavior was observed with alternative termination routes and higher-order iterations, we envision our approach to be broadly applicable to other iterative pathways besides the rBOX. Here, considering that high throughput, automated strain construction using combinatorial promoter and RBS libraries remain out of reach for many researchers, especially in academia, tools like the TriO system could democratize the testing and evaluation of pathway designs by reducing cost, time and infrastructure requirements.

59 BASIC BIOLOGICAL SCIENCES↗

Engineering growth factors for regenerative medicine applications.

Growth factors are important morphogenetic proteins that instruct cell behavior and guide tissue repair and renewal. Although their therapeutic potential holds great promise in regenerative medicine applications, translation of growth factors into clinical treatments has been hindered by limitations including poor protein stability, low recombinant expression yield, and suboptimal efficacy. This review highlights current tools, technologies, and approaches to design integrated and effective growth factor-based therapies for regenerative medicine applications. The first section describes rational and combinatorial protein engineering approaches that have been utilized to improve growth factor stability, expression yield, biodistribution, and serum half-life, or alter their cell trafficking behavior or receptor binding affinity. The second section highlights elegant biomaterial-based systems, inspired by the natural extracellular matrix milieu, that have been developed for effective spatial and temporal delivery of growth factors to cell surface receptors. Although appearing distinct, these two approaches are highly complementary and involve principles of molecular design and engineering to be considered in parallel when developing optimal materials for clinical applications.

Biomaterials↗

Machine Learning-Enabled Image Classification for Automated Electron Microscopy

Abstract Traditionally, materials discovery has been driven more by evidence and intuition than by systematic design. However, the advent of “big data” and an exponential increase in computational power have reshaped the landscape. Today, we use simulations, artificial intelligence (AI), and machine learning (ML) to predict materials characteristics, which dramatically accelerates the discovery of novel materials. For instance, combinatorial megalibraries, where millions of distinct nanoparticles are created on a single chip, have spurred the need for automated characterization tools. This paper presents an ML model specifically developed to perform real-time binary classification of grayscale high-angle annular dark-field images of nanoparticles sourced from these megalibraries. Given the high costs associated with downstream processing errors, a primary requirement for our model was to minimize false positives while maintaining efficacy on unseen images. We elaborate on the computational challenges and our solutions, including managing memory constraints, optimizing training time, and utilizing Neural Architecture Search tools. The final model outperformed our expectations, achieving over 95% precision and a weighted F-score of more than 90% on our test data set. This paper discusses the development, challenges, and successful outcomes of this significant advancement in the application of AI and ML to materials discovery.

Materials Science↗

Reducing model error using optimized galaxy selection: weak lensing cluster mass estimation

Galaxy clusters are one of the most powerful probes to study extensions of General Relativity and the Standard Cosmological Model. Upcoming surveys like the Vera Rubin Observatory’s Legacy Survey of Space and Time are expected to revolutionise the field, by enabling the analysis of cluster samples of unprecedented size and quality. To reach this era of high-precision cluster cosmology, the mitigation of sources of systematic error is crucial. A particularly important challenge is bias in cluster mass measurements induced by the mismodelling of photometric redshift estimates of source galaxies. This work proposes a method to optimise the source sample selection in cluster weak lensing analyses drawn from wide-field survey lensing catalogs to reduce the bias on reconstructed cluster masses. We use a combinatorial optimisation scheme and methods from variational inference to select galaxies in latent space to produce a probabilistic galaxy source sample catalog for highly accurate cluster mass estimation. We show that our method reduces the critical surface mass density Σ crit relative modelling bias on the 60-70% level, while maintaining up to 90% of galaxies. We highlight that our methodology has applications beyond cluster mass estimation as an approach to jointly combine galaxy selection and model inference under sources of systematics.

