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At least 217 records · Page 12

ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules

One of the grand challenges in modern theoretical chemistry is designing and implementing approximations that expedite ab initio methods without loss of accuracy. Machine learning (ML) methods are emerging as a powerful approach to constructing various forms of transferable atomistic potentials. They have been successfully applied in a variety of applications in chemistry, biology, catalysis, and solid-state physics. However, these models are heavily dependent on the quality and quantity of data used in their fitting. Fitting highly flexible ML potentials, such as neural networks, comes at a cost: a vast amount of reference data is required to properly train these models. We address this need by providing access to a large computational DFT database, which consists of more than 20 M off equilibrium conformations for 57,462 small organic molecules. We believe it will become a new standard benchmark for comparison of current and future methods in the ML potential community.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Statistics of base polytopes in F-theory

We propose a new statistical ensemble of toric bases for elliptic Calabi-Yaus used in F-theory models, by focusing on only the convex hull of the base, i.e., the base polytope. This physically motivated coarse-graining greatly simplifies the combinatorial complexity of the part of the 4d F-theory landscape with toric bases. We develop a Monte Carlo approach that randomly samples the base polytopes within fixed boxes, with proper statistical weights. We first apply the algorithm to the set of 2d base polytopes, generating an enlarged set of toric 2d bases that include certain types of codimension-two (4,6) points, and we validate our approach against exact numbers. We then explore the set of 3d base polytopes which fit in a set of “maximal” 3d boxes, and estimate the total number of inequivalent 3d base polytopes to be 10 85 –10 90 . We provide statistical data such as the distribution of non-Higgsable gauge groups on these bases. Amusingly, a similar method can also be applied to generate reflexive polytopes in various dimensions. In both the reflexive and base polytope cases, the number of relevant polytopes obeys a Gaussian distribution as a function of the number of vertices, which can be understood in terms of other results on random polytopes in the math literature.

Differential and algebraic geometry↗

Accelerated discovery of metallic glasses through iteration of machine learning and high-throughput experiments

With more than a hundred elements in the periodic table, a large number of potential new materials exist to address the technological and societal challenges we face today; however, without some guidance, searching through this vast combinatorial space is frustratingly slow and expensive, especially for materials strongly influenced by processing. We train a machine learning (ML) model on previously reported observations, parameters from physiochemical theories, and make it synthesis method–dependent to guide high-throughput (HiTp) experiments to find a new system of metallic glasses in the Co-V-Zr ternary. Experimental observations are in good agreement with the predictions of the model, but there are quantitative discrepancies in the precise compositions predicted. We use these discrepancies to retrain the ML model. The refined model has significantly improved accuracy not only for the Co-V-Zr system but also across all other available validation data. We then use the refined model to guide the discovery of metallic glasses in two additional previously unreported ternaries. Although our approach of iterative use of ML and HiTp experiments has guided us to rapid discovery of three new glass-forming systems, it has also provided us with a quantitatively accurate, synthesis method–sensitive predictor for metallic glasses that improves performance with use and thus promises to greatly accelerate discovery of many new metallic glasses. We believe that this discovery paradigm is applicable to a wider range of materials and should prove equally powerful for other materials and properties that are synthesis path–dependent and that current physiochemical theories find challenging to predict.

36 MATERIALS SCIENCE↗

Crystal structure of the V(D)J recombinase RAG1–RAG2

V(D)J recombination in the vertebrate immune system generates a highly diverse population of immunoglobulins and T-cell receptors by combinatorial joining of segments of coding DNA. The RAG1–RAG2 protein complex initiates this site-specific recombination by cutting DNA at specific sites flanking the coding segments. Here we report the crystal structure of the mouse RAG1–RAG2 complex at 3.2 Å resolution. The 230-kilodalton RAG1–RAG2 heterotetramer is ‘Y-shaped’, with the amino-terminal domains of the two RAG1 chains forming an intertwined stalk. Each RAG1–RAG2 heterodimer composes one arm of the ‘Y’, with the active site in the middle and RAG2 at its tip. The RAG1–RAG2 structure rationalizes more than 60 mutations identified in immunodeficient patients, as well as a large body of genetic and biochemical data. Here, the architectural similarity between RAG1 and the hairpin-forming transposases Hermes and Tn5 suggests the evolutionary conservation of these DNA rearrangements.

