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At least 91 records · Page 5

Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS

The APBS software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages. APBS has enjoyed widespread adoption throughout the biomedical community and is used in numerous applications involving biomolecular structures. However, visualization of complex biomolecular electrostatic properties can be challenging for two-dimensional graphics systems. Therefore, advanced visualization and manipulation capabilities have been incorporated. In particular, APBS tools have been integrated with the UnityMolX virtual reality platform to provide an immersive experience for preparing biomolecular systems for calculations as well as visualizing and comparing calculated results.

electrostatics, molecular visualization, solvation↗

Spin disorder in a stacking polytype of a layered magnet

Strongly correlated ground states and exotic quasiparticle excitations in low-dimensional systems are central research topics in the solid-state research community. The present work develops a layered material and explores the physical properties. Single crystals of 3⁢R–Na 2 ⁢MnTe⁢O 6 were synthesized via a flux method. Single-crystal x-ray diffraction and transmission electron microscopy reveal a crystal structure with ABC-type stacking and an R–3 space group, which establishes this material as a stacking polytype to previously reported 2⁢H–Na 2 ⁢MnTe⁢O 6 . Magnetic- and heat-capacity measurements demonstrate dominant antiferromagnetic interactions, the absence of long-range magnetic order down to 0.5 K, and field-dependent short-range magnetic correlations. A structural transition at ~23 K observed in dielectric measurements may be related to displacements of the Na positions. In conclusion, our results demonstrate that 3⁢R–Na 2 ⁢MnTe⁢O 6 displays low-dimensional magnetism, disordered structure and spins, and the system displays a rich structure variety.

36 MATERIALS SCIENCE↗

Towards engineering ectomycorrhization into switchgrass bioenergy crops via a lectin receptor‐like kinase

Summary Soil‐borne microbes can establish compatible relationships with host plants, providing a large variety of nutritive and protective compounds in exchange for photosynthesized sugars. However, the molecular mechanisms mediating the establishment of these beneficial relationships remain unclear. Our previous genetic mapping and whole‐genome resequencing studies identified a gene deletion event of a Populus trichocarpa lectin receptor‐like kinase gene PtLecRLK1 in Populus deltoides that was associated with poor‐root colonization by the ectomycorrhizal fungus Laccaria bicolor . By introducing PtLecRLK1 into a perennial grass known to be a non‐host of L. bicolor , switchgrass ( Panicum virgatum L.), we found that L. bicolor colonizes ZmUbipro‐PtLecRLK1 transgenic switchgrass roots, which illustrates that the introduction of PtLecRLK1 has the potential to convert a non‐host to a host of L. bicolor . Furthermore, transcriptomic and proteomic analyses on inoculated‐transgenic switchgrass roots revealed genes/proteins overrepresented in the compatible interaction and underrepresented in the pathogenic defence pathway, consistent with the view that pathogenic defence response is down‐regulated during compatible interaction. Metabolomic profiling revealed that root colonization in the transgenic switchgrass was associated with an increase in N‐containing metabolites and a decrease in organic acids, sugars, and aromatic hydroxycinnamate conjugates, which are often seen in the early steps of establishing compatible interactions. These studies illustrate that PtLecRLK1 is able to render a plant susceptible to colonization by the ectomycorrhizal fungus L. bicolor and shed light on engineering mycorrhizal symbiosis into a non‐host to enhance plant productivity and fitness on marginal lands.

59 BASIC BIOLOGICAL SCIENCES↗

Identification, Expression, and Interaction Analysis of Ovate Family Proteins in Populus trichocarpa Reveals a Role of PtOFP1 Regulating Drought Stress Response

Ovate family proteins (OFPs) are a family of plant growth regulators that play diverse roles in many aspects of physiological processes. OFPs have been characterized in various plant species including tomato, Arabidopsis , and rice. However, little is known about OFPs in woody species. Here, a total of 30 PtOFP genes were identified from the genome of Populus trichocarpa and were further grouped into four subfamilies based on their sequence similarities. Gene expression analysis indicated that some members of the PtOFP gene family displayed tissue/organ-specific patterns. Analysis of cis -acting elements in the promoter as well as gene expression by hormone treatment revealed putative involvement of PtOFPs in hormonal response. Furthermore, PtOFP1 (Potri.006G107700) was further experimentally demonstrated to act as a transcriptional repressor. Yeast two-hybrid assay showed physical interactions of PtOFP1 with other proteins, which suggests that they might function in various cellular processes by forming protein complexes. In addition, overexpression of PtOFP1 in Arabidopsis conferred enhanced tolerance to PEG-induced drought stress at seedling stage, as well as a higher survival rate than the wild type at mature stage. These results provide a systematic analysis of the Populus OFP gene family and lay a foundation for functional characterization of this gene family.

