A Graph Model for DynamicWaveband Switching in WDM Mesh Networks

We investigate the problem of waveband switching (WBS) in a wavelength-division multiplexing (WDM) mesh network with dynamic traffic requests. To solve the WBS problem in a homogeneous dynamic WBS network, where every node is a multi-granular optical cross-connect (MG-OXC), we construct an auxiliary graph. Based on the auxiliary graph, we develop two heuristic on-line WBS algorithms with different grouping policies, namely the wavelength-first WBS algorithm based on the auxiliary graph (WFAUG) and the waveband-first WBS algorithm based on the auxiliary graph (BFAUG). Our results show that the WFAUG algorithm outperforms the BFAUG algorithm.

Least-cost Disjoint Paths with Dependent Cost Structure in Wavelength Continuous Optical WDM Networks

One of the important issues in establishing a fault tolerant connection in a wavelength division multiplexing optical network is computing a pair of disjoint working and protection paths and a free wavelength along the paths. While most of the earlier research focused only on computing disjoint paths, in this work we consider computing both disjoint paths and a free wavelength along the paths. The concept of dependent cost structure (DCS) of protection paths to enhance their resource sharing ability was proposed in our earlier work. In this work we extend the concept of DCS of protection paths to wavelength continuous networks. We formalize the problem of computing disjoint paths with DCS in wavelength continuous networks and prove that it is NP-complete. We present an iterative heuristic that uses a layered graph model to compute disjoint paths with DCS and identify a free wavelength.

A macroscopic kinetic model for DNA polymerase elongation and high-fidelity nucleotide election

The enzymatically catalyzed template-directed extension of ssDNA/primer complex is an impor-tant reaction of extraordinary complexity. The DNA polymerase does not merely facilitate the insertion of dNMP, but it also performs rapid screening of substrates to ensure a high degree of fidelity. Several kinetic studies have determined rate constants and equilibrium constants for the elementary steps that make up the overall pathway. The information is used to develop a macro-scopic kinetic model, using an approach described by Ninio [Ninio J., 1987. Alternative to the steady-state method: derivation of reaction rates from first-passage times and pathway probabili-ties. Proc. Natl. Acad. Sci. U.S.A. 84, 663–667]. The principle idea of the Ninio approach is to track a single template/primer complex over time and to identify the expected behavior. The average time to insert a single nucleotide is a weighted sum of several terms, in-cluding the actual time to insert a nucleotide plus delays due to polymerase detachment from ei-ther the ternary (template-primer-polymerase) or quaternary (+nucleotide) complexes and time delays associated with the identification and ultimate rejection of an incorrect nucleotide from the binding site. The passage times of all events and their probability of occurrence are ex-pressed in terms of the rate constants of the elementary steps of the reaction pathway. The model accounts for variations in the average insertion time with different nucleotides as well as the in-fluence of G+C content of the sequence in the vicinity of the insertion site. Furthermore the model provides estimates of error frequencies. If nucleotide extension is recognized as a compe-tition between successful insertions and time delaying events, it can be described as a binomial process with a probability distribution. The distribution gives the probability to extend a primer/template complex with a certain number of base pairs and in general it maps annealed complexes into extension products.