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At least 235 records · Page 13

Evolutionary inverse design of defects at graphene 2D lateral interfaces

Grain boundaries (GBs) in two-dimensional (2D) materials often have a profound impact on various material properties from mechanical to optical to electronic, yet predicting all possible GB formations is a challenge. Here, we introduce a workflow based on an evolutionary algorithm for exploring possible GBs formed at a lateral 2D interface. In a departure from conventional genetic algorithm based structure optimization methods, we perform genetic operations in the near interface region that allow us to be computationally efficient. We benchmark our method using graphene, which is a well-studied 2D material with a wide range of point defects. An empirical potential was used as the surrogate of the evolutionary search. More than 11.5 × 106 structures in total were evaluated for 128 GB orientations, and for each orientation, the ten best structures are recorded. A subset of low energy GBs predicted by empirical potential based search was relaxed by first-principles calculations and used to validate the energetic rank order. With the validated formation energy, we rank-ordered the best 128 GB structures and performed a detailed statistical analysis of primitive rings to find the correlation between the ring distribution and the formation energy. We found that for low energy GBs (below 0.5eV/Å), Stone–Wales defects will dominate, while structures with a higher energy (0.5–1.1eV/Å) show an increasing population of heptagons and nine-membered rings to form seven-nine defect pairs. For structures with energy higher than 1.1eV/Å, the percentage of octagons and nine-membered rings increases, which indicates that these two types of rings are not energetically favorable. Our proposed methodology is broadly applicable to explore defective low dimensional materials and represents a powerful tool that enables a systematic search of GBs of lateral interfaces for 2D materials.

Zhang, Jianan↗

Determining Partial Atomic Charges for Liquid Water: Assessing Electronic Structure and Charge Models

Partial atomic charges provide an intuitive and efficient way to describe the charge distribution and the resulting intermolecular electrostatic interactions in liquid water. Many charge models exist and it is unclear which model provides the best assignment of partial atomic charges in response to the local molecular environment. In this work, we systematically scrutinize various electronic structure methods and charge models (Mulliken, natural population analysis, CHelpG, RESP, Hirshfeld, Iterative Hirshfeld, and Bader) by evaluating their performance in predicting the dipole moments of isolated water, water clusters, and liquid water as well as charge transfer in the water dimer and liquid water. Although none of the seven charge models is capable of fully capturing the dipole moment increase from isolated water (1.85 D) to liquid water (about 2.9 D), the Iterative Hirshfeld method performs best for liquid water, reproducing its experimental average molecular dipole moment, yielding a reasonable amount of intermolecular charge transfer, and showing modest sensitivity to the local water environment. The performance of the charge model is dependent on the choice of the density functional and the quantum treatment of the environment. The computed molecular dipole moment of water generally increases with the percentage of the exact Hartree–Fock exchange in the functional, whereas the amount of charge transfer between molecules decreases. For liquid water, including two full solvation shells of surrounding water molecules (within about 5.5 Å of the central water) in the quantum chemical calculation converges the charges of the central water molecule. Furthermore, our final pragmatic quantum chemical charge-assigning protocol for liquid water is the Iterative Hirshfeld method with M06-HF/aug-cc-pVDZ and a quantum region cutoff radius of 5.5 Å.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural inference of networked dynamical systems with universal differential equations

Networked dynamical systems are common throughout science in engineering; e.g., biological networks, reaction networks, power systems, and the like. For many such systems, nonlinearity drives populations of identical (or near-identical) units to exhibit a wide range of nontrivial behaviors, such as the emergence of coherent structures (e.g., waves and patterns) or otherwise notable dynamics (e.g., synchrony and chaos). Here, we seek to infer (i) the intrinsic physics of a base unit of a population, (ii) the underlying graphical structure shared between units, and (iii) the coupling physics of a given networked dynamical system given observations of nodal states. These tasks are formulated around the notion of the Universal Differential Equation, whereby unknown dynamical systems can be approximated with neural networks, mathematical terms known a priori (albeit with unknown parameterizations), or combinations of the two. We demonstrate the value of these inference tasks by investigating not only future state predictions but also the inference of system behavior on varied network topologies. The effectiveness and utility of these methods are shown with their application to canonical networked nonlinear coupled oscillators.