36 MATERIALS SCIENCE↗

Metrics for Intercomparison of Remapping Algorithms (MIRA) protocol applied to Earth system models

Abstract. Strongly coupled nonlinear phenomena such as those described by Earth system models (ESMs) are composed of multiple component models with independent mesh topologies and scalable numerical solvers. A common operation in ESMs is to remap or interpolate component solution fields defined on their computational mesh to another mesh with a different combinatorial structure and decomposition, e.g., from the atmosphere to the ocean, during the temporal integration of the coupled system. Several remapping schemes are currently in use or available for ESMs. However, a unified approach to compare the properties of these different schemes has not been attempted previously. We present a rigorous methodology for the evaluation and intercomparison of remapping methods through an independently implemented suite of metrics that measure the ability of a method to adhere to constraints such as grid independence, monotonicity, global conservation, and local extrema or feature preservation. A comprehensive set of numerical evaluations is conducted based on a progression of scalar fields from idealized and smooth to more general climate data with strong discontinuities and strict bounds. We examine four remapping algorithms with distinct design approaches, namely ESMF Regrid (Hill et al., 2004), TempestRemap (Ullrich and Taylor, 2015), generalized moving least squares (GMLS) (Trask and Kuberry, 2020) with post-processing filters, and WLS-ENOR (Li et al., 2020). By repeated iterative application of the high-order remapping methods to the test fields, we verify the accuracy of each scheme in terms of their observed convergence order for smooth data and determine the bounded error propagation using challenging, realistic field data on both uniform and regionally refined mesh cases. In addition to retaining high-order accuracy under idealized conditions, the methods also demonstrate robust remapping performance when dealing with non-smooth data. There is a failure to maintain monotonicity in the traditional L2-minimization approaches used in ESMF and TempestRemap, in contrast to stable recovery through nonlinear filters used in both meshless GMLS and hybrid mesh-based WLS-ENOR schemes. Local feature preservation analysis indicates that high-order methods perform better than low-order dissipative schemes for all test cases. The behavior of these remappers remains consistent when applied on regionally refined meshes, indicating mesh-invariant implementations. The MIRA intercomparison protocol proposed in this paper and the detailed comparison of the four algorithms demonstrate that the new schemes, namely GMLS and WLS-ENOR, are competitive compared to standard conservative minimization methods requiring computation of mesh intersections. The work presented in this paper provides a foundation that can be extended to include complex field definitions, realistic mesh topologies, and spectral element discretizations, thereby allowing for a more complete analysis of production-ready remapping packages.

58 GEOSCIENCES↗

A combinatorially complete epistatic fitness landscape in an enzyme active site

Protein engineering often targets binding pockets or active sites which are enriched in epistasis—nonadditive interactions between amino acid substitutions—and where the combined effects of multiple single substitutions are difficult to predict. Few existing sequence-fitness datasets capture epistasis at large scale, especially for enzyme catalysis, limiting the development and assessment of model-guided enzyme engineering approaches. We present here a combinatorially complete, 160,000-variant fitness landscape across four residues in the active site of an enzyme. Assaying the native reaction of a thermostable β-subunit of tryptophan synthase (TrpB) in a nonnative environment yielded a landscape characterized by significant epistasis and many local optima. These effects prevent simulated directed evolution approaches from efficiently reaching the global optimum. There is nonetheless wide variability in the effectiveness of different directed evolution approaches, which together provide experimental benchmarks for computational and machine learning workflows. The most-fit TrpB variants contain a substitution that is nearly absent in natural TrpB sequences—a result that conservation-based predictions would not capture. Thus, although fitness prediction using evolutionary data can enrich in more-active variants, these approaches struggle to identify and differentiate among the most-active variants, even for this near-native function. Overall, this work presents a large-scale testing ground for model-guided enzyme engineering and suggests that efficient navigation of epistatic fitness landscapes can be improved by advances in both machine learning and physical modeling.

biocatalysis↗

Progress in Understanding the Origins of Excellent Corrosion Resistance in Metallic Alloys: From Binary Polycrystalline Alloys to Metallic Glasses and High Entropy Alloys

