Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of physically relevant pseudoknots. Here, we present a method for computing base-pairing probabilities starting from the output of this partition function algorithm. The approach relies on the calculation of recursion probabilities that are computed...

Anomaly detection algorithms have been proved to be useful in the search of new physics beyond Standard Model. However, a prerequisite for using an anomaly algorithm is that signal sought indeed anomalous. This does not always hold true, example when interference between and Model becomes important. In this case, no longer detection. To overcome difficulty, we propose nested algorithm, which ap...

In this paper we describe an hybrid algorithm for an even number of processors based on an algorithm for two processors and the Overlapping Partition Method for tridiagonal systems. Moreover, we compare this hybrid method with the Partition Wang’s method in a BSP computer. Finally, we compare the theoretical computation cost of both methods for a Cray T3D computer, using the cost model that BSP...

In this paper we present a new version of the derefinement algorithm developed by Plaza et al. (in Numerical Methodr in Engineering, Elsevier Science, Amsterdam, 1992, pp. 225-232; in Algorithms, Software, Architecture, Elsevier Science, Amsterdam, 1992, pp. 409-415; A. Plaza, PhD thesis, University of Las Palmas de Gran Canaria, 1993; Commun. Numer. Meth. Engng, 1994, 10, 403-412).‘-4 The purp...

We develop a method to obtain an optimal solution for a constrained distribution system with several items and multi-retailers. The objective is to determine the procurement frequency as well as the joint shipment interval for each retailer in order to minimize the total costs. The proposed method is applicable to both nested and non-nested policies and ends up with an optimal solution. To solv...

We report a remarkable success of nested pricing rules over major pivot rules commonly used in practice, such as Dantzig’s original rule as well as the steepest-edge rule and Devex rule.

Chvátal defined a skew partition of a graph G to be a partition of its vertex set into two non-empty parts A and B such that A induces a disconnected subgraph of G and B induces a disconnected subgraph of G. Skew partitions are important in the characterization of perfect graphs. De Figuereido et al. presented a polynomial time algorithm which given a graph either finds a skew partition or dete...

In this paper we describe an hybrid algorithm for an even number of processors based on an algorithm for two processors and the Overlapping Partition Method for tridiagonal systems. Moreover, we compare this hybrid method with the Partition Wang’s method in a BSP computer. Finally, we compare the theoretical computation cost of both methods for a Cray T3D computer, using the cost model that BSP...

We present an efficient numerical algorithm for simulating chemical kinetic systems with multiple time scales. This algorithm is an improvement of the traditional stochastic simulation algorithm (SSA), also known as Gillespie’s algorithm. It is in the form of a nested SSA and uses an outer SSA to simulate the slow reactions with rates computed from realizations of inner SSAs that simulate the f...