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At least 163 records · Page 9

Active Learning A Neural Network Model For Gold Clusters & Bulk From Sparse First Principles Training Data

Small metal clusters are of fundamental scientific interest and of tremendous significance in catalysis. These nanoscale clusters display diverse geometries and structural motifs depending on the cluster size; a knowledge of this size-dependent structural motifs and their dynamical evolution has been of longstanding interest. Given the high computational cost of first-principles calculations, molecular modeling and atomistic simulations such as molecular dynamics (MD) has proven to be an important complementary tool to aid this understanding. Classical MD typically employ predefined functional forms which limits their ability to capture such complex size-dependent structural and dynamical transformation. Neural Network (NN) based potentials represent flexible alternatives and in principle, well-trained NN potentials can provide high level of flexibility, transferability and accuracy on-par with the reference model used for training. A major challenge, however, is that NN models are interpolative and requires large quantities (similar to 10 4 or greater) of training data to ensure that the model adequately samples the energy landscape both near and far-from-equilibrium. A highly desirable goal is minimize the number of training data, especially if the underlying reference model is first-principles based and hence expensive. In this work, we introduce an active learning (AL) scheme that trains a NN model on-the-fly with minimal amount of first-principles based training data. Our AL workflow is initiated with a sparse training dataset (similar to 1 to 5 data points) and is updated on-the-fly via a Nested Ensemble Monte Carlo scheme that iteratively queries the energy landscape in regions of failure and updates the training pool to improve the network performance. Using a representative system of gold clusters, we demonstrate that our AL workflow can train a NN with similar to 500 total reference calculations. Using an extensive DFT test set of similar to 1100 configurations, we show that our AL-NN is able to accurately predict both the DFT energies and the forces for clusters of a myriad of different sizes. Our NN predictions are within 30 meV/atom and 40 meV/angstrom of the reference DFT calculations. Moreover, our AL-NN model also adequately captures the various size-dependent structural and dynamical properties of gold clusters in excellent agreement with DFT calculations and available experiments. We finally show that our AL-NN model also captures bulk properties reasonably well, even though they were not included in the training data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

PDBspheres: a method for finding 3D similarities in local regions in proteins

Abstract We present a structure-based method for finding and evaluating structural similarities in protein regions relevant to ligand binding. PDBspheres comprises an exhaustive library of protein structure regions (‘spheres’) adjacent to complexed ligands derived from the Protein Data Bank (PDB), along with methods to find and evaluate structural matches between a protein of interest and spheres in the library. PDBspheres uses the LGA (Local–Global Alignment) structure alignment algorithm as the main engine for detecting structural similarities between the protein of interest and template spheres from the library, which currently contains >2 million spheres. To assess confidence in structural matches, an all-atom-based similarity metric takes side chain placement into account. Here, we describe the PDBspheres method, demonstrate its ability to detect and characterize binding sites in protein structures, show how PDBspheres—a strictly structure-based method—performs on a curated dataset of 2528 ligand-bound and ligand-free crystal structures, and use PDBspheres to cluster pockets and assess structural similarities among protein binding sites of 4876 structures in the ‘refined set’ of the PDBbind 2019 dataset.

59 BASIC BIOLOGICAL SCIENCES↗

Structure and Stability of the Ionic Liquid Clusters [EMIM]n[BF4]n+1- (n = 1 – 9): Implications for Electrochemical Separations

Precise functionalization of electrodes with size-selected ionic liquid (IL) clusters may improve the application of ILs in electrochemical separations. Herein, we report our combined experimental and theoretical investigation of the IL clusters [EMIM]????[BF4]????+1- (n = 1 – 9) and demonstrate their selectivity and efficiency towards targeted adsorption of molecules from solution. The structures and energies of the IL clusters, predicted with global optimization, agree with and help interpret the ion abundances and stabilities measured by high mass resolution electrospray ionization mass spectrometry and collision induced dissociation experiments. The [EMIM][BF4]2- cluster, which was identified as the most stable IL cluster, was selectively soft landed onto a working electrode. Electrochemical impedance spectroscopy revealed a lower charge transfer resistance on the soft-landed electrode containing [EMIM] [BF_4 ]_2^- compared to an electrode prepared by drop casting of IL solution, which contains the full range of IL clusters. Our findings indicate that specific IL clusters may be used to increase the efficiency of electrochemical separations by lowering the overpotentials involved.

