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Results for “cluster characterization”
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Permutation-adapted complete and independent basis for atomic cluster expansion descriptors
In many recent applications, particularly in the field of atom-centered descriptors for interatomic potentials, tensor products of spherical harmonics have been used to characterize complex atomic environments. When coupled with a radial basis, the atomic cluster expansion (ACE) basis is obtained. However, symmetrization with respect to both rotation and permutation results in an overcomplete set of ACE descriptors with linear dependencies occurring within blocks of functions corresponding to particular generalized Wigner symbols. All practical applications of ACE employ semi-numerical constructions to generate a complete, fully independent basis. While computationally tractable, the resultant basis cannot be expressed analytically, is susceptible to numerical instability, and thus has limited reproducibility. Here we present a procedure for generating explicit analytic expressions for a complete and independent set of ACE descriptors. The procedure uses a coupling scheme that is maximally symmetric w.r.t. permutation of the atoms, exposing the permutational symmetries of the generalized Wigner symbols, and yields a permutation-adapted rotationally and permutationally invariant basis (PA-RPI ACE). Theoretical support for the approach is presented, as well as numerical evidence of completeness and independence. A summary of explicit enumeration of PA-RPI functions up to rank 6 and polynomial degree 32 is provided. The PA-RPI blocks corresponding to particular generalized Wigner symbols may be either larger or smaller than the corresponding blocks in the simpler rotationally invariant basis. Finally, we demonstrate that basis functions of high polynomial degree persist under strong regularization, indicating the importance of not restricting the maximum degree of basis functions in ACE models a priori.
Confining platinum clusters in indium-modified ZSM-5 zeolite to promote propane dehydrogenation
Designing highly active and stable catalytic sites is often challenging due to the complex synthesis procedure and the agglomeration of active sites during high-temperature reactions. Here, we report a facile two-step method to synthesize Pt clusters confined by In-modified ZSM-5 zeolite. In-situ characterization confirms that In is located at the extra-framework position of ZSM-5 as In + , and the Pt clusters are stabilized by the In-ZSM-5 zeolite. The resulting Pt clusters confined in In-ZSM-5 show excellent propane conversion, propylene selectivity, and catalytic stability, outperforming monometallic Pt, In, and bimetallic PtIn alloys. The incorporation of In + in ZSM-5 neutralizes Brønsted acid sites to inhibit side reactions, as well as tunes the electronic properties of Pt clusters to facilitate propane activation and propylene desorption. The strategy of combining precious metal clusters with metal cation-exchanged zeolites opens the avenue to develop stable heterogeneous catalysts for other reaction systems.
First Principles Modeling of Cluster-Based Solid Electrolytes (Final Technical Report)
Given the trend of global warming and the urgent need to transition from fossil fuels to green energy, lithium-ion batteries continue to be an integral part of our lives. Design, development, and understanding of novel solid-state electrolyte materials play the key role for achieving next-generation all-solid-state batteries with high energy and great safety. The current modeling schemes to develop advanced solid electrolytes are focusing on materials in which the building blocks are individual atoms. Our theoretical approach is a paradigm shift in solid-state electrolyte design. Instead of atoms, we focus on clusters as the building blocks and model these solid electrolytes and their interfaces with electrodes, especially Li-metal anode, for their successful implementation in solid-state batteries. The advantage of using the cluster ions to replace elemental ions is that the size, composition, and shape of the former can be tailored to achieve higher ionic conductivity at room temperature, electrochemical stability, and charge transfer across solid-solid interfaces than conventional materials. Specifically, the project includes: (1) Developing cluster-based solid electrolytes, where the halogen components are replaced by cluster ions that mimic the chemistry of halogens but are characterized by additional degrees of freedom, including the size, shape, composition, and motional dynamics under excitation. (2) Providing a fundamental understanding of the ion conduction mechanism in the developed cluster-based solid electrolytes; (3) Modeling the interfacial properties (i.e., structural, chemical, and transport properties) between the cluster-based solid electrolytes and electrodes at the atomic level. For the cluster-based solid electrolytes incompatible with the Li-metal anode or cathode materials, potential candidates for interfacial coatings are identified and studied. (4) Providing a theoretical framework towards optimizing critical parameters of the solid-state electrolytes that guides experimentalists to attain desired cathode-electrode interface for cluster-based solid-state electrolytes.