97 MATHEMATICS AND COMPUTING↗

Enhancing Biopreparedness through a Model System to Understand the Molecular Mechanisms that Lead to Pathogenesis and Disease Transmission: NW-BRaVE

The science of biopreparedness to counter biological threats hinges on understanding the fundamental principles and molecular mechanisms that lead to pathogenesis and disease transmission. Our vision to address this challenge is to create a powerful and user-friendly platform to elucidate the fundamental principles of how molecular interactions drive pathogen-host relationships and host shifts. We will enable groundbreaking discoveries by integrating a wide range of structural, genomics, proteomics, and other advanced omics measurements, along with evolutionary and artificial intelligence predictions. To make sure the system is applicable to real-world problems, we will develop it in the context of a tractable model system, the small, abundant, and accessible photosynthetic cyanobacteria and their constantly co-adapting viral pathogens, cyanophages. This model will maintain the system’s applicability to real-world problems and techniques, but the overall focus will be on elucidating general principles of detecting, assessing, and surveilling molecular interaction, adaptation, and coevolution that are system agnostic and therefore extensible to other viral-host interactions. Our overall objectives are to (1) identify the molecular complexes that comprise the cyanobacteria redox macromolecular subsystem and how they dynamically change with bacteriophage infection in situ, using cryo-electron tomography; (2) profile regulatory changes during infection using proteomics, multiomics, and experimental validation, and integrate the data with in situ structures; (3) use genomics and metagenomics to determine environmental and population factors across time scales that impact the interactions between marine cyanobacteria and their cyanophage parasites, predicting the evolutionary origins of in situ structural and functional interactions, convergence and coevolution; and (4) develop a data integration and transformation platform that facilitates the integration of in situ, proteomic, and evolutionary measurements of molecular interactions to surveil diverse hosts and parasites in various environmental contexts. These objectives address Focus Area 2 Reveal Molecular Interactions Across Biological Scales for Design of Targeted Interventions. Our powerful and user-friendly platform will enhance connections between the often-siloed fields of structure, molecular phenotype, and evolutionary genomics that are key to biopreparedness, but in need of integration (Figure 1). We will build an integrated navigation tool to facilitate the effective use of globally distributed experimental data for integrated analysis and predictive modeling. The project will develop, implement, and test a platform to assess host-pathogen molecular interactions, adaptation to hosts and host shifts, and coevolution between hosts and pathogens, successfully impacting the research community by revolutionizing abilities to study any host-pathogen interaction, encourage diverse community contributions, and gain fundamental insights into how proteins adapt to new contexts. This ability will be critical for designing early interventions to address future threats. We will build surveillance training capability, aiming for a fair and equitable response to future pandemics and biothreats.

59 BASIC BIOLOGICAL SCIENCES↗

Ternary Complexes of BiI 3 /CuI and SbI 3 /CuI with Tetrahydrothiophene

Reactions of BiI 3 /CuI mixtures with tetrahydrothiophene (THT) in toluene produce 2-D sheet networks BiCu 3 I 6 (THT) n (n = 2, 3, or 4), depending on reaction conditions. All three structures are based on BiI 6 octahedra, which share pairs of (μ 2 -I) 2 with Cu 3 (THT) n units. BiCu 3 I 6 (THT) 2 features Cu 2 (μ 2 -I) 2 rhombs with close Cu···Cu interactions and is accompanied by formation of the very complex HBi 3 Cu 12 I 22 (THT) 8 . Reactions of SbI 3 /CuI with THT in toluene produced a SbCu 3 I 6 (THT) 2 network shows Cu 3 (μ 2 -THT) 2 units, like its Bi congener, but Cu 6 (μ 2 -I) 6 barrels rather than rhombs. Isolated SbI 3 units are stacked above the Cu 6 I 6 barrels. A molecular compound, Sb 3 Cu 3 I 12 (THT) 6 consists of a face-sharing Sb 3 I 12 stack, in which the Cu-THT units are bonded in asymmetric fashion about the central SbI 6 . Metal-halide bonds were investigated via QTAIM and NLMO analyses, demonstrating that these bonds are largely ionic and occur between the Bi/Sb and I p orbitals. Hirshfeld analysis shows significant H···H and H···I interactions. Diffuse reflectance spectroscopy (DRS) reveals band edges for the Bi species of 1.71–1.82 eV, while those for the neutral Sb complexes are in the range of 1.94–2.06 eV. Mapping of the electronic structure via density of state calculations indicates population of antibonding Bi/Sb–I orbitals in the excited state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ion Pairing Mediates Molecular Organization Across Liquid/Liquid Interfaces