59 BASIC BIOLOGICAL SCIENCES↗

Aerobic oxidation of alcohols over Ru-Mn-Ce and Ru-Co-Ce catalysts: The effect of calcination temperature

We report two ternary mixed oxides, Ru-Mn-Ce and Ru-Co-Ce, were prepared by a co-precipitation method and used in the aerobic oxidation of alcohols to corresponding aldehydes (ketones). Interestingly, different catalytic results were obtained when these compounds were calcined. The calcination temperature had an adverse effect on the catalytic performance of Ru-Mn-Ce catalysts, while being beneficial to the Ru-Co-Ce catalysts. To illustrate these effects, these materials were characterized using X-ray diffraction (XRD), Fourier transformed infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS), Temperature-programmed reduction (TPR), Electron paramagnetic resonance (EPR) and other techniques. The data showed that ruthenium oxides were uniformly dispersed in the mixed oxides, and phase transformations occur after calcination. Mn 3 O 4 was transformed to MnO 2 for the Ru-Mn-Ce catalyst, while CoO(OH) was transformed to Co 3 O 4 in the Ru-Co-Ce catalyst. The interactions between ruthenium oxides and Co (Mn)-Ce mixed oxides of the former strengthened while the latter weakened. Calcination decreased the content of adsorbed oxygen and restricted oxygen transfer mechanism in the manganese system, while the opposite effect was observed with the cobalt-containing catalyst. Under optimal reaction conditions, various kinds of alcohols were transformed to corresponding aldehydes (ketones) in high yields over the Ru-Mn-Ce catalyst suggesting these ternary oxides are environmental friendly and economical catalytic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cr 2.37 Ga 3 Se 8 : A Quasi-Two-Dimensional Magnetic Semiconductor

We present a novel magnetic semiconductor, Cr 2.37 Ga 3 Se 8 , synthesized by partially replacing magnetic Cr 3+ in antiferromagnetic Cr 5+δ Se 8 with nonmagnetic Ga 3+ . The crystal structure of Cr 2.37 Ga 3 Se 8 was determined by both powder and single-crystal X-ray diffraction. The title compound crystallizes in a monoclinic structure with space group C2/m (No. 12). In Cr 2.37 Ga 3 Se 8 , the Cr atoms are surrounded by 6 Se atoms and form filled octahedral clusters, while Ga atoms are centered in the Se 4 tetrahedral clusters. The two kinds of clusters pack alternatingly along the c-axis, which results in a quasi-two-dimensional layered structure. The magnetization (M) measurement shows the development of short-range ferromagnetic coupling below the Curie-Weiss (CW) temperature θ CW ~ 92 K, evidenced by the nonlinear field dependence of M. However, the magnetic susceptibility exhibits a peak at low fields at ~18 K, indicating the existence of an antiferromagnetic interaction as well. Electronic structure calculations using the WIEN2k program in the local spin density approximation indicate that the magnetism arises exclusively from local moments of the Cr atoms. Here, the electrical resistivity measurement of the Cr 2.37 Ga 3 Se 8 sample confirms that this material is a semiconductor with the band gap ~0.26 eV. Meanwhile, the experimental band gap (~0.26 eV) is close to the theoretical prediction using the WIEN2k program (~0.35 eV).

