The entropy of a complex molecule.

Entropy is a central concept in the theory of coarse-graining. Through Einstein's formula, it provides the equilibrium probability distribution of the coarse-grained variables used to describe the system of interest. We study with molecular dynamics simulations the equilibrium probability distribution of thermal blobs representing at a coarse-grained level star polymer molecules in melt. Thermal blobs are characterized by the positions and momenta of the centers of mass, and internal energies of the molecules. We show that the entropy of the level of description of thermal blobs can be very well approximated as the sum of the thermodynamic entropy of each single molecule considered as isolated thermodynamic systems. The entropy of a single molecule depends on the intrinsic energy, involving only contributions from the atoms that make the molecule and not from the interactions with atoms of other molecules.

Local density dependent potential for compressible mesoparticles.

This work proposes a coarse grained description of molecular systems based on mesoparticles representing several molecules, where interactions between mesoparticles are modelled by an interparticle potential of molecular type. Since strong non-equilibrium situations over a wide range of pressure and density are targeted, the internal compressibility of the mesoparticles has to be considered. This is done by introducing a dependence of the potential on the local environment of the mesoparticles. To define local densities, we resort to a three-dimensional Voronoi tessellation instead of standard local, spherical averages. As an example, a local density dependent potential is fitted to reproduce the Hugoniot curve of a model of nitromethane over a large range of pressures and densities.

Size consistency in smoothed dissipative particle dynamics.

Smoothed dissipative particle dynamics (SDPD) is a mesoscopic method that allows one to select the level of resolution at which a fluid is simulated. In this work, we study the consistency of the resulting thermodynamic properties as a function of the size of the mesoparticles, both at equilibrium and out of equilibrium. We also propose a reformulation of the SDPD equations in terms of energy variables. This increases the similarities with dissipative particle dynamics with energy conservation and opens the way for a coupling between the two methods. Finally, we present a numerical scheme for SDPD that ensures the conservation of the invariants of the dynamics. Numerical simulations illustrate this approach.