Atomistic models articles within Nature Communications

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  • Article
    | Open Access

    Modelling of acidic zeolites, one of the key industrial catalysts, under realistic operating conditions is currently limited to specific cases. Here, the authors report a machine learning framework allowing for accurate high-throughput modelling.

    • Andreas Erlebach
    • , Martin Šípka
    •  & Lukáš Grajciar

  • Article
    | Open Access

    Adupa et al show how the anti-amyloidogenic molecular chaperone DNAJB6 adopts three conformational states that determine the accessibility of its substrate binding domain. In all states, interactions with HSP70 are shielded, suggesting that functional interactions only may occur upon substrate binding.

    • Vasista Adupa
    • , Elizaveta Ustyantseva
    •  & Patrick R. Onck

  • Article
    | Open Access

    CALF-20 MOF is considered a benchmark sorbent for industrial scale CO2 capture. Here authors use machine-learning potential simulations to show that CALF-20 exhibits anomalous structural responses to temperature and strain stimuli, with potential applications in mechanical/thermal sensing.

    • Dong Fan
    • , Supriyo Naskar
    •  & Guillaume Maurin

  • Article
    | Open Access

    The hydration of tricalcium aluminate is an important initial step in the structural build-up of Portland cement. Here the authors use ab initio and accelerated dynamics to describe the reactions and dynamics of this process at the molecular level.

    • Xing Ming
    • , Wen Si
    •  & Zongjin Li

  • Article
    | Open Access

    By performing long ab initio molecular dynamics simulations of water under external electric fields, for up to 500 picoseconds, the authors identify a transition to a ferroelectric amorphous phase at ambient conditions.

    • Giuseppe Cassone
    •  & Fausto Martelli

  • Article
    | Open Access

    Magnitude of the ideal strength achievable in experiments for metals remains to be known. Here, the authors show that the spall strength of Cu50Zr50 amorphous alloy exceeds the E/10 limit at extreme strain rates, showing the void nucleation and growth as the primary failure mechanism.

    • Wenqing Zhu
    • , Zhi Li
    •  & Xiaoding Wei

  • Article
    | Open Access

    Alternatives to lithium-ion electrochemistry present challenges due to undesirable phenomena at the electrode-electrolyte interface. Through simulations, the authors find that the performance of a calcium-based electrolyte is driven entirely by molecular-scale processes within approximately 1 nm of the electrode.

    • Ana Sanz Matias
    • , Fabrice Roncoroni
    •  & David Prendergast

  • Article
    | Open Access

    Little is known about how the states in glass are connected to each other. Here, the authors perform molecular dynamics simulation of relaxation in a prototypical metallic glass to show that the energy barriers separating these states are very low, and even be overcome by quantum fluctuations.

    • Leo Zella
    • , Jaeyun Moon
    •  & Takeshi Egami

  • Article
    | Open Access

    Conduction in solid-state electrolytes composed of monatomic ions is found to be analogous to the paddle-wheel mechanism in molecular solid electrolytes, facilitated by rotational motion of lone pair electrons, helping unify understanding of mechanisms.

    • Harender S. Dhattarwal
    • , Rahul Somni
    •  & Richard C. Remsing

  • Article
    | Open Access

    It is still challenging to study the atomistic mechanism of inelastic deformation in metallic glasses owing to their amorphous structure. Here, the authors report an anomalous temperature dependence of the onset of plasticity in metallic glasses at low temperature.

    • Yifan Wang
    • , Jing Liu
    •  & Wei Cai

  • Article
    | Open Access

    Ultrafast spectroscopy enables characterization and control of non-equilibrium states. Here the authors introduce a stochastic thermodynamics approach to calculate entropy production in a material under ultrafast excitation, using ionic displacement data from time-resolved X-ray scattering experiments.

    • Lorenzo Caprini
    • , Hartmut Löwen
    •  & R. Matthias Geilhufe

  • Article
    | Open Access

    The nucleation of calcium silicate hydrate is a crucial step in cement hydration, but is still a poorly understood process. Here the authors use atomistic simulations to study primary particles and their aggregation, revealing a potential C-S-H “basic building block”.