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Long-range magnetic order with disordered spin orientations in a high-entropy antiferromagnet

Disorder in magnetic systems typically suppresses long-range order, promoting short-range states such as spin glasses and magnetic clusters. This is particularly prominent in high-entropy materials, characterized by the random distributions of local magnetic entities and exchange interactions. However, in rare exceptions, long-range magnetic order can persist in high-entropy systems, while the microscopic characters and underlying mechanisms remain elusive, especially the magnetic behaviors of individual elements. Here, combining neutron diffraction and resonant soft x-ray scattering, we have conducted an element-specific investigation into the magnetic order of a high-entropy honeycomb-lattice van der Waals material (Mn 1/4 Fe 1/4 Co 1/4 Ni 1/4 )PS 3 . Despite significant atomic disorder, long-range zigzag antiferromagnetic order is observed below 72 K, with all four transition-metal elements participating in a unified phase transition. However, the spin orientations of various elements are distinct, attributed to the competition between single-ion anisotropies and exchange interactions. Our findings showcase a novel form of long-range magnetic order with disordered spin orientations, which is synergically stabilized by distinct magnetic elements in a high entropy magnet, offering a new paradigm for understanding complex magnetic systems.

Shen, Yao [Chinese Academy of Sciences (CAS), Beij↗

MOOSE–Workbench Integration and MOOSE Meshing Capability Enhancements to Facilitate Inputs and Outputs for Multiphysics Modeling

The Multiphysics Object-Oriented Simulation Environment (MOOSE) is an open-source framework that supports many of the US Department of Energy’s (DOE’s) Nuclear Energy Advanced Modeling and Simulation (NEAMS) technical areas (TA). These TAs develop and use NEAMS physics and coupling modules in multiple ways to enable the research and development of complex physics models. In addition to the MOOSE framework, the NEAMS Workbench user interface provides a common analysis environment with user-interaction accelerators that streamline the tasks of model creation, review, execution, and output inspection. In FY 2024, objectives were realized in the MOOSE framework application development support and user-oriented improvements. Application development improvements support both developers and users with an expanded Reactor Module and Mesh System, stateful material property support for mortar contact, and customizable convergence criteria. Additionally, new user-oriented features were implemented in the MOOSE framework language server, including autocompletion snippets, definition from source and find reference navigations, and syntax overrides. Lastly, improvements were made to the input interpreter necessary to support the MOOSE language server and the NEAMS Workbench so that they can interact with syntactically incomplete user inputs. These improvements and more were intended to address stakeholder feedback and improve developer and user ability to conduct advanced nuclear energy modeling and simulation in support of DOE and industry needs.

97 - MATHEMATICS AND COMPUTING↗

pyXPCSviewer : an open-source interactive tool for X-ray photon correlation spectroscopy visualization and analysis

pyXPCSviewer , a Python-based graphical user interface that is deployed at beamline 8-ID-I of the Advanced Photon Source for interactive visualization of XPCS results, is introduced. pyXPCSviewer parses rich X-ray photon correlation spectroscopy (XPCS) results into independent PyQt widgets that are both interactive and easy to maintain. pyXPCSviewer is open-source and is open to customization by the XPCS community for ingestion of diversified data structures and inclusion of novel XPCS techniques, both of which are growing demands particularly with the dawn of near-diffraction-limited synchrotron sources and their dedicated XPCS beamlines.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Accurate simulation of surfaces and interfaces of ten FCC metals and steel using Lennard–Jones potentials

Abstract The earlier integration of validated Lennard–Jones (LJ) potentials for 8 fcc metals into materials and biomolecular force fields has advanced multiple research fields, for example, metal–electrolyte interfaces, recognition of biomolecules, colloidal assembly of metal nanostructures, alloys, and catalysis. Here we introduce 12-6 and 9-6 LJ parameters for classical all-atom simulations of 10 further fcc metals (Ac, Ca (α), Ce (γ), Es (β), Fe (γ), Ir, Rh, Sr (α), Th (α), Yb (β)) and stainless steel. The parameters reproduce lattice constants, surface energies, water interfacial energies, and interactions with (bio)organic molecules in 0.1 to 5% agreement with experiment, as well as qualitative mechanical properties under standard conditions. Deviations are reduced up to a factor of one hundred in comparison to earlier Lennard–Jones parameters, embedded atom models, and density functional theory. We also explain a quantitative correlation between atomization energies from experiments and surface energies that supports parameter development. The models are computationally very efficient and applicable to an exponential space of alloys. Compatibility with a wide range of force fields such as the Interface force field (IFF), AMBER, CHARMM, COMPASS, CVFF, DREIDING, OPLS-AA, and PCFF enables reliable simulations of nanostructures up to millions of atoms and microsecond time scales. User-friendly model building and input generation are available in the CHARMM-GUI Nanomaterial Modeler. As a limitation, deviations in mechanical properties vary and are comparable to DFT methods. We discuss the incorporation of reactivity and features of the electronic structure to expand the range of applications and further increase the accuracy.