Zhang, Jun↗

The completed SDSS-IV extended Baryon Oscillation Spectroscopic Survey: measurement of the growth rate of structure from the small-scale clustering of the luminous red galaxy sample

ABSTRACT We measure the small-scale clustering of the Data Release 16 extended Baryon Oscillation Spectroscopic Survey Luminous Red Galaxy sample, corrected for fibre-collisions using Pairwise Inverse Probability weights, which give unbiased clustering measurements on all scales. We fit to the monopole and quadrupole moments and to the projected correlation function over the separation range $7-60\, h^{-1}{\rm Mpc}$ with a model based on the aemulus cosmological emulator to measure the growth rate of cosmic structure, parametrized by fσ8. We obtain a measurement of fσ8(z = 0.737) = 0.408 ± 0.038, which is 1.4σ lower than the value expected from 2018 Planck data for a flat ΛCDM model, and is more consistent with recent weak-lensing measurements. The level of precision achieved is 1.7 times better than more standard measurements made using only the large-scale modes of the same sample. We also fit to the data using the full range of scales $0.1\text{--}60\, h^{-1}{\rm Mpc}$ modelled by the aemulus cosmological emulator and find a 4.5σ tension in the amplitude of the halo velocity field with the Planck + ΛCDM model, driven by a mismatch on the non-linear scales. This may not be cosmological in origin, and could be due to a breakdown in the Halo Occupation Distribution model used in the emulator. Finally, we perform a robust analysis of possible sources of systematics, including the effects of redshift uncertainty and incompleteness due to target selection that were not included in previous analyses fitting to clustering measurements on small scales.

79 ASTRONOMY AND ASTROPHYSICS↗

Adaptive Conformer Sampling for Property Prediction Using the Conductor-like Screening Model for Real Solvents

The valorization of lignocellulose-derived bioproducts requires effective separation from excessive water. Liquid–liquid extraction is a promising low-energy separation technology, but effective extraction requires solvent selection based on the thermodynamic properties of the bioproduct and solvent components. We propose a computational framework for predicting such properties by developing an adaptive conformer selection approach for use with COSMO-RS (conductor-like screening model for real solvents) calculations. In this framework, molecular dynamics simulations are used to generate many molecular structures (conformers) at representative temperatures in varying solvent environments. Conformers are then clustered based on structural metrics in a low-dimensional space and selected using a mixed-integer quadratic programming problem to iteratively insert a sampled conformer. At each iteration, we determine bioproduct properties using COSMO-RS. Here, we demonstrate the capability of the proposed framework on representative bioproducts to show convergence of the adaptive sampling toward experimentally measured properties with fewer calculations than required by random conformer sampling, enabling the improved screening of solvent systems for liquid-phase separation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Formation and transformation of iron oxy-hydroxide precursor clusters to ferrihydrite

