Molecular dynamics articles within Nature Communications

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  • 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

  • Article
    | Open Access

    The subtle connections between water’s supercooled liquid and glassy states are difficult to characterize. Gartner et al. suggest with MD simulations that the long-range structure of glassy water may reflect signatures of water’s debated second critical point in the supercooled liquid.

    • Thomas E. Gartner III
    • , Salvatore Torquato
    •  & Pablo G. Debenedetti

  • Article
    | Open Access

    Determining the structure of amorphous solids is important for optimization of pharmaceutical formulations, but direct relation of molecular dynamics (MD) simulations and NMR to achieve this is challenging. Here, the authors use a machine learning model of chemical shifts to solve the atomic-level structure of the hydrated amorphous drug AZD5718 by combining dynamic nuclear polarization-enhanced solid-state NMR with predicted shifts for MD simulations of large systems.

    • Manuel Cordova
    • , Martins Balodis
    •  & Lyndon Emsley

  • Article
    | Open Access

    The structure of water around Brønsted acid sites in zeolites is shown to influence their catalytic activity. Here the authors shed light on confinement effects in different pores zeolites/water interfaces acidic strength by means of ab-initio molecular dynamics and enhanced sampling metadynamics techniques.

    • Emanuele Grifoni
    • , GiovanniMaria Piccini
    •  & Michele Parrinello

  • Article
    | Open Access

    Engineering efforts have focused on acyltransferase (AT) domains of modular polyketide synthases (PKSs) to site-selectively modify the resulting polyketides, but critical AT residues involved in substrate selection have not been fully elucidated. Here, the authors use molecular dynamics to pinpoint mutations that impact AT domain selectivity and exchange structural motifs to obtain chimeric PKS modules with expanded substrate specificity.

    • Edward Kalkreuter
    • , Kyle S. Bingham
    •  & Gavin J. Williams

  • Article
    | Open Access

    The relationship between the strain rate and micro-scale deformation in metals is still poorly understood. Here the authors use discrete dislocation dynamics and molecular dynamics to establish a universal relationship between material strength, dislocation density, strain rate and dislocation mobility in fcc metals.

    • Haidong Fan
    • , Qingyuan Wang
    •  & Michael Zaiser

  • Article
    | Open Access

    Connecting conformational dynamics and epistasis has so far been limited to a few proteins and a single fitness trait. Here, the authors provide evidence of positive epistasis on multiple catalytic traits in the evolution and dynamics of engineered cytochrome P450 monooxygenase, offering insights for in silico protein design.

    • Carlos G. Acevedo-Rocha
    • , Aitao Li
    •  & Manfred T. Reetz

  • Article
    | Open Access

    The accuracy of a machine-learned potential is limited by the quality and diversity of the training dataset. Here the authors propose an active learning approach to automatically construct general purpose machine-learning potentials here demonstrated for the aluminum case.

    • Justin S. Smith
    • , Benjamin Nebgen
    •  & Kipton Barros

  • Article
    | Open Access

    The diffusion of fluids in complex nanoporous geometries represents a challenge for modelling approaches. Here, the authors describe the macroscopic diffusivity of a simple fluid in disordered nanoporous materials by bridging microscopic and mesoscopic dynamics with parameters obtained from simple physical laws.

    • Colin Bousige
    • , Pierre Levitz
    •  & Benoit Coasne

  • Article
    | Open Access

    The nature of the bulk hydrated electron has been a challenge for both experiment and theory. Here the authors use a machine-learning model trained on MP2 data to achieve an accurate determination of the structure, diffusion mechanisms, and vibrational spectroscopy of the solvated electron.

    • Jinggang Lan
    • , Venkat Kapil
    •  & Vladimir V. Rybkin

  • Article
    | Open Access

    The inclusion of nuclear quantum effects (NQE) in atomistic simulations of chemical systems is of key importance. Here the authors use machine learned force fields trained on coupled cluster reference data to show the dynamical strengthening of covalent and non-covalent molecular interactions induced by NQE.

    • Huziel E. Sauceda
    • , Valentin Vassilev-Galindo
    •  & Alexandre Tkatchenko

  • Article
    | Open Access

    Machine learning potentials do not account for long-range charge transfer. Here the authors introduce a fourth-generation high-dimensional neural network potential including non-local information of charge populations that is able to provide forces, charges and energies in excellent agreement with DFT data.

    • Tsz Wai Ko
    • , Jonas A. Finkler
    •  & Jörg Behler

  • Article
    | Open Access

    Semilocal density functionals, while computationally efficient, do not account for non-local correlation. Here, the authors propose a machine-learning approach to DFT that leads to non-local and transferable functionals applicable to non-covalent, ionic and covalent interactions across system of different sizes.

