30 research outputs found
Two infinite families of polyominoes that tile the plane by translation in two distinct ways
It has been proved that, among the polyominoes that tile the plane by translation, the so-called squares tile the plane in at most two distinct ways. In this paper, we focus on double squares, that is, the polyominoes that tile the plane in exactly two distinct ways. Our approach is based on solving equations on words, which allows us to exhibit properties about their shape. Moreover, we describe two infinite families of double squares. The first one is directly linked to Christoffel words and may be interpreted as segments of thick straight lines. The second one stems from the Fibonacci sequence and reveals some fractal features
Combinatorial aspects of Escher tilings
International audienceIn the late 30's, Maurits Cornelis Escher astonished the artistic world by producing some puzzling drawings. In particular, the tesselations of the plane obtained by using a single tile appear to be a major concern in his work, drawing attention from the mathematical community. Since a tile in the continuous world can be approximated by a path on a sufficiently small square grid - a widely used method in applications using computer displays - the natural combinatorial object that models the tiles is the polyomino. As polyominoes are encoded by paths on a four letter alphabet coding their contours, the use of combinatorics on words for the study of tiling properties becomes relevant. In this paper we present several results, ranging from recognition of these tiles to their generation, leading also to some surprising links with the well-known sequences of Fibonacci and Pell.Lorsque Maurits Cornelis Escher commença à la fin des années 30 à produire des pavages du plan avec des tuiles, il étonna le monde artistique par la singularité de ses dessins. En particulier, les pavages du plan obtenus avec des copies d'une seule tuile apparaissent souvent dans son œuvre et ont attiré peu à peu l'attention de la communauté mathématique. Puisqu'une tuile dans le monde continu peut être approximée par un chemin sur un réseau carré suffisamment fin - une méthode universellement utilisée dans les applications utilisant des écrans graphiques - l'objet combinatoire qui modèle adéquatement la tuile est le polyomino. Comme ceux-ci sont naturellement codés par des chemins sur un alphabet de quatre lettres, l'utilisation de la combinatoire des mots devient pertinente pour l'étude des propriétés des tuiles pavantes. Nous présentons dans ce papier plusieurs résultats, allant de la reconnaissance de ces tuiles à leur génération, conduisant à des liens surprenants avec les célèbres suites de Fibonacci et de Pell
Heesch numbers of unmarked polyforms
A shape's Heesch number is the number of layers of copies of the shape that can be placed around it without gaps or overlaps. Experimentation and exhaustive searching have turned up examples of shapes with finite Heesch numbers up to six, but nothing higher. The computational problem of classifying simple families of shapes by Heesch number can provide more experimental data to fuel our understanding of this topic. I present a technique for computing Heesch numbers of nontiling polyforms using a SAT solver, and the results of exhaustive computation of Heesch numbers up to 19-ominoes, 17-hexes, and 24-iamonds
An aperiodic monotile
A longstanding open problem asks for an aperiodic monotile, also known as an
"einstein": a shape that admits tilings of the plane, but never periodic
tilings. We answer this problem for topological disk tiles by exhibiting a
continuum of combinatorially equivalent aperiodic polygons. We first show that
a representative example, the "hat" polykite, can form clusters called
"metatiles", for which substitution rules can be defined. Because the metatiles
admit tilings of the plane, so too does the hat. We then prove that generic
members of our continuum of polygons are aperiodic, through a new kind of
geometric incommensurability argument. Separately, we give a combinatorial,
computer-assisted proof that the hat must form hierarchical -- and hence
aperiodic -- tilings.Comment: 89 pages, 57 figures; Minor corrections, renamed "fylfot" to
"triskelion", added the name "turtle", added references, new H7/H8 rules (Fig
2.11), talk about reflection
Enumeration of polyominoes defined in terms of pattern avoidance or convexity constraints
In this thesis, we consider the problem of characterizing and enumerating
sets of polyominoes described in terms of some constraints, defined either by
convexity or by pattern containment. We are interested in a well known subclass
of convex polyominoes, the k-convex polyominoes for which the enumeration
according to the semi-perimeter is known only for k=1,2. We obtain, from a
recursive decomposition, the generating function of the class of k-convex
parallelogram polyominoes, which turns out to be rational. Noting that this
generating function can be expressed in terms of the Fibonacci polynomials, we