79 ASTRONOMY AND ASTROPHYSICS↗

cuAlign: Scalable Network Alignment on GPU Accelerators

Given two graphs, the objective of network alignment is to find the best one-to-one mapping of vertices in one graph (??) to vertices in the other (??), such that the number of overlaps is maximized. We say that edges(??, ??) ???and(??', ??') ??? are overlapped if ?? is mapped to ??' and ?? is mapped to??'. Network alignment is an important optimization problem with several applications in bioinformatics, computer vision and ontology matching. Since it is an NP-hard problem, efficient heuristics and scalable implementations are necessary. In this work, we introduce a new framework that combines the concepts of intra-network proximity using vertex embedding,Belief Propagation (BP) and approximate weighted matching, and provides qualitative improvements up to22%over state-of-the-art approaches. We also provide scalable implementations on GPU accelerators, demonstrating up to19×speedup for Belief Propagation and 3× speedup for approximate weighted matching relative to previous multithreaded implementation. A combination of combinatorial and algebraic kernels within the network alignment algorithm poses significant hurdles for parallelization. Load imbalance and irregular DRAM traffic limit achievable performance on GPUs. Our novel approach identifies and exploits unique structural proper-ties of the BP-based algorithm and employs code fusion to reduce data movement between different steps of the algorithm. Using a diverse set of inputs, we demonstrate qualitative improvements of our algorithms, and performance gains of our GPU-accelerated implementation. We believe that our work will enable algorithmic improvements and practical applications of network alignment.

Xiang, Lizhi↗

Identification of 2-Hydroxyacyl-CoA Synthases with High Acyloin Condensation Activity for Orthogonal One-Carbon Bioconversion

One-carbon (C1) compounds are emerging as cost-effective and potentially carbon-negative feedstocks for biomanufacturing, which require efficient, versatile metabolic platforms for the synthesis of value-added products. Synthetic formyl-CoA elongation (FORCE) pathways allow diverse product synthesis from C1 compounds via iterative C1 elongation, operating independently from the host metabolism with reduced engineering complexity and improved theoretical yields. However, a major bottleneck was identified as the suboptimal kinetics of the core C1–C1 condensation enzyme, 2-hydroxyacyl-CoA synthase (HACS), catalyzing the acyloin condensation reaction between formaldehyde and formyl-CoA. Furthermore, we used a combinatorial approach of bioprospecting and rational protein engineering to identify multiple HACS variants with significantly improved activities toward C1 substrates. Sequence and structure alignment of the active variants elucidated the key regions for the catalytic function, which were targeted for mutagenesis, leading to improved catalytic efficiency. In parallel, a consecutive round of bioprospecting for homologs with high similarity with active variants revealed a highly active HACS variant exhibiting up to 7-fold improvement in catalytic efficiency (k cat /K M ) and 14-fold improvement in the FORCE pathway flux in vivo compared to the previous reports. Upon further optimization of the downstream pathway, the orthogonal C1-to-product bioconversion system showed a metabolic flux of up to 700 μM glycolate OD –1 h –1 (2.1 mmol gDCW –1 h –1 ) and an industrially relevant glycolate titer, rate, and yield of 5.2 g L –1 (67.8 mM), 0.22 g L –1 h –1 , and 94% carbon yield, respectively.

2-hydroxyacyl-CoA synthase↗

Enhancing Electron Microscopy Image Classification Using Data Augmentation

Manual labeling for machine learning tasks such as image classification is tedious and labor-intensive; as a result, scientific datasets suitable for deep learning applications are scarce and limited. While data augmentation techniques have shown promise for extending image datasets, very little work has been done to understand the impact of combining multiple augmentation methods sequentially or the limits of their effectiveness when combined. Our work addresses this gap by examining how standard and combinatorial data augmentation affects the performance of machine learning models when trained on small datasets for label classification tasks. For our analysis, we generate single, double and quadruple-augmented datasets for a microscopy image classification task using six standard augmentation methods, and compare the resultant improvements observed in binary classification accuracy with three standard image classification models (DenseNet169, MobileNetV2, ResNet101V2). Our experiments show a non-monotonic relationship between the number of simultaneous augmentation methods and classification accuracy, indicating that there is a trade-off between the degree of augmentation and the model performance. These findings suggest that the optimal number of augmentation methods will vary by domain and use case. We also find that the order in which augmentation methods are applied to a limited dataset matters when combining augmentation schemes, with our use case showing performance differences up to 2.6% when the augmentation order is reversed for double-augmented datasets. Our work offers insights to the limits of data augmentation when working on image classification tasks with limited datasets.

