Coarse-grained models articles within Nature Communications

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  • Article
    | Open Access

    Authors predict polar Bloch points with negative capacitance in tensile-strained ultrathin ferroelectric PbTiO3 film by phase-field simulations, observing their polarization structures by scanning transmission electron microscopic imaging.

    • Yu-Jia Wang
    • , Yan-Peng Feng
    •  & Xiu-Liang Ma

  • Article
    | Open Access

    The self-assembly of nanocrystals into checkerboard lattice patterns is difficult to control. Here, the authors investigate the formation of such patterns from hydrophilic/hydrophobic bifunctionalized Ag nanocubes and use multiscale simulations to understand the effects of physical forces.

    • Yufei Wang
    • , Yilong Zhou
    •  & Andrea R. Tao

  • Article
    | Open Access

    The self-assembly process of DNA nanostructures is still not well understood, especially for DNA origami. Here, the authors present a mesoscopic model that uses a switchable force field to capture the mechanical behavior of single- and double-stranded DNA motifs and transition between them, allowing access to the long assembly timescales of DNA origami up to several kilobases in size.

    • Marcello DeLuca
    • , Daniel Duke
    •  & Gaurav Arya

  • Article
    | Open Access

    Computational frameworks for structural dynamics are in continuous need of being developed. Here the authors present a a computational framework based on Langevin dynamics to analyze structural dynamics and reconfiguration of DNA assemblies, offering a rational method for designing responsive and reconfigurable DNA machines

    • Jae Young Lee
    • , Heeyuen Koh
    •  & Do-Nyun Kim

  • Article
    | Open Access

    Thermodynamics predicts equilibrium crystal structures and kinetics discover the pathway to form them. The authors investigate the interplay of thermodynamics and kinetics in the formation of colloidal clusters and reveal a bifurcation at an early stage of the crystallization process.

    • Chrameh Fru Mbah
    • , Junwei Wang
    •  & Michael Engel

  • 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

    As lamellar materials, smectics exhibit both liquid and solid characteristics, making them difficult to model at the mesoscale. Paget et al. propose a complex tensor order parameter that reflects the smectic symmetries, capable of describing complex defects including dislocations and disclinations.

    • Jack Paget
    • , Marco G. Mazza
    •  & Tyler N. Shendruk

  • Article
    | Open Access

    The dynamic structure of supramolecular polymers is challenging to determine both in experiments and in simulations. Here the authors use coarse-grained molecular models to provide a comprehensive analysis of the molecular communication in these complex molecular systems.

    • Martina Crippa
    • , Claudio Perego
    •  & Giovanni M. Pavan

  • Article
    | Open Access

    Direct laser writing is an effective technique for fabrication of complex 3D polymer networks using ultrashort laser pulses but to date it is difficult to obtain a time-resolved microscopic picture of the printing process in operando. Here, the use molecular dynamics simulation to model direct laser writing and investigate the effect of writing condition and aspect ratio on the mechanical properties of the printed polymer network.

    • Elaheh Sedghamiz
    • , Modan Liu
    •  & Wolfgang Wenzel

  • Article
    | Open Access

    Ordinary cracks in bulk materials feature square root singular deformation fields near their edge. Here, the authors show that rupture fronts propagating along frictional interfaces, while resembling ordinary cracks in some respects, feature edge sigularity that differs from the conventional square root one.

    • Efim A. Brener
    •  & Eran Bouchbinder

  • Article
    | Open Access

    Identifying optimal materials in multiobjective optimization problems represents a challenge for new materials design approaches. Here the authors develop an active-learning algorithm to optimize the Pareto-optimal solutions successfully applied to the in silico polymer design for a dispersant-based application.

    • Kevin Maik Jablonka
    • , Giriprasad Melpatti Jothiappan
    •  & Brian Yoo

  • Article
    | Open Access

    Despite the fact that layered materials are often employed as lubricants, many of the underlying mechanisms are still controversial. Here the authors present a fundamental model for describing friction on atomically thin sheets that reveals the dynamics of strengthening and layer-number dependence of the friction.

    • David Andersson
    •  & Astrid S. de Wijn

  • Article
    | Open Access

    Glass transition in soft materials can be affected by the topology of constituent particles, but the detail remains elusive. Here, Smrek et al. show that the interplay between circular topology of ring polymers and their active segments generates a new state of matter, namely active topological glass.

    • Jan Smrek
    • , Iurii Chubak
    •  & Kurt Kremer

  • Article
    | Open Access

    Current interest in tuning optoelectronic properties of two-dimensional materials focuses on phase and strain engineering. Here the authors propose a novel approach to achieve nanoscale composition/strain patterns and 3D objects with tailored properties using 2D transition metal dicalchogenide alloys.

