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Volume 3 Issue 5, May 2023

Predicting interactions at the nanoscale

The cover depicts a computer-generated graphic of a lysine-specific molecular tweezer (metallic scaffolding) binding to a 14-3-3 protein from Homo sapiens (white mass). The protein's target lysine site is indicated by the glowing region. The approach introduced by Saldinger et al. in this issue was designed to accurately predict protein–nanoparticle interactions such as the one illustrated on the cover.

See Saldinger et al.

Image: Matt Raymond, Violi Group, University of Michigan. Cover design: Alex Wing

Editorial

  • Even though Nature Computational Science is a computational-focused journal, some studies submitted to our journal might require experimental validation in order to verify the reported results and to demonstrate the usefulness of the proposed methods.

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Comment & Opinion

  • As artificial intelligence (AI) proliferates, synthetic chemistry stands to benefit from its progress. Despite hidden variables and ‘unknown unknowns’ in datasets that may impede the realization of a digital twin for the laboratory flask, there are many opportunities to leverage AI and large datasets to advance synthesis science.

    • Nicholas David
    • Wenhao Sun
    • Connor W. Coley
    Comment
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Research Highlights

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News & Views

  • An image-inspired deep-learning model is developed to generate realistic de novo protein structures and scaffolds around functional sites, which helps the search for new structures and functions in protein engineering.

    • Ava P. Amini
    • Kevin K. Yang
    News & Views
  • A computational tool based on an additive approach and linear algebra has been developed together with a fabrication strategy for the systematic exploration of rigid-deployable, compact and reconfigurable kirigami patterns.

    • Alberto Corigliano
    News & Views
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Research Briefings

  • We often encounter mental conflict in our lives. Such mental conflict has long been regarded as subjective. However, a machine learning method can be used to quantify the temporal dynamics of conflict between reward and curiosity from behavioral time-series.

    Research Briefing
  • A graph neural network — GAME-Net — has been developed to predict the adsorption energy of organic molecules on metal surfaces, which is a key descriptor of heterogeneous catalytic activity. This method allows for the study of large molecules derived from raw materials such as plastic waste, avoiding the use of costly and time-intensive first-principles simulations.

    Research Briefing
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Reviews

  • While digital twins have been recently used to represent cities and their physical structures, integrating complexity science into the digital twin approach will be key to deliver more explicable and trustworthy models and results.

    • G. Caldarelli
    • E. Arcaute
    • J. L. Fernández-Villacañas
    Perspective
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