Liquid/liquid interfaces play a central role in scientific fields ranging from nanomaterial synthesis and soft matter electronics to nuclear waste remediation and chemical separations. This diversity of functions arises from an interface’s ability to respond to changing conditions in its neighboring bulk phases. Understanding what drives this interfacial flexibility can provide novel avenues for designing new functional interfaces. However, limiting this progress is an inadequate understanding of the subtle intermolecular and interphase interactions taking place at the molecular level. Here, we use surface-specific vibrational sum frequency generation spectroscopy combined with atomistic molecular dynamics simulations to investigate the self-assembly and structure of model ionic oligomers consisting of an oligodimethylsiloxane (ODMS) tail covalently attached to a positively charged methyl imidazolium (MIM + ) head group at buried oil/aqueous interfaces. We show how the presence of seemingly innocuous salts can impart dramatic changes to the ODMS tail conformations in the oil phase via specific ion effects and ion-pairing interactions taking place in the aqueous phase. These specific ion interactions are shown to drive enhanced amphiphile adsorption, induce morphological changes, and disrupt emergent hydrogen-bonding structures at the interface. Tuning these interactions allows for independent control over the oligomer structure in the oil phase versus interfacial population changes and represents key mechanistic insight that is needed to control chemical reactions at liquid/liquid interfaces.

36 MATERIALS SCIENCE↗

The Materials Provenance Store

Abstract We present a database resulting from high throughput experimentation, primarily on metal oxide solid state materials. The central relational database, the Materials Provenance Store (MPS), manages the metadata and experimental provenance from acquisition of raw materials, through synthesis, to a broad range of materials characterization techniques. Given the primary research goal of materials discovery of solar fuels materials, many of the characterization experiments involve electrochemistry, along with optical, structural, and compositional characterizations. The MPS is populated with all information required for executing common data queries, which typically do not involve direct query of raw data. The result is a database file that can be distributed to users so that they can independently execute queries and subsequently download the data of interest. We propose this strategy as an approach to manage the highly heterogeneous and distributed data that arises from materials science experiments, as demonstrated by the management of over 30 million experiments run on over 12 million samples in the present MPS release.

36 MATERIALS SCIENCE↗

Electronic heat generation in semiconductors: Non-equilibrium excitation and evolution of zone-edge phonons via electron–phonon scattering in photo-excited germanium

We investigate experimentally and using first-principles theory the generation of phonons and the relaxation of carriers on picosecond timescales across the Brillouin zone of photo-excited Ge by inter-valley electron–phonon scattering. The phonons generated are typical of those generated in semiconductor devices, contributing to the accumulation of heat within the material. We simulate the time-evolution of phonon populations, based on first-principles band structure and electron–phonon and phonon–phonon matrix elements, and compare them to data from time-resolved x-ray diffuse scattering experiments, performed at the Linac Coherent Light Source x-ray free-electron laser facility, following photo-excitation by a 50 fs near-infrared optical pulse. We show that the intensity of the non-thermal x-ray diffuse scattering signal, which is observed to grow substantially near the L-point of the Brillouin zone over 3–5 ps, is due to phonons generated by scattering of carriers between the Δ and L valleys. These phonons have low group velocities, resulting in a heat bottleneck. With the inclusion of phonon decay through 3-phonon processes, the simulations also account for other non-thermal features observed in the x-ray diffuse scattering intensity, which are due to anharmonic phonon–phonon scattering of the phonons initially generated by electron–phonon scattering.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

SASHIMI-SIDM: semi-analytical subhalo modelling for self-interacting dark matter at sub-galactic scales

