Related papers: Combinatorial RNA Design Designability and Structu…
We have considered the problem of protein design based on a model where the contact energy between amino acid residues is fitted phenomenologically using the Miyazawa--Jernigan matrix. Due to the simple form of the contact energy function,…
In this paper we enumerate $k$-noncrossing RNA pseudoknot structures with given minimum stack-length. We show that the numbers of $k$-noncrossing structures without isolated base pairs are significantly smaller than the number of all…
Rising costs in recent years of developing new drugs and treatments have led to extensive research in optimization techniques in biomolecular design. Currently, the most widely used approach in biomolecular design is directed evolution,…
We describe a combinatorial approach for investigating properties of rational numbers. The overall approach rests on structural bijections between rational numbers and familiar combinatorial objects, namely rooted trees. We emphasize that…
We present a novel topological classification of RNA secondary structures with pseudoknots. It is based on the topological genus of the circular diagram associated to the RNA base-pair structure. The genus is a positive integer number,…
Motivated by the study of matrix elimination orderings in combinatorial scientific computing, we utilize graph sketching and local sampling to give a data structure that provides access to approximate fill degrees of a matrix undergoing…
Regular $A_n$-, $B_n$- and $C_n$-crystals are edge-colored directed graphs, with ordered colors $1,2,...,n$, which are related to representations of quantized algebras $U_q(\mathfrak{sl}_{n+1})$, $U_q(\mathfrak{sp}_{2n})$ and…
Data centers require high-performance network equipment that consume low power and support high bandwidth requirements. In this context, a combinatorial approach was proposed to design data center network (DCN) equipment from a library of…
Assembly Theory, as developed by Cronin and co-workers, assigns to an object an assembly index: the minimal number of binary join operations required to build at least one copy of the object from a specified set of basic building blocks,…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
We consider the problem of designing (or augmenting) an electric power system at a minimum cost such that it satisfies the N-k-e survivability criterion. This survivability criterion is a generalization of the well-known N-k criterion, and…
In this paper, we use the biological domain knowledge incorporated into stochastic models for ab initio RNA secondary-structure prediction to improve the state of the art in joint compression of RNA sequence and structure data (Liu et al.,…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
RNAs self-interact through hydrogen-bond base-pairing between nucleotides and fold into specific, stable structures that substantially govern their biochemical behaviour. Experimental characterization of these structures remains difficult,…
The structure of an RNA molecule plays a significant role in its biological function. Predicting structure given a one dimensional sequence of RNA nucleotide bases is a difficult and important problem. Many computer programs (known as in…
Modeling potential alloys requires the exploration of all possible configurations of atoms. Additionally, modeling the thermal properties of materials requires knowledge of the possible ways of displacing the atoms. One solution to finding…
We study the problem of causal structure learning from a combination of observational and interventional data generated by a linear non-Gaussian structural equation model that might contain cycles. Recent results show that using mere…
Given a random RNA secondary structure, $S$, we study RNA sequences having fixed ratios of nuclotides that are compatible with $S$. We perform this analysis for RNA secondary structures subject to various base pairing rules and minimum arc-…
The constraints of lightweight distributed computing environments such as wireless sensor networks lend themselves to the use of symmetric cryptography to provide security services. The lack of central infrastructure after deployment of…
We present a simple kinetic model for the assembly of small single-stranded RNA viruses that can be used to carry out analytical packaging contests between different types of RNA molecules. The RNA selection mechanism is purely kinetic and…