Molecular dynamics articles within Nature Communications

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  • Article
    | Open Access

    Cis-trans lactam amide rotation is a fundamental process and its understanding might aid molecular design. Here, the authors report the synthesis and study of bicyclic lactams which undergo spin through 360 degrees as in open-chain amides, due to the occurrence of nitrogen pyramidalization.

    • Yuko Otani
    • , Xin Liu
    •  & Tomohiko Ohwada

  • 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

    Ionic liquid electrolytes can impart increased operational voltage and energy density in supercapacitors, but water may diminish performance. Here the authors show that the hydrophilicity/hydrophobicity of ionic liquids can influence electrosorption of water and ultimately the supercapacitor performance.

    • Sheng Bi
    • , Runxi Wang
    •  & Guang Feng

  • Article
    | Open Access

    Water uptake of natural polymers is accompanied by swelling and changes in the internal structure of the polymeric system but the exact mechanism of water-uptake and swelling remained unknown. Here the authors use atom-scale simulations to identify a molecular mechanism which is responsible for hysteresis in sorption-induced swelling in natural polymers.

    • Mingyang Chen
    • , Benoit Coasne
    •  & Jan Carmeliet

  • Article
    | Open Access

    Scalable graphene production from graphite via an intercalation-oxidation-reduction process is still hampered by low reproducibility and many lattice defects. Here, the authors show that reducing molecular friction by using highly crystalline graphite and mild oxidizing conditions is the key to high quality graphene.

    • Steffen Seiler
    • , Christian E. Halbig
    •  & Siegfried Eigler

  • Article
    | Open Access

    The electron affinity of liquid water is a fundamental property which has not yet been accurately measured. Here, the authors predict this property by coupling path-integral molecular dynamics with ab initio potentials and electronic structure calculations, revisiting several estimates used in the literature.

    • Alex P. Gaiduk
    • , Tuan Anh Pham
    •  & Giulia Galli

  • Article
    | Open Access

    Heterogeneous nucleation is a process that mediates the birth of many crystalline materials, but is not fully understood. Here, the authors show that the study of precritical cluster fluctuations paves new ways for the identification of polymorphism, polymorphic control and theoretical modeling.

    • Martin Fitzner
    • , Gabriele C. Sosso
    •  & Angelos Michaelides

  • Article
    | Open Access

    Local hydration structures at solid-liquid interfaces are important in catalytic, electrochemical, and biological processes. Here, the authors demonstrate atomic-scale 3D hydration structures around the boundary on a heterogeneous mineral surface using atomic force microscopy experiments and molecular dynamics simulations.

    • Kenichi Umeda
    • , Lidija Zivanovic
    •  & Hirofumi Yamada

  • Article
    | Open Access

    Clay is thought to have played a part in the origin of life. Here, the authors show that layered double hydroxides, a type of clay little studied despite its presumed prevalence on the early Earth, can facilitate the formation of small proteins.

    • Valentina Erastova
    • , Matteo T. Degiacomi
    •  & H. Chris Greenwell

  • Article
    | Open Access

    Knowledge of the energy transfer pathways in transition metal dichalcogenides is essential to design efficient optoelectronic devices. Here, the authors use megaelectronvolt ultrafast electron diffraction to unveil the sub-picosecond lattice dynamics in MoSe2 following photoexcitation of charge carriers

    • Ming-Fu Lin
    • , Vidya Kochat
    •  & Uwe Bergmann

  • Article
    | Open Access

    Cationic metal-organic frameworks provide promising opportunities to capture anionic pollutants, but stable frameworks with sufficiently large pores are lacking. Here the authors present a thorium-based mesoporous, cationic and hydrolytically-stable MOF that can rapidly trap inorganic and organic anionic pollutants.

    • Yuxiang Li
    • , Zaixing Yang
    •  & Shuao Wang

  • Article
    | Open Access

    The timescale of isomerization in molecules involving ultrafast migration of constituent atoms is difficult to measure. Here the authors report that sub-100 fs isomerization time on acetylene dication in lower electronic states is not possible and point to misinterpretation of recent experimental results.

    • Zheng Li
    • , Ludger Inhester
    •  & Todd J. Martinez

  • Article
    | Open Access

    Soft solids have important applications in industry but their material properties can be compromised by aging. Here Bouzidet al. present a large-scale study of a model gel to investigate the aging of soft matter which can help unravel the microscopic dynamics in a range of soft solids.

    • Mehdi Bouzid
    • , Jader Colombo
    •  & Emanuela Del Gado

  • Article
    | Open Access

    Understanding ice nucleation is important for the development of accurate cloud models. Here Biet al. show that sharp wedges can enhance ice nucleation both when the wedge geometry matches the ice lattice and when such matching is absent, in which case nucleation is promoted by topological defects.

