IDEAS home Printed from https://ideas.repec.org/a/wsi/ijmpcx/v18y2007i04ns0129183107010759.html
   My bibliography  Save this article

A Coupled Molecular-Continuum Hybrid Model For The Simulation Of Macromolecular Dynamics

Author

Listed:
  • GIOVANNI GIUPPONI

    (Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon street, London WC1H 0AJ, UK)

  • GIANNI DE FABRITIIS

    (Computational Biochemistry and Biophysics Lab (GRIB-IMIM/UPF), Barcelona Biomedical Research Park, C/Doctor Aiguader 88, 08003 Barcelona, Spain)

  • PETER V. COVENEY

    (Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon street, London WC1H 0AJ, UK)

Abstract

We describe a hybrid simulation method that captures the combined effects of molecular and hydrodynamic forces which influence macromolecules in solution. In this method, the solvent contribution is accounted for implicitly as the Navier-Stokes equations are solved on a grid using a finite volume method, while we use coarse-grained molecular dynamics to describe the macromolecule. The two systems are coupled by a dissipative Stokesian force. We show that our method correctly captures the hydrodynamically enhanced self-diffusion of a single monomer for different fluids and grid sizes. Moreover, the monomer diffusion does not depend on the monomer mass for the mass range used, as postulated by polymer dynamics theories. We also show that the dynamical properties of the chain do not depend on the grid sizeawhen the chain radius of gyrationRg≫ a.

Suggested Citation

  • Giovanni Giupponi & Gianni De Fabritiis & Peter V. Coveney, 2007. "A Coupled Molecular-Continuum Hybrid Model For The Simulation Of Macromolecular Dynamics," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 18(04), pages 520-527.
    • Handle: RePEc:wsi:ijmpcx:v:18:y:2007:i:04:n:s0129183107010759
    DOI: 10.1142/S0129183107010759
    as

    Download full text from publisher

    File URL: http://www.worldscientific.com/doi/abs/10.1142/S0129183107010759
    Download Restriction: Access to full text is restricted to subscribers
    File URL: https://libkey.io/10.1142/S0129183107010759?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:wsi:ijmpcx:v:18:y:2007:i:04:n:s0129183107010759. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Tai Tone Lim (email available below). General contact details of provider: http://www.worldscinet.com/ijmpc/ijmpc.shtml .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.