Some of the factors responsible for good corrosion resistance of select polycrystalline and emerging alloys in chloride solutions are discussed with a goal of providing some perspectives on the current status and future directions. Traditional metallic glass alloys, single phase high entropy alloys (HEAs), early metallic glasses, and high entropy metallic glasses are all emerging corrosion-resistant alloys (CRAs) that utilize traditional strategies for improved corrosion resistance as well as take advantage of some other novel beneficial attributes. These materials enjoy many degrees of freedom as far as choice of both composition and structure, providing great flexibility in the pursuit of superior corrosion resistance. The new materials depart from classical solvent-solute type polycrystalline binary or ternary alloys. Thus, such emerging materials provide significant opportunities to achieve even greater improvements in corrosion resistance in harsh environments. Several examples of the unique corrosion properties of selected materials in the context of modern theories of corrosion are discussed herein. Discussion is restricted to solid-solution binary or ternary polycrystalline alloys, several metallic glass alloys, and single phase HEAs. A common feature of many CRAs is that composition and microstructure often affect both passivity and resistance to localized corrosion that can be divided into initiation, stabilization, and propagation stages. Enormous complexities in protective oxide structures and chemistries and the large number of combinatorial possibilities in newer materials such as HEAs preclude trial-and-error approaches and perhaps even combinatorial experimental design. Computational materials methodologies will be required in the search for new corrosion-resistant alloys in these material classes. The search must consider the best scientific insights available regarding how major and minor alloy additions, as well as various microstructural attributes, contribute to corrosion mitigation. Additional scientific insights, as they emerge, will enable choices beyond the reliance on high concentrations of alloying elements that are known to affect passivity breakdown and pit stabilization. A challenge is to connect the “basic attributes” of an alloy with its properties. The strength of this connection will likely require new scientific principles enabling deep multiphysics insights in order to link feature(s) such as composition and metallurgical phases to the desired corrosion properties. Application of data informatics will likely also play a role given the plethora of variables that are important in corrosion and the difficulty in assessing all relationships. Here, the opportunity exists to accelerate the design of emerging materials for high corrosion resistance.

36 MATERIALS SCIENCE↗

Combinatorial Exploration and Mapping of Phase Transformation in a Ni–Ti–Co Thin Film Library

Combinatorial synthesis and high-throughput characterization of a Ni–Ti–Co thin film materials library are reported for exploration of reversible martensitic transformation. The library was prepared by magnetron co-sputtering, annealed in vacuum at 500 °C without atmospheric exposure, and evaluated for shape memory behavior as an indicator of transformation. Composition, structure, and transformation behavior of the 177 pads in the library were characterized using high-throughput wavelength dispersive spectroscopy (WDS), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), and four-point probe temperature-dependent resistance (R(T)) measurements. A new, expanded composition space having phase transformation with low thermal hysteresis and Co > 10 at. % is found. Unsupervised machine learning methods of hierarchical clustering were employed to streamline data processing of the large XRD and XPS data sets. Through cluster analysis of XRD data, we identified and mapped the constituent structural phases. Finally, composition–structure–property maps for the ternary system are made to correlate the functional properties to the local microstructure and composition of the Ni–Ti–Co thin film library.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Data for Metabolic Engineering of Rhodotorula toruloides IFO0880 Improves C16 and C18 Fatty Alcohol Production from Synthetic Media

The oleaginous, carotenogenic yeast Rhodotorula toruloides has been increasingly explored as a platform organism for the production of terpenoids and fatty acid derivatives. Fatty alcohols, a fatty acid derivative widely used in the production of detergents and surfactants, can be produced microbially with the expression of a heterologous fatty acyl-CoA reductase. Due to its high lipid production, R. toruloides has high potential for fatty alcohol production, and in this study several metabolic engineering approaches were investigated to improve the titer of this product. Fatty acyl-CoA reductase from Marinobacter aqueolei was co-expressed with SpCas9 in R. toruloides IFO0880 and a panel of gene overexpressions and Cas9-mediated gene deletions were explored to increase the fatty alcohol production. Two overexpression targets (ACL1 and ACC1, improving cytosolic acetyl-CoA and malonyl-CoA production, respectively) and two deletion targets (the acyltransferases DGA1 and LRO1) resulted in significant (1.8 to 4.4-fold) increases to the fatty alcohol titer in culture tubes. Combinatorial exploration of these modifications in bioreactor fermentation culminated in a 3.7 g/L fatty alcohol titer in the LRO1Δ mutant. As LRO1 deletion was not found to be beneficial for fatty alcohol production in other yeasts, a lipidomic comparison of the DGA1 and LRO1 knockout mutants was performed, finding that DGA1 is the primary acyltransferase responsible for triacylglyceride production in R. toruloides , while LRO1 disruption simultaneously improved fatty alcohol production, increased diacylglyceride and triacylglyceride production, and increased glucose consumption. The fatty alcohol titer of fatty acyl-CoA reductase-expressing R. toruloides was significantly improved through the deletion of LRO1, or the deletion of DGA1 combined with overexpression of ACC1 and ACL1. Disruption of LRO1 surprisingly increased both lipid and fatty alcohol production, creating a possible avenue for future study of the lipid metabolism of this yeast.

