Article
Chemistry, Physical
Nathan J. Szymanski, Zhengyan Lun, Jue Liu, Ethan C. Self, Christopher J. Bartel, Jagjit Nanda, Bin Ouyang, Gerbrand Ceder
Summary: Pair distribution function (PDF) analysis is a powerful technique for characterizing short-range order (SRO) in disordered materials. This study outlines an approach to model SRO using first-principles calculations based on the cluster-expansion formalism and validates it on neutron scattering data from two disordered rocksalt oxyfluorides. The results demonstrate the importance of considering local variations in site occupancies and bond lengths in accurately interpreting experimental PDF data.
CHEMISTRY OF MATERIALS
(2023)
Article
Materials Science, Multidisciplinary
N. Qureshi, H. E. Fischer, S. X. M. Riberolles, T. C. Hansen, M. Ciomaga Hatnean, O. A. Petrenko
Summary: In this study, we investigate the short-range magnetic spin correlations in two compounds of rare-earth strontium oxides using total-scattering powder neutron diffraction, reverse Monte Carlo simulations, and magnetic pair-distribution function analysis. The compounds exhibit a distorted honeycomb lattice, leading to significant geometrical frustration due to antiferromagnetic exchange between magnetic ions. The results demonstrate the ordering of the short-range spin correlations above the respective Néel temperatures, indicating the dominance of nearest and next-nearest interactions.
Article
Materials Science, Ceramics
R. Toyoda, K. Usui, T. Hirota, K. Kimura, Y. Onodera, M. R. Cicconi, R. Belli, M. Brehl, J. Lubauer, U. Lohbauer, H. Tajiri, K. Ikeda, T. Hayakawa, D. de Ligny, S. Kohara, K. Hayashi
Summary: A structural model of ZrO2-doped Li2O-SiO2-based multi-component glass was constructed using the MD-RMC method, based on X-ray and neutron scattering data. Local structural information around Zr was successfully extracted from the model. The presence of edge-sharing structural units around Zr-O and Li-O polyhedra resulted in a densely packed configuration of O atoms.
JOURNAL OF NON-CRYSTALLINE SOLIDS
(2023)
Article
Physics, Condensed Matter
Yinze Qin, Shidong Zhang, Sijie Zhang, Matthew G. Tucker, David A. Keen, Guanqun Cai, Anthony E. Phillips, Martin T. Dove
Summary: We report a study on the orientational order and phase transitions in crystalline deuterated methane using neutron total scattering and the reverse Monte Carlo method. The results show that this approach provides more accurate information than fitting the bond orientational distribution function (ODF) to diffraction data, and is suitable for studying orientationally-disordered crystals.
JOURNAL OF PHYSICS-CONDENSED MATTER
(2022)
Article
Chemistry, Multidisciplinary
Zhu-Lin Xie, Xiaolin Liu, Andrew J. S. Valentine, Vincent M. Lynch, David M. Tiede, Xiaosong Li, Karen L. Mulfort
Summary: High-energy X-ray scattering and pair distribution function analysis is a powerful method for detecting the structure of molecular complexes in solution, revealing pairwise distances in local coordination spheres of metal centers and metal...metal distances. Comparing metal...metal distances detected in solution with crystal structure and molecular models can confirm unique distortions to metal bridging ligands in the solid state. This work demonstrates the potential for observing sub-angstrom conformational differences by comparing solution and solid-state structures directly.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Nanoscience & Nanotechnology
Loku Singgappulige Rosantha Kumara, Okkyun Seo, Jaemyung Kim, Fenglong Wang, Yanna Chen, Ibrahima Gueye, Chulho Song, Koji Ohara, Kohei Kusada, Hiroshi Kitagawa, Osami Sakata
Summary: Solid-solution alloy nanoparticles consisting of a noble metal and a transition metal were studied for their crystal structures using high-energy X-ray diffraction and the reverse Monte Carlo method. The results showed that these nanoparticles have highly disordered spherical configurations with random mixing of copper and iridium atoms. The local structures of the nanoparticles were investigated using persistence diagrams and bond orientational orders, providing evidence for the presence of active sites on the nanoparticle surface and enhancing the oxygen-evolution reaction.
ACS APPLIED NANO MATERIALS
(2023)
Article
Physics, Condensed Matter
Shidong Zhang, Yinze Qin, Sijie Zhang, Min Gao, Matthew G. Tucker, David A. Keen, Guanqun Cai, Anthony E. Phillips, Martin T. Dove
Summary: The orientational disorder in crystalline sulfur hexafluoride (SF6) has been studied using neutron total scattering and the reverse Monte Carlo method. Analysis of the atomic configurations and distributions of F-F distances provide insights into the extent of disorder and correlations between neighbouring molecules.
