Mesoscale biosimulations within a unified framework: from proteins to plasmids

ABSTRACT

The simulation of large biomolecules and biological assemblies requires to achieve an optimal balance between physical realism and computational efficiency. We describe how an effective strategy is based on a dual representation, whereby macromolecules are described by means of a coarse grained, particle-based representation, while aqueous solvent and electrolytes are represented by a mesoscopic, kinetic treatment. The joint usage of the Molecular Dynamics and Lattice Boltzmann techniques provides an optimal combination for these representations and allows simulating from proteins to polynucleotides under a wide range of equilibrium and off-equilibrium conditions.

KEYWORDS:

• Mesoscale simulations
• hydrokinetic modelling
• proteins
• plasmids

Acknowledgments

This work benefitted from delightful discussions with Sauro Succi, Umberto Marini Bettolo Marconi and Paolo Bettotti.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

Support from the ANR LABEX Grant ‘DYNAMO’ (ANR-11-LABX-0011) is kindly acknowledged.