Molecular dynamics articles within Nature Communications

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  • Article
    | Open Access

    While clusters in calcium orthophosphate nucleation have long been known, their speciation and mechanistic pathways to hydroxyapatite remain debated. Here the authors report a revision of ion association in the calcium phosphate system and explore the consequences thereof on the early stages of phase separation.

    • David P. McDonogh
    • , Julian D. Gale
    •  & Denis Gebauer

  • Article
    | Open Access

    Solvated electrons can be formed through photo-induced charge-transfer-to-solvent electronic states of halide ions in water. Here, the authors use machine learning accelerated molecular dynamics simulations to follow the evolution of these states for aqueous iodide in detail.

    • Jinggang Lan
    • , Majed Chergui
    •  & Alfredo Pasquarello

  • 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

    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

    Here, authors report chemokine receptors structures obtained using coarse-grained metadynamics. CCR5 and CXCR4 homo- and heterodimers differ in the conformations of ligand binding sites and of the G protein interaction interface, suggesting structural basis for the rational design of biased ligands.

    • Daniele Di Marino
    • , Paolo Conflitti
    •  & Vittorio Limongelli

  • Article
    | Open Access

    Understanding protein dynamics is a complex scientific challenge. Here, authors construct coarse-grained molecular potentials using artificial neural networks, significantly accelerating protein dynamics simulations while preserving their thermodynamics.

    • Maciej Majewski
    • , Adrià Pérez
    •  & Gianni De Fabritiis

  • Article
    | Open Access

    The hydrophobic gating is believed to function in various ion channels. Here, the authors use MD simulations to assess how dewetting of the channel pore modulates the function and conformational transition of the potassium channels.

    • Ruo-Xu Gu
    •  & Bert L. de Groot

  • Article
    | Open Access

    Here the authors report SBCG2 an update to the neural network based, Shape-Based Coarse Graining (SBCG) approach for creating coarse grained molecular topologies with atomistic detail. They show how SBCG2 can reduce the computational costs of simulating very large assemblies like the HIV-1 capsid allowing simulation on commodity hardware.

    • Alexander J. Bryer
    • , Juan S. Rey
    •  & Juan R. Perilla

  • Article
    | Open Access

    Direct spectroscopic probes of the impact of structure on dynamical processes in liquids remain scarce. Here, the authors use molecular dynamics simulations to show that the correlation between vibrational coupling and the local tetrahedral structure of liquid water can be studied via hybrid terahertz- and infrared-Raman spectroscopy.

    • Tomislav Begušić
    •  & Geoffrey A. Blake

  • Article
    | Open Access

    Aqueous CO2 under nanoconfinement is of great importance to the carbon storage and transport in Earth. Here, the authors apply ab initio molecular dynamics simulations to study the effects of confinement and interfaces, and show that that CO(aq) reacts more in nanoconfinement than in bulk.

    • Nore Stolte
    • , Rui Hou
    •  & Ding Pan

  • Article
    | Open Access

    Energy transfer between the electromagnetic field and atoms or molecules is fundamentally interesting. Here the authors demonstrate stepwise energy transfer between broadband mid-infrared optical pulses and vibrating methylsulfonylmethane molecules in aqueous solution.

    • Martin T. Peschel
    • , Maximilian Högner
    •  & Ioachim Pupeza

  • Article
    | Open Access

    Hybrid light-matter states formed in the strong light-matter coupling regime can alter the molecular ground-state reactivity. Here, Li et al. computationally demonstrate that pumping a collection of solvent molecules forming hybrid vibrational light-matter states in an optical cavity can excite solute molecules to very high excited states.

    • Tao E. Li
    • , Abraham Nitzan
    •  & Joseph E. Subotnik

  • Article
    | Open Access

    The rigidity of solid nanocontacts formed when metals touch is apparently lost liquidlike under large mechanical oscillations. As we show theoretically, there is no melting but oscillated nanocontacts undergo a remarkable reversible stick-slip rheology.

    • Ali Khosravi
    • , Antoine Lainé
    •  & Erio Tosatti

  • 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

    The authors report non-adiabatic first principles molecular dynamics to show how an achiral molecule can be converted to a chiral one upon photoexcitation. These results demonstrate the possibility of asymmetric photochemistry starting from achiral reactants.

    • Umberto Raucci
    • , Hayley Weir
    •  & Todd J. Martínez

  • 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

    The application of photoswitches as light-responsive triggers for phase transitions of porous materials remains poorly explored. Here, the authors report a light-responsive flexible metal-organic framework which undergoes pore contraction upon combined application of light irradiation and adsorption stress via a buckling process of the framework-embedded azobenzene photoswitch.

