Guilherme L. Moritz

Time-Switching Uplink Network-Coded Cooperative Communication With Downlink Energy Transfer

In this work, we consider a multiuser cooperative wireless network where the energy-constrained sources have independent information to transmit to a common destination, which is assumed to be externally powered and responsible for transferring energy wirelessly to the sources. The source nodes may cooperate, under either decode-and-forward or network coding-based protocols. Taking into account the fact that the energy harvested by the source nodes is a function of the fading realization of inter-user channels and user-destination channels, we obtain a closed-form approximation for the system outage probability, as well as an approximation for the optimal energy transfer period that minimizes such outage probability. It is also shown that, even though the achievable diversity order is reduced due to wireless energy transfer process, it is very close to the one achieved for a network without energy constraints. Numerical results are also presented to validate the theoretical results.

A distributed approach for a multiple sequence alignment algorithm using a parallel virtual machine

Multiple sequence alignment is a central topic of extensive research in computational biology. Basically, two or more protein sequences are compared so as to evaluate their similarity. This work reports a methodology for parallel processing of a multiple sequence alignment algorithm (ClustalW) in an environment of networked computers. A detailed description of the modules that compose the distributed system is provided, giving special attention to the way a dynamic programming algorithm can be executed in parallel. Extensive experiments were done to evaluate performance and scalability of the method. Results show that the proposed method is efficient and offers a real advantage for large-scale multiple protein sequence alignment

Implementation of a Parallel Algorithm for Protein Pairwise Alignment Using Reconfigurable Computing

This paper describes the design and implementation of a parallel pairwise alignment hardware, implemented in a FPGA