    • Yuanfei Bi
    • , Boxiao Cao
    •  & Tianshu Li

  • Article
    | Open Access

    Ice recrystallization is important for a range of research fields, both applied and fundamental, however the effect of ions on this process is not well known. Here the authors discover an ion-specific Hofmeister type effect on ice recrystallization, using this phenomenon to prepare porous materials with tuneable pore sizes.

    • Shuwang Wu
    • , Chongqin Zhu
    •  & Jianjun Wang

  • Article
    | Open Access

    Liquid crystal mixtures are used in commercial applications and their composition affects their properties. Here Rahimiet al. use atomistic simulations to show that defects influence the molecular arrangement of the mixture components leading to a deviation of the local order from that of the bulk.

    • Mohammad Rahimi
    • , Hadi Ramezani-Dakhel
    •  & Juan J. de Pablo

  • Article
    | Open Access

    Controlling the self-assembly of oligothiophene complexes that are used in multi-functional thin films can be challenging. Here the authors show a hierarchy of non-covalent interactions for robust self-assembly that orders Saturn-like complexes of fullerenes with oligothiophene macrocycles.

    • José D. Cojal González
    • , Masahiko Iyoda
    •  & Jürgen P. Rabe

  • Article
    | Open Access

    Natural supplies of bryostatin, a compound in clinical trials for Alzheimer’s disease, cancer, and HIV, are scarce. Here, the authors perform molecular dynamics simulations to understand how bryostatin interacts with membrane-bound protein kinase C, offering insights for the design of bryostatin analogs.

    • Steven M. Ryckbosch
    • , Paul A. Wender
    •  & Vijay S. Pande

  • Article
    | Open Access

    G-protein-coupled receptors trigger several signalling pathways and their activity was proposed to be allosteric modulated by cholesterol. Here the authors use molecular dynamics simulations and ligand binding assays to show that membrane cholesterol can bind to adenosine A2Areceptor orthosteric site.

    • Ramon Guixà-González
    • , José L. Albasanz
    •  & Jana Selent

  • Article
    | Open Access

    It is commonly held that van der Waals wells are inevitable in chemical reactions. Here, the authors show that weak van der Waals forces in the entrance channel of a prototypical complex-forming reaction cause a van der Waals saddle instead, with different dynamical effects from a well at low collision energies.

    • Zhitao Shen
    • , Haitao Ma
    •  & Jianwei Cao

  • Article
    | Open Access

    Antimicrobial peptides (AMPs) selectively form pores in microbial membranes in process not fully understood. Here the authors use experimentally guided molecular dynamics to study maculatin pore formation, showing how this AMP assembles into transient and structurally diverse oligomeric pores in cell membranes.

    • Yukun Wang
    • , Charles H. Chen
    •  & Jakob P. Ulmschneider

  • Article
    | Open Access

    The organization of supramolecular peptide polymers determines their properties; however, controlling their dimensions still remains a problem. Here, Gazitet al. show the spontaneous elongation and shortening of these polymers at an individual nano-assembly level by using a microfluidic platform.

    • Zohar A. Arnon
    • , Andreas Vitalis
    •  & Ehud Gazit

  • Article
    | Open Access

    Tetrameric cationic channels specificity is determined by the sequence and structural conformation of their selectivity filter. Here, the authors show that a cationic channel from Tsukamurella paurometabola is non-selective due to a Ca2+-binding motif within its unusual proline-rich filter.

    • Balasundaresan Dhakshnamoorthy
    • , Ahmed Rohaim
    •  & Benoît Roux

  • Article
    | Open Access

    Thermal management is important for designing bio-nano interfaces for biosensing and thermotherapic applications. Here the authors perform simulations showing that nm-thick water layers between graphene and cell membranes display layered ordering, promoting interfacial thermal coupling and thermal dissipation.

    • Yanlei Wang
    • , Zhao Qin
    •  & Zhiping Xu

  • Article
    | Open Access

    Nitrogen vacancy centres in diamond form spin-1 defects which may be exploited as sensitive probes of nanoscale magnetic phenomena. Here, the authors use individual nitrogen vacancies to perform nuclear magnetic resonance measurements of the 1H spins of adsorbed organic molecules.

    • T. Staudacher
    • , N. Raatz
    •  & J. Wrachtrup

  • Article
    | Open Access

    Materials that are tolerant to radiation damage are important for use in nuclear reactors or the storage of nuclear materials. Here, the authors show that pre-introduced nanovoids in nanotwinned copper improve self-healing of the material and therefore enhance its radiation tolerance.