Characterizing the Effect of Capillary Heterogeneity on Multiphase Flow Pulsation in an Intermediate–Scale Beadpack Experiment using Time Series Clustering and Frequency Analysis
An intermediate-scale beadpack drainage experiment was conducted to investigate how simple layered lamination heterogeneity affects CO 2 flow. Two simple layers of capillary barriers are manually packed in the tank and slow drainage was carried out using analog fluids to mimic the capillary- and gravity-dominated CO 2 upward migration process in deep saline aquifers. Nonwetting phase saturation time series clustering analysis and frequency analysis have been conducted on the experimental data. Additionally, modified invasion percolation numerical simulations were done on a digital model of the beadpack to compare to experimental results. Results show that capillary barriers can lead to strong pulsation behavior, which in turn can cause unexpected early breaching through other barriers. The inlet pressure is found to be able to respond to saturation changes in far regions of the domain, indicating that the wetting phase can transmit pressure changes from the other phase. Although static simulations were not able to capture all the dynamic behavior observed in the experiment, Monte Carlo composite simulation results combining many different realizations can better illustrate how the nonwetting phase will behave in the heterogeneous domain. Furthermore, our results suggest the need for CO 2 storage site selection with preference given to aquifers with more capillary barriers with finer grain sizes to avoid flow pulsation and to retard plume upward migration.
Redshift inference from the combination of galaxy colours and clustering in a hierarchical Bayesian model – Application to realistic N -body simulations
ABSTRACT Photometric galaxy surveys constitute a powerful cosmological probe but rely on the accurate characterization of their redshift distributions using only broad-band imaging, and can be very sensitive to incomplete or biased priors used for redshift calibration. A hierarchical Bayesian model has recently been developed to estimate those from the robust combination of prior information, photometry of single galaxies, and the information contained in the galaxy clustering against a well-characterized tracer population. In this work, we extend the method so that it can be applied to real data, developing some necessary new extensions to it, especially in the treatment of galaxy clustering information, and we test it on realistic simulations. After marginalizing over the mapping between the clustering estimator and the actual density distribution of the sample galaxies, and using prior information from a small patch of the survey, we find the incorporation of clustering information with photo-z’s tightens the redshift posteriors and overcomes biases in the prior that mimic those happening in spectroscopic samples. The method presented here uses all the information at hand to reduce prior biases and incompleteness. Even in cases where we artificially bias the spectroscopic sample to induce a shift in mean redshift of $\Delta \bar{z} \approx 0.05,$ the final biases in the posterior are $\Delta \bar{z} \lesssim 0.003.$ This robustness to flaws in the redshift prior or training samples would constitute a milestone for the control of redshift systematic uncertainties in future weak lensing analyses.
Archaeal protein containing domain of unknown function 2193 undergoes oligomeric reconfiguration upon iron–sulfur cluster binding
Methanogenic archaea are particularly rich in iron–sulfur proteins, yet their roles remain largely enigmatic. Here, we characterized aMethanococcus voltae(Mvo) protein from the domain of unknown function (DUF) 2193 family, a group of proteins present primarily in archaea and characterized by a conserved cysteine‐rich C‐terminal motif.MvoDUF2193 was heterologously expressed and characterized by a range of spectroscopic and analytical methods. The results demonstrate thatMvoDUF2193 binds a single [4Fe–4S] cluster per subunit and that cluster occupancy regulates the transition from an apo tetramer to a [4Fe–4S] monomeric form. We hypothesize thatMvoDUF2193 serves a regulatory role in the cell, mediated by [Fe–S] cluster binding and changes in oligomeric state.
Trade-Offs Between Growth Rate and Other Fungal Traits
If we better understand how fungal responses to global change are governed by their traits, we can improve predictions of fungal community composition and ecosystem function. Specifically, we can examine trade-offs among traits, in which the allocation of finite resources toward one trait reduces the investment in others. We hypothesized that trade-offs among fungal traits relating to rapid growth, resource capture, and stress tolerance sort fungal species into discrete life history strategies. We used the Biolog Filamentous Fungi database to calculate maximum growth rates of 37 fungal species and then compared them to their functional traits from the fun fun database. In partial support of our hypothesis, maximum growth rate displayed a negative relationship with traits related to resource capture. Moreover, maximum growth rate displayed a positive relationship with amino acid permease, forming a putative Fast Growth life history strategy. A second putative life history strategy is characterized by a positive relationship between extracellular enzymes, including cellobiohydrolase 6, cellobiohydrolase 7, crystalline cellulase AA9, and lignin peroxidase. These extracellular enzymes were negatively related to chitosanase 8, an enzyme that can break down a derivative of chitin. Chitosanase 8 displayed a positive relationship with many traits that were hypothesized to cluster separately, forming a putative Blended life history strategy characterized by certain resource capture, fast growth, and stress tolerance traits. These trait relationships complement previously explored microbial trait frameworks, such as the Competitor-Stress Tolerator-Ruderal and the Yield-Resource Acquisition-Stress Tolerance schemes.