    • Xabier M. Aretxabaleta
    • , Jon López-Zorrilla
    •  & Hegoi Manzano

  • Article
    | Open Access

    Spin defects in semiconductors are promising for quantum technologies but understanding of defect formation processes in experiment remains incomplete. Here the authors present a computational protocol to study the formation of spin defects at the atomic scale and apply it to the divacancy defect in SiC.

    • Cunzhi Zhang
    • , Francois Gygi
    •  & Giulia Galli

  • Article
    | Open Access

    Level of atomic disorder in materials is critical to understanding the effect of local structure on materials properties. Here the authors present a workflow combining structure-aware graph neural networks and physics-inspired order parameter to characterize structural disorder on a per atom basis.

    • James Chapman
    • , Tim Hsu
    •  & Brandon C. Wood

  • Article
    | Open Access

    In solid-state lithium metal batteries, the crystallization of Li-ions deposited at interfaces remains unclear. Here, authors use molecular dynamics simulations to reveal lithium crystallization pathways and energy barriers, guiding improved interfacial engineering and accelerated crystal growth.

    • Menghao Yang
    • , Yunsheng Liu
    •  & Yifei Mo

  • Article
    | Open Access

    It remains challenging to understand the relation between mechanical properties of glasses close to the yielding point and plastic behaviors at microscales. Wu et al. examine the plasticity using topological properties of the vibrational modes and identify a correlation between defects and plastic events.

    • Zhen Wei Wu
    • , Yixiao Chen
    •  & Limei Xu

  • Article
    | Open Access

    Recent experiments reveal undetermined crystalline phases near the melting minimum region in lithium. Here, the authors use a crystal structure search method combined with machine learning to explore the energy landscape of lithium and predict complex crystal structures.

    • Xiaoyang Wang
    • , Zhenyu Wang
    •  & Yanming Ma

  • Article
    | Open Access

    Luminescent metal-organic frameworks are an emerging class of optical sensors capable to capture and detect toxic gases. Here, the authors report the incorporation of synergistic binding sites in MOF-808 through post-synthetic modification with copper for optical sensing of NO2 at remarkably low concentrations.

    • Isabel del Castillo-Velilla
    • , Ahmad Sousaraei
    •  & Ana E. Platero-Prats

  • Article
    | Open Access

    Lithium graphite intercalation compounds are important for developing Li-ion batteries. Here authors simulate the interaction of high energy X-rays with Li ions intercalated in graphite and show that Li ions behave in an unexpected non-Gaussian fashion, leading to increasingly chaotic behaviour as the ion concentration reduces.

    • Sasawat Jamnuch
    •  & Tod A. Pascal

  • Article
    | Open Access

    The paper presents a method that allows scaling machine learning interatomic potentials to extremely large systems, while at the same time retaining the remarkable accuracy and learning efficiency of deep equivariant models. This is obtained with an E(3)- equivariant neural network architecture that combines the high accuracy of equivariant neural networks with the scalability of local methods.

    • Albert Musaelian
    • , Simon Batzner
    •  & Boris Kozinsky

  • Article
    | Open Access

    Many ceramics and semiconductors are brittle at moderate temperatures, which can be a concern for applications. Here authors present a theoretical approach based on local misfit energy to accurately derive the Peierls stress and model the dislocation process in SrTiO3, which provides insights into the plasticity around room temperature.

    • Yi Li
    • , Xiangyang Liu
    •  & Chunlei Wan

  • Article
    | Open Access

    Improving the efficiency of light-driven molecular rotary motors is a challenging task. Here, the authors combine theoretical modeling, synthesis and spectroscopy to prepare a prototype molecular motor capable of avoiding inefficient thermally activated motion; thus offering prospects to implement a 2-stroke photon-only molecular motor.

    • Michael Filatov(Gulak)
    • , Marco Paolino
    •  & Massimo Olivucci

  • Article
    | Open Access

    Predicting structures and stabilities of solid-solid interfaces presents an ongoing and increasingly important challenge for development of new technologies. Here authors report an unconstrained and generally applicable non-periodic screening method for systematic exploration of material´s interfaces.

