Analytical study of the effect of recombination on evolution via DNA shuffling

We investigate a multi-locus evolutionary model which is based on the DNA shuffling protocol widely applied in \textit{in vitro} directed evolution. This model incorporates selection, recombination and point mutations. The simplicity of the model allows us to obtain a full analytical treatment of both its dynamical and equilibrium properties, for the case of an infinite population. We also briefly discuss finite population size corrections

Absorbing-state phase transitions in fixed-energy sandpiles

We study sandpile models as closed systems, with conserved energy density $\zeta$ playing the role of an external parameter. The critical energy density, $\zeta_c$, marks a nonequilibrium phase transition between active and absorbing states. Several fixed-energy sandpiles are studied in extensive simulations of stationary and transient properties, as well as the dynamics of roughening in an interface-height representation. Our primary goal is to identify the universality classes of such models, in hopes of assessing the validity of two recently proposed approaches to sandpiles: a phenomenological continuum Langevin description with absorbing states, and a mapping to driven interface dynamics in random media. Our results strongly suggest that there are at least three distinct universality classes for sandpiles.Comment: 41 pages, 23 figure

Novel charges in CFT's

In this paper we construct two infinite sets of self-adjoint commuting charges for a quite general CFT. They come out naturally by considering an infinite embedding chain of Lie algebras, an underlying structure that share all theories with gauge groups U(N), SO(N) and Sp(N). The generality of the construction allows us to carry all gauge groups at the same time in a unified framework, and so to understand the similarities among them. The eigenstates of these charges are restricted Schur polynomials and their eigenvalues encode the value of the correlators of two restricted Schurs. The existence of these charges singles out restricted Schur polynomials among the number of bases of orthogonal gauge invariant operators that are available in the literature.Comment: 58 page

Gravitational Dynamics of an Infinite Shuffled Lattice: Particle Coarse-grainings, Non-linear Clustering and the Continuum Limit

We study the evolution under their self-gravity of infinite ``shuffled lattice'' particle distributions, focussing specifically on the comparison of this evolution with that of ``daughter'' particle distributions, defined by a simple coarse-graining procedure. We consider both the case that such coarse-grainings are performed (i) on the initial conditions, and (ii) at a finite time with a specific additional prescription. In numerical simulations we observe that, to a first approximation, these coarse-grainings represent well the evolution of the two-point correlation properties over a significant range of scales. We note, in particular, that the form of the two-point correlation function in the original system, when it is evolving in the asymptotic ``self-similar'' regime, may be reproduced well in a daughter coarse-grained system in which the dynamics are still dominated by two-body (nearest neighbor) interactions. Using analytical results on the early time evolution of these systems, however, we show that small observed differences between the evolved system and its coarse-grainings at the initial time will in fact diverge as the ratio of the coarse-graining scale to the original inter-particle distance increases. The second coarse-graining studied, performed at a finite time in a specified manner, circumvents this problem. It also makes more physically transparent why gravitational dynamics from these initial conditions tends toward a ``self-similar'' evolution. We finally discuss the precise definition of a limit in which a continuum (specifically Vlasov-like) description of the observed linear and non-linear evolution should be applicable.Comment: 21 pages, 8 eps figures, 2 jpeg figures (available in high resolution at http://pil.phys.uniroma1.it/~sylos/PRD_dec_2006/

Cutting and Shuffling a Line Segment: Mixing by Interval Exchange Transformations

We present a computational study of finite-time mixing of a line segment by cutting and shuffling. A family of one-dimensional interval exchange transformations is constructed as a model system in which to study these types of mixing processes. Illustrative examples of the mixing behaviors, including pathological cases that violate the assumptions of the known governing theorems and lead to poor mixing, are shown. Since the mathematical theory applies as the number of iterations of the map goes to infinity, we introduce practical measures of mixing (the percent unmixed and the number of intermaterial interfaces) that can be computed over given (finite) numbers of iterations. We find that good mixing can be achieved after a finite number of iterations of a one-dimensional cutting and shuffling map, even though such a map cannot be considered chaotic in the usual sense and/or it may not fulfill the conditions of the ergodic theorems for interval exchange transformations. Specifically, good shuffling can occur with only six or seven intervals of roughly the same length, as long as the rearrangement order is an irreducible permutation. This study has implications for a number of mixing processes in which discontinuities arise either by construction or due to the underlying physics.Comment: 21 pages, 10 figures, ws-ijbc class; accepted for publication in International Journal of Bifurcation and Chao