Development of platforms for functional characterization and production of phenazines using a multi-chassis approach via CRAGE
Phenazines (Phzs), a family of chemicals with a phenazine backbone, are secondary metabolites with diverse properties such as antibacterial, anti-fungal, or anticancer activity. The core derivatives of phenazine, phenazine-1-carboxylic acid (PCA) and phenazine-1,6-dicarboxylic acid (PDC), are themselves precursors for various other derivatives. Recent advances in genome mining tools have enabled researchers to identify many biosynthetic gene clusters (BGCs) that might produce novel Phzs. Here, to characterize the function of these BGCs efficiently, we performed modular construct assembly and subsequent multi-chassis heterologous expression using chassis-independent recombinase-assisted genome engineering (CRAGE). CRAGE allowed rapid integration of a PCA BGC into 23 diverse γ-proteobacteria species and allowed us to identify top PCA producers. We then used the top five chassis hosts to express four partially refactored PDC BGCs. A few of these platforms produced high levels of PDC. Specifically, Xenorhabdus doucetiae and Pseudomonas simiae produced PDC at a titer of 293 mg/L and 373 mg/L, respectively, in minimal media. These titers are significantly higher than those previously reported. Furthermore, selectivity toward PDC production over PCA production was improved by up to 9-fold. The results show that these strains are promising chassis for production of PCA, PDC, and their derivatives, as well as for function characterization of Phz BGCs identified via bioinformatics mining.
Ion soft landing: A unique tool for understanding electrochemical processes
Ion soft landing (SL) is a preparative mass spectrometry approach that enables deposition of mass- and charge-selected gaseous ions onto surfaces with controlled kinetic energy. The unique capabilities of SL provide an opportunity to populate electrode–electrolyte interfaces (EEIs) with well-defined intact electroactive ions of known composition, thereby facilitating the characterization of their intrinsic electrochemical properties. Here, in this perspective, we describe the SL technique and discuss how it may be used to study the effect of the charge state, stoichiometry, and composition of large redox active molecules and clusters on their electron transfer kinetics. SL has enabled the characterization of redox-active species that cannot be purified and examined using conventional bulk-phase separation and deposition approaches. Furthermore, precise control over the deposition process provides an opportunity to prepare and characterize well-defined EEIs relevant to energy storage and conversion, catalysis, and sensing.
The hierarchical growth of bright central galaxies and intracluster light as traced by the magnitude gap
Using a sample of 2800 galaxy clusters identified in the Dark Energy Survey across the redshift range 0.20 < z < 0.60, we characterize the hierarchical assembly of bright central galaxies (BCGs) and the surrounding intracluster light (ICL). To quantify hierarchical formation we use the stellar mass–halo mass (SMHM) relation, comparing the halo mass, estimated via the mass–richness relation, to the stellar mass within the BCG + ICL system. Moreover, we incorporate the magnitude gap (M14), the difference in brightness between the BCG (measured within 30 kpc) and fourth brightest cluster member galaxy within 0.5 $R_{200,c}$, as a third parameter in this linear relation. The inclusion of M14, which traces BCG hierarchical growth, increases the slope and decreases the intrinsic scatter, highlighting that it is a latent variable within the BCG + ICL SMHM relation. Moreover, the correlation with M14 decreases at large radii. However, the stellar light within the BCG + ICL transition region (30 –80 kpc) most strongly correlates with halo mass and has a statistically significant correlation with M14. Since the transition region and M14 are independent measurements, the transition region may grow due to the BCG’s hierarchical formation. Additionally, as M14 and ICL result from hierarchical growth, we use a stacked sample and find that clusters with large M14 values are characterized by larger ICL and BCG + ICL fractions, which illustrates that the merger processes that build the BCG stellar mass also grow the ICL. Furthermore, this may suggest that M14 combined with the ICL fraction can identify dynamically relaxed clusters.
