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

Combinatorial Hopf algebra structure on packed square matrices

We construct a new bigraded Hopf algebra whose bases are indexed by square matrices with entries in the alphabet $\{0, 1, ..., k\}$, $k \geq 1$, without null rows or columns. This Hopf algebra generalizes the one of permutations of Malvenuto and Reutenauer, the one of $k$-colored permutations of Novelli and Thibon, and the one of uniform block permutations of Aguiar and Orellana. We study the algebraic structure of our Hopf algebra and show, by exhibiting multiplicative bases, that it is free. We moreover show that it is self-dual and admits a bidendriform bialgebra structure. Besides, as a Hopf subalgebra, we obtain a new one indexed by alternating sign matrices. We study some of its properties and algebraic quotients defined through alternating sign matrices statistics.Comment: 35 page

Hopf algebras and Markov chains: Two examples and a theory

The operation of squaring (coproduct followed by product) in a combinatorial Hopf algebra is shown to induce a Markov chain in natural bases. Chains constructed in this way include widely studied methods of card shuffling, a natural "rock-breaking" process, and Markov chains on simplicial complexes. Many of these chains can be explictly diagonalized using the primitive elements of the algebra and the combinatorics of the free Lie algebra. For card shuffling, this gives an explicit description of the eigenvectors. For rock-breaking, an explicit description of the quasi-stationary distribution and sharp rates to absorption follow.Comment: 51 pages, 17 figures. (Typographical errors corrected. Further fixes will only appear on the version on Amy Pang's website, the arXiv version will not be updated.

Avoiding and Enforcing Repetitive Structures in Words

The focus of this thesis is on the study of repetitive structures in words, a central topic in the area of combinatorics on words. The results presented in the thesis at hand are meant to extend and enrich the existing theory concerning the appearance and absence of such structures. In the first part we examine whether these structures necessarily appear in infinite words over a finite alphabet. The repetitive structures we are concerned with involve functional dependencies between the parts that are repeated. In particular, we study avoidability questions of patterns whose repetitive structure is disguised by the application of a permutation. This novel setting exhibits the surprising behaviour that avoidable patterns may become unavoidable in larger alphabets. The second and major part of this thesis deals with equations on words that enforce a certain repetitive structure involving involutions in their solution set. Czeizler et al. (2009) introduced a generalised version of the classical equations u` Æ vmwn that were studied by Lyndon and Schützenberger. We solve the last two remaining and most challenging cases and thereby complete the classification of these equations in terms of the repetitive structures appearing in the admitted solutions. In the final part we investigate the influence of the shuffle operation on words avoiding ordinary repetitions. We construct finite and infinite square-free words that can be shuffled with themselves in a way that preserves squarefreeness. We also show that the repetitive structure obtained by shuffling a word with itself is avoidable in infinite words

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/

From Aztec diamonds to pyramids: steep tilings

We introduce a family of domino tilings that includes tilings of the Aztec diamond and pyramid partitions as special cases. These tilings live in a strip of $\mathbb{Z}^2$ of the form $1 \leq x-y \leq 2\ell$ for some integer $\ell \geq 1$, and are parametrized by a binary word $w\in\{+,-\}^{2\ell}$ that encodes some periodicity conditions at infinity. Aztec diamond and pyramid partitions correspond respectively to $w=(+-)^\ell$ and to the limit case $w=+^\infty-^\infty$. For each word $w$ and for different types of boundary conditions, we obtain a nice product formula for the generating function of the associated tilings with respect to the number of flips, that admits a natural multivariate generalization. The main tools are a bijective correspondence with sequences of interlaced partitions and the vertex operator formalism (which we slightly extend in order to handle Littlewood-type identities). In probabilistic terms our tilings map to Schur processes of different types (standard, Pfaffian and periodic). We also introduce a more general model that interpolates between domino tilings and plane partitions.Comment: 36 pages, 22 figures (v3: final accepted version with new Figure 6, new improved proof of Proposition 11