Iron (Fe) oxy-hydroxide minerals such as ferrihydrite (Fh) are ubiquitous in Earth-surface environments and important in biogeochemical element cycling. Recent research has suggested that their formation is preceded by the precipitation of ultrasmall (~1 nm) Keggin-like Fe oxy-hydroxide clusters. However, relatively little is understood about the structure of the precursor clusters and the impacts of pH and time on their growth and transformation to more stable phases. Here, we used a new method that involves mixed flow reactors (MFR) to synthesize these Fe oxy-hydroxide precursor clusters at pH 1.0, 1.5, 2.5, and 4.5. In situ and ex situ synchrotron scattering measurements and laboratory small-angle X-ray scattering (SAXS) were used to study the structure and size of Fe oxy-hydroxide clusters and their transformation products, respectively. Results show that with increasing pH, the particle size and structural order of samples increase, forming solids that resemble 2-line Fh at pH 4.5. The experimental data were compared with X-ray pair distribution functions (PDF) calculated for a range of Fe(III) oxyhydroxide clusters, including Fe 13 Keggin isomers computed previously using density functional theory (DFT), which yielded at best only partial agreement at short range (<5 Å). Aging of the clusters synthesized at pH 1.5 and 2.5 results in growth and transformation via Ostwald ripening to mixtures of goethite (Gt) and lepidocrocite (Lp). This process was inhibited by immediately reacting the early-formed clusters with phosphate (PO 4 3– ), suggesting that oxyanion surface complexes can stabilize the initial clusters by preventing growth and crystallization to more stable phases.

58 GEOSCIENCES↗

The Signatures of Self-interacting Dark Matter and Subhalo Disruption on Cluster Substructure

The abundance, distribution, and inner structure of satellites of galaxy clusters can be sensitive probes of the properties of dark matter. We run 30 cosmological zoom-in simulations with self-interacting dark matter (SIDM), with a velocity-dependent cross section, to study the properties of subhalos within cluster-mass hosts. We find that the abundance of subhalos that survive in the SIDM simulations are suppressed relative to their cold dark matter (CDM) counterparts. Once the population of disrupted subhalos—which may host orphan galaxies—is taken into account, satellite galaxy populations in CDM and SIDM models can be reconciled. However, even in this case, the inner structures of subhalos are significantly different in the two dark matter models. We study the feasibility of using the weak-lensing signal from the subhalo density profiles to distinguish between the cold and self-interacting dark matter while accounting for the potential contribution of orphan galaxies. We find that the effects of self-interactions on the density profile of subhalos can appear degenerate with subhalo disruption in CDM, when orphans are accounted for. With current error bars from the Subaru Hyper Suprime-Cam Strategic Program, we find that subhalos in the outskirts of clusters (where disruption is less prevalent) can be used to constrain dark matter physics. In the future, the Vera C. Rubin Observatory Legacy Survey of Space and Time will give precise measurements of the weak-lensing profile and can be used to constrain σ $_{T}$/m at the ∼1 cm$^{2}$ g$^{−1}$ level at v ∼ 2000 km s$^{−1}$.

79 ASTRONOMY AND ASTROPHYSICS↗

Search for interacting galaxy clusters from SDSS DR-17 employing optimized friends-of-friends algorithm and multimessenger tracers

ABSTRACT In the theoretical framework of hierarchical structure formation, galaxy clusters evolve through continuous accretion and mergers of substructures. Cosmological simulations have revealed the best picture of the universe as a 3D filamentary network of dark-matter distribution called the cosmic web. Galaxy clusters are found to form at the nodes of this network and are the regions of high merging activity. Such mergers being highly energetic, contain a wealth of information about the dynamical evolution of structures in the Universe. Observational validation of this scenario needs a colossal effort to identify numerous events from all-sky surveys. Therefore, such efforts are sparse in literature and tend to focus on individual systems. In this work, we present an improved search algorithm for identifying interacting galaxy clusters and have successfully produced a comprehensive list of systems from SDSS DR-17. By proposing a set of physically motivated criteria, we classified these interacting clusters into two broad classes, ‘merging’ and ‘pre-merging/postmerging’ systems. Interestingly, as predicted by simulations, we found that most cases show cluster interaction along the prominent cosmic filaments of galaxy distribution (i.e. the proxy for dark matter filaments), with the most violent ones at their nodes. Moreover, we traced the imprint of interactions through multiband signatures, such as diffuse cluster emissions in radio or X-rays. Although we could not find direct evidence of diffuse emission from connecting filaments and ridges; our catalogue of interacting clusters will ease locating such faintest emissions as data from sensitive telescopes such as eROSITA or SKA, becomes accessible.