Welsman, Jordan A↗

The 2019 materials by design roadmap

Advances in renewable and sustainable energy technologies critically depend on our ability to design and realize materials with optimal properties. Materials discovery and design efforts ideally involve close coupling between materials prediction, synthesis and characterization. Increased use of computational tools, the generation of materials databases, and advances in experimental methods have substantially accelerated these activities. It is therefore an opportune time to consider future prospects for materials by design approaches. The purpose of this roadmap is to present an overview of the current state of computational materials prediction, synthesis and characterization approaches, materials design needs for various technologies, and future challenges and opportunities that must be addressed. Perspectives cover topics on computational techniques, validation, materials databases, materials informatics, high-throughput combinatorial methods, advanced characterization approaches, and materials design issues in thermoelectrics, photovoltaics, solid state lighting, catalysts, batteries, metal alloys, complex oxides and transparent conducting materials. It is our hope that this roadmap will guide researchers and funding agencies in identifying new prospects for materials design.

36 MATERIALS SCIENCE↗

Ultra-rapid, physics-based development pathway for reactor-relevant RF antenna materials

This paper presents a rapid, atomistically-informed, experimental development pathway for fusion reactor-relevant radio frequency (RF) antenna materials in the Cu-Cr-(Nb,Al,Zr) composition system, with the goal of improving upon GRCop-84. RF antennas in a tokamak fusion reactor will face a unique set of challenges as both structural and functional materials. The desired material must simultaneously achieve and maintain high electrical conductivity, high strength, high thermal conductivity, resist high temperatures, possess low nuclear activation, and incur low damage due to neutron bombardment. The GRCop-84 alloy serves as a starting point for iterative improvement, with the desire to reduce or eliminate Nb from the material to minimize nuclear activation. The rapid development pathway makes use of a multi-target combinatorial thick film sputtering process to produce full ternary phase diagrams on a Si wafer substrate. Transient grating spectroscopy (TGS), a laser-ultrasonic method, will determine spatially-varying thermo-elastic properties, while four terminal electrical conductivity measurements will map out the best per- forming regions of the sample for in-depth study at larger length scales. High energy proton and self-ion irradiation emulates the effects of neutron damage on the thermal/electric properties. With rapid turnaround time (∼days) in terms of mapping radiation damage-induced material property changes in the full ternary system, these techniques allow rapid iteration towards an optimal material, testing hundreds of nearby compositions in the time it took to test one. Focused testing of larger, single composition samples (produced in an arc furnace or by laser sintering) provides data on structural and high power RF properties, and validates our thick-film based workflow.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations

Publicly available collections of drug-like molecules have grown to comprise tens of billions of compounds due to advances in combinatorial chemistry. Traditional methods for identifying "hit" molecules from a large collection of potential drug-like candidates have relied 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 the major drawback that they require exceptional computing capabilities for even relatively small collections of molecules. Hyperdimensional Computing (HDC) is a recently-proposed learning paradigm that represents data with high-dimension binary vectors; this 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. We consider existing HDC approaches for molecular property classification and introduce two novel encodings of a commonly-used molecular representation, the extended connectivity fingerprint (ECFP). We show that HDC-based inference methods are as much as 91 times more efficient than traditional machine learning methods, and achieve an acceleration of nearly nine orders of magnitude compared to molecular docking. Our results show that HDC accelerated methods retain competitive accuracy on a number of well-studied tasks such as molecular property predictions using the MoleculeNet dataset, and bind/no-bind activity classification using the DUD-E and LIT-PCBA datasets. Our work thus motivates further investigation into molecular representation learning to develop ultraefficient pre-screening tools.

Jones, William↗

Combinatorial alloying improves bismuth vanadate photoanodes via reduced monoclinic distortion

Improving the efficiency of solar-powered oxygen evolution is both critical for development of solar fuels technologies and challenging due to the broad set of properties required of a solar fuels photoanode. Bismuth vanadate, in particular the monoclinic clinobisvanite phase, has received substantial attention and has exhibited the highest radiative efficiency among metal oxides with a band gap in the visible range. Efforts to further improve its photoelectrochemical performance have included alloying one or more metals onto the Bi and/or V sites, with progress on this frontier stymied by the difficulty in computational modelling of substitutional alloys and the high dimensionality of co-alloying composition spaces. Since substitutional alloying concurrently changes multiple materials properties, understanding the underlying cause for performance improvements is also challenging, motivating our application of combinatorial materials science techniques to map photoelectrochemical performance of 948 unique bismuth vanadate alloy compositions comprising 0 to 8% alloys of P, Ca, Mo, Eu, Gd, and W along with a variety of compositions from each pairwise combination of these elements. Upon identification of substantial improvements in the (Mo,Gd) co-alloying space, structural mapping was performed to reveal a remarkable correlation between performance enhancement and a lowered monoclinic distortion. Lastly, first-principles density functional theory calculations indicate that the improvements are due to a lowered hole effective mass and hole polaron formation energy, and collectively, our results identify the monoclinic distortion as a critical parameter in the optimization and understanding of bismuth vanadate-based photoanodes.

