Free energy calculations of elemental sulphur crystals via molecular dynamics simulations

Free energy calculations of two crystalline phases of the molecular compound S8 were performed via molecular dynamics simulations of these crystals. The elemental sulphur S8 molecule model used in our MD calculations consists of a semi-flexible closed chain, with fixed bond lengths and intra-molecular potentials for its bending and torsional angles. The intermolecular potential is of the atom-atom Lennard-Jones type. Two free energy calculation methods were implemented: the accurate thermodynamic integration method proposed by Frenkel and Ladd and an estimation that takes into account the contribution of the zero point energy and the entropy of the crystalline vibrational modes to the free energy of the crystal. The last estimation has the enormous advantage of being easily obtained from a single MD simulation. Here we compare both free energy calculation methods and analyze the reliability of the fast estimation via the vibrational density of states obtained from constrained MD simulations. New results on alpha- and alpha'- S8 crystals are discussedComment: 18 pages, 2 figures, submitted to J. Chem. Phy

Toward an anisotropic atom-atom model for the crystalline phases of the molecular S8 compound

We analize two anisotropic atom-atom models used to describe the crystalline alpha,beta and gamma phases of S8 crystals, the most stable compound of elemental sulfur in solid phases, at ambient pressure and T<=400 K. The calculations are performed via a series of classical molecular dynamics (MD) simulations, with flexible molecular models and using a constant pressure-constant temperature algorithm for the numerical simulations. All intramolecular modes that mix with lattice modes, and are therefore relevant on the onset of structural phase transitions, are taken into account. Comparisons with experimental data and previous results obtained with an isotropic atom-atom molecular model are also performed.Comment: Major changes, new simulations and figures added, revtex4, to appear in J. Chem. Phy

Test of a simple and flexible molecule model for alpha-, beta- and gamma-S8 crystals

S8 is the most stable compound of elemental sulfur in solid and liquid phases, at ambient pressure and below 400K. Three crystalline phases of S8 have been clearly identified in this range of thermodynamic parameters, although no calculation of its phase diagram has been performed yet. alpha- and gamma-S8 are orientationally ordered crystals while beta-S8 is measured as orientationally disordered. In this paper we analyze the phase diagram of S8 crystals, as given by a simple and flexible molecule model, via a series of molecular dynamics (MD) simulations. The calculations are performed in the constant pressure- constant temperature ensemble, using an algorithm that is able to reproduce structural phase transitions.Comment: RevTex,7 pages, 5 figures,to appear in J. Chem. Phy

Cyclic motion and inversion of surface flow direction in a dense polymer brush under shear

Using molecular simulations, we study the properties of a polymer brush in contact with an explicit solvent under Couette and Poiseuille flow. The solvent is comprised of chemically identical chains. We present evidence that individual, unentangled chains in the dense brush exhibit cyclic, tumbling motion and non-Gaussian fluctuations of the molecular orientations similar to the behaviour of isolated tethered chains in shear flow. The collective molecular motion gives rise to an inversion of hydrodynamic flow direction in the vicinity of the brush-coated surface. Utilising Couette and Poiseuille flow, we investigate to what extend the effect of a brush-coated surface can be described by a Navier slip condition.Comment: 6 pages, 6 figures, submitted for publicatio

Comparison of Dissipative Particle Dynamics and Langevin thermostats for out-of-equilibrium simulations of polymeric systems

In this work we compare and characterize the behavior of Langevin and Dissipative Particle Dynamics (DPD) thermostats in a broad range of non-equilibrium simulations of polymeric systems. Polymer brushes in relative sliding motion, polymeric liquids in Poiseuille and Couette flows, and brush-melt interfaces are used as model systems to analyze the efficiency and limitations of different Langevin and DPD thermostat implementations. Widely used coarse-grained bead-spring models under good and poor solvent conditions are employed to assess the effects of the thermostats. We considered equilibrium, transient, and steady state examples for testing the ability of the thermostats to maintain constant temperature and to reproduce the underlying physical phenomena in non-equilibrium situations. The common practice of switching-off the Langevin thermostat in the flow direction is also critically revisited. The efficiency of different weight functions for the DPD thermostat is quantitatively analyzed as a function of the solvent quality and the non-equilibrium situation.Comment: 12 pages, introduction improved, references added, to appear in Phys. Rev.

