Repetitions in infinite palindrome-rich words

Rich words are characterized by containing the maximum possible number of distinct palindromes. Several characteristic properties of rich words have been studied; yet the analysis of repetitions in rich words still involves some interesting open problems. We address lower bounds on the repetition threshold of infinite rich words over 2 and 3-letter alphabets, and construct a candidate infinite rich word over the alphabet $\Sigma_2=\{0,1\}$ with a small critical exponent of $2+\sqrt{2}/2$. This represents the first progress on an open problem of Vesti from 2017.Comment: 12 page

On Words with the Zero Palindromic Defect

We study the set of finite words with zero palindromic defect, i.e., words rich in palindromes. This set is factorial, but not recurrent. We focus on description of pairs of rich words which cannot occur simultaneously as factors of a longer rich word

On morphisms preserving palindromic richness

It is known that each word of length $n$ contains at most $n+1$ distinct palindromes. A finite rich word is a word with maximal number of palindromic factors. The definition of palindromic richness can be naturally extended to infinite words. Sturmian words and Rote complementary symmetric sequences form two classes of binary rich words, while episturmian words and words coding symmetric $d$-interval exchange transformations give us other examples on larger alphabets. In this paper we look for morphisms of the free monoid, which allow to construct new rich words from already known rich words. We focus on morphisms in Class $P_{ret}$. This class contains morphisms injective on the alphabet and satisfying a particular palindromicity property: for every morphism $\varphi$ in the class there exists a palindrome $w$ such that $\varphi(a)w$ is a first complete return word to $w$ for each letter $a$. We characterize $P_{ret}$ morphisms which preserve richness over a binary alphabet. We also study marked $P_{ret}$ morphisms acting on alphabets with more letters. In particular we show that every Arnoux-Rauzy morphism is conjugated to a morphism in Class $P_{ret}$ and that it preserves richness

Decision Algorithms for Ostrowski-Automatic Sequences

We extend the notion of automatic sequences to a broader class, the Ostrowski-automatic sequences. We develop a procedure for computationally deciding certain combinatorial and enumeration questions about such sequences that can be expressed as predicates in first-order logic. In Chapter 1, we begin with topics and ideas that are preliminary to this work, including a small introduction to non-standard positional numeration systems and the relationship between words and automata. In Chapter 2, we define the theoretical foundations for recognizing addition in a generalized Ostrowski numeration system and formalize the general theory that develops our decision procedure. Next, in Chapter 3, we show how to implement these ideas in practice, and provide the implementation as an integration to the automatic theorem-proving software package -- Walnut. Further, we provide some applications of our work in Chapter 4. These applications span several topics in combinatorics on words, including repetitions, pattern-avoidance, critical exponents of special classes of words, properties of Lucas words, and so forth. Finally, we close with open problems on decidability and higher-order numeration systems and discuss future directions for research

