Clustering and coalescence from multiplicative noise: the Kraichnan ensemble

We study the dynamics of the two-point statistics of the Kraichnan ensemble which describes the transport of a passive pollutant by a stochastic turbulent flow characterized by scale invariant structure functions. The fundamental equation of this problem consists in the Fokker-Planck equation for the two-point correlation function of the density of particles performing spatially correlated Brownian motions with scale invariant correlations. This problem is equivalent to the stochastic motion of an effective particle driven by a generic multiplicative noise. In this paper we propose an alternative and more intuitive approach to the problem than the original one leading to the same conclusions. The general features of this new approach make possible to fit it to other more complex contexts.Comment: IOP-LaTeX, 17 pages J. Phys. A: Theor. Mat. 2008 in pres

Transport and fluctuation-dissipation relations in asymptotic and pre-asymptotic diffusion across channels with variable section

We study the asymptotic and pre-asymptotic diffusive properties of Brownian particles in channels whose section varies periodically in space. The effective diffusion coefficient $D_{\mathrm{eff}}$ is numerically determined by the asymptotic behavior of the root mean square displacement in different geometries, considering even cases of steep variations of the channel boundaries. Moreover, we compared the numerical results to the predictions from the various corrections proposed in the literature to the well known Fick-Jacobs approximation. Building an effective one dimensional equation for the longitudinal diffusion, we obtain an approximation for the effective diffusion coefficient. Such a result goes beyond a perturbation approach, and it is in good agreement with the actual values obtained by the numerical simulations. We discuss also the pre-asymptotic diffusion which is observed up to a crossover time whose value, in the presence of strong spatial variation of the channel cross section, can be very large. In addition, we show how the Einstein's relation between the mean drift induced by a small external field and the mean square displacement of the unperturbed system is valid in both asymptotic and pre-asymptotic regimes.Comment: RevTeX 4-1, 11 Pages, 11 pdf figure

Computational analysis of folding and mutation properties of C5 domain from Myosin binding protein C

Thermal folding Molecular Dynamics simulations of the domain C5 from Myosin Binding Protein C were performed using a native-centric model to study the role of three mutations related to Familial Hypertrophic Cardiomyopathy. Mutation of Asn755 causes the largest shift of the folding temperature, and the residue is located in the CFGA' beta-sheet featuring the highest Phi-values. The mutation thus appears to reduce the thermodynamic stability in agreement with experimental data. The mutations on Arg654 and Arg668, conversely, cause a little change in the folding temperature and they reside in the low Phi-value BDE beta-sheet, so that their pathologic role cannot be related to impairment of the folding process but possibly to the binding with target molecules. As the typical signature of Domain C5 is the presence of a longer and destabilizing CD-loop with respect to the other Ig-like domains we completed the work with a bioinformatic analysis of this loop showing a high density of negative charge and low hydrophobicity. This indicates the CD-loop as a natively unfolded sequence with a likely coupling between folding and ligand binding.Comment: RevTeX, 10 pages, 9 eps-figure

Kinetics of self-induced aggregation in Brownian particles

We study a model of interacting random walkers that proposes a simple mechanism for the emergence of cooperation in group of individuals. Each individual, represented by a Brownian particle, experiences an interaction produced by the local unbalance in the spatial distribution of the other individuals. This interaction results in a nonlinear velocity driving the particle trajectories in the direction of the nearest more crowded regions; the competition among different aggregating centers generates nontrivial dynamical regimes. Our simulations show that for sufficiently low randomness, the system evolves through a coalescence behavior characterized by clusters of particles growing with a power law in time. In addition, the typical scaling properties of the general theory of stochastic aggregation processes are verified.Comment: RevTeX, 9 pages, 9 eps-figure

Mean Field Approach for a Statistical Mechanical Model of Proteins

We study the thermodynamical properties of a topology-based model proposed by Galzitskaya and Finkelstein for the description of protein folding. We devise and test three different mean-field approaches for the model, that simplify the treatment without spoiling the description. The validity of the model and its mean-field approximations is checked by applying them to the $\beta$-hairpin fragment of the immunoglobulin-binding protein (GB1) and making a comparison with available experimental data and simulation results. Our results indicate that this model is a rather simple and reasonably good tool for interpreting folding experimental data, provided the parameters of the model are carefully chosen. The mean-field approaches substantially recover all the relevant exact results and represent reliable alternatives to the Monte Carlo simulations.Comment: RevTeX-4, 11 pages, 6 eps-figures, To Appear on J.Chem.Phy

Driven diffusion against electrostatic or effective energy barrier across Alpha-Hemolysin

We analyze the translocation of a charged particle across an Alpha-Hemolysin (aHL) pore in the framework of a driven diffusion over an extended energy barrier generated by the electrical charges of the aHL. A one-dimensional electrostatic potential is extracted from the full 3D solution of the Poisson's equation. We characterize the particle transport under the action of a constant forcing by studying the statistics of the translocation time. We derive an analytical expression of translocation time average that compares well with the results from Brownian dynamic simulations of driven particles over the electrostatic potential. Moreover, we show that the translocation time distributions can be perfectly described by a simple theory which replaces the true barrier by an equivalent structureless square barrier. Remarkably our approach maintains its accuracy also for low-applied voltage regimes where the usual inverse-Gaussian approximation fails. Finally we discuss how the comparison between the simulated time distributions and their theoretical prediction results to be greatly simplified when using the notion of the empirical Laplace transform technique.Comment: RevTeX 4-1, 11 pages, 6 pdf figures, J. Chem. Phys. 2015 in pres