Conversion↗

K-decompositions and 3d gauge theories

This paper combines several new constructions in mathematics and physics. Mathematically, we study framed flat PGL(K, C)-connections on a large class of 3-manifolds M with boundary. We introduce a moduli space $\mathcal{L}$ K (M) of framed flat connections on the boundary ∂M that extend to M. Our goal is to understand an open part of $\mathcal{L}$ K (M) as a Lagrangian subvariety in the symplectic moduli space X un K (∂M) of framed flat connections on the boundary — and more so, as a “K 2 -Lagrangian,” meaning that the K 2 -avatar of the symplectic form restricts to zero. We construct an open part of $\mathcal{L}$ K (M) from elementary data associated with the hypersimplicial K-decomposition of an ideal triangulation of M, in a way that generalizes (and combines) both Thurston’s gluing equations in 3d hyperbolic geometry and the cluster coordinates for framed flat PGL(K, C)-connections on surfaces. By using a canonical map from the complex of configurations of decorated flags to the Bloch complex, we prove that any generic component of $\mathcal{L}$ K (M) is K 2 -isotropic as long as ∂M satisfies certain topological constraints (theorem 4.2). In some cases this easily implies that $\mathcal{L}$ K (M) is K 2 -Lagrangian. For general M, we extend a classic result of Neumann and Zagier on symplectic properties of PGL(2) gluing equations to reduce the K 2 -Lagrangian property to a combinatorial statement. Physically, we translate the K-decomposition of an ideal triangulation of M and its symplectic properties to produce an explicit construction of 3d N = 2 superconformal field theories T K [M] resulting (conjecturally) from the compactification of K M5-branes on M. This extends known constructions for K = 2. Just as for K = 2, the theories T K [M] are described as IR fixed points of abelian Chern-Simons-matter theories. Changes of triangulation (2-3 moves) lead to abelian mirror symmetries that are all generated by the elementary duality between N f = 1 SQED and the XYZ model. In the large K limit, we find evidence that the degrees of freedom of T K [M] grow cubically in K.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Nuclear level density, thermalization, chaos, and collectivity

The knowledge of the level density is necessary for understanding nuclear reactions involving excited nuclear states. In particular, it is an important element in description of astrophysical processes and in technological applications. This review article explains main ideas of physics forming the level density in complex nuclei that grows very fast due to combinatorial complexity of total excitation energy shared by many constituents. This can be translated into a language of statistical physics by the Darwin–Fowler method. We briefly go through the historical development from the nuclear Fermi-gas model to the self-consistent mean field including the pairing effects. At the next step we introduce the ideas of thermalization in a closed mesoscopic system and quantum chaos with very complicated eigenfunctions. This is supported by the experience of the shell model in a limited orbital space that either provides an exact solution or uses the Monte Carlo approach. The statistical method of moments allows one to avoid the exact diagonalization keeping intact the quality of the results. We discuss the popular “constant temperature model” that describes well available data and the shell-model results; it is shown that its success cannot be explained by the phase transition from superfluid to a normal phase. The interpretation is suggested, supported by the numerical studies, in terms of dynamical chaotization including the collective enhancement of the level density. The role of incoherent collision-like interactions is stressed as a necessary element of the thermalization process.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Machine Learning Applied to Zeolite Synthesis: The Missing Link for Realizing High-Throughput Discovery