Mean properties and Free Energy of a few hard spheres confined in a spherical cavity

We use analytical calculations and event-driven molecular dynamics simulations to study a small number of hard sphere particles in a spherical cavity. The cavity is taken also as the thermal bath so that the system thermalizes by collisions with the wall. In that way, these systems of two, three and four particles, are considered in the canonical ensemble. We characterize various mean and thermal properties for a wide range of number densities. We study the density profiles, the components of the local pressure tensor, the interface tension, and the adsorption at the wall. This spans from the ideal gas limit at low densities to the high-packing limit in which there are significant regions of the cavity for which the particles have no access, due the conjunction of excluded volume and confinement. The contact density and the pressure on the wall are obtained by simulations and compared to exact analytical results. We also obtain the excess free energy for N=4, by using a simulated-assisted approach in which we combine simulation results with the knowledge of the exact partition function for two and three particles in a spherical cavity.Comment: 11 pages, 9 figures and two table

Social Cognition in Neurodevelopmental Disorders and Epilepsy

Introduction: The purpose of our study was to perform a comparative analysis of social cognition in children and adolescents with epilepsy, autism spectrum disorder (ASD), specific learning disorder (SLD) and in typical development (TD) controls. The secondary aim was to relate social cognition to some clinical and demographic characteristics. Methods: Our work is a transversal observational study. The recruits were 179 children and adolescents aged between 6 and 18 years diagnosed with epilepsy, ASD, or SLD and 32 subjects with TD. All the participants underwent neuropsychological assessment of Emotion Recognition (ER) and Theory of Mind (ToM) skills. Results: All three clinical groups performed significantly worse than controls in ER and ToM. The ASD group achieved significantly lower performance than the other groups; however, the scores of SLD and epilepsy groups were comparable. The ER performances are related to non-verbal intelligence only in the group with epilepsy. Conclusion: Children and adolescents with focal epilepsy, SLD, or ASD may present a deficit of varying extent in emotion recognition and ToM, compared with TD peers. These difficulties are more pronounced in individuals with ASD, but impairment worthy of clinical attention also emerges in individuals with SLD and epilepsy

Static and dynamic properties of the interface between a polymer brush and a melt of identical chains

Molecular dynamics simulations of a short-chain polymer melt between two brush-covered surfaces under shear have been performed. The end-grafted polymers which constitute the brush have the same chemical properties as the free chains in the melt and provide a soft deformable substrate. Polymer chains are described by a coarse-grained bead-spring model with Lennard-Jones interactions between the beads and a FENE potential between nearest neighbors along the backbone of the chains. The grafting density of the brush layer offers a way of controlling the behavior of the surface without altering the molecular interactions. We perform equilibrium and non-equilibrium Molecular Dynamics simulations at constant temperature and volume using the Dissipative Particle Dynamics thermostat. The equilibrium density profiles and the behavior under shear are studied as well as the interdigitation of the melt into the brush, the orientation on different length scales (bond vectors, radius of gyration, and end-to-end vector) of free and grafted chains, and velocity profiles. The viscosity and slippage at the interface are calculated as functions of grafting density and shear velocity.Comment: 12 pages, submitted to J Chem Phy

Nanotribology of biopolymer brushes in aqueous solution using dissipative particle dynamics simulations: an application to PEG covered liposomes in theta solvent

We undertake the investigation of sheared polymer chains grafted on flat surfaces to model liposomes covered with polyethylene glycol brushes as a case study for the mechanisms of efficient drug delivery in biologically relevant situations, for example, as carriers for topical treatments of illnesses in the human vasculature. For these applications, specific rheological properties are required, such as low viscosity at high shear rate to improve the transport of the liposomes. Therefore non - equilibrium, DPD simulations of polymer brushes of various length and shear rates are performed to obtain the average viscosity and friction coefficient of the system as functions of the shear rate and polymerization degree under theta solvent conditions, and find that the brushes experience shear thinning at large shear rates.The viscosity and the friction coefficient are shown to obey scaling laws at high shear rate in theta solvent, irrespective of the brushes degree of polymerization. These results confirm recent scaling predictions and reproduce very well trends in measurements of the viscosity at high shear of red blood cells in a liposome containing medium.Comment: 32 pages, 8 figure