describe a bijection between the class of k-parallelogram polyominoes and the
class of planted planar trees having height less than k+3. In the second part
of the thesis we examine the notion of pattern avoidance, which has been
extensively studied for permutations. We introduce the concept of pattern
avoidance in the context of matrices, more precisely permutation matrices and
polyomino matrices. We present definitions analogous to those given for
permutations and in particular we define polyomino classes, i.e. sets downward
closed with respect to the containment relation. So, the study of the old and
new properties of the redefined sets of objects has not only become
interesting, but it has also suggested the study of the associated poset. In
both approaches our results can be used to treat open problems related to
polyominoes as well as other combinatorial objects.Comment: PhD thesi
Programmation et indécidabilités dans les systèmes complexes
N/AUn système complexe est un système constitué d'un ensemble d'entités quiinteragissent localement, engendrant des comportements globaux, émergeant dusystème, qu'on ne sait pas expliquer à partir du comportement local, connu, desentités qui le constituent. Nos travaux ont pour objet de mieux cerner lesliens entre certaines propriétés des systèmes complexes et le calcul. Parcalcul, il faut entendre l'objet d'étude de l'informatique, c'est-à-dire ledéplacement et la combinaison d'informations. À l'aide d'outils issus del'informatique, l'algorithmique et la programmation dans les systèmes complexessont abordées selon trois points de vue. Une première forme de programmation,dite externe, consiste à développer l'algorithmique qui permet de simuler lessystèmes étudiés. Une seconde forme de programmation, dite interne, consiste àdévelopper l'algorithmique propre à ces systèmes, qui permet de construire desreprésentants de ces systèmes qui exhibent des comportements programmés. Enfin,une troisième forme de programmation, de réduction, consiste à plonger despropriétés calculatoires complexes dans les représentants de ces systèmes pourétablir des résultats d'indécidabilité -- indice d'une grande complexitécalculatoire qui participe à l'explication de la complexité émergente. Afin demener à bien cette étude, les systèmes complexes sont modélisés par desautomates cellulaires. Le modèle des automates cellulaires offre une dualitépertinente pour établir des liens entre complexité des propriétés globales etcalcul. En effet, un automate cellulaire peut être décrit à la fois comme unréseau d'automates, offrant un point de vue familier de l'informatique, etcomme un système dynamique discret, une fonction définie sur un espacetopologique, offrant un point de vue familier de l'étude des systèmesdynamiques discrets.Une première partie de nos travaux concerne l'étude de l'objet automatecellulaire proprement dit. L'observation expérimentale des automatescellulaires distingue, dans la littérature, deux formes de dynamiques complexesdominantes. Certains automates cellulaires présentent une dynamique danslaquelle émergent des structures simples, sortes de particules qui évoluentdans un domaine régulier, se rencontrent lors de brèves collisions, avant degénérer d'autres particules. Cette forme de complexité, dans laquelletransparaît une notion de quanta d'information localisée en interaction, estl'objet de nos études. Un premier champ de nos investigations est d'établir uneclassification algébrique, le groupage, qui tend à rendre compte de ce type decomportement. Cette classification met à jour un type d'automate cellulaireparticulier : les automates cellulaires intrinsèquement universels. Un automatecellulaire intrinsèquement universel est capable de simuler le comportement detout automate cellulaire. C'est l'objet de notre second champ d'investigation.Nous caractérisons cette propriété et démontrons son indécidabilité. Enfin, untroisième champ d'investigation concerne l'algorithmique des automatescellulaires à particules et collisions. Étant donné un ensemble de particuleset de collisions d'un tel automate cellulaire, nous étudions l'ensemble desinteractions possibles et proposons des outils pour une meilleure programmationinterne à l'aide de ces collisions.Une seconde partie de nos travaux concerne la programmation par réduction. Afinde démontrer l'indécidabilité de propriétés dynamiques des automatescellulaires, nous étudions d'une part les problèmes de pavage du plan par desjeux de tuiles finis et d'autre part les problèmes de mortalité et depériodicité dans les systèmes dynamiques discrets à fonction partielle. Cetteétude nous amène à considérer des objets qui possèdent la même dualité entredescription combinatoire et topologique que les automates cellulaires. Unenotion d'apériodicité joue un rôle central dans l'indécidabilité des propriétésde ces objets
A chiral aperiodic monotile
The recently discovered "hat" aperiodic monotile mixes unreflected and
reflected tiles in every tiling it admits, leaving open the question of whether
a single shape can tile aperiodically using translations and rotations alone.
