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Biomedical subjects

Gianni De Fabritiis

Publications and source records attributed to Gianni De Fabritiis.

2 recordsLinked to original sources

Energy controlled insertion of polar molecules in dense fluids.

We present a method to search low energy configurations of polar molecules in the complex potential energy surfaces associated with dense fluids. The search is done in the configurational space of the translational and rotational degrees of freedom of the molecule, combining steepest-descent and Newton-Raphson steps which embed information on the average sizes of the potential energy wells obtained from prior inspection of the liquid structure. We perform a molecular dynamics simulation of a liquid water shell which demonstrates that the method enables fast and energy-controlled water molecule insertion in aqueous environments. The algorithm finds low energy configurations of incoming water molecules around three orders of magnitude faster than direct random insertion. This method represents an important step towards dynamic simulations of open systems and it may also prove useful for energy-biased ensemble average calculations of the chemical potential.

Journal Article↗

Multiscale dissipative particle dynamics.

We present a simplified kinetic derivation of the multiscale Voronoi-based dissipative particle dynamics (DPD) method. The Voronoi tessellation is used to coarse-grain the molecular level of a fluid, resulting in mesoscopic equations of motion for local mass, momentum and energy. The dissipative particles follow the dynamics of extended objects subject to forces including pressure and stresses. The stresses and heat fluxes are computed through constitutive relations, which lead to fluctuating Navier-Stokes hydrodynamics for the solvent. The present formulation is based on the use of statistical mechanical distribution functions and the connection with the underlying molecular description of the fluid is maintained through the pair-distribution function and the intermolecular potential. The main features of this DPD method are the adaptivity of the dissipative particles to the important length-scales of the problem and the explicit role played by the molecular pair-distribution function.

Biological Transport↗