O nekim reverznoinvarijantnim merama složenosti visearnih reči

We focus on two complexity measures of words that are invariant under the operation of reversal of a word: the palindromic defect and the MP-ratio.The palindromic defect of a given word w is dened by jwj + 1   jPal(w)j, where jPal(w)j denotes the number of palindromic factors of w. We study innite words, to which this de  nition can be naturally extended. There are many results in the literature about the so- called rich words (words  of defect 0), while words of nite positive defect have been studied signicantly less; for some time (until recently) it was not known whether there even exist such words that additionally are aperiodic and have their set of factors closed under reversal. Among the rst examples that appeared were the so-called highly potential words. In this  thesis we present a much more general construction,which gives a wider class of words, named generalized highly potential words, and analyze their signicance within the frames of combinatorics on words.The MP-ratio of a given n-ary  word w is dened as the quotient jrwsj jwj ,where r and s are words such that the word rws is minimal- palindromic and that the length jrj + jsj is minimal possible; here, an n-ary word is called minimal-palindromic if it does not contain palindromic subwords of length greater than jwj n . In the binary case, it was proved that the MP-ratio is well-dened and that it is bounded from above by 4, which is the best possible upper bound. The question of well- denedness of the MP-ratio for larger alphabets was left open. In this thesis we solve that  question in the ternary case: we show that the MP-ratio is indeed well-dened in the ternary case, that it is bounded from above by the constant 6 and that this is the best possible upper bound.Izucavamo dve mere slozenosti reci koje su invarijantne u odnosu na operaciju preokretanja reci: palindromski defekt i MP-razmeru date reci.Palindromski defekt reci w denise se kao jwj + 1   jPal(w)j, gde jPal(w)j predstavlja broj palindromskih faktora reci w. Mi izucavamo beskonacne reci, na koje se ova denicija moze prirodno prosiriti. Postoje mnogobrojni rezultati u vezi sa tzv. bogatim recima (reci cije je defekt 0), dok se o recima sa konacnim pozitivnim defektom relativno malo zna; tokom jednog perioda (donedavno) nije bilo poznato ni da li uopste postoje takve reci koje su,dodatno, aperiodi cne i imaju skup faktora zatvoren za preokretanje. Medu prvim primerima koji su se pojavili u literaturi su bile tzv. visokopotencijalne reci. U disertaciji cemo predstaviti znatno opstiju konstrukciju, kojom se dobija znacajno sira klasa reci, nazvanih uop stene visokopotencijalne reci, i analiziracemo njihov znacaj u okvirima kombinatorike na recima.MP-razmera date n-arne reci w denise se kao kolicnik jrwsj jwj , gde su r i s takve da je rec rws minimalno-palindromicna, i duzina jrj + jsj je najmanja moguca; ovde, za n-arnu rec kazemo da je minimalno-palindromicna ako ne sadrzi palindromsku podrec duzine vece od  jwj n  . U binarnom slucaju dokazano je da je MP-razmera dobro  denisana i da je ogranicena odozgo konstantom 4, sto je i najbolja moguca granica. Dobra denisanost MP-razmere za vece alfabete je ostavljena kao otvoren problem. U ovoj tezi resavamo taj problem u ternarnom slucaju: pokazacemo da MP- razmera jeste dobro de-nisana u ternarnom slucaju, da je ogranicena odozgo sa 6, i da se ta granica ne moze poboljsati.

DNA Computing: Modelling in Formal Languages and Combinatorics on Words, and Complexity Estimation

DNA computing, an essential area of unconventional computing research, encodes problems using DNA molecules and solves them using biological processes. This thesis contributes to the theoretical research in DNA computing by modelling biological processes as computations and by studying formal language and combinatorics on words concepts motivated by DNA processes. It also contributes to the experimental research in DNA computing by a scaling comparison between DNA computing and other models of computation. First, for theoretical DNA computing research, we propose a new word operation inspired by a DNA wet lab protocol called cross-pairing polymerase chain reaction (XPCR). We define and study a word operation called word blending that models and generalizes an unexpected outcome of XPCR. The input words are uwx and ywv that share a non-empty overlap w, and the output is the word uwv. Closure properties of the Chomsky families of languages under this operation and its iterated version, the existence of a solution to equations involving this operation, and its state complexity are studied. To follow the XPCR experimental requirement closely, a new word operation called conjugate word blending is defined, where the subwords x and y are required to be identical. Closure properties of the Chomsky families of languages under this operation and the XPCR experiments that motivate and implement it are presented. Second, we generalize the sequence of Fibonacci words inspired by biological concepts on DNA. The sequence of Fibonacci words is an infinite sequence of words obtained from two initial letters f(1) = a and f(2)= b, by the recursive definition f(n+2) = f(n+1)*f(n), for all positive integers n, where * denotes word concatenation. After we propose a unified terminology for different types of Fibonacci words and corresponding results in the extensive literature on the topic, we define and explore involutive Fibonacci words motivated by ideas stemming from theoretical studies of DNA computing. The relationship between different involutive Fibonacci words and their borderedness and primitivity are studied. Third, we analyze the practicability of DNA computing experiments since DNA computing and other unconventional computing methods that solve computationally challenging problems often have the limitation that the space of potential solutions grows exponentially with their sizes. For such problems, DNA computing algorithms may achieve a linear time complexity with an exponential space complexity as a trade-off. Using the subset sum problem as the benchmark problem, we present a scaling comparison of the DNA computing (DNA-C) approach with the network biocomputing (NB-C) and the electronic computing (E-C) approaches, where the volume, computing time, and energy required, relative to the input size, are compared. Our analysis shows that E-C uses a tiny volume compared to that required by DNA-C and NB-C, at the cost of the E-C computing time being outperformed first by DNA-C and then by NB-C. In addition, NB-C appears to be more energy efficient than DNA-C for some input sets, and E-C is always an order of magnitude less energy efficient than DNA-C