Zeolites are microporous crystalline materials with well-defined cavities and pores, which can be prepared under different pore topologies and chemical compositions. Their preparation is typically defined by multiple interconnected variables (e.g., reagent sources, molar ratios, aging treatments, reaction time and temperature, among others), but unfortunately their distinctive influence, particularly on the nucleation and crystallization processes, is still far from being understood. Thus, the discovery and/or optimization of specific zeolites is closely related to the exploration of the parametric space through trial-and-error methods, generally by studying the influence of each parameter individually. In the past decade, machine learning (ML) methods have rapidly evolved to address complex problems involving highly nonlinear or massively combinatorial processes that conventional approaches cannot solve. Considering the vast and interconnected multiparametric space in zeolite synthesis, coupled with our poor understanding of the mechanisms involved in their nucleation and crystallization, the use of ML is especially timely for improving zeolite synthesis. Indeed, the complex space of zeolite synthesis requires drawing inferences from incomplete and imperfect information, for which ML methods are very well-suited to replace the intuition-based approaches traditionally used to guide experimentation. In this Account, we contend that both existing and new ML approaches can provide the “missing link” needed to complete the traditional zeolite synthesis workflow used in our quest to rationalize zeolite synthesis. Within this context, we have made important efforts on developing ML tools in different critical areas, such as (1) data-mining tools to process the large amount of data generated using high-throughput platforms; (2) novel complex algorithms to predict the formation of energetically stable hypothetical zeolites and guide the synthesis of new zeolite structures; (3) new “ab initio” organic structure directing agent predictions to direct the synthesis of hypothetical or known zeolites; (4) an automated tool for nonsupervised data extraction and classification from published research articles. ML has already revolutionized many areas in materials science by enhancing our ability to map intricate behavior to process variables, especially in the absence of well-understood mechanisms. Undoubtedly, ML is a burgeoning field with many future opportunities for further breakthroughs to advance the design of molecular sieves. For this reason, this Account includes an outlook of future research directions based on current challenges and opportunities. We envision this Account will become a hallmark reference for both well-established and new researchers in the field of zeolite synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modeling Intercalation Chemistry with Multiredox Reactions by Sparse Lattice Models in Disordered Rocksalt Cathodes

Modern battery materials can contain many elements with substantial site disorder, and their configurational state has been shown to be critical for their performance. The intercalation voltage profile is a critical parameter to evaluate the performance of energy storage. The application of commonly used cluster expansion techniques to model the intercalation thermodynamics of such systems ab initio is challenged by the combinatorial increase in configurational degrees of freedom as the number of species grows. Such challenges necessitate the efficient generation of lattice models without overfitting and proper sampling of the configurational space under the requirement of charge balance in ionic systems. In this work, we introduce a combined approach that addresses these challenges by (1) constructing a robust cluster expansion Hamiltonian using the sparse regression technique, including -norm regularization and structural hierarchy; and (2) implementing semigrand-canonical Monte Carlo to sample charge-balanced ionic configurations using the table-exchange method and an ensemble average approach. These techniques are applied to a disordered rocksalt oxyfluoride (LMNOF) that is part of a family of promising earth-abundant cathode materials. The simulated voltage profile is found to be in good agreement with experimental data and particularly provides a clear demonstration of the and oxygen contributions to the redox potential as a function of content.

25 ENERGY STORAGE↗

Efficient, Predictive Tomography of Multi-Qubit Quantum Processors

After decades of R&D, quantum computers comprising more than 2 qubits are appearing. If this progress is to continue, the research community requires a capability for precise characterization (“tomography”) of these enlarged devices, which will enable benchmarking, improvement, and finally certification as mission-ready. As world leaders in characterization -- our gate set tomography (GST) method is the current state of the art – the project team is keenly aware that every existing protocol is either (1) catastrophically inefficient for more than 2 qubits, or (2) not rich enough to predict device behavior. GST scales poorly, while the popular randomized benchmarking technique only measures a single aggregated error probability. This project explored a new insight: that the combinatorial explosion plaguing standard GST could be avoided by using an ansatz of few-qubit interactions to build a complete, efficient model for multi-qubit errors. We developed this approach, prototyped it, and tested it on a cutting-edge quantum processor developed by Rigetti Quantum Computing (RQC), a US-based startup. We implemented our new models within Sandia’s PyGSTi open-source code, and tested them experimentally on the RQC device by probing crosstalk. We found two major results: first, our schema worked and is viable for further development; second, while the Rigetti device is indeed a “real” 8-qubit quantum processor, its behavior fluctuated significantly over time while we were experimenting with it and this drift made it difficult to fit our models of crosstalk to the data.

97 MATHEMATICS AND COMPUTING↗

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↗

PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions

Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

59 BASIC BIOLOGICAL SCIENCES↗

Combinatorial pulsed laser deposition of doped yttrium iron garnet films on yttrium aluminium garnet

We investigate the crystalline growth of yttrium iron garnet (YIG) films doped with bismuth (Bi) and cerium (Ce) by combinatorial pulsed laser deposition, co-ablating a YIG target and either a Bi{sub 2}O{sub 3} or a CeO{sub 2} target, for applications in microwave and optical communications. Substrate temperature is critical for crystalline growth of YIG with simultaneous inclusion of Bi in the garnet lattice, whereas Ce is not incorporated in the garnet structure, but forms a separate CeO{sub 2} phase.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