    • Johannes T. Margraf
    •  & Karsten Reuter

  • Article
    | Open Access

    Narrowing pores filled with an electrolyte usually slows down their charge-discharge dynamics. Here the authors demonstrate through molecular dynamics simulations and experiments with novolac-derived carbon electrodes how non-linear voltage sweeps can accelerate charging and discharging of subnanometer pores.

    • Konrad Breitsprecher
    • , Mathijs Janssen
    •  & Svyatoslav Kondrat

  • Article
    | Open Access

    Molecular understanding of water is challenging due to the structural complexity of liquid water and the large number of ice phases. Here the authors use a machine-learning potential trained on liquid water to demonstrate the structural similarity of liquid water and that of 54 real and hypothetical ice phases.

    • Bartomeu Monserrat
    • , Jan Gerit Brandenburg
    •  & Bingqing Cheng

  • Article
    | Open Access

    Citrate-stabilized metallic colloids are key materials towards chemosensing and catalysis applications. Here the authors introduce a new theoretical model to estimate how the stoichiometry of citrate molecules absorbed onto spherical metallic nanoparticles influences their aggregation phenomena.

    • Sebastian Franco-Ulloa
    • , Giuseppina Tatulli
    •  & Marco De Vivo

  • Article
    | Open Access

    Hydrogen has multiple molecular phases which are challenging to explore computationally. The authors develop a machine-learning approach, learning from reference ab initio molecular dynamics simulations, to derive a transferable hierarchical force model that provides insight into high pressure phases and the melting line of H2.

    • Hongxiang Zong
    • , Heather Wiebe
    •  & Graeme J. Ackland

  • Article
    | Open Access

    Heterogenous ice nucleation is a ubiquitous phenomenon, but predicting the ice nucleation ability of a substrate is challenging. Here the authors develop a machine-learning data-driven approach to predict the ice nucleation ability of substrates, which is based on four descriptors related to physical properties of the interface.

    • Martin Fitzner
    • , Philipp Pedevilla
    •  & Angelos Michaelides

  • Article
    | Open Access

    Currently the cost of CO2 chemical fixation remains high because of harsh reaction conditions. Here, the authors report a covalent organic framework screened from 10994 candidates as the efficient CO2 fixation catalyst under ambient conditions based on the finding of a “pore enrichment effect”.

    • Wei Zhou
    • , Qi-Wen Deng
    •  & Wei-Qiao Deng

  • Article
    | Open Access

    Supercooled liquids near the glass transition show remarkable non-Arrhenius transport phenomena, whose origin is yet to be clarified. Here, the authors use GPU molecular dynamics simulations for various binary mixtures in the supercooled regime to show the validity of a quasiuniversal excess-entropy scaling relation for viscosity and diffusion.

    • Ian H. Bell
    • , Jeppe C. Dyre
    •  & Trond S. Ingebrigtsen

  • Article
    | Open Access

    Increasing the non-locality of the exchange and correlation functional in DFT theory comes at a steep increase in computational cost. Here, the authors develop NeuralXC, a supervised machine learning approach to generate density functionals close to coupled-cluster level of accuracy yet computationally efficient.

    • Sebastian Dick
    •  & Marivi Fernandez-Serra

  • Article
    | Open Access

    Mitochondrial apoptosis is controlled by BCL2 family proteins, and the BH3-only proteins often act as sensors that transmit apoptotic signals. Here the authors show how the BH3-only proteins BMF and HRK can directly activate the BCL2 protein BAK and interact with BAK through an alternative binding groove.

    • Kaiqin Ye
    • , Wei X. Meng
    •  & Haiming Dai

  • Article
    | Open Access

    Salts in water at extreme conditions play a fundamental role in determining the properties of the Earthʼs mantle constituents. Here the authors shed light on ion-water and ion-ion interactions for NaCl dissolved in water at conditions relevant to the Earthʼs upper mantle by molecular dynamics simulations.

    • Cunzhi Zhang
    • , Federico Giberti
    •  & Giulia Galli

  • Article
    | Open Access

    Potassium (K+) channels, such as MthK, are essentional for many biological processes, but how lipid-protein interactions regulate ion permeation of K+ channels remained unclear. Here authors conducted molecular dynamics simulations of MthK and observed different ion permeation rates of MthK in membranes with different properties.

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

  • Article
    | Open Access

    Graphene oxide holds great promise for water purification applications, though its chemical reactivity in water is yet to be clarified. Here the authors show by first principles molecular dynamics that graphene oxide structures with correlated functional groups and regions of pristine graphene are the most stable in liquid water.

    • Félix Mouhat
    • , François-Xavier Coudert
    •  & Marie-Laure Bocquet

  • Article
    | Open Access

    Tripartite-motif containing (TRIM) proteins modulate cellular responses to viral infection. Here the authors use molecular dynamics simulations to demonstrate that TRIM5α uses a two-dimensional lattice hopping mechanism to aggregate on the HIV capsid surface and initiate lattice growth.

