Developing frameworks for protocol implementation

This paper presents a method to develop frameworks for protocol implementation. Frameworks are software structures developed for a specific application domain, which can be reused in the implementation of various different concrete systems in this domain. The use of frameworks support a protocol implementation process connected with formal design methods and produce an implementation code easy to extend and to reuse

Interplay between structure and density anomaly for an isotropic core-softened ramp-like potential

Using molecular dynamics simulations and integral equations we investigate the structure, the thermodynamics and the dynamics of a system of particles interacting through a continuous core- softened ramp-like interparticle potential. We found density, dynamic and structural anomalies similar to that found in water. Analysis of the radial distribution function for several temperatures at fixed densities show a pattern that may be related to the origin of density anomaly.Comment: 7 pages, 3 figure

Water-like hierarchy of anomalies in a continuous spherical shouldered potential

We investigate by molecular dynamics simulations a continuous isotropic core-softened potential with attractive well in three dimensions, introduced by Franzese [cond-mat/0703681, to appear on Journal of Molecular Liquids], that displays liquid-liquid coexistence with a critical point and water-like density anomaly. Here we find diffusion and structural anomalies. These anomalies occur with the same hierarchy that characterizes water. Yet our analysis shows differences with respect to the water case. Therefore, many of the anomalous features of water could be present in isotropic systems with soft-core attractive potentials, such as colloids or liquid metals, consistent with recent experiments showing polyamorphism in metallic glasses.Comment: 27 pages, 9 figures. to appear in J. Chem. Phy

An ubiquitous mechanism for waterlike anomalies

Using collision driven molecular dynamics a system of spherical particles interacting through an effective two length scales potential is studied. The potential can be tuned by means of a single parameter, $\lambda$, from a ramp $(\lambda=0.5)$ to a square-shoulder potential $(\lambda=1.0)$ representing a family of two length scales potential in which the shortest interaction distance has higher potential energy than the largest interaction distance. For all the potentials, ranging between the ramp and the square-shoulder, density and structural anomalies were found, while the diffusion anomaly is found in all but in the square-shoulder potential. The presence anomalies in square-shoulder potential, not observed in previous simulations, confirm the assumption that the two length scales potential is an ubiquitous ingredient for a system to exhibit water-like anomaliesComment: 6 pages, 7 figure

Thermodynamic and dynamic anomalies for a three dimensional isotropic core-softened potential

Using molecular dynamics simulations and integral equations (Rogers-Young, Percus-Yevick and hypernetted chain closures) we investigate the thermodynamic of particles interacting with continuous core-softened intermolecular potential. Dynamic properties are also analyzed by the simulations. We show that, for a chosen shape of the potential, the density, at constant pressure, has a maximum for a certain temperature. The line of temperatures of maximum density (TMD) was determined in the pressure-temperature phase diagram. Similarly the diffusion constant at a constant temperature, $D$, has a maximum at a density $\rho_{max}$ and a minimum at a density $\rho_{min}<\rho_{max}$. In the pressure-temperature phase-diagram the line of extrema in diffusivity is outside of TMD line. Although in this interparticle potential lacks directionality, this is the same behavior observed in SPC/E water.Comment: 16 page

Liquid crystal phase and waterlike anomalies in a core-softened shoulder-dumbbells system

Using molecular dynamics we investigate the thermodynamics, dynamics and structure of 250 diatomic molecules interacting by a core-softened potential. This system exhibits thermodynamics, dynamics and structural anomalies: a maximum in density-temperature plane at constante pressure and maximum and minimum points in the diffusivity and translational order parameter against density at constant temperature. Starting with very dense systems and decreasing density the mobility at low temperatures first increases, reach a maximum, then decreases, reach a minimum and finally increases. In the pressure-temperature phase diagram the line of maximum translational order parameter is located outside the line of diffusivity extrema that is enclosing the temperature of maximum density line. We compare our results with the monomeric system showing that the anisotropy due to the dumbbell leads to a much larger solid phase and to the appearance of a liquid crystal phase. the double ranged thermodynamic and dynamic anomalies.Comment: 14 pages, 5 figure

Entropy, diffusivity and the energy landscape of a water-like fluid

Molecular dynamics simulations and instantaneous normal mode (INM) analysis of a fluid with core-softened pair interactions and water-like liquid-state anomalies are performed to obtain an understanding of the relationship between thermodynamics, transport properties and the poten- tial energy landscape. Rosenfeld-scaling of diffusivities with the thermodynamic excess and pair correlation entropy is demonstrated for this model. The INM spectra are shown to carry infor- mation about the dynamical consequences of the interplay between length scales characteristic of anomalous fluids, such as bimodality of the real and imaginary branches of the frequency distribu- tion. The INM spectral information is used to partition the liquid entropy into two contributions associated with the real and imaginary frequency modes; only the entropy contribution from the imaginary branch captures the non-monotonic behaviour of the excess entropy and diffusivity in the anomalous regime of the fluid

Postmenopausal Osteoporosis reference genes for qPCR expression assays

Osteoporosis (OP) is a multifactorial disease influenced by genetic factors in more than half of the cases. In spite of the efforts to clarify the relationship among genetic factors and susceptibility to develop OP, many genetic associations need to be further functionally validated. Besides, some limitations as the choice of stably expressed reference genes (RG) should be overcome to ensure the quality and reproducibility of gene expression assays. To our knowledge, a validation study for RG in OP is still missing. We compared the expression levels, using polymerase chain reaction quantitative real time (qPCR) of 10 RG (G6PD, B2M, GUSB, HSP90, EF1A, RPLP0, GAPDH, ACTB, 18 S and HPRT1) to assess their suitability in OP analysis by using GeNorm, Normfinder, BestKeeper and RefFinder programs. A minimal number of two RG was recommended by GeNorm to obtain a reliable normalization. RPLP0 and B2M were identified as the most stable genes in OP studies while ACTB, 18 S and HPRT1 were inadequate for normalization in our data set. Moreover, we showed the dramatic effects of suboptimal RG choice on the quantification of a target gene, highlighting the importance in the identification of the most appropriate reference gene to specific diseases. We suggest the use of RPLP0 and B2M as the most stable reference genes while we do not recommend the use of the least stable reference genes HPRT1, 18 S and ACTB in OP expression assays using PBMC as biological source. Additionally, we emphasize the importance of individualized and careful choice in software and reference genes selection