14 SOLAR ENERGY↗

Design and Performance of a Smartphone-based Cosmic Ray Observatory

This dissertation examines the feasibility of appropriating the global network of smartphones as an observatory for ultra-high-energy cosmic rays. An application and cloud-based data-acquisition system are first proposed for such an observatory, in which heterogenous devices self-calibrate and server feedback optimizes individual device triggers. Methods of monitoring and manually controlling this network are also examined. Detection efficiencies for cosmic muons, MeV-scale gamma rays, and 120 GeV protons are then measured for this trigger, with which a Monte Carlo pixel model is fine-tuned. Extending this model to cosmic ray showers, the effective area of the observatory for super-GZK primaries is shown to equal that of the Pierre Auger Observatory with a global participation rate under 0.1%, far below initial estimates presented in Ref. [83]. A vastly improved sensitivity to photons and more precise modeling of electrons are primarily responsible for this discrepancy, though more refined models of the combinatorial background may yet lead to more stringent requirements.

Swaney, Jeff↗

Novel Chalcopyrites for Advanced Photoelectrochemical Water Splitting

With the support of DoE’s EERE office, our team has established a unique tool-chest of capabilities, including theoretical modeling (Lawrence Livermore National Laboratory: LLNL), state-of-the-art synthesis (Hawaii Natural Energy Institute: HNEI, Stanford, and the National Renewable Energy Laboratory: NREL) and advanced materials and interfaces characterization (University of Nevada, Las Vegas: UNLV, and Lawrence Berkeley National Laboratory: LBNL), to accelerate the development of high efficiency and durable chalcopyrite materials for advanced photoelectrochemical (PEC) water splitting. Using this synergistic approach, we have successfully created new wide bandgap chalcopyrite photocathodes generating over 10 mA/cm 2 , developed innovative strategies to protect them from corrosion, and engineered novel integration methods to circumvent thin film materials mechanical, chemical and thermal incompatibility. In Task 1 “Modeling and synthesis of chalcopyrite photocathodes”, we expanded our library of wide bandgap chalcopyrites for PEC water splitting. With support from LLNL’s “Computational Materials Diagnostics and Optimization of PEC Devices”, LBNL’s “photophysical” and NREL’s “I-III-VI Compound Semiconductors for Water-Splitting” nodes, we investigated two new chalcopyrite candidates for PEC water splitting: Cu(In,Al)Se 2 and Cu(In,B)Se 2 . We also further developed ordered vacancy compounds, such as CuGa 3 Se 5 , with unprecedented durability during PEC waters splitting in acidic solutions. In Task 2 “Interfaces engineering for enhanced efficiency and durability”, we addressed both the non-ideal band-edge positions of chalcopyrites with respect to water redox potentials, as well as their chemical instability under PEC water splitting, with a buried-junctions approach. With help from NREL’s “High-Throughput Experimental Thin Film Combinatorial Capabilities” and “Corrosion Analysis of Materials” nodes, we engineered environmentally friendly n-type buffers, including Mn x Zn 1-x O, to adjust the chalcopyrite band-edge positions and achieved photovoltages as high as 925 mV. Also, we integrated non-precious catalytic-protecting layers, such as WO 3 , to enhance the water splitting long-term stability of chalcopyrite absorbers. Finally, in Task 3 “Hybrid photoelectrode device integration”, we proposed an innovative method to bond wide bandgap photocathodes onto narrow bandgap PV drivers at room temperature using conductive polymers. Our semi-monolithic approach addressed fundamental processing incompatibility issues, as both the photocathode and the PV driver are processed separately. Proof-of-concept whole-chalcopyrite tandems were obtained by consecutive exfoliation and transfer of fully integrated 1.85 eV CuGa 3 Se 5 and 1.13 eV CuInGaSe 2 stacks from their Mo/SLG substrates onto a new single FTO host substrate.