Kanhaiya, Krishan (ORCID:0000000236222655)↗

Nontraditional Approaches To Enable High-Energy and Long-Life Lithium–Sulfur Batteries

In this study, lithium-sulfur (Li-S) batteries are promising for automotive applications due to their high theoretical energy density (2600 Wh/kg). In addition, the natural abundance of sulfur could mitigate the global raw material supply chain challenge of commercial lithium-ion batteries that use critical elements, such as nickel and cobalt. However, due to persistent polysulfide shuttling and uncontrolled lithium dendrite growth, Li-S batteries using nonencapsulated sulfur cathodes and conventional ether-based electrolytes suffer from rapid cell degradation upon cycling. Despite significant improvements in recent decades, there is still a big gap between lab research and commercialization of the technology. To date, the reported cell energy densities and cycling life of practical Li-S pouch cells remain largely unsatisfactory. Traditional approaches to improving Li-S performance are primarily focused on confining polysulfides using electronically conductive hosts. However, these micro- and mesoporous hosts suffer from limited pore volume to accommodate high sulfur loading and the associated volume change during cycling. Moreover, they fail to balance adsorption-conversion of polysulfides during charge-discharge, leading to the formation of massive dead sulfur. Such hosts are themselves electrochemically inactive, which decreases the practical energy density. In contrast, a series of nontraditional approaches, paired with advances in multiscale mechanistic understanding, have recently demonstrated exciting performance outcomes not only in conventional coin cells but also in practical pouch cells. In this Account, we first introduce our novel cathode design strategies to overcome polysulfide shuttling and sluggish redox kinetics in thick S cathodes via selenium-sulfur chemistry and cathode host engineering. Next, we gain a mechanistic understanding of Li-S batteries in various types of electrolytes via a series of spectroscopic, nuclear magnetic resonance, and electrochemical methods. Meanwhile, a novel cathode solid electrolyte interphase encapsulation strategy via nonviscous highly fluorinated ether-based electrolyte is introduced. The established selection rule by investigating how solvating power retards the shuttle effect and induces robust cathode/solid-electrolyte interphase formation is also included. We then discuss how the synergistic interactions between rational cathode structures and electrolytes can be exploited to tailor the reaction pathways and kinetics of S cathodes under high mass loading and lean electrolyte conditions. In addition, a novel interlayer design to simultaneously overcome degradation processes (polysulfide shuttling and lithium dendrite formation) and accelerate redox reaction kinetics is presented. Finally, this Account concludes with an overview of the challenges and strategies to develop Li-S pouch cells with high practical energy density, long cycle life, and fast-charging capability.

25 ENERGY STORAGE↗

Stable Hydrazone-Linked Covalent Organic Frameworks Containing O,N,O'-Chelating Sites for Fe(III) Detection in Water

Two stable crystalline hydrazone-linked covalent organic frameworks (COFs) (Bth-Dha and Bth-Dma) containing functional O,N,O'-chelating sites have been designed and successfully synthesized by the Schiff-base condensation reactions between benzene-1,3,5-tricarbohydrazide (Bth) and 2,5-dihydroxyterephthalaldehyde (Dha) or 2,5-dimethoxyterephthal-aldehyde (Dma), respectively. Bth-Dma exhibits strong fluorescence in the solid state and in an aqueous dispersion, while no fluorescence can be observed for Bth-Dha. Interestingly, the as-synthesized Bth-Dma can be used as a turn-off fluorescence sensor for the Fe(III) ion in aqueous solution with outstanding selectivity and sensitivity. Here, the recognition process can be attributed to the coordination interaction between Fe(III) ion and the O,N,O'-chelating sites in the pore wall of Bth-Dma COF, as verified by X-ray photoelectron spectroscopy and 1 H NMR spectroscopy. To the best of our knowledge, this is the first report on the rational design of luminescent COF with predesigned O,N,O'-chelating sites as a fluorescence sensor for highly selective and sensitive metal ion detection. This work may pave the way for designing luminescent COF sensors with functional binding sites for detecting specific metal ions.