Oak, Tejas↗

Localized Flexoelectric Effect Around Ba(CuNb) Nano‐Clusters in Epitaxial BiFeO 3 Films for Enhancement of Electric and Multiferroic Properties

Abstract Room‐temperature (RT) multiferroic materials have received significant research attention for various potential applications; however, their properties are not suitable for real‐world implementation. In this study, a nano‐scale localized flexoelectric effect is introduced to enhance the RT multiferroic performance of epitaxial bismuth iron oxide (BiFeO 3 ; BFO) thin films by embedding 10 mol% Ba(Cu 1/3 Nb 2/3 )O 3 (BCN) nano‐clusters into the host BFO film, which originally has a rhombohedral crystal structure. By utilizing nano‐clustering, a large out‐of‐plane coherent strain is localized around the nano‐clusters, resulting in a highly strained tetragonality of the BFO structure; subsequently, the films exhibit peculiar types of domains and domain walls, such as nano‐scale rotational vortices and antiparallel dipole configurations. These peculiar domain structures, which originate from the localized flexoelectric effect at the nano‐scale, enable excellent ferroelectric, ferromagnetic, and RT multiferroic magnetoelectric coupling. This study reveals that the local variation in the localized flexoelectric field around nano‐clusters considerably impacts the formation of unusual domain‐wall structures. This suggests that the controlled introduction of nano‐clusters with different crystal structures is promising for achieving the desired multiferroic properties.

Song, Hyunseok↗

Synergistic Density Functional Theory and Molecular Dynamics Approach to Elucidate PNIPAM–Water Interaction Mechanisms

This study employs Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations to investigate interactions between water molecules and Poly(N-isopropylacrylamide) (PNIPAM). DFT reveals preferential water binding sites, with enhanced binding energy observed in the linker zone. Quantum Theory of Atoms in Molecules (QTAIM) and electron localization function (ELF) analyses highlight the roles of hydrogen bonding and steric hindrance. MD simulations unveil temperature-dependent hydration dynamics, with structural transitions marked by changes in the radius of gyration (Rg) and the radial distribution function (RDF), aligning with DFT findings. Our work goes beyond prior studies by combining a DFT, QTAIM and MD simulations approach across different PNIPAM monomer-to-30mer structures. It introduces a systematic quantification of pseudo-saturation thresholds and explores water clustering dynamics with structural specificity, which have not been previously reported in the literature. These novel insights establish a more complete molecular-level picture of PNIPAM hydration behavior and temperature responsiveness, emphasizing the importance of amide hydrogen and carbonyl oxygen sites in hydrogen bonding, which weakens above the lower critical solution temperature (LCST), resulting in increased hydrophobicity and paving the way for understanding water sorption mechanisms, offering guidance for future applications such as dehumidification and atmospheric water harvesting.

08 HYDROGEN↗

A computational study of Al n - and Al n -1 1Pt - clusters: the effects of doping and a uniform tuning gauge for single-atom nanocatalysts

Results of density functional theory calculations on Al n - and Al n -1 1Pt - , n = 2-8, clusters are presented and analyzed. The analysis includes different structural forms of the clusters characterized in terms of binding energy, spin and symmetry, and a comparative evaluation of various properties of the two systems viewed as connected through a single-Pt substitutional doping and examined in terms of their respective most stable structures. Furthermore, the Al n -1 1Pt - clusters are then used as a paradigmatic (model) case of single-atom nanocatalysts, with Pt as the catalytic center and Al n-1 as its support, to implement a uniform descriptor for gauging the tuning effects of all the parameters ( "knobs ") of a nanocatalyst that include the identity of the active center and the material and size of its support.