Structure-dependent clustering-to-declustering solute segregation transitions near disconnections
Grain-boundary disconnections, characterized by a step and a dislocation, are pervasive interfacial line defects that play a critical role in governing the properties and performance of nanocrystalline alloys. Although segregation of alloying elements is frequently observed at GB disconnections, the underlying mechanisms remain poorly understood, particularly at elevated temperatures and non-dilute conditions. In this study, we employ atomistic simulations to study the segregation behavior of Ag at various faulted disconnections in Cu as a model material system. Our results demonstrate a pronounced size and compactness effect on the segregation behavior: more compact faulted disconnection structures promote the formation of Ag segregation clusters due to a highly localized tensile field, whereas more spread faulted disconnection structures (i.e., with wider partial dislocation spacing) exhibit much weaker clustering tendencies. Furthermore, with increasing temperature, Ag clustering in small disconnections initially intensifies and then disappears, indicating a thermally driven transition from clustering to declustering segregation behavior.
Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation
ABSTRACT Marine fungi remain poorly covered in global genome sequencing campaigns; the 1000 fungal genomes (1KFG) project attempts to shed light on the diversity, ecology and potential industrial use of overlooked and poorly resolved fungal taxa. This study characterizes the genomes of three marine fungi: Emericellopsis sp. TS7, wood-associated Amylocarpus encephaloides and algae-associated Calycina marina. These species were genome sequenced to study their genomic features, biosynthetic potential and phylogenetic placement using multilocus data. Amylocarpus encephaloides and C. marina were placed in the Helotiaceae and Pezizellaceae (Helotiales) , respectively, based on a 15-gene phylogenetic analysis. These two genomes had fewer biosynthetic gene clusters (BGCs) and carbohydrate active enzymes (CAZymes) than Emericellopsis sp. TS7 isolate. Emericellopsis sp. TS7 ( Hypocreales , Ascomycota ) was isolated from the sponge Stelletta normani . A six-gene phylogenetic analysis placed the isolate in the marine Emericellopsis clade and morphological examination confirmed that the isolate represents a new species, which is described here as E. atlantica . Analysis of its CAZyme repertoire and a culturing experiment on three marine and one terrestrial substrates indicated that E. atlantica is a psychrotrophic generalist fungus that is able to degrade several types of marine biomass. FungiSMASH analysis revealed the presence of 35 BGCs including, eight non-ribosomal peptide synthases (NRPSs), six NRPS-like, six polyketide synthases, nine terpenes and six hybrid, mixed or other clusters. Of these BGCs, only five were homologous with characterized BGCs. The presence of unknown BGCs sets and large CAZyme repertoire set stage for further investigations of E. atlantica . The Pezizellaceae genome and the genome of the monotypic Amylocarpus genus represent the first published genomes of filamentous fungi that are restricted in their occurrence to the marine habitat and form thus a valuable resource for the community that can be used in studying ecological adaptions of fungi using comparative genomics.
Neutron Irradiation Induced Changes in Isotopic Abundance of 6Li and 3D Nanoscale Distribution of Tritium in LiAlO2 Pellets Analyzed by Atom Probe Tomography
Tritium, a radioactive isotope of hydrogen is produced by neutron irradiation of 6Li enriched LiAlO2 pellets in Tritium producing burnable absorber rods (TPBARs). Three-dimensional nanoscale mapping of Tritium in irradiated pellets is critical to understand its spatial variation and its association with various microstructural features in the pellets. Spatially resolved analysis of 6Li isotopic enrichment in such ceramic pellets before and after irradiation can provide insights to heterogeneities in Li isotopic distribution. However, Li being a light isotope, its spatially resolved compositional or isotopic analysis is a challenging task to most analytical methods. Here we used atom probe tomography, to evaluate the Li isotopic enrichment in both the LiAlO¬2 matrix and the Li deficient secondary phase LiAl5O8 before irradiation. These results were then compared with 6Li isotopic ratio measured by APT analysis of neutron irradiated pellets to clearly demonstrate the unique capability of APT to quantitatively analyze the isotopic enrichment of 6Li as well as for other light elements present in these materials. Evidence for heterogenous nanoscale distribution of 3H and O3H within irradiated pellet microstructure is also provided, which is attributed to 3H trapping in irradiation induced vacancy clusters or voids within the LiAlO2 matrix. The characterization results given here, now prove the feasibility for using APT for analyzing nanoscale spatially resolved isotopic enrichment of Li as well as other light elements such as Tritium in TPBARs. This work also paves way to adopt APT for analyzing light elements such as Li and tritium in materials used for nuclear fusion reactor applications, geochemistry, astrophysics as well as for energy storage applications.