We combine the semi-analytical structure formation model, SASHIMI, which predicts subhalo populations in collisionless, cold dark matter (CDM), with a parametric model that maps CDM halos to self-interacting dark matter (SIDM) halos. The resulting model, SASHIMI-SIDM, generates SIDM subhalo populations down to sub-galactic mass scales, for an arbitrary input cross section, in minutes. We show that SASHIMI-SIDM agrees with SIDM subhalo populations from high-resolution cosmological zoom-in simulations in resolved regimes. Crucially, we predict that the fraction of core-collapsed subhalos peaks at a mass scale determined by the input SIDM cross section and decreases toward higher halo masses, consistent with the predictions of gravothermal models and cosmological simulations. For the first time, we also show that the core-collapsed fraction decreases toward lower halo masses. While the dependence of the collapse time on mass and concentration implies such behaviour, our semi-analytical approach allows us to quantify and illustrate this trend clearly across the full mass spectrum of subhalos, including for subhalo masses below the resolution limit of any current cosmological SIDM simulation. As a proof of principle, we apply SASHIMI-SIDM to predict the boost to the local dark matter density and annihilation rate from core-collapsed SIDM subhalos, which can be enhanced relative to CDM by an order of magnitude for viable SIDM models. Thus, SASHIMI-SIDM provides an efficient and reliable tool for scanning SIDM parameter space and testing it with astrophysical observations. The code is publicly available at https://github.com/shinichiroando/sashimi-si.

cosmological simulations↗

Determining population densities in bimodal micellar solutions using contrast-variation small angle neutron scattering

Self-assembly of amphiphilic polymers in water is of fundamental and practical importance. Significant amounts of free unimers and associated micellar aggregates often coexist over a wide range of phase regions. The thermodynamic and kinetic properties of the microphase separation are closely related to the relative population density of unimers and micelles. Although the scattering technique has been employed to identify the structure of micellar aggregates as well as their time-evolution, the determination of the population ratio of micelles to unimers remains a challenging problem due to their difference in scattering power. In this work, using small-angle neutron scattering (SANS), we present a comprehensive structural study of amphiphilic n-dodecyl-PNIPAm polymers, which shows a bimodal size distribution in water. By adjusting the deuterium/hydrogen ratio of water, the intra-micellar polymer and water distributions are obtained from the SANS spectra. The micellar size and number density are further determined, and the population densities of micelles and unimers are calculated to quantitatively address the degree of micellization at different temperatures. Our method can be used to provide an in-depth insight into the solution properties of microphase separation, which are present in many amphiphilic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The satellite population around luminous red galaxies in the 25 deg2 DESI Legacy Imaging Surveys Early Data Release

ABSTRACT Luminous red galaxies, or LRGs, are representative of the most massive galaxies and were originally selected in the Sloan Digital Sky Survey as good tracers of large-scale structure. They are dominated by by uniformly old stellar populations, have low star formation rates, early type morphologies, and little cold gas. Despite having old stellar populations and little in situ star formation, studies have shown that they have grown their stellar mass since z = 1, implying that they grow predominantly via the accretion of satellites. Tests of this picture have been limited because of the lack of deep imaging data sets that both covers a large enough area of the sky to contain substantial numbers of LRGs and that also is deep enough to detect faint satellites. We use the 25 deg2 Early Data Release (EDR) of the DESI Legacy Imaging Surveys to characterize the satellite galaxy population of LRGs out to z = 0.65. The DESI Legacy Imaging Surveys are comprised of grz imaging to 2–2.5 mag deeper than SDSS and with better image quality. We use a new statistical background technique to identify excess populations of putative satellite galaxies around 1823 LRGs at 0.2 < z < 0.65. In three redshift and luminosity bins we measure the numbers of satellite galaxies and their r−z colour distribution down to rest-frame g-band luminosity limits at least 3.6 times fainter than L*. In addition, we develop a forward modeling technique and apply it to constrain the mean number of satellites in each of our redshift and luminosity bins. Finally, we use these estimates to determine the amount of stellar mass growth in LRGs down to the local Universe.

