Molecular dynamics articles within Nature

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  • Article |

    Machine learning models enable atomistic simulations of phase transitions in amorphous silicon, predict electronic fingerprints, and show that the pressure-induced crystallization occurs over three distinct stages.

    • Volker L. Deringer
    • , Noam Bernstein
    •  & Stephen R. Elliott

  • News & Views |

    A combination of vibrational spectroscopy and molecular calculations reveals that only the surface layer of water at the interface with air has a distinctly different structure from the bulk liquid. See Letter p.192

    • Pavel Jungwirth

  • Letter |

    The mechanism of action of general anaesthetics is poorly understood, although there is some evidence that their principal protein targets are pentameric ligand-gated ion channels (pLGICs). Here, the X-ray crystal structures of propofol and desflurane bound to a bacterial homologue of the pLGIC family are solved. The structures reveal a common binding site for these two anaesthetics in the upper part of the transmembrane domain of each protomer.

    • Hugues Nury
    • , Catherine Van Renterghem
    •  & Pierre-Jean Corringer

  • Letter |

    The X-ray crystal structure of the human β2 adrenergic receptor, a G-protein-coupled receptor (GPCR), covalently bound to a small-molecule agonist is solved. Comparison of this structure with structures of this GPCR in an inactive state and in an antibody-stabilized active state reveals how binding events at both the extracellular and intracellular surfaces stabilize the active conformation of the receptor. Molecular dynamics simulations suggest that the agonist-bound active state spontaneously relaxes to an inactive-like state in the absence of a G protein.

    • Daniel M. Rosenbaum
    • , Cheng Zhang
    •  & Brian K. Kobilka

  • Letter |

    Attosecond (10−18 s) laser pulses make it possible to peer into the inner workings of atoms and molecules on the electronic timescale — phenomena in solids have already been investigated in this way. Here, an attosecond pump–probe experiment is reported that investigates the ionization and dissociation of hydrogen molecules, illustrating that attosecond techniques can also help explore the prompt charge redistribution and charge localization that accompany photoexcitation processes in molecular systems.

    • G. Sansone
    • , F. Kelkensberg
    •  & M. J. J. Vrakking

  • Letter |

    Stop codons in messenger RNA define when a protein sequence has been completely synthesized; such codons bind release factors (RFs), which cause the newly made protein to be released. Structures of RFs alone and in combination with the ribosome have been reported, but the energetics of the reaction in the presence of codons had not been determined. Here, molecular dynamics simulations of 14 termination complexes are used to define how termination is achieved and how the RFs distinguish different sequences.

    • Johan Sund
    • , Martin Andér
    •  & Johan Åqvist

  • News & Views |

    Catastrophic breakage of brittle materials such as ceramics is usually triggered by the rapid spreading of cracks. Computer simulations have now cracked the three-dimensional details of this process.

    • Markus J. Buehler
    •  & Zhiping Xu

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