Biomedical subjects

Giulio Costantini

Publications and source records attributed to Giulio Costantini.

5 recordsLinked to original sources

PubMed2006

Transport of a heated granular gas in a washboard potential.

We study numerically the motion of a one dimensional array of Brownian particles in a washboard potential, driven by an external stochastic force and interacting via short range repulsive forces. In particular, we investigate the role of instantaneous elastic and inelastic collisions on the system dynamics and transport. The system displays a locked regime, where particles may move only via activated processes and a running regime where particles drift along the direction of the applied field. By tuning the value of the friction parameter controlling the Brownian motion we explore both the overdamped dynamics and the underdamped dynamics. In the two regimes we considered the mobility and the diffusivity of the system as functions of the tilt and other relevant control parameters such as coefficient of restitution, particle size, and total number of particles. We find that while in the overdamped regime the results for the interacting systems present similarities with the known noninteracting case, in the underdamped regime the inelastic collisions determine a rich variety of behaviors among which is an unexpected enhancement of the inelastic diffusion.

Algorithms↗

PubMed2006

Inelastic Takahashi hard-rod gas.

We study a one-dimensional fluid of hard rods interacting with each other via binary inelastic collisions and a short-ranged square-well potential. Upon tuning the depth and the sign of the well, we investigate the interplay between dissipation and cohesive or repulsive forces. Molecular-dynamics simulations of the cooling regime indicate that the presence of this simple interparticle interaction is sufficient to significantly modify the energy dissipation rates expected by Haff's law for the free cooling. The simplicity of the model makes it amenable to an analytical approach based on the Boltzmann-Enskog transport equation which allows deriving the behavior of the granular temperature. Furthermore, in the elastic limit, the model can be solved exactly to provide a full thermodynamic description. A meaningful theoretical approximation explaining the properties of the inelastic system in interaction with a thermal bath can be directly extrapolated from the properties of the corresponding elastic system, upon a proper redefinition of the relevant observables. Simulation results both in the cooling and driven regimes can be fairly interpreted according to our theoretical approach and compare rather well to our predictions.

Journal Article↗

PubMed2005

The inelastic hard dimer gas: a nonspherical model for granular matter.

We study a two-dimensional gas of inelastic smooth hard dimers. Since the collisions between dimers are dissipative, being characterized by a coefficient of restitution alpha<1, and no external driving force is present, the energy of the system decreases in time and no stationary state is achieved. However, the resulting nonequilibrium state of the system displays several interesting properties in close analogy with systems of inelastic hard spheres, whose relaxational dynamics has been thoroughly explored. We generalize to inelastic systems a recently method introduced [G. Ciccotti and G. Kalibaeva, J. Stat. Phys. 115, 701 (2004)] to study the dynamics of rigid elastic bodies made up of different spheres held together by rigid bonds. Each dimer consists of two hard disks of diameter d, whose centers are separated by a fixed distance a. By describing the rigid bonds by means of holonomic constraints and deriving the appropriate collision rules between dimers, we reduce the dynamics to a set of equations which can be solved by means of event-driven simulation. After deriving the algorithm we study the decay of the total kinetic energy, and of the ratio between the rotational and the translational kinetic energy of inelastic dimers. We show numerically that the celebrated Haff's homogeneous cooling law t(-2), describing how the kinetic energy of an inelastic hard-sphere system with a constant coefficient of restitution decreases in time, holds even in the case of these nonspherical particles. We fully characterize this homogeneous decay process in terms of appropriate decay constants and confirm numerically the scaling behavior of the velocity distributions.

Journal Article↗

PubMed2003

A combined atomic force microscopy and molecular dynamics simulation study on a plastocyanin mutant chemisorbed on a gold surface.

A mutant of copper plastocyanin, covalently bound to an Au (111) surface through an engineered disulfide bridge, was investigated in aqueous medium by atomic force microscopy (AFM) and molecular dynamics (MD) simulations. Tapping-mode AFM images revealed adsorption of single molecules which are homogeneously distributed over the substrate and strongly bound to gold and display uniform lateral size. A statistical analysis of the height of the macromolecules on the gold substrate evidenced a distribution around a mean value consistent with that expected from the crystallographic data and with a relatively large standard deviation. A 10-ns classical MD simulation of mutated plastocyanin, hydrated by a layer of water, covalently bound to a gold surface by one or two sulfur atoms, was performed. The simulations indicate that the bound protein retains, in both cases, its overall tertiary structure during the dynamic evolution. Moreover, the macro-molecule can assume different orientations with respect to the gold substrate, which give rise to a distribution of heights on the gold substrate. Experimental and MD simulation results are compared and discussed in connection with the topological and dynamical properties of the protein system.

Adsorption↗

PubMed2003

MD simulation of a plastocyanin mutant adsorbed onto a gold surface.

MD simulation of plastocyanin, an electron transfer protein, adsorbed onto a gold surface, has been performed for 10 ns. Starting from the crystallographic structure of a poplar plastocyanin mutant engineered with the insertion of a disulfide bridge, the protein has been anchored to a gold substrate modeled by a cluster of three layers in the Au<111> configuration. A number of significant structural and dynamical properties of the protein molecule, covalently bound through either one or two sulfur atoms to the gold surface, has been extracted and compared with those of the free protein. Attention has been paid to investigate the dynamical aspects putatively related to the electron transfer process. In particular, the cross-correlation function between specific active site vibrations and all the other protein atom motions and the principal component analysis have been calculated in order to put into evidence dynamical correlation of some functional relevance. The results are discussed also in connection with related experiments.

Absorption↗