Astronomy & Astrophysics↗

Exploring the stellar populations of backsplash galaxies

Backsplash galaxies are those that traverse and overshoot cluster cores as they fall into these structures. They are affected by environment, and should stand out in contrast to the infalling population. We target galaxies in the vicinity of clusters (R≳R 200 ) and select a sample in projected phase space (PPS), from the compilation of Sampaio et al. based on SDSS data. We present a statistical analysis, comparing two regions in PPS, with the same projected distance to the cluster but different velocity. The analysis relies on the presence of variations in the stellar population content of backsplash galaxies. We find a lower limit in the fractional contribution of ∼5 per cent with respect to the general sample of infalling galaxies at similar group-centric distance when using single line strength analysis, or ∼15-30 per cent when adopting bivariate distributions. The stellar populations show a subtle but significant difference towards older ages, and a higher fraction of quiescent galaxies. We also compare this set with a general field sample, where a substantially larger difference in galaxy properties is found, with the field sample being consistently younger, metal poorer and with a lower fraction of quiescent galaxies. Noting that our ‘cluster’ sample is located outside of the virial radius, we expect this difference to be caused by pre-processing of the infalling galaxies in the overall higher density regions.

79 ASTRONOMY AND ASTROPHYSICS↗

Characterizing the γ-Ray Emission from FR0 Radio Galaxies

Abstract FR0 galaxies constitute the most abundant jet population in the local Universe. With their compact jet structure, they are broadband photon emitters and have been proposed as multimessenger sources. Recently, these sources have been detected for the first time inγrays. Using a revised FR0 catalog, we confirm that the FR0 population as a whole areγ-ray emitters, and we also identify two significant sources. For the first time, we find a correlation between the 5 GHz core radio luminosity andγ-ray luminosity in the 1–800 GeV band, having a 4.8σstatistical significance. This is clear evidence that the jet emission mechanism is similar in nature for FR0s and the well-studied canonical FR (FRI and FRII) radio galaxies. Furthermore, we perform broadband spectral energy distribution modeling for the significantly detected sources as well as the subthreshold source population using a one-zone synchrotron self-Compton model. Within the maximum jet power budget, our modeling shows that the detectedγrays from the jet can be explained as inverse Compton photons. To explain the multiwavelength observations for these galaxies, the modeling results stipulate a low bulk Lorentz factor and a jet composition far from equipartition, with the particle energy density dominating over the magnetic field energy density.

Astronomy & Astrophysics↗

Nuclear structure advancements with multi-nucleon transfer reactions

Multi-Nucleon Transfer (MNT) reactions have been used for decades as a reaction mechanism, in order to populate excited states in nuclei far from stability and to perform nuclear structure studies. Nevertheless, the development of set-ups involving high acceptance tracking magnetic spectrometers (mainly existing in Europe), coupled with the Advanced GAmma Tracking Array (AGATA) opens new possibilities, especially if they are used in conjunction with high-intensity stable beams or ISOL RIBs. In this article, we will discuss the capabilities of such set-ups aiming at different goals, including complete information in high-resolution spectroscopy as well as lifetime measurements.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Many-Exciton Quantum Dynamics in a Ruddlesden–Popper Tin Iodide

We present a study on the many-body exciton interactions in a Ruddlesden–Popper tin halide, namely, (PEA) 2 SnI 4 (PEA = phenylethylammonium), using coherent two-dimensional electronic spectroscopy. The optical dephasing times of the third-order polarization observed in these systems are determined by exciton many-body interactions and lattice fluctuations. We investigate the excitation-induced dephasing (EID) and observe a significant reduction of the dephasing time with increasing excitation density as compared to its lead counterpart (PEA) 2 PbI 4 , which we have previously reported in a separate publication [J. Chem. Phys. 2020, 153, 164706]. Surprisingly, we find that the EID interaction parameter is four orders of magnitude higher in (PEA) 2 SnI 4 than that in (PEA) 2 PbI 4 . This increase in the EID rate may be due to exciton localization arising from a more statically disordered lattice in the tin derivative. This is supported by the observation of multiple closely spaced exciton states and the broadening of the linewidth with increasing population time (spectral diffusion), which suggests a static disordered structure relative to the highly dynamic lead-halide. Additionally, we find that the exciton nonlinear coherent lineshape shows evidence of a biexcitonic state with low binding energy (<10 meV) not observed in the lead system. We model the lineshapes based on a stochastic scattering theory that accounts for the interaction with a nonstationary population of dark background excitations. Our study provides evidence of differences in the exciton quantum dynamics between tin- and lead-based Ruddlesden–Popper metal halides (RPMHs) and links them to the exciton–exciton interaction strength and the static disorder aspect of the crystalline structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Real-time tracking of protein unfolding with time-resolved x-ray solution scattering