36 MATERIALS SCIENCE↗

Fluctuating Hydrodynamics Methods for Dynamic Coarse-Grained Implicit-Solvent Simulations in LAMMPS

We present a software package integrated with the molecular dynamics software LAMMPS for fluctuating hydrodynamics simulations of fluid-structure interactions subject to thermal fluctuations. The package is motivated to provide dynamic thermostats to extend implicit-solvent coarse-grained (IS-CG) models by incorporating kinetic contributions from the solvent to facilitate their use in a wider range of applications. To capture the thermal and hydrodynamic contributions of the solvent to dynamics, we introduce momentum conserving thermostats and computational methods based on fluctuating hydrodynamics and the stochastic Eulerian Lagrangian method (SELM). SELM couples the coarse-grained microstructure degrees of freedom to continuum stochastic fields to capture both the relaxation of hydrodynamic modes and thermal fluctuations. Features of the SELM software include (i) numerical time-step integrators for SELM fluctuating hydrodynamics in inertial and quasi-steady regimes, (ii) Lees--Edwards-style methods for imposing shear, (iii) a Java-based graphical user interface (GUI) for setting up models and simulations, (iv) standardized XML formats for parametrization and data output, and (v) standardized formats VTK for continuum fields and microstructures. The SELM software package facilitates for pre-established models in LAMMPS easy adoption of the SELM fluctuating hydrodynamics thermostats. We offer here an overview of the SELM software package, computational methods, and applications.

97 MATHEMATICS AND COMPUTING↗

Electrostatic Self-Assembly Enabling Integrated Bulk and Interfacial Sodium Storage in 3D Titania-Graphene Hybrid

Room temperature sodium-ion batteries have attracted increased attention for energy storage due to the natural abundance of sodium. However, it remains a huge challenge to develop versatile electrode materials with favorable properties, which requires smart structure design and good mechanistic understanding. Herein, we reported a general and scalable approach to synthesize 3D titania-graphene hybrid via electrostatic-interaction-induced self-assembly. Synchrotron X-ray probe, transmission electron microscopy and computational modeling revealed that the strong interaction between Titania and graphene through comparably strong van-der-Waals forces not only facilitates bulk Na+ intercalation but also enhances the interfacial sodium storage. As a result, the titania-graphene hybrid exhibits exceptional long-term cycle stability up to 5000 cycles, and ultrahigh rate capability up to 20 C for sodium storage. Furthermore, density function theory calculation indicated that the interfacial Li+, K+, Mg2+ and Al3+ storage can be enhanced as well. The proposed general strategy opens up new avenues to create versatile materials for advanced battery systems.

25 ENERGY STORAGE↗

Visualizing interfacial collective reaction behaviour of Li–S batteries

Benefiting from high energy density (2,600 Wh kg -1 )) and low cost, lithium-sulfur (Li-S) batteries are considered promising candidates for advanced energy-storage systems. Despite tremendous efforts in suppressing the long-standing shuttle effect of lithium polysulfides, understanding of the interfacial reactions of lithium polysulfides at the nanoscale remains elusive. This is mainly because of the limitations of in situ characterization tools in tracing the liquid-solid conversion of unstable lithium polysulfides at high temporal-spatial resolution. There is an urgent need to understand the coupled phenomena inside Li-S batteries, specifically, the dynamic distribution, aggregation, deposition and dissolution of lithium polysulfides. Here, by using in situ liquid-cell electrochemical transmission electron microscopy, we directly visualized the transformation of lithium polysulfides over electrode surfaces at the atomic scale. Notably, an unexpected gathering-induced collective charge transfer of lithium polysulfides was captured on the nanocluster active-centre-immobilized surface. It further induced an instantaneous deposition of nonequilibrium Li2S nanocrystals from the dense liquid phase of lithium polysulfides. Without mediation of active centres, the reactions followed a classical single-molecule pathway, lithium polysulfides transforming into Li 2 S 2 and Li 2 S step by step. Molecular dynamics simulations indicated that the long-range electrostatic interaction between active centres and lithium polysulfides promoted the formation of a dense phase consisting of Li + and S n 2- (2 < n ≤ 6), and the collective charge transfer in the dense phase was further verified by ab initio molecular dynamics simulations. Finally, the collective interfacial reaction pathway unveils a new transformation mechanism and deepens the fundamental understanding of Li-S batteries.