JOURNAL OF PHYSICS-CONDENSED MATTER
(2022)
Article
Biochemistry & Molecular Biology
Fernando T. Tanouye, Jozismar R. Alves, Francesco Spinozzi, Rosangela Itri
Summary: In this study, protein interactions were investigated using in-solution small angle X-Ray scattering (SAXS) experiments and Monte Carlo (MC) simulations under different conditions. The analysis of experimental data using the HSDY/RPA model combined with MC simulations showed limitations in describing the protein-protein pair potential for highly concentrated systems at low ionic strength. SAXS/MC results revealed that lysozyme concentrations between 2 and 20 mg/mL exhibited similar protein-protein pair potentials, with a surface net charge of around 7 e, protein diameter of 28 Å, attractive well potential decay range of 3 Å, and a depth varying from 1 to 5 kBT depending on temperature and salt addition. Additionally, a novel method combining SAXS with MC simulations was proposed to overcome the limitations of closure relationships in analyzing interacting protein SAXS data.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Materials Science, Multidisciplinary
Tom Vieijra, Jutho Haegeman, Frank Verstraete, Laurens Vanderstraeten
Summary: The study introduces a new sampling algorithm for generating independent samples from PEPS, bypassing issues related to autocorrelation times and dependent samples in traditional algorithms. By introducing an auxiliary probability distribution and combining it with importance sampling, accurate evaluation of expectation values is achieved.
Review
Chemistry, Multidisciplinary
He Zhu, Yalan Huang, Jincan Ren, Binghao Zhang, Yubin Ke, Alex K. -Y. Jen, Qiang Zhang, Xun-Li Wang, Qi Liu
Summary: The correlation between structure and function is crucial in materials science and engineering. Modern functional materials often exhibit inhomogeneities at the atomic level, giving them unique properties related to electrons, phonons, and magnetic moments. The pair distribution function (PDF) technique has emerged as a powerful tool for detecting local structure away from average in functional materials, with the advancements in crystallographic techniques and the availability of synchrotron X-rays, spallation neutrons, and advanced computing power.
Article
Materials Science, Multidisciplinary
Inga Pudza, Andris Anspoks, Giuliana Aquilanti, Alexei Kuzmin
Summary: The effect of tungsten substitution with molybdenum on the structure of CuMo1_xWxO4 solid solutions was studied. It was found that the structure is mainly determined by the tungsten-related sublattice, while molybdenum atoms adapt to a locally distorted environment.
MATERIALS RESEARCH BULLETIN
(2022)
Article
Materials Science, Multidisciplinary
Magnus M. Nygard, Oystein S. Fjellvag, Magnus H. Sorby, Kouji Sakaki, Kazutaka Ikeda, Jeff Armstrong, Ponniah Vajeeston, Wojciech A. Slawinski, Hyunjeong Kim, Akihiko Machida, Yumiko Nakamura, Bjorn C. Hauback
Summary: The study investigated the local structure in TiVCrNbDx to explore how to destabilize the remaining sites with respect to hydrogen/deuterium occupation. The analysis revealed a body-centred tetragonal structure for partially desorbed deuteride (x = 2.2), with a higher portion of occupied sites with low valence-electron concentration. Further strategies for destabilization of the hydride were motivated based on these observations.
Article
Chemistry, Physical
Vera P. Pakharukova, Dmitriy A. Yatsenko, Evgeny Yu Gerasimov, Evgeniya N. Vlasova, Galina A. Bukhtiyarova, Sergey Tsybulya
Summary: Total X-ray scattering and atomic pair distribution analysis were used to study the structure of anisotropic two-dimensional MoS2 nanoparticles in MoS2/Al2O3 catalysts. PDF analysis not only helped determine atomic ordering, but also assess the geometry and size of the nanoparticles. Discrete atomistic modeling was used in refinement of PDFs to account for finite size and shape effects, revealing that MoS2 slab length was smaller than values obtained from high-resolution TEM data due to defectiveness and multi-domain structure of the nanoparticles. The study also suggested that increasing the heat treatment temperature of oxide precursors decreased deformation of MoS2 nanoparticles in sulfided catalysts.
COLLOID AND INTERFACE SCIENCE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Masatsugu Yoshimoto, Takuya Kimura, Atsushi Sakuda, Chie Hotehama, Yuji Shiramata, Akitoshi Hayashi, Kazuhiko Omote
Summary: Solid electrolytes, such as sulfide glasses, are crucial for the practical application of all-solid-state Li-ion batteries. This study evaluated the local structure of a Li3PS4 glass and found that the structure of the PS4 anion remains unchanged during crystallization, but the correlation of inter-PS4 distances changes. Additionally, the study revealed that the distribution of Li ions is wider in the glassy state and narrows during crystallization.
