We show how an existing concurrent multi-scale method named hybrid particle field-molecular dynamics (hPF-MD) can be adapted to enable the simulation of structure and/or structural dynamics in... Show moreWe show how an existing concurrent multi-scale method named hybrid particle field-molecular dynamics (hPF-MD) can be adapted to enable the simulation of structure and/or structural dynamics in compressible systems. Implementing such new equations of state (EOS) into hPF-MD, while conserving the efficiency associated with treating intermolecular interactions in a continuum fashion, opens this method up to describe a new class of phenomena in which non-uniform densities play a role, for example, evaporation and crystallization. We carefully consider how compressible hPF-MD compares to its mean-field counterpart for two particular EOS, adopted from the Cell Model for polymers and the Carnahan-Starling expression for hard spheres. Here, we performed a very basic analysis for a single-component system, focusing on the significance of various particle-based parameters and the particle-to-field projection. Our results illustrate the key role of the particle density per field grid cell and show that projection based on a Gaussian kernel is preferred over the standard cloud-in-cell projection. They also suggest that the behavior of hPF-MD close to the critical point is non-classical, i.e., in agreement with a critical exponent for a pure particle description, despite the mean-field origin of the method. Show less
Nicola, A. de; Soares, T.A.; Santos, D.E.S.; Bore, S.L.; Sevink, G.J.A.; Cascella, M.; Milano, G. 2020
Lipid A is one of the three components of bacterial lipopolysaccharides constituting the outer membrane of Gram-negative bacteria, and is recognized to have an important biological role in the... Show moreLipid A is one of the three components of bacterial lipopolysaccharides constituting the outer membrane of Gram-negative bacteria, and is recognized to have an important biological role in the inflammatory response of mammalians. Its biological activity is modulated by the number of acyl-chains that are present in the lipid and by the dielectric medium, i.e., the type of counter-ions, through electrostatic interactions. In this paper, we report on a coarse-grained model of chemical variants of Lipid A based on the hybrid particle-field/molecular dynamics approach (hPF-MD). In particular, we investigate the stability of Lipid A bilayers for two different hexa- and tetra-acylated structures. Comparing particle density profiles along bilayer cross-sections, we find good agreement between the hPF-MD model and reference all-atom simulation for both chemical variants of Lipid A. hPF-MD models of constituted bilayers composed by hexa-acylated Lipid A in water are stable within the simulation time. We further validate our model by verifying that the phase behavior of Lipid A/counterion/water mixtures is correctly reproduced. In particular, hPF-MD simulations predict the correct self-assembly of different lamellar and micellar phases from an initially random distribution of Lipid A molecules with counterions in water. Finally, it is possible to observe the spontaneous formation and stability of Lipid A vesicles by fusion of micellar aggregates. Show less
Nicola, A. de; Munao, G.; Grizzuti, N.; Auriemma, F.; Rosa, C. de; Sevink, G.J.A.; Milano, G. 2020
The tacticity of vinyl polymer chains strongly affects the physical properties of polymeric materials, as example the chain conformations and stiffness. In the present work we tested how the hybrid... Show moreThe tacticity of vinyl polymer chains strongly affects the physical properties of polymeric materials, as example the chain conformations and stiffness. In the present work we tested how the hybrid Particle-Field Molecular Dynamics (PF-MD) technique is capable to describe conformational differences of polymer chains as function of the tacticity. In particular, we focus on tacticity effect of atactic, isotactic, and syndiotactic polypropylene (PP) homopolymer melts. We found that PF-MD simulations exhibit dependence of Flory's Characteristic Ratio from the fraction of racemo diads along the PP chains in qualitative agreement with Small Angle Neutron Scattering (SANS) experiments and theoretical previsions. Finally, we calculated and compared the packing length parameter on very high stereoregular syndiotactic PP systems with rheological measurements. A qualitative agreement between the calculated and experimental packing length is found. Show less
Pizzirusso, A.; Nicola, A. de; Sevink, G.J.A.; Correa, A.; Cascella, M.; Kawakatsu, T.; ... ; Milano, G. 2017
