相关论文: The Expected Order of Saturated RNA Secondary Stru…

We study the space requirements of a sorting algorithm where only items that at the end will be adjacent are kept together. This is equivalent to the following combinatorial problem: Consider a string of fixed length n that starts as a…

The Human Genome Project has led to an exponential increase in data related to the sequence, structure, and function of biomolecules. Bioinformatics is an interdisciplinary research field that primarily uses computational methods to analyze…

Karp et al. (1988) described Deferred Data Structures for Multisets as "lazy" data structures which partially sort data to support online rank and select queries, with the minimum amount of work in the worst case over instances of size $n$…

Integrative biomolecular modeling of RNA relies on structural refined collections and accurate experimental data that reflect binding and folding behavior. However, the prediction of such collections remains challenging due to the rugged…

A matrix (and any associated linear system) will be referred to as structured if it has a small displacement rank. It is known that the inverse of a structured matrix is structured, which allows fast inversion (or solution), and reduced…

The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…

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…

RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main…

We develop a formal hierarchy of the expressive capacity of RNN architectures. The hierarchy is based on two formal properties: space complexity, which measures the RNN's memory, and rational recurrence, defined as whether the recurrent…

The properties of the number of iterations in random sequential adsorption protocol needed to generate finite saturated random packing of spherically symmetric shapes were studied. Numerical results obtained for one, two, and three…

Let $A$ be a static array storing $n$ elements from a totally ordered set. We present a data structure of optimal size at most $n\log_2(3+2\sqrt{2})+o(n)$ bits that allows us to answer the following queries on $A$ in constant time, without…

Characterizations of finite sequences $\beta_{1}<\cdots<\beta_{n}$ representing expected values of order statistics from a random sample of size $n$ are given. As a by-product, a characterization of binomial mixtures, when the mixing random…

High energy x-ray diffraction is used to investigate the bulk oxygen ordering properties of YBa_2Cu_3O_{6+x}. Superstructures of Cu-O chains aligned along the b axis and ordered with periodicity ma, along the a axis have been observed. For…

Prediction of one-dimensional protein structures such as secondary structures and contact numbers is useful for the three-dimensional structure prediction and important for the understanding of sequence-structure relationship. Here we…

It is a common belief that the order of a Boolean network is mainly determined by its attractors, including fixed points and cycles. Using semi-tensor product (STP) of matrices and the algebraic state-space representation (ASSR) of Boolean…

Ordering process of stripe order in La{2-x}Sr{x}NiO{4} with x being around 1/3 was investigated by neutron diffraction experiments. When the stripe order is formed at high temperature, incommensurability \epsilon of the stripe order has a…

Background: We study the sparsification of dynamic programming folding algorithms of RNA structures. Sparsification applies to the mfe-folding of RNA structures and can lead to a significant reduction of time complexity. Results: We analyze…

The second-largest order statistic is of special importance in reliability theory since it represents the time to failure of a $2$-out-of-$n$ system. Consider two $2$-out-of-$n$ systems with heterogeneous random lifetimes. The lifetimes are…

We prove several results of the following type: given finite dimensional normed space V there exists another space X with log (dim X) = O(log (dim V)) and such that every subspace (or quotient) of X, whose dimension is not "too small,"…

We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…