08 HYDROGEN↗

Combinatorial sputtering of Ga-doped (Zn,Mg)O for contact applications in solar cells

In this study, the development of tunable contact materials based on environmentally friendly chemical elements using scalable deposition approaches is necessary for existing and emerging solar energy conversion technologies. In this paper, the properties of ZnO alloyed with magnesium (Mg), and doped with gallium (Ga) are studied using combinatorial thin film experiments. As a result of these studies, the optical band gap of the sputtered Zn 1-x Mg x O thin films was determined to vary from 3.3 to 3.6 eV for a compositional spread of Mg content in the 0.04 < x < 0.17 range. Depending on whether or not Ga dopants were added, the electron concentrations were on the order of 10 17 cm -3 or 10 20 cm -3 , respectively. Based on these results and on the Kelvin Probe work function measurements, a band diagram was derived using basic semiconductor physics equations. The quantitative determination of how the energy levels of Ga-doped (Zn, Mg)O thin films change as a function of Mg composition presented here, will facilitate their use as optimized contact layers for both Cu 2 ZnSnS 4 (CZTS), Cu(In, Ga)Se 2 (CIGS) and other solar cell absorbers.

14 SOLAR ENERGY↗

Two-Stage Adaptive Restoration Decision Support System for a Self-Healing Power Grid

Power outages cost American industries and businesses billions of dollars and jeopardize the lives of hospital patients. The losses can be greatly reduced with a fast, reliable, and flexible self-healing tool. This paper is aimed to tackle the challenging task of developing an adaptive restoration decision support system (RDSS). The proposed RDSS determines restoration actions both in planning and real-time phases and adapts to constantly changing system conditions. The comprehensive formulation encompasses practical constraints including ac power flow, dynamic reserve, and load modeling. Here, the combinatorial problem is decomposed into a two-stage formulation solved by an integer L-shaped algorithm. The two stages are then executed online in the RDSS framework employing a sliding window method. The IEEE 39-bus system has been studied under normal and contingency conditions to demonstrate the effectiveness and efficiency of the proposed online RDSS.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Solid Phase Gradient Alloying Method via ShAPE

Alloying has been used to confer desirable properties to various metallic systems since the bronze age. For example, Ni, Mn, and Cr are alloyed into an Fe matrix to make steel, which has improved strength and corrosion resistance (as displayed in Fig. 1). In addition to the type of alloying elements, the amount of alloying elements added into a matrix is also very critical for a material’s mechanical property, physical property, machinability, and cost. Conventionally, new alloys are discovered by combining alloy precursors and elemental constituents into a mixture and melting them together. The solidified product or ingot represents a usually non-homogeneous combination of the chemistry with a microstructure dictated by the physics of solidification. It is time and energy intensive to optimize the alloying amounts via the casting process and hence, economically not conducive to rapid alloy discovery. In addition, the cast microstructure seen in the as-cast ingot is often not the ideal, nor even desired structure for optimized performance. Cast materials often need further processing such as homogenization, annealing, and deformation work put in through rolling, forging, extruding, etc. to have favorable microstructures and properties. A faster method to discover new alloy combinations and evaluate them in their worked or processed form is needed. Recently, Laser Engineered Net Shaping was applied to fabricate gradient compositional material for alloy designing. However, the mechanical properties of this gradient alloy were poor due to the existence of impurities, oxidation and cracks that are inherent in the melt-solidification process. Because of these limitations, we propose to use a solid-phase process (ShAPE) to create bulk materials (extrudates) that vary in composition from one end of the extruded solid to the other. Various manufacturing methods for alloy design including conventional casting method, laser based combinatorial method and current solid phase gradient alloying method are displayed and compared in Fig. 2. ShAPE machine and a schematic of ShAPE process are displayed in Fig. 3. Starting material is processed by a rotating and plunging die to form an extrudate. We are proposing through this methodology to invent a new, bulk-scale combinatorial technique. With this novel technique, alloying element can be dissolved into the matrix with a continued gradient without bulk melting. Formation of inter-metallics and defects originating from melt processing can be avoided. In addition, the ShAPE process creates the mixed alloy chemistry, and meanwhile subjects the material to severe plastic strain, which induces the favorable “worked” microstructure. Products from the ShAPE process can be tested in hardness directly providing a path to rapid evaluation of mechanical properties. The ability to create graded structures using friction stir processing (FSP) has been demonstrated, however using the ShAPE process we believe will lead to much faster and higher fidelity results. When combined with high throughput screening methods of physical, mechanical and microstructural property characterization, efficiency and accuracy of alloy design can be significantly improved.

36 MATERIALS SCIENCE↗