Related papers: Stacks in canonical RNA pseudoknot structures
We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is…
A fundamental algorithmic problem in computational biology is to find all subgraphs of a given type (superbubbles, snarls, and ultrabubbles) in a directed or bidirected input graph. These correspond to regions of genetic variation and are…
We study RNA foldings and investigate their topology using a combination of knot theory and embedded rigid vertex graphs. Knot theory has been helpful in modeling biomolecules, but classical knots place emphasis on a biomolecule's…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
An endhered (end-adhered) pattern is a subset of arcs in matchings, such that the corresponding starting points are consecutive and the same holds for the ending points. Such patterns are in one-to-one correspondence with the permutations.…
Accurate prediction of RNA secondary structure underpins transcriptome annotation, mechanistic analysis of non-coding RNAs, and RNA therapeutic design. Recent gains from deep learning and RNA foundation models are difficult to interpret…
We present a differentiable stack data structure that simultaneously and tractably encodes an exponential number of stack configurations, based on Lang's algorithm for simulating nondeterministic pushdown automata. We call the combination…
In the analysis of Markov chains and processes, it is sometimes convenient to replace an unbounded state space with a "truncated" bounded state space. When such a replacement is made, one often wants to know whether the equilibrium behavior…
A graph $G$ is pseudo 2--factor isomorphic if the parity of the number of cycles in a 2--factor is the same for all 2--factors of $G$. In \cite{ADJLS} we proved that pseudo 2--factor isomorphic $k$--regular bipartite graphs exist only for…
Cross-diffusion systems play a central role in mathematical modelling, in which density-dependent dispersal and multiscale mechanisms can lead to spatial segregation and diffusion-driven instabilities. In several relevant examples,…
Stochasticity is introduced to a well studied class of recursively grown graphs: $(u,v)$-flower nets, which have power-law degree distributions as well as small-world properties (when $u=1$). The stochastic variant interpolates between…
We investigate a broad family of non weakly reversible stochastically modeled reaction networks (CRN), by looking at their steady-state distributions. Most known results on stationary distributions assume weak reversibility and zero…
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of…
We prove general equidistribution statements (both conditional and unconditional) relating to the Fourier coefficients of arithmetically normalized holomorphic Hecke cusp forms $f_1,\ldots,f_k$ without complex multiplication, of equal…
We prove that a generic $k$-parameter bifurcation of a dynamical system with a monoid symmetry occurs along a generalized kernel or center subspace of a particular type. More precisely, any (complementable) subrepresentation $U$ is given a…
In this work we investigate the process of pattern formation in a two dimensional domain for a reaction-diffusion system with nonlinear diffusion terms and the competitive Lotka-Volterra kinetics. The linear stability analysis shows that…
A $k$-stack layout (also called a $k$-page book embedding) of a graph consists of a total order of the vertices, and a partition of the edges into $k$ sets of non-crossing edges with respect to the vertex order. The stack number (book…
Let U be a Haar distributed unitary matrix in U(n)or O(n). We show that after centering the double index process $$ W^{(n)} (s,t) = \sum_{i \leq \lfloor ns \rfloor, j \leq \lfloor nt\rfloor} |U_{ij}|^2 $$ converges in distribution to the…
We examine reaction networks (CRNs) through their associated continuous-time Markov processes. Studying the dynamics of such networks is in general hard, both analytically and by simulation. In particular, stationary distributions of…