97 MATHEMATICS AND COMPUTING↗

Unveiling Synergetic Photocatalytic Activity from Heterometallic Ti/Ce Clusters

Titanium-oxo clusters, with their robust structure and suitable optical and electronic properties, have been widely investigated as photocatalysts. Heterometallic Ti/M-oxo clusters provide additional tunability and functionality, which enable systematic structure-activity investigations to elucidate reaction mechanisms and improve catalyst de-sign. Incorporating cerium into Ti-oxo clusters can provide additional redox (Ce IV /Ce III ) and oxygen harvesting ability, but to date only limited number of structurally defined titanium-cerium (Ti/Ce) clusters have been reported due to their synthetic challenges. Herein, we report the synthesis and photocatalytic properties of two structurally defined Ti/Ce-oxo clusters, Ti 8 Ce 2 (BA) 16 and Ti 9 Ce 4 (BA) 20 , as well as a TiCe-BA cluster with a calculated formula of Ti 20 Ce 9 O 36 (BA) 42 . Photocatalytic study of these clusters demonstrates that the amount of Ce 3+ species greatly impacts its photocatalytic oxidation performance, and their superior photocatalytic reactivity towards aerobic alcohol oxidation can be contributed to the synergistic effects of the multiple radical species generated upon light absorption. Furthermore, this work represents a significant milestone in the construction of stable Ti/Ce-oxo clusters, enriching the current library of known heterometallic Ti/M-oxo clusters, and providing a series of crystalline materials with great promise of photo-luminescence and photovoltaic chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Surface structure of mass-selected niobium oxide nanoclusters on Au(111)

The structures formed by the deposition of mass-selected niobium oxide clusters, Nb 3 O y ( y = 5, 6, 7), onto Au(111) were studied by scanning tunneling microscopy. The as-deposited Nb 3 O 7 clusters assemble into large dendritic structures that grow on the terraces as well as extend from the top and bottom of step edges. The Nb 3 O 6 cluster also forms dendritic assemblies but they are generally much smaller in size. The assemblies are composed of smaller discrete structures (<1 nm) which are likely to be single clusters. Furthermore, the dendritic assemblies for both the Nb 3 O 7 and Nb 3 O 6 clusters have fractal dimensions of about 1.7 which is very close to that expected for simple diffusion limited aggregation. Annealing the Nb 3 O 7,6 /Au(111) surfaces up to 550 K results in changes in assembly sizes and increases in heights, while heating to 700 results in the disruption of the assemblies into smaller structures. By contrast, the as-deposited Nb 3 O 5 /Au(111) surface at RT exhibits compact cluster structures which become 3D nanoparticles when annealed above 550 K. Differences in the observed surface structures and thermal stability are attributed to differences in metal-oxygen stoichiometry which can influence cluster binding energies, mobility and inter-cluster interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Free Energies of Hydrated Halide Anions: High Through-Put Computations on Clusters to Treat Rough Energy-Landscapes

With a longer-term goal of addressing the comparative behavior of the aqueous halides F−, Cl−, Br−, and I− on the basis of quasi-chemical theory (QCT), here we study structures and free energies of hydration clusters for those anions. We confirm that energetically optimal (H2O)nX clusters, with X = Cl−, Br−, and I−, exhibit surface hydration structures. Computed free energies, based on optimized surface hydration structures utilizing a harmonic approximation, typically (but not always) disagree with experimental free energies. To remedy the harmonic approximation, we utilize single-point electronic structure calculations on cluster geometries sampled from an AIMD (ab initio molecular dynamics) simulation stream. This rough-landscape procedure is broadly satisfactory and suggests unfavorable ligand crowding as the physical effect addressed. Nevertheless, this procedure can break down when n≳4, with the characteristic discrepancy resulting from a relaxed definition of clustering in the identification of (H2O)nX clusters, including ramified structures natural in physical cluster theories. With ramified structures, the central equation for the present rough-landscape approach can acquire some inconsistency. Extension of these physical cluster theories in the direction of QCT should remedy that issue, and should be the next step in this research direction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