In situ TEM annealing of neutron-irradiated Ti reveals a two-stage mechanism for elevated temperature radiation damage recovery
Understanding how irradiation-induced defects evolve at elevated temperatures is of critical importance to predicting materials' behavior under steady-state and accident scenarios. However, such mechanistic insight into microstructural evolution is limited by the nature of ex situ annealing and subsequent imaging. Here we show direct observation and quantification of defect recovery in neutron-irradiated Ti using in situ transmission electron microscopy (TEM) annealing experiments. In agreement with our prior work, and at temperatures below the irradiation temperature (T irr = 300 °C), dislocation loops are observed to glide. At elevated temperatures (>500 °C), dislocation lines become mobile and promote significant recovery of the microstructure. These mechanisms challenge the established electron irradiation-based model for radiation damage recovery, which originally suggests dissolution of static defect clusters, and demonstrates the importance of in situ characterization in understanding defect evolution in irradiated materials.
Three-state majority-vote model on small-world networks
Abstract In this work, we study the opinion dynamics of the three-state majority-vote model on small-world networks of social interactions. In the majority-vote dynamics, an individual adopts the opinion of the majority of its neighbors with probability 1- q , and a different opinion with chance q , where q stands for the noise parameter. The noise q acts as a social temperature, inducing dissent among individual opinions. With probability p , we rewire the connections of the two-dimensional square lattice network, allowing long-range interactions in the society, thus yielding the small-world property present in many different real-world systems. We investigate the degree distribution, average clustering coefficient and average shortest path length to characterize the topology of the rewired networks of social interactions. By employing Monte Carlo simulations, we investigate the second-order phase transition of the three-state majority-vote dynamics, and obtain the critical noise $$q_c$$ q c , as well as the standard critical exponents $$\beta /\nu$$ β / ν , $$\gamma /\nu$$ γ / ν , and $$1/\nu$$ 1 / ν for several values of the rewiring probability p . We conclude that the rewiring of the lattice enhances the social order in the system and drives the model to different universality classes from that of the three-state majority-vote model in two-dimensional square lattices.
Modeling of Thermal Decomposition of TATB-Based Explosive for Safety Analysis
We investigate and model the cook-off behavior of LX-17 to understand the response of explosive systems in abnormal thermal environments. Decomposition has been explored via conventional ODTX (One-Dimensional Time-to-eXplosion), PODTX (ODTX with pressure-measurement), TGA (Thermo-Gravimetric Analysis), and DSC (Differential Scanning Calorimetry) experiments under isothermal and ramped temperature profiles. The data were used to fit reaction rate parameters for proposed schemes in an ALE3D computational model. This model includes chemical reactions, thermo- and hydro-dynamics, and material properties, including thermal expansion, compressibility, and strength. These parameterizations were carried out utilizing a Python evolutionary optimization method on LLNL’s high-performance computing clusters. Additional experiments are being developed to further characterize and monitor decomposition intermediates to improve the model. Once experimentally validated, this model will be scalable to several applications involving LX-17. Furthermore, the optimization methodology developed herein should be applicable to other high explosive materials.
A glimpse into the fungal metabolomic abyss: Novel network analysis reveals relationships between exogenous compounds and their outputs
Fungal specialized metabolites are a major source of beneficial compounds that are routinely isolated, characterized, and manufactured as pharmaceuticals, agrochemical agents, and industrial chemicals. The production of these metabolites is encoded by biosynthetic gene clusters that are often silent under standard growth conditions. There are limited resources for characterizing the direct link between abiotic stimuli and metabolite production. Herein, we introduce a network analysis-based, data-driven algorithm comprising two routes to characterize the production of specialized fungal metabolites triggered by different exogenous compounds: the direct route and the auxiliary route. Both routes elucidate the influence of treatments on the production of specialized metabolites from experimental data. The direct route determines known and putative metabolites induced by treatments and provides additional insight over traditional comparison methods. The auxiliary route is specific for discovering unknown analytes, and further identification can be curated through online bioinformatic resources. We validated our algorithm by applying chitooligosaccharides and lipids at two different temperatures to the fungal pathogen Aspergillus fumigatus. After liquid chromatography–mass spectrometry quantification of significantly produced analytes, we used network centrality measures to rank the treatments’ ability to elucidate these analytes and confirmed their identity through fragmentation patterns or in silico spiking with commercially available standards. Later, we examined the transcriptional regulation of these metabolites through real-time quantitative polymerase chain reaction. Our data-driven techniques can complement existing metabolomic network analysis by providing an approach to track the influence of any exogenous stimuli on metabolite production. Our experimental-based algorithm can overcome the bottlenecks in elucidating novel fungal compounds used in drug discovery.