The correct folding of proteins is of paramount importance for their function, and protein misfolding is believed to be the primary cause of a wide range of diseases. Protein folding has been investigated with time-averaged methods and time-resolved spectroscopy, but observing the structural dynamics of the unfolding process in real-time is challenging. Here, we demonstrate an approach to directly reveal the structural changes in the unfolding reaction. We use nano- to millisecond time-resolved x-ray solution scattering to probe the unfolding of apomyoglobin. The unfolding reaction was triggered using a temperature jump, which was induced by a nanosecond laser pulse. We demonstrate a new strategy to interpret time-resolved x-ray solution scattering data, which evaluates ensembles of structures obtained from molecular dynamics simulations. We find that apomyoglobin passes three states when unfolding, which we characterize as native, molten globule, and unfolded. The molten globule dominates the population under the conditions investigated herein, whereas native and unfolded structures primarily contribute before the laser jump and 30 μs after it, respectively. The molten globule retains much of the native structure but shows a dynamic pattern of inter-residue contacts. Our study demonstrates a new strategy to directly observe structural changes over the cause of the unfolding reaction, providing time- and spatially resolved atomic details of the folding mechanism of globular proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Genetic underpinnings of arthropod community distributions in Populus trichocarpa

Community genetics seeks to understand the mechanisms by which natural genetic variation in heritable host phenotypes can encompass assemblages of organisms such as bacteria, fungi, and many animals including arthropods. Prior studies that focused on plant genotypes have been unable to identify genes controlling community composition, a necessary step to predict ecosystem structure and function as underlying genes shift within plant populations. Here, we surveyed arthropods within an association population of Populus trichocarpa in three common gardens to discover plant genes that contributed to arthropod community composition. We analyzed our surveys with traditional single-trait genome-wide association analysis (GWAS), multitrait GWAS, and functional networks built from a diverse set of plant phenotypes. Plant genotype was influential in structuring arthropod community composition among several garden sites. Candidate genes important for higher level organization of arthropod communities had broadly applicable functions, such as terpenoid biosynthesis and production of dsRNA binding proteins and protein kinases, which may be capable of targeting multiple arthropod species. We have demonstrated the ability to detect, in an uncontrolled environment, individual genes that are associated with the community assemblage of arthropods on a host plant, further enhancing our understanding of genetic mechanisms that impact ecosystem structure.

Community genetics↗

Designed Spin‐Texture‐Lattice to Control Anisotropic Magnon Transport in Antiferromagnets

Abstract Spin waves in magnetic materials are promising information carriers for future computing technologies due to their ultra‐low energy dissipation and long coherence length. Antiferromagnets are strong candidate materials due, in part, to their stability to external fields and larger group velocities. Multiferroic antiferromagnets, such as BiFeO 3 (BFO), have an additional degree of freedom stemming from magnetoelectric coupling, allowing for control of the magnetic structure, and thus spin waves, with the electric field. Unfortunately, spin‐wave propagation in BFO is not well understood due to the complexity of the magnetic structure. In this work, long‐range spin transport is explored within an epitaxially engineered, electrically tunable, 1D magnonic crystal. A striking anisotropy is discovered in the spin transport parallel and perpendicular to the 1D crystal axis. Multiscale theory and simulation suggest that this preferential magnon conduction emerges from a combination of a population imbalance in its dispersion, as well as anisotropic structural scattering. This work provides a pathway to electrically reconfigurable magnonic crystals in antiferromagnets.

36 MATERIALS SCIENCE↗