    • Alvin Yu
    • , Katarzyna A. Skorupka
    •  & Gregory A. Voth

  • Article
    | Open Access

    The determination of the speciation of ions and molecules in supercritical aqueous fluids under pressure is key to understanding their mass transport in the Earth’s interior. Here the authors present a strategy based on ab-initio molecular dynamics to determine the speciation of carbonates in aqueous fluids.

    • Ding Pan
    •  & Giulia Galli

  • Article
    | Open Access

    Understanding the dynamic evolution of the catalysts’ structure under reaction conditions is crucial in heterogeneous catalysis. Here the authors use ab initio molecular dynamics simulations to show an anomalous decrease in reaction free energies and barriers on dynamical sub-nanometer Au clusters supported on MgO(001).

    • Juan-Juan Sun
    •  & Jun Cheng

  • Article
    | Open Access

    The properties of water under confinement are significantly altered with respect to the bulk phase. Here the authors use infrared spectroscopy and many-body molecular dynamics simulations to show the structure and dynamics of confined water as a function of relative humidity within a metal-organic framework.

    • Adam J. Rieth
    • , Kelly M. Hunter
    •  & Francesco Paesani

  • Article
    | Open Access

    While aluminosilicate zeolites are of interest for many applications, the affect of water on zeolite stability in mild aqueous conditions has yet to be established. Here, using ab initio calculations and NMR spectroscopy, the authors show that covalent bonds in the zeolite chabazite are labile when in contact with neutral liquid water.

    • Christopher J. Heard
    • , Lukas Grajciar
    •  & Russell E. Morris

  • Article
    | Open Access

    Understanding vibrational energy transfer in macromolecules has been challenging to both theory and experiment. Here the authors use non-equilibrium molecular dynamics to reveal the relationship between heat transport in a model peptide, emergent nonlinearity, and the underlying free energy landscape.

    • Justin E. Elenewski
    • , Kirill A. Velizhanin
    •  & Michael Zwolak

  • Article
    | Open Access

    Allosteric GPCR modulators can achieve exquisite subtype selectivity, but the underlying mechanism is unclear. Using molecular dynamics simulations, the authors here identify a previously undetected dynamic pocket in muscarinic GPCRs that is critical for subtype selectivity of allosteric modulators.

    • Scott A. Hollingsworth
    • , Brendan Kelly
    •  & Ron O. Dror

  • Article
    | Open Access

    The structural origin of the mid-gap states responsible for the time-dependent resistance drift in phase-change materials is still under debate. Here the authors use machine learning and density functional theory to identify the structural motifs of the mid-gap defects in the prototypical Ge2Sb2Te5 phase-change alloy.

    • Konstantinos Konstantinou
    • , Felix C. Mocanu
    •  & Stephen R. Elliott

  • Article
    | Open Access

    It is well known that fluids become opaque at the liquid–vapor critical point, but a description of the underlying mechanical instability is still missing. Das and Green leverage nonlinear dynamics to quantify the role of chaos in the emergence of this critical phenomenon.

    • Moupriya Das
    •  & Jason R. Green

  • Article
    | Open Access

    The origins of the different charging processes observed in graphene and boron-nitride nanofluidics are still under debate. Here, using ab-initio molecular dynamics, the authors show that hydroxide species in water exhibits physisorption on graphene but strong chemisorption on boron-nitride.

    • Benoît Grosjean
    • , Marie-Laure Bocquet
    •  & Rodolphe Vuilleumier

  • Article
    | Open Access

    Aqueous proton-selective membranes are vital for methanol fuel cells and flow batteries, but suffer from crossover issues. Here the authors use ab initio molecular dynamics simulations to show that graphyne is an ideal candidate for a proton-selective membrane that can be tailored for methanol impermeability

    • Le Shi
    • , Ao Xu
    •  & Tianshou Zhao

  • Article
    | Open Access

    Understanding how nuclear motions affect vibrational motions in molecular liquids remains challenging in modern condensed matter physics. Here the authors study the vibrational quantum effects in liquid water and show the sensitivity on the coherent evolution of OH bonds in core-excited states.

    • Vinícius Vaz da Cruz
    • , Faris Gel’mukhanov
    •  & Michael Odelius

  • Article
    | Open Access

    A number of disease-causing human transthyretin (TTR) mutations are known to lead to amyloid formation. Here the authors combine neutron crystallography, native mass spectrometry and modelling studies to characterize the T119M and S52P-TTR mutants, providing mechanistic insights into TTR amyloidosis.

    • Ai Woon Yee
    • , Matteo Aldeghi
    •  & V. Trevor Forsyth

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