Design Of An All-Optical WDM Lightpath Concentrator

A design of a nonblocking, all-optical lightpath concentrator using wavelength exchanging optical crossbars and WDM crossbar switches is presented. The proposed concentrator is highly scalable, cost-efficient, and can switch signals in both space and wavelength domains without requiring a separate wavelength conversion stage

Selection Of Switching Sites In All-Optical Network Topology Design

In this paper, we consider the problem of topology design for both unprotected and one-link protected all-optical networks. We investigate the problem of selecting switching sites to minimize total cost of the network. The cost of an optical network is expressed as a sum of three main factors: the site cost, the link cost, and the switch cost. For unprotected networks with linear cost model, we present a mixed integer linear programming (MILP) formulation of the problem. We also present an efficient heuristic to approximate the solution. The experimental results show good performance of the linear cost model heuristic. In 16% of the experiments with 10 nodes network topologies, the linear cost model heuristic had no error. Moreover, for 54% and 86% of the experiments with 10 nodes network topologies, the linear cost model heuristic’s solution is within 2% and 5% of its optimal value respectively. Finally, we extend our approach to one-link protected networks, and present an efficient survivable heuristic, and representative experimental results

DESIGN FOR TESTABILITY AND TEST GENERATION WITH TWO CLOCKS

We propose a novel design for testability method that enhances the controllability of storage elements by use of additional clock lines Our scheme is applicable to synchronous circuits but is otherwise transparent to the designer. The associated area and speed penalties are minimal compared to scan based methods, however, a sequential ATPG system is necessary for test generation. The basic idea Is to use independent clock lines to control disjoint groups of flip-flops. No cyclic path are permitted among the flip-flops of the same group. During testing, a selected group can be made to hold its state by disabling its clock lines In the normal mode, all clock lines carry the same system clock signal. With the appropriate partitioning of flip-flops, the length of the vector sequence produced by the test generator for a fault is drastically reduced. An n-stage binary counter is used for experimental verification of reduction in test length by the proposed technique

Network Coding for WDM All-Optical Multicast

Network coding has become a useful means for achieving efficient multicast, and the optical community has started to examine its application to optical networks. However, a number of challenges, including limited processing capability and coarse bandwidth granularity, need to be overcome before network coding can be effectively used in optical networks. In this paper, we address some of these problems. We consider the problem of finding efficient routes to use with coding, and we study the effectiveness of using network coding for optical-layer dedicated protection of multicast traffic. We also propose architectures for all-optical circuits capable of performing the processing required for network coding. Our experiments show that network coding provides a moderate improvement in bandwidth efficiency for unprotected multicast while significantly outperforming existing approaches for dedicated multicast protection

M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species

BACKGROUND: Due to recent advances in whole genome shotgun sequencing and assembly technologies, the financial cost of decoding an organism's DNA has been drastically reduced, resulting in a recent explosion of genomic sequencing projects. This increase in related genomic data will allow for in depth studies of evolution in closely related species through multiple whole genome comparisons. RESULTS: To facilitate such comparisons, we present an interactive multiple genome comparison and alignment tool, M-GCAT, that can efficiently construct multiple genome comparison frameworks in closely related species. M-GCAT is able to compare and identify highly conserved regions in up to 20 closely related bacterial species in minutes on a standard computer, and as many as 90 (containing 75 cloned genomes from a set of 15 published enterobacterial genomes) in an hour. M-GCAT also incorporates a novel comparative genomics data visualization interface allowing the user to globally and locally examine and inspect the conserved regions and gene annotations. CONCLUSION: M-GCAT is an interactive comparative genomics tool well suited for quickly generating multiple genome comparisons frameworks and alignments among closely related species. M-GCAT is freely available for download for academic and non-commercial use at:

Selection of Switching Sites in All-Optical Nework Topology Design

In this paper, we consider the problem of topology design for optical networks. We investigate the problem of selecting switching sites to minimize total cost of the optical network. The cost of an optical network can be expressed as a sum of three main factors: the site cost, the link cost, and the switch cost. To the best of our knowledge, this problem has not been studied in its general form as investigated in this paper. We present a mixed integer quadratic programming (MIQP) formulation of the problem to find the optimal value of the total network cost. We also present an efficient heuristic to approximate the solution in polynomial time. The experimental results show good performance of the heuristic. The value of the total network cost computed by the heuristic varies within 2% to 21% of its optimal value in the experiments with 10 nodes. The total network cost computed by the heuristic for 51% of the experiments with 10 node network topologies varies within 8% of its optimal value. We also discuss the insight gained from our experiments

Yeast pheromone pathway modeling using Petri nets

Background: Our environment is composed of biological components of varying magnitude. The relationships between the different biological elements can be represented as a biological network. The process of mating in S. cerevisiae is initiated by secretion of pheromone by one of the cells. Our interest lies in one particular question: how does a cell dynamically adapt the pathway to continue mating under severe environmental changes or under mutation (which might result in the loss of functionality of some proteins known to participate in the pheromone pathway). Our work attempts to answer this question. To achieve this, we first propose a model to simulate the pheromone pathway using Petri nets. Petri nets are directed graphs that can be used for describing and modeling systems characterized as concurrent, asynchronous, distributed, parallel, non-deterministic, and/or stochastic. We then analyze our Petri net-based model of the pathway to investigate the following: 1) Given the model of the pheromone response pathway, under what conditions does the cell respond positively, i.e., mate? 2) What kinds of perturbations in the cell would result in changing a negative response to a positive one? Method: In our model, we classify proteins into two categories: core component proteins (set ψ) and additional proteins (set λ). We randomly generate our model’s parameters in repeated simulations. To simulate the pathway, we carry out three different experiments. In the experiments, we simply change the concentration of the additional proteins (λ) available to the cell. The concentration of proteins in ψ is varied consistently from 300 to 400. In Experiment 1, the range of values for λ is set to be 100 to 150. In Experiment 2, it is set to be 151 to 200. In Experiment 3, the set λ is further split into σ and ς, with the idea that proteins in σ are more important than those in ς. The range of values for s is set to be between 151 to 200 while that of σ is 100 to 150. Decision trees were derived from each of the first two experiments to allow us to more easily analyze the conditions under which the pheromone is expressed. Conclusion: The simulation results reveal that a cell can overcome the detrimental effects of the conditions by using more concentration of additional proteins in l. The first two experiments provide evidence that employing more concentration of proteins might be one of the ways that the cell uses to adapt itself in inhibiting conditions to facilitate mating. The results of the third experiment reveal that in some case the protein set s is sufficient in regulating the response of the cell. Results of Experiments 4 and 5 reveal that there are certain conditions (parameters) in the model that are more important in determining whether a cell will respond positively or not