    • Joel Berry
    • , Simeon Ristić
    •  & David J. Srolovitz

  • Article
    | Open Access

    Predicting alloy microstructures with parameter-free theoretical schemes remains a challenge. Here the authors derive a general phase field approach to reproduce the microstructural evolution of a nickel-aluminum alloy as a function of composition only and without empirical thermodynamic parameters.

    • Swastibrata Bhattacharyya
    • , Ryoji Sahara
    •  & Kaoru Ohno

  • Article
    | Open Access

    Solutions of proteins and other molecules can host puzzling, solute-rich inclusions of mesoscopic dimensions. Here the authors report a mechanism by which mesoscopic clusters can nucleate and ripen, requiring that the solute form long-lived complexes, with implications for biologically and industrially relevant systems.

    • Ho Yin Chan
    •  & Vassiliy Lubchenko

  • Article
    | Open Access

    A computationally efficient description of ice-water systems at the mesoscopic scale is challenging due to system size and timescale limitations. Here the authors develop a machine-learned coarse-grained water model to elucidate the ice nucleation process much more efficiently than previous models.

    • Henry Chan
    • , Mathew J. Cherukara
    •  & Subramanian K. R. S. Sankaranarayanan

  • Article
    | Open Access

    Gels filtering particles by interactions are a goal of nanotechnology; this is difficult when particles are larger than the mesh of the gel. Here, the authors present an equilibrium mechanism where binding dynamics of crosslinks are affected by interacting particles so that particles experience enhanced diffusion.

    • Carl P. Goodrich
    • , Michael P. Brenner
    •  & Katharina Ribbeck

  • Article
    | Open Access

    Conventional grain growth models assume the velocity of a grain boundary is proportional to its curvature but cannot account for the many deviations observed experimentally. Here, the authors present a model that connects grain growth directly to the disconnection mechanism of grain boundary migration and can account for these deviations.

    • Spencer L. Thomas
    • , Kongtao Chen
    •  & David J. Srolovitz

  • Article
    | Open Access

    Flexoelectric coupling between strain gradients and polarization influences the physics of ferroelectric devices but it is difficult to directly probe its effects. Here, Li et al. use principal component analysis to compare STEM images with phase-field modeling and extract the flexoelectric contributions.

    • Q. Li
    • , C. T. Nelson
    •  & S. V. Kalinin

  • Article
    | Open Access

    Accessing the dynamics of soft self-assembled materials at high resolution is very difficult. Here the authors show atomistic and coarse-grained modelling combined with enhanced sampling to characterize the molecular mechanisms and kinetics of monomer exchange in synthetic supramolecular polymers.

    • Davide Bochicchio
    • , Matteo Salvalaglio
    •  & Giovanni M. Pavan

  • Article
    | Open Access

    A thin elastic sheet can develop wrinkles which arrange into patterns similar to those characteristic of liquid crystals. Here the authors use this analogy to propose a mapping between the elastic sheet problem and the smectic liquid crystal problem which can enable a better understanding of wrinkling.

    • Hillel Aharoni
    • , Desislava V. Todorova
    •  & Eleni Katifori

  • Article
    | Open Access

    The universality class for plastic yield in amorphous materials remains controversial. Here authors present a tensorial mesoscale model that captures both complex shear patterns and avalanche scaling behaviour, which differs from mean-field models and suggests a distinct type of critical phenomenon.

    • Zoe Budrikis
    • , David Fernandez Castellanos
    •  & Stefano Zapperi

  • Article
    | Open Access

    Determining the spatial dynamics of excited carriers will provide a more complete understanding of ultrafast carrier dynamics in materials. Using scanning ultrafast electron microscopy, Najafiet al. are able to observe the spatiotemporal dynamics of excited electron and hole carriers in silicon.

    • Ebrahim Najafi
    • , Vsevolod Ivanov
    •  & Marco Bernardi

  • Article
    | Open Access

    Computational design of functional materials with broken inversion symmetry is a complex task. Here, the authors demonstrate an approach that integrates symmetry analysis, data science methods, and density functional theory to accelerate the selection and identification process in complex oxides.

    • Prasanna V. Balachandran
    • , Joshua Young
    •  & James M. Rondinelli

  • Article
    | Open Access

    Molecular self-assembly is controlled by chemical and entropic factors, but theory has not been able to differentiate the role of each. Here, the authors unambiguously address this question for self-assembly on metal surfaces, using a new computational method that bridges coarse-grained and atomistic approaches.

    • Daniel M. Packwood
    • , Patrick Han
    •  & Taro Hitosugi

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