SOLID STATE IONICS
(2023)
Article
Materials Science, Ceramics
Shinya Hosokawa, Jean-Francois Berar, Nathalie Boudet, Wolf-Christian Pilgrim, Laszlo Pusztai, Satoshi Hiroi, Shinji Kohara, Hidemi Kato, Henry E. Fischer, Anita Zeidler
Summary: By comparing the structures of Pd40Cu40P20 metallic glass and Pd40Cu40P20 alloy glass, key factors influencing the GFA characteristics were identified.
JOURNAL OF NON-CRYSTALLINE SOLIDS
(2021)
Article
Geochemistry & Geophysics
Hui Zhang, Piotr Zarzycki, Benjamin Gilbert, Jillian F. Banfield
Summary: The study using low-dose high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) revealed the polytypic structures of lizardite and amesite, identifying both long-term non-standard and short-term ordered polytypes, and revealing some atomic combinations. This method provides a new way to study beam-sensitive minerals and has the potential to resolve the structural details of more abundant but less ordered minerals.
AMERICAN MINERALOGIST
(2022)
Article
Instruments & Instrumentation
Joseph B. Nichols, Marco Voltolini, Benjamin Gilbert, Alastair A. MacDowell, Michael W. Czabaj
Summary: Beamline 11.3.1 at the Advanced Light Source is equipped with a new full-field, nanoscale transmission x-ray microscope for imaging composite and porous materials. The microscope has high resolutions and is used in tandem with a phase-type zone plate magnifying objective.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2022)
Review
Multidisciplinary Sciences
Pupa U. P. A. Gilbert, Kristin D. Bergmann, Nicholas Boekelheide, Sylvie Tambutte, Tali Mass, Frederic Marin, Jess F. Adkins, Jonathan Erez, Benjamin Gilbert, Vanessa Knutson, Marjorie Cantine, Javier Ortega Hernandez, Andrew H. Knoll
Summary: Calcium carbonate biomineralizing organisms have had significant roles in the history of life and the global carbon cycle. By integrating mechanisms of CaCO3 skeleton formation with evolutionary history, omics, and isotopic data, a model for CaCO3 biomineralization applicable to all phyla is proposed, aiding in understanding the environmental sensitivity of marine calcifiers and their resilience in 21st century acidifying oceans.
Article
Multidisciplinary Sciences
Michael L. Whittaker, David Ren, Colin Ophus, Yugang Zhang, Laura Waller, Benjamin Gilbert, Jillian F. Banfield
Summary: This study investigates the visualization of hydrated interfaces and proposes a new method for direct imaging the electric double layer (EDL) structure of layered minerals. The presence of hydrated ion waves and their interactions with minerals are revealed. This research is of great significance for understanding geochemical processes and mineral behavior.
NATURE COMMUNICATIONS
(2022)
Article
Physics, Condensed Matter
Nigel Lee En Hew, Dino Spagnoli, Lorenzo Faraone
Summary: The study uses density functional theory to investigate the core structure energetics of partial dislocations in HgTe, CdTe, and Hg0.7Cd0.3Te, and the density of states of these dislocations in CdTe and Hg0.7Cd0.3Te. Stable dislocation pairs were found for both 30 degrees and 90 degrees partial dislocations, with energetically favorable segregation of Hg atoms to the dislocation cores in Hg0.7Cd0.3Te. The 90 degrees partial dislocations were found to introduce more mid-gap states compared to the 30 degrees partial dislocations in CdTe and Hg0.7Cd0.3Te, suggesting a greater detrimental effect on the material's optoelectronic properties.
PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS
(2022)
Article
Geochemistry & Geophysics
Lucien Stolze, Bhavna Arora, Dipankar Dwivedi, Carl Steefel, Zhi Li, Sergio Carrero, Benjamin Gilbert, Peter Nico, Markus Bill
Summary: The weathering of shale plays a crucial role in the hydrochemical fluxes to river systems and has a significant impact on global biogeochemical cycles. However, there is still a lack of quantitative understanding regarding shale weathering and its influence on these cycles due to the complex interactions between hydrological, biogeochemical, and physical processes. In this study, a novel modeling approach was developed to quantitatively interpret the long-term chemical weathering of shale and its effect on geochemical conditions. The model considers multiple processes involved in shale weathering, including infiltration of meteoric water, mineral-water interactions, microbial oxidation of organic matter, mineral reactions-induced evolution of porosity, and gas exchange between the subsurface and atmosphere.