    • Giovanni Di Liberto
    • , Ángel Morales-García
    •  & Stefan T. Bromley

  • Article
    | Open Access

    Evaporation and crystal growth occur at different rates on different surfaces. Here authors show dissociative evaporation from ZnO (0001) polar surfaces is accelerated by the formation of a Zn-deficient quasi-liquid layer derived from the formation and inward diffusion of Zn vacancies that stabilize the polar surface.

    • Zhen Wang
    • , Jinho Byun
    •  & Sang Ho Oh

  • Article
    | Open Access

    The effect of aliovalent doping on grain boundary is not yet fully understood at the atomic level. Here, the authors report grain boundary structural transformation in α-Al2O3 is induced by co-segregation of multiple dopants using atomic-resolution electron microscopy and theoretical calculations.

    • Toshihiro Futazuka
    • , Ryo Ishikawa
    •  & Yuichi Ikuhara

  • Article
    | Open Access

    The oxygen-redox mechanism in lithium-rich disordered rocksalt cathode materials is still not well understood. Here, the authors show that in Li2MnO2F, molecular oxygen forms in the bulk during charge and is re-incorporated into the structure as oxygen anions on discharge, but this process is associated with irreversible Mn migration, causing voltage hysteresis.

    • Kit McColl
    • , Robert A. House
    •  & M. Saiful Islam

  • Article
    | Open Access

    Most machine-learning force fields dismiss long-range interactions. Here the authors demonstrate the BIGDML approach for building materials’ potential energy surfaces that enables a broad range of materials simulations within accuracies better than 1 meV/atom using just 10–200 structures for training.

    • Huziel E. Sauceda
    • , Luis E. Gálvez-González
    •  & Alexandre Tkatchenko

  • Article
    | Open Access

    The sheer number of parameters in deep learning makes the physical interpretation of failure predictions in glasses challenging. Here the authors use Grad-CAM to reveal the role of topological defects and local potential energies in failure predictions.

    • Francesc Font-Clos
    • , Marco Zanchi
    •  & Stefano Zapperi

  • Article
    | Open Access

    The current study explores by ab-initio molecular dynamics simuations the concept of hypervalency in amorphous chalcogenide materials, from which a unified conceptual framework for understanding chemical bonding, microscopic structures, and structure-property relationships is established.

    • T. H. Lee
    •  & S. R. Elliott

  • Article
    | Open Access

    Understanding incipient plasticity has been experimentally limited by spatial and temporal resolution. Here the authors report ultra-fast, in situ electron diffraction measurement of dislocation defect dynamics in the early stage of plastic deformation in Al under laser-driven compression.

    • Mianzhen Mo
    • , Minxue Tang
    •  & Siegfried Glenzer

  • Article
    | Open Access

    High pressure can modify the chemical properties of the elements, giving rise to exotic bonding. Here the authors report the prediction of a nitrogen-rich iodine nitride compound IN6 where the iodine atom has an unusual twelve-fold coordination, stable above 100 GPa.

    • Yan Liu
    • , Rui Wang
    •  & Tian Cui

  • Article
    | Open Access

    Reinforcement learning algorithms are emerging as powerful machine learning approaches. This paper introduces a novel machine-learning approach for learning in continuous action space and applies this strategy to the generation of high dimensional potential models for a wide variety of materials.

    • Sukriti Manna
    • , Troy D. Loeffler
    •  & Subramanian K. R. S. Sankaranarayanan

  • Article
    | Open Access

    The origins of deformation twins in Mg have remained unclear in the past. Here the authors, by combining in situ experimental observations and atomistic simulations, capture the rapid twinning phenomena in Mg crystals and show that twinning occurs through pure atomic shuffle.

    • Lin Jiang
    • , Mingyu Gong
    •  & Julie M. Schoenung

  • Article
    | Open Access

    In-plane polarized ferroelectric thin films typically exhibit complicated multidomain states, not desirable for optoelectronic device performance. Here, the authors combine interfacial symmetry engineering and anisotropic strain to design single-domain in-plane polarized ferroelectric BaTiO3 films.

    • J. W. Lee
    • , K. Eom
    •  & C. B. Eom

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