Related papers: Stacks in canonical RNA pseudoknot structures
For a Fermat quasi-homogeneous polynomial $W$, we study a family of K-theoretic quantum invariants parametrized by a positive rational number $\epsilon$. We prove a wall-crossing formula by showing the generating functions lie on the…
The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on…
Motivated by bacterial chemotaxis and multi-species ecological interactions in heterogeneous environments, we study a general one-dimensional reaction-cross-diffusion system in the presence of spatial heterogeneity in both transport and…
Extensive studies have been done to understand the principles behind architectures of real networks. Recently, evidences for hierarchical organization in many real networks have also been reported. Here, we present a new hierarchical model…
Coding techniques may be useful for data center data survivability as well as for reducing traffic congestion. We present a queued cross-bar network (QCN) method that can be used for traffic analysis of both replication/uncoded and coded…
In large data centers, storage nodes are organized in racks, and the cross-rack transmission dominates the bandwidth cost. For the repair of single node failures, codes achieving the tradeoff between the storage redundancy and cross-rack…
We present a general setting for structure-sequence comparison in a large class of RNA structures that unifies and generalizes a number of recent works on specific families on structures. Our approach is based on tree decomposition of…
In this paper we address the characterization of the structure of condensed materials, periodic and non-periodic. Carrying out an extensive study of over 7000 different groundstate structures of a 2D lattice model of binary packing, we find…
A $(0,1)$-matrix has the Consecutive Ones Property (C1P) for the rows if there is a permutation of its columns such that the ones in each row appear consecutively. We say a $(0, 1)$-matrix is nested if it has the consecutive ones property…
A {\it stuck knot} is a knot diagram containing designated crossings, called {\it stuck crossings}, whose incident strands are required to remain locally non-separable. These rigidity constraints restrict the allowable ambient isotopies and…
Existing state-of-the-art methods that take a single RNA sequence and predict the corresponding RNA secondary-structure are thermodynamic methods. These predict the most stable RNA structure, but do not consider the process of structure…
In this paper we compute the bivariate generating function of $\gamma$-matchings over two backbones, filtered by the number of arcs and the topological genus. $\gamma$-matchings over two backbones are chord-diagrams, obtained via…
We describe a family of graphs with queue-number at most 4 but unbounded stack-number. This resolves open problems of Heath, Leighton and Rosenberg (1992) and Blankenship and Oporowski (1999).
We investigate the bifurcation structure of equilibria in a class of non-autonomous ordinary differential equations governed by a season length parameter, $\tau$, which determines the alternation between growth and decline dynamics. This…
Graphs of the most probable transitions for a transition probability matrix, $e^{\tau K}$, i.e., the time evolution matrix of the transition rate matrix $K$ over a finite time interval $\tau$, are considered. We study how the graph…
In this paper, we introduce polynomial time algorithms that generate random 3-noncrossing partitions and 2-regular, 3-noncrossing partitions with uniform probability. A 3-noncrossing partition does not contain any three mutually crossing…
We consider crack propagation in a crystalline material in terms of bifurcation analysis. We provide evidence that the stress intensity factor is a natural bifurcation parameter, and that the resulting bifurcation diagram is a periodic…
A growing number of RNA sequences are now known to have distributions of multiple stable sequences. Recent algorithms use the list of nucleotides in a sequence and auxiliary experimental data to predict such distributions. Although the…
Graph spanners are fundamental graph structures with a wide range of applications in distributed networks. We consider a standard synchronous message passing model where in each round $O(\log n)$ bits can be transmitted over every edge (the…
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…