We show that a close relative of the hat -- the equilateral member of the
continuum to which it belongs -- is a weakly chiral aperiodic monotile: it
admits only non-periodic tilings if we forbid reflections by fiat. Furthermore,
by modifying this polygon's edges we obtain a family of shapes called Spectres
that are strictly chiral aperiodic monotiles: they admit only chiral
non-periodic tilings based on a hierarchical substitution system.Comment: 23 pages, 12 figure
Development of Atomistic Potentials for Silicate Materials and Coarse-Grained Simulation of Self-Assembly at Surfaces
This thesis is composed of two parts. The first is a study of evolutionary strategies for parametrization of empirical potentials, and their application in development of a charge-transfer potential for silica. An evolutionary strategy was meta-optimized for use in empirical potential parametrization, and a new charge-transfer empirical model was developed for use with isobaric-isothermal ensemble molecular dynamics simulations. The second is a study of thermodynamics and self-assembly in a particular class of athermal two-dimensional lattice models. The effects of shape on self-assembly and thermodynamics for polyominoes and tetrominoes were examined. Many interesting results were observed, including complex clustering, non-ideal mixing, and phase transitions. In both parts, computational efficiency and performance were important goals, and this was reflected in method and program development
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Modelling the evolution of biological complexity with a two-dimensional lattice self-assembly process
Self-assembling systems are prevalent across numerous scales of nature, lying at the heart of diverse physical and biological phenomena.
Individual protein subunits self-assembling into complexes is often a vital first step of biological processes.
Errors during protein assembly, due to mutations or misfolds, can have devastating effects and are responsible for an assortment of protein diseases, known as proteopathies.
With proteins exhibiting endless layers of complexity, building any all-encompassing model is unrealistic.
Coarse-grained models, despite not faithfully capturing every detail of the original system, have massive potential to assist understanding complex phenomenon.
A principal actor in self-assembly is the binding interactions between subunits, and so geometric constraints, polarity, kinetic forces, etc. can often be marginalised.
This work explores how self-assembly and its outcomes are inextricably tied to the involved interactions through the use of a two-dimensional lattice polyomino model.
%Armed with this tractable model, we can probe how dynamics acting on evolution are reflected in interaction properties.
First, this thesis addresses how the interaction characteristics of self-assembly building blocks determine what structures they form.
Specifically, if the same structures are consistently produced and remain finite in size.
Assembly graphs store subunit interaction information and are used in classifying these two properties, the determinism and boundedness respectively.
Arbitrary sets of building blocks are classified without the costly overhead of repeated stochastic assembling, improving both the analysis speed and accuracy.
Furthermore, assembly graphs naturally integrate combinatorial and graph techniques, enabling a wider range of future polyomino studies.
The second part narrows in on implications of nondeterministic assembly on interaction strength evolution.
Generalising subunit binding sites with mutable binary strings introduces such interaction strengths into the polyomino model.
Deterministic assemblies obey analytic expectations.
Conversely, interactions in nondeterministic assemblies rapidly diverge from equilibrium to minimise assembly inconsistency.
Optimal interaction strengths during assembly are also reflected in evolution.
Transitions between certain polyominoes are strongly forbidden when interaction strengths are misaligned.
The third aspect focuses on genetic duplication, an evolutionary event observed in organisms across all taxa.
Through polyomino evolutions, a duplication-heteromerisation pathway emerges as an efficient process.
This pathway exploits the advantages of both self-interactions and pairwise-interactions, and accelerates evolution by avoiding complexity bottlenecks.
Several simulation predictions are successfully validated against a large data set of protein complexes.
These results focus on coarse-grained models rather than quantified biological insight.
Despite this, they reinforce existing observations of protein complexes, as well as posing several new mechanisms for the evolution of biological complexity