Related papers: Combinatorics of $\gamma$-structures
Every finitely generated self-similar group naturally produces an infinite sequence of finite $d$-regular graphs $\Gamma_n$. We construct self-similar groups, whose graphs $\Gamma_n$ can be represented as an iterated zig-zag product and…
There is a long history of studying Ramsey theory using the algebraic structure of the Stone-\v{C}ech compactification of discrete semigroup. It has been shown that various Ramsey theoretic structures are contained in different algebraic…
We compare several classes of biparameter persistence modules: $\gamma$-products of monoparameter modules, hook-decomposable modules, modules admitting a Smith-type structure theorem, and modules of projective dimension at most 1. We…
This document presents a combinatorial framework for analyzing assembly systems using generating functions. We explore the theory through concrete examples, such as linear polymers, and develop recursive equations to characterize valid…
The unordered configuration space of $n$ points on a graph $\Gamma,$ denoted here by $UC^n(\Gamma),$ can be viewed as the space of all configurations of $n$ unlabeled robots on a system of one-dimensional tracks, which is interpreted as a…
Purpose: To develop the algebraic foundation of finite commutative ternary $\Gamma$-semirings by identifying their intrinsic invariants, lattice organization, and radical behavior that generalize classical semiring and $\Gamma$-ring…
DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…
A combinatorial structure, $\mathcal{F}$, with counting sequence $\{a_n\}_{n\ge 0}$ and ordinary generating function $G_\mathcal{F}=\sum_{n\ge0} a_n x^n$, is positive algebraic if $G_\mathcal{F}$ satisfies a polynomial equation…
Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with…
The motivation of this work is to define cohomology classes in the space of knots that are both easy to find and to evaluate, by reducing the problem to simple linear algebra. We achieve this goal by defining a combinatorial graded cochain…
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…
We study, to certain Banach spaces $X$, families of weighted composition operators. Notably, we show that if this family form a strongly continuous semigroup, then its infinitesimal generator ($\Gamma, D(\Gamma)$) is given by $\Gamma f =…
Some sum of squares (SOS) polynomials admit decomposition certificates, or positive semidefinite Gram matrices, with additional structure. In this work, we use the structure of Gram matrices to relate the representation theory of $SL(2)$ to…
The theory of bottom tangles is used to construct a quantum fundamental group. On the other hand, the skein module is considered as a quantum analogue of the $SL(2)$ representation of the fundamental group. Here we construct the skein…
Canonical functions are a powerful concept with numerous applications in the study of groups, monoids, and clones on countable structures with Ramsey-type properties. In this short note, we present a proof of the existence of canonical…
Exponential Puiseux semirings are additive submonoids of $\qq_{\geq 0}$ generated by almost all of the nonnegative powers of a positive rational number, and they are natural generalizations of rational cyclic semirings. In this paper, we…
Let $\Sigma$ be a surface of negative Euler characteristic together with a pants decomposition $\P$. Kra's plumbing construction endows $\Sigma$ with a projective structure as follows. Replace each pair of pants by a triply punctured sphere…
We give explicit structure of the graded ring of modular forms with respect to Gamma(N) (N=1,2,3,4,5,6,7,8,9,10,12,16,18) and for some other congruence groups. We also study the modular forms of half-integer weight for certain groups.
Searching new molecules in areas like drug discovery often starts from the core structures of candidate molecules to optimize the properties of interest. The way as such has called for a strategy of designing molecules retaining a…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…