Editorial overview: Folding and binding: In silico, in vitro and in cellula

The essence of any biological processes relies on the conformational states of macromolecules and their interactions. It comes therefore with no surprises that the study of folding and binding has been centre stage since the birth of structural biology. In this context, the collaborative efforts of experimen- talists and theoreticians have tremendously increased our current knowl- edge on macromolecular structure and recognition. Nevertheless, several challenges and open questions are still present and a multidisciplinary approach would appear the most appropriate means to shed light onto the mechanisms of folding and binding to the highest level of detail. This thematic issue brings together a collection of reviews describing our current understanding of folding and binding, looking at these fundamental pro- blems from a wide perspective ranging from the single molecule to the complexity of the living cell, drawing on approaches that span from compu- tational (in silico), to the test tube (in vitro) and cell cultures (in cellula)

Local modularity measure for network clusterizations

Many complex networks have an underlying modular structure, i.e., structural subunits (communities or clusters) characterized by highly interconnected nodes. The modularity $Q$ has been introduced as a measure to assess the quality of clusterizations. $Q$ has a global view, while in many real-world networks clusters are linked mainly \emph{locally} among each other (\emph{local cluster-connectivity}). Here, we introduce a new measure, localized modularity $LQ$, which reflects local cluster structure. Optimization of $Q$ and $LQ$ on the clusterization of two biological networks shows that the localized modularity identifies more cohesive clusters, yielding a complementary view of higher granularity.Comment: 5 pages, 4 figures, RevTex4; Changed conten

Level Set Approach to Reversible Epitaxial Growth

We generalize the level set approach to model epitaxial growth to include thermal detachment of atoms from island edges. This means that islands do not always grow and island dissociation can occur. We make no assumptions about a critical nucleus. Excellent quantitative agreement is obtained with kinetic Monte Carlo simulations for island densities and island size distributions in the submonolayer regime.Comment: 7 pages, 9 figure

On Strong Convergence to Equilibrium for the Boltzmann Equation with Soft Potentials

The paper concerns $L^1$- convergence to equilibrium for weak solutions of the spatially homogeneous Boltzmann Equation for soft potentials (-4\le \gm<0), with and without angular cutoff. We prove the time-averaged $L^1$-convergence to equilibrium for all weak solutions whose initial data have finite entropy and finite moments up to order greater than 2+|\gm|. For the usual $L^1$-convergence we prove that the convergence rate can be controlled from below by the initial energy tails, and hence, for initial data with long energy tails, the convergence can be arbitrarily slow. We also show that under the integrable angular cutoff on the collision kernel with -1\le \gm<0, there are algebraic upper and lower bounds on the rate of $L^1$-convergence to equilibrium. Our methods of proof are based on entropy inequalities and moment estimates.Comment: This version contains a strengthened theorem 3, on rate of convergence, considerably relaxing the hypotheses on the initial data, and introducing a new method for avoiding use of poitwise lower bounds in applications of entropy production to convergence problem

Sharp interface limits of phase-field models

The use of continuum phase-field models to describe the motion of well-defined interfaces is discussed for a class of phenomena, that includes order/disorder transitions, spinodal decomposition and Ostwald ripening, dendritic growth, and the solidification of eutectic alloys. The projection operator method is used to extract the ``sharp interface limit'' from phase field models which have interfaces that are diffuse on a length scale $\xi$. In particular,phase-field equations are mapped onto sharp interface equations in the limits $\xi \kappa \ll 1$ and $\xi v/D \ll 1$, where $\kappa$ and $v$ are respectively the interface curvature and velocity and $D$ is the diffusion constant in the bulk. The calculations provide one general set of sharp interface equations that incorporate the Gibbs-Thomson condition, the Allen-Cahn equation and the Kardar-Parisi-Zhang equation.Comment: 17 pages, 9 figure

The Moment Guided Monte Carlo method for the Boltzmann equation

In this work we propose a generalization of the Moment Guided Monte Carlo method developed in [11]. This approach permits to reduce the variance of the particle methods through a matching with a set of suitable macroscopic moment equations. In order to guarantee that the moment equations provide the correct solutions, they are coupled to the kinetic equation through a non equilibrium term. Here, at the contrary to the previous work in which we considered the simplified BGK operator, we deal with the full Boltzmann operator. Moreover, we introduce an hybrid setting which permits to entirely remove the resolution of the kinetic equation in the limit of infinite number of collisions and to consider only the solution of the compressible Euler equation. This modification additionally reduce the statistical error with respect to our previous work and permits to perform simulations of non equilibrium gases using only a few number of particles. We show at the end of the paper several numerical tests which prove the efficiency and the low level of numerical noise of the method.Comment: arXiv admin note: text overlap with arXiv:0908.026

Pricing and Hedging Asian Basket Options with Quasi-Monte Carlo Simulations

In this article we consider the problem of pricing and hedging high-dimensional Asian basket options by Quasi-Monte Carlo simulation. We assume a Black-Scholes market with time-dependent volatilities and show how to compute the deltas by the aid of the Malliavin Calculus, extending the procedure employed by Montero and Kohatsu-Higa (2003). Efficient path-generation algorithms, such as Linear Transformation and Principal Component Analysis, exhibit a high computational cost in a market with time-dependent volatilities. We present a new and fast Cholesky algorithm for block matrices that makes the Linear Transformation even more convenient. Moreover, we propose a new-path generation technique based on a Kronecker Product Approximation. This construction returns the same accuracy of the Linear Transformation used for the computation of the deltas and the prices in the case of correlated asset returns while requiring a lower computational time. All these techniques can be easily employed for stochastic volatility models based on the mixture of multi-dimensional dynamics introduced by Brigo et al. (2004).Comment: 16 page

Motion of a vortex sheet on a sphere with pole vortices

We cons i der the motion of a vortex sheet on the surface of a unit sphere in the presence of point vortices xed on north and south poles.Analytic and numerical research revealed that a vortex sheet in two-dimensional space has the following three properties.First,the vortex sheet is linearly unstable due to Kelvin-Helmholtz instability.Second,the curvature of the vortex sheet diverges in nite time.Last,the vortex sheet evolves into a rolling-up doubly branched spiral,when the equation of motion is regularized by the vortex method.The purpose of this article is to investigate how the curvature of the sphere and the presence of the pole vortices