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.
Mesoscale biosimulations within a unified framework: from proteins to plasmids
Melchionna S
2021
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.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
