A characterization of balanced episturmian sequences

It is well known that Sturmian sequences are the aperiodic sequences that are balanced over a 2-letter alphabet. They are also characterized by their complexity: they have exactly $(n+1)$ factors of length $n$. One possible generalization of Sturmian sequences is the set of infinite sequences over a $k$-letter alphabet, $k \geq 3$, which are closed under reversal and have at most one right special factor for each length. This is the set of episturmian sequences. These are not necessarily balanced over a $k$-letter alphabet, nor are they necessarily aperiodic. In this paper, we characterize balanced episturmian sequences, periodic or not, and prove Fraenkel's conjecture for the class of episturmian sequences. This conjecture was first introduced in number theory and has remained unsolved for more than 30 years. It states that for a fixed $k> 2$, there is only one way to cover $\Z$ by $k$ Beatty sequences. The problem can be translated to combinatorics on words: for a $k$-letter alphabet, there exists only one balanced sequence up to letter permutation that has different letter frequencies

Evolution of Brain Tumor and Stability of Geometric Invariants

This paper presents a method to reconstruct and to calculate geometric invariants on brain tumors. The geometric invariants considered in the paper are the volume, the area, the discrete Gauss curvature, and the discrete mean curvature. The volume of a tumor is an important aspect that helps doctors to make a medical diagnosis. And as doctors seek a stable calculation, we propose to prove the stability of some invariants. Finally, we study the evolution of brain tumor as a function of time in two or three years depending on patients with MR images every three or six months

Enumerating Abelian Returns to Prefixes of Sturmian Words

We follow the works of Puzynina and Zamboni, and Rigo et al. on abelian returns in Sturmian words. We determine the cardinality of the set $\mathcal{APR}_u$ of abelian returns of all prefixes of a Sturmian word $u$ in terms of the coefficients of the continued fraction of the slope, dependingly on the intercept. We provide a simple algorithm for finding the set $\mathcal{APR}_u$ and we determine it for the characteristic Sturmian words.Comment: 19page

Describing the set of words generated by interval exchange transformation

Let $W$ be an infinite word over finite alphabet $A$. We get combinatorial criteria of existence of interval exchange transformations that generate the word W.Comment: 17 pages, this paper was submitted at scientific council of MSU, date: September 21, 200

On the Language of Standard Discrete Planes and Surfaces

International audienceA standard discrete plane is a subset of Z^3 verifying the double Diophantine inequality mu =< ax+by+cz < mu + omega, with (a,b,c) != (0,0,0). In the present paper we introduce a generalization of this notion, namely the (1,1,1)-discrete surfaces. We first study a combinatorial representation of discrete surfaces as two-dimensional sequences over a three-letter alphabet and show how to use this combinatorial point of view for the recognition problem for these discrete surfaces. We then apply this combinatorial representation to the standard discrete planes and give a first attempt of to generalize the study of the dual space of parameters for the latter [VC00]

Beta-Strand Interfaces of Non-Dimeric Protein Oligomers Are Characterized by Scattered Charged Residue Patterns

Protein oligomers are formed either permanently, transiently or even by default. The protein chains are associated through intermolecular interactions constituting the protein interface. The protein interfaces of 40 soluble protein oligomers of stœchiometries above two are investigated using a quantitative and qualitative methodology, which analyzes the x-ray structures of the protein oligomers and considers their interfaces as interaction networks. The protein oligomers of the dataset share the same geometry of interface, made by the association of two individual β-strands (β-interfaces), but are otherwise unrelated. The results show that the β-interfaces are made of two interdigitated interaction networks. One of them involves interactions between main chain atoms (backbone network) while the other involves interactions between side chain and backbone atoms or between only side chain atoms (side chain network). Each one has its own characteristics which can be associated to a distinct role. The secondary structure of the β-interfaces is implemented through the backbone networks which are enriched with the hydrophobic amino acids favored in intramolecular β-sheets (MCWIV). The intermolecular specificity is provided by the side chain networks via positioning different types of charged residues at the extremities (arginine) and in the middle (glutamic acid and histidine) of the interface. Such charge distribution helps discriminating between sequences of intermolecular β-strands, of intramolecular β-strands and of β-strands forming β-amyloid fibers. This might open new venues for drug designs and predictive tool developments. Moreover, the β-strands of the cholera toxin B subunit interface, when produced individually as synthetic peptides, are capable of inhibiting the assembly of the toxin into pentamers. Thus, their sequences contain the features necessary for a β-interface formation. Such β-strands could be considered as ‘assemblons’, independent associating units, by homology to the foldons (independent folding unit). Such property would be extremely valuable in term of assembly inhibitory drug development

Further steps on the reconstruction of convex polyominoes from orthogonal projections

A remarkable family of discrete sets which has recently attracted the attention of the discrete geometry community is the family of convex polyominoes, that are the discrete counterpart of Euclidean convex sets, and combine the constraints of convexity and connectedness. In this paper we study the problem of their reconstruction from orthogonal projections, relying on the approach defined by Barcucci et al. (Theor Comput Sci 155(2):321–347, 1996). In particular, during the reconstruction process it may be necessary to expand a convex subset of the interior part of the polyomino, say the polyomino kernel, by adding points at specific positions of its contour, without losing its convexity. To reach this goal we consider convexity in terms of certain combinatorial properties of the boundary word encoding the polyomino. So, we first show some conditions that allow us to extend the kernel maintaining the convexity. Then, we provide examples where the addition of one or two points causes a loss of convexity, which can be restored by adding other points, whose number and positions cannot be determined a priori