25 ENERGY STORAGE↗

Development of high-energy non-aqueous lithium-sulfur batteries via redox-active interlayer strategy

Abstract Lithium-sulfur batteries have theoretical specific energy higher than state-of-the-art lithium-ion batteries. However, from a practical perspective, these batteries exhibit poor cycle life and low energy content owing to the polysulfides shuttling during cycling. To tackle these issues, researchers proposed the use of redox-inactive protective layers between the sulfur-containing cathode and lithium metal anode. However, these interlayers provide additional weight to the cell, thus, decreasing the practical specific energy. Here, we report the development and testing of redox-active interlayers consisting of sulfur-impregnated polar ordered mesoporous silica. Differently from redox-inactive interlayers, these redox-active interlayers enable the electrochemical reactivation of the soluble polysulfides, protect the lithium metal electrode from detrimental reactions via silica-polysulfide polar-polar interactions and increase the cell capacity. Indeed, when tested in a non-aqueous Li-S coin cell configuration, the use of the interlayer enables an initial discharge capacity of about 8.5 mAh cm −2 (for a total sulfur mass loading of 10 mg cm −2 ) and a discharge capacity retention of about 64 % after 700 cycles at 335 mA g −1 and 25 °C.

25 ENERGY STORAGE↗

Scalar electroweak multiplet dark matter

We revisit the theory and phenomenology of scalar electroweak multiplet thermal dark matter. We derive the most general, renormalizable scalar potential, assuming the presence of the Standard Model Higgs doublet, H , and an electroweak multiplet Φ of arbitrary SU(2) L rank and hypercharge, Y . We show that, in general, the Φ- H Higgs portal interactions depend on three, rather than two independent couplings as has been previously considered in the literature. For the phenomenologically viable case of Y = 0 multiplets, we focus on the septuplet and quintuplet cases, and consider the interplay of relic density and spin-independent direct detection cross section. We show that both the relic density and direct detection cross sections depend on a single linear combination of Higgs portal couplings, λ eff . For λ eff ~ \( \mathcal{O} \) (1), present direct detection exclusion limits imply that the neutral component of a scalar electroweak multiplet would comprise a subdominant fraction of the observed DM relic density.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Control simulations of many-body quantum systems by a synergism of discrete real-time learning and optimal control theory

We present a self-consistent algorithm for optimal control simulations of many-body quantum systems. The algorithm features a two-step synergism that combines discrete real-time machine learning (DRTL) with Quantum Optimal Control Theory (QOCT) using the time-dependent Schrödinger equation. Specifically, in step (1), DRTL is employed to identify a compact working space (i.e., the important portion of the Hilbert space) for the time evolution of the many-body quantum system in the presence of a control field (i.e., the initial or previously updated field), and in step (2), QOCT utilizes the DRTL-determined working space to find a newly updated control field for a chosen objective. Steps 1 and 2 are iterated until a self-consistent control objective value is reached such that the resulting optimal control field yields the same targeted objective value when the corresponding working space is systematically enlarged. Furthermore, to demonstrate this two-step self-consistent DRTL-QOCT synergistic algorithm, we perform optimal control simulations of strongly interacting 1D as well as 2D Heisenberg spin systems. In both scenarios, only a single spin (at the left end site for 1D and the upper left corner site for 2D) is driven by the time-dependent control fields to create an excitation at the opposite site as the target. It is found that, starting from all spin-down zero excitation states, the synergistic method is able to identify working spaces and convergence of the desired controlled dynamics with just a few iterations of the overall algorithm. In the cases studied, the dimensionality of the working space scales only quasi-linearly with the number of spins.

Artificial neural networks↗