GEOCHIMICA ET COSMOCHIMICA ACTA
(2023)
Article
Geochemistry & Geophysics
Sergio Carrero, Sarah P. Slotznick, Sirine C. Fakra, M. Cole Sitar, Sharon E. Bone, Jeffrey L. Mauk, Andrew H. Manning, Nicholas L. Swanson-Hysell, Kenneth H. Williams, Jillian F. Banfield, Benjamin Gilbert
Summary: The oxidative weathering of sulfidic rock has significant impacts on watersheds through the release of acidity and metals. By utilizing a combination of mineralogical and geochemical techniques, researchers were able to develop a weathering model that accurately predicts the pathways and controls of mineral transformation. This study provides valuable insights into the weathering processes of sulfidic sedimentary rocks and their implications for water quality.
GEOCHIMICA ET COSMOCHIMICA ACTA
(2023)
Article
Engineering, Geological
Mengsu Hu, Carl Steefel, Jonny Rutqvist, Benjamin Gilbert
Summary: In this study, the impacts of geometry and temperature on pressure solution in natural salt rock are investigated through microscale modeling. It is found that geometric features dominate stress distribution and thus control the occurrence of pressure solution.
ROCK MECHANICS AND ROCK ENGINEERING
(2023)
Article
Nanoscience & Nanotechnology
Evgeny Ogorodnik, Kang-Hsin Wang, Benjamin Gilbert, Fu-tong Liu, Dominik R. Haudenschild, Gang-yu Liu
Summary: High aspect ratio nanomaterials, such as nanowires, have unique properties and diverse applications due to their geometry and small diameters. This study investigates the interactions between living cells and silver nanowires (AgNWs) using high-resolution laser scanning confocal microscopy. The results reveal direct piercing of AgNWs into cells, frustrated phagocytosis, and failed attempts by AgNWs to pierce due to membrane wrapping. The comprehensive understanding of AgNW-cell interactions is crucial for nanotoxicity research and the development of preventive measures.
ACS APPLIED NANO MATERIALS
(2023)
Article
Chemistry, Medicinal
Chunhui Li, Benjamin Gilbert, Steven Farrell, Piotr Zarzycki
Summary: Molecular dynamics simulation is crucial for understanding the behavior and phases of atoms and molecules. However, long simulation times are needed to obtain convergence, resulting in high computational costs. In this study, a point cloud-based deep learning strategy was developed to rapidly predict the structural properties of liquids from a single molecular configuration. The approach was successfully tested on different liquids under various pressure and temperature conditions.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Materials Science, Multidisciplinary
Mehdi Eskandari-Ghadi, Seiji Nakagawa, Hang Deng, Steve Pride, Benjamin Gilbert, Yida Zhang
Summary: This paper develops a surface-force-based fracture theory to explain the multi-stage characteristics of subcritical crack growth (SCG) in brittle solids. By integrating surface force models and fluid transport models, a numerical model based on SFFT is developed and validated by experimental data. The results show that the shape and changes of SCG curves critically depend on the assumed transport models.
JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS
(2023)
Article
Multidisciplinary Sciences
Benjamin Gilbert, Sergio Carrero, Wenming Dong, Claresta Joe-Wong, Bhavna Arora, Patricia Fox, Peter Nico, Kenneth H. Williams
Summary: Daily measurements of river concentration of thorium (Th) provide novel insights into bedrock fracture processes. River Th concentrations show distinct patterns, uncorrelated with precipitation or atmospheric deposition. There is a weak statistical correlation between Th and seismic motion caused by distant earthquakes.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Michael L. Whittaker, Mohammad Shoaib, Laura N. Lammers, Yugang Zhang, Christophe Tournassat, Benjamin Gilbert
Summary: This study investigates the structure and swelling pressure of swelling clay minerals and finds that clay swelling is osmotic swelling, with attractive osmotic pressure at high clay activities. The hyperdiffusive layer dynamics are driven by hydration-mediated interfacial charge.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
J. Collen Aldum, Isabelle Jones, Paul R. McGonigal, Dino Spagnoli, Nicholas D. Stapleton, Gemma F. Turner, Stephen A. Moggach
Summary: The crystal structure of a new polymorph of methanol (the epsilon polymorph) has been determined at 5.09 GPa using single crystal X-ray diffraction. The polymorph exhibits a 4-membered hydrogen bonded ring structure, which has never been observed before in any crystal structure of methanol. Interestingly, the presence of another crystallite led to the serendipitous seeding of the epsilon phase, enabling crystallization at conditions 2 GPa lower than previously reported.
Article
Chemistry, Physical
Vivien Ramothe, Laurent Charlet, Benjamin Gilbert, Pauline Simonnin, Michel Sassi, Kevin M. Rosso
Summary: Using density functional theory (DFT) calculations, the process of H2S sorption and reaction on Ag(100) surfaces relevant to Ag nanowires (AgNWs) was examined, revealing the mechanism of dissociative chemisorption and the influence of complex environmental media.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)