    • Simon Krause
    • , Jack D. Evans
    •  & Ben L. Feringa

  • Article
    | Open Access

    The reaction region is commonly considered to be the direct catalyst surface. Here, the authors challenge this view and use molecular dynamics simulations to reveal a solvated hydroxide species dynamically confined in a pseudo-adsorption state at a few water layers away from the active site during oxygen reduction reaction on single atom electrocatalyst.

    • Jie-Wei Chen
    • , Zisheng Zhang
    •  & Yang-Gang Wang

  • 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

    Modelling the growth of carbon nanoclusters in shock experiments is computationally demanding. Here the authors employ a machine-learned reactive interatomic model to perform large-scale simulations of nanocarbon formation from prototypical shocked C/O-containing precursor.

    • Rebecca K. Lindsey
    • , Nir Goldman
    •  & Sorin Bastea

  • Article
    | Open Access

    Dissolution of minerals in water is ubiquitous in nature, its mechanism at the atomic level still under debate. Here, the authors investigate the dissolution mechanism of tricalcium silicate at early stage by ab initio molecular dynamics and metadynamics simulations.

    • Yunjian Li
    • , Hui Pan
    •  & Zongjin Li

  • Article
    | Open Access

    The reactive uptake of N2O5 to aqueous aerosol is a major loss channel for nitrogen oxides in the troposphere. Here authors report a theoretical investigation on the N2O5 uptake into aqueous aerosol and determine the hydrolysis rates by numerically solving a molecularly detailed reaction–diffusion equation.

    • Vinícius Wilian D. Cruzeiro
    • , Mirza Galib
    •  & Andreas W. Götz

  • Article
    | Open Access

    By advanced machine learning techniques, first-principles simulations find that dissolving salt in water does not change water structure drastically. It is contrary to the notion of “pressure effect” which has been widely applied over past 25 years.

    • Chunyi Zhang
    • , Shuwen Yue
    •  & Xifan Wu

  • Article
    | Open Access

    Theoretical studies of the air-water interface of a water droplet show a wide distribution of strong electric fields at the surface that can make or break chemical bonds to accelerate chemical reactions over the bulk water phase.

    • Hongxia Hao
    • , Itai Leven
    •  & Teresa Head-Gordon

  • Article
    | Open Access

    No existing density functional correctly describes the properties of water across the entire phase diagram. The authors report a data-driven many-body potential energy function based on density-corrected SCAN functional that quantitatively reproduces the energetics of gas-phase water clusters, and correctly predicts the properties of liquid water.

    • Saswata Dasgupta
    • , Eleftherios Lambros
    •  & Francesco Paesani

  • Article
    | Open Access

    Achieving ultra-low friction at macroscopic scales is highly desirable. In this work molecular dynamics simulations of graphitic contacts incorporating corrugated grain boundaries reveal an unusual non-monotonic variation of friction with normal load and temperature due to dynamic buckling effects.

    • Xiang Gao
    • , Wengen Ouyang
    •  & Oded Hod

  • Article
    | Open Access

    Aqueous solutions under nanoscale confinement exhibit interesting physicochemical properties. This work reports evidence on the spontaneous formation of two-dimensional alkali chloride crystalline/non-crystalline nanostructures in dilute aqueous solution under nanoscale confinement by computer simulations.

    • Wenhui Zhao
    • , Yunxiang Sun
    •  & Xiao Cheng Zeng

  • Article
    | Open Access

    Multistep nucleation phenomena are of considerable fundamental interest. Here the authors combine molecular dynamics, machine learning and molecular cluster analysis to investigate the multistep nucleation of smectic clusters from a nematic fluid that cannot be accounted for by the classical nucleation theory.

    • Kazuaki Z. Takahashi
    • , Takeshi Aoyagi
    •  & Jun-ichi Fukuda

  • Article
    | Open Access

    Nematic liquid crystals with polar order bear great potential for many applications but their rational design is difficult. Mandle et al. outline a set of design principles for this new phase of matter, guided by experiments and simulation, showing polar order to be driven by steric interactions.

    • Richard J. Mandle
    • , Nerea Sebastián
    •  & Alenka Mertelj

  • Article
    | Open Access

    hNEIL1 (human endonuclease VIII-like 1) is a broadly specific DNA glycosylase for base excision repair. Here, the authors show that hNEIL1 can assume activated or triage conformations: the structural basis for the mechanism that enables broad specificity and reduces futile repair of normal bases.

    • Menghao Liu
    • , Jun Zhang
    •  & Chengqi Yi

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