    • Y. Chen
    • , K Y. Yu
    •  & X. Zhang

  • Article
    | Open Access

    Increasing the resolution of fluorescence microscopy is a fundamental need for modern cell biology. Lanzanò et al.demonstrate that arbitrary spatial resolution is, in principle, possible by encoding the fluorophore's spatial distribution information in the temporal dynamics of the fluorophore's transition.

    • Luca Lanzanò
    • , Iván Coto Hernández
    •  & Giuseppe Vicidomini

  • Article |

    Self-assembling of complex molecular structures with a target topology is of importance to design and synthesize functional materials. Here, Polles et al. demonstrate the spontaneous formation of closed knotted structures from simple helical building blocks with sticky ends in simulations.

    • Guido Polles
    • , Davide Marenduzzo
    •  & Cristian Micheletti

  • Article |

    It is challenging to determine thermodynamic quantities for single molecules. Here, the authors access single-molecule thermodynamic information via a microscopic and computational study of a confined molecule, for which the resulting patterns represent a real-space equilibrium probability distribution.

    • Carlos-Andres Palma
    • , Jonas Björk
    •  & Johannes V. Barth

  • Article |

    Gold nanoparticles coated with amphiphilic ligands can spontaneously insert into lipid bilayers, reducing hydrophobic interactions. Here, the authors show the key step in this process is similar to vesicle fusion: lipid tails from the bilayer protrude into water before encountering the nanoparticle.

    • Reid C. Van Lehn
    • , Maria Ricci
    •  & Alfredo Alexander-Katz

  • Article |

    Photoexciting molecules provides insights into their different degrees of freedom if the ultrafast electron and nuclei motion can be properly analysed. To this end, McFarland et al.use X-ray pump-probe techniques to show that Auger spectra can unveil information on nuclear relaxation in molecules.

    • B. K. McFarland
    • , J. P. Farrell
    •  & M. Gühr

  • Article |

    Nanopores of porous electrodes have key roles in enhancing supercapacitor performance, but little is known at the atomic level. Merlet et al. perform molecular dynamics simulations and report the effects of confinement of electrolyte ions inside the pores on charge storage efficiency.

    • C. Merlet
    • , C. Péan
    •  & M. Salanne

  • Article |

    The mechanical properties of brittle materials are largely determined by how cracks propagate through them. Contrary to expectations, Kermodeet al.show that a crack propagating below a critical speed through a silicon crystal can be scattered by a single isolated boron impurity.

    • J.R. Kermode
    • , L. Ben-Bashat
    •  & A. De Vita

  • Article |

    Intercalation materials are of interest for batteries because of their capability of accommodating ions in their layered structures. Mashtalir et al. develop a new battery electrode material using two-dimensional intercalated carbides, which exhibit high lithium-ion conductivity and capacity.

    • Olha Mashtalir
    • , Michael Naguib
    •  & Yury Gogotsi

  • Article
    | Open Access

    Cell-penetrating peptides can deliver molecular cargoes into living cells, and cross biological membranes by transduction—a non-endocytic mechanism. Here, the transduction efficiency of cyclic arginine-rich peptides is shown to be higher than that of more flexible linear peptides.

    • Gisela Lättig-Tünnemann
    • , Manuel Prinz
    •  & M. Cristina Cardoso

  • Article |

    The detailed interactions of membrane proteins with their lipid environment are poorly understood. Sonntaget al. use low-resolution X-ray crystallographic data and molecular dynamics simulations to study the manner in which the sarcoendoplasmic reticulum Ca2+–ATPase adapts to different membrane environments.

    • Yonathan Sonntag
    • , Maria Musgaard
    •  & Lea Thøgersen

  • Article |

    The formation of hydrophilic protein–protein interactions cannot be explained by charge–charge interactions. Here, molecular simulations reveal that water forms an adhesive hydrogen-bonded network between proteins, stabilizing intermediate states before the bound complex forms.

    • Mazen Ahmad
    • , Wei Gu
    •  & Volkhard Helms

  • Article |

    The unusual magnetic fields of Uranus and Neptune are important considerations when developing hydrodynamic models of the planetary interiors. In this study, molecular dynamics simulations are used to study how chemical processes could create the interior structures predicted from the planets' magnetic fields.

    • Ricky Chau
    • , Sebastien Hamel
    •  & William J. Nellis

  • Article |

    The interiors of outer solar planets are believed to contain water–methane mixtures that are subject to extreme pressures. Lee and Scandolo use molecular dynamics simulations to show that at high pressures there can be enhanced mixing and ionization, with consequences for the origin of the planetary magnetic field.

    • Mal-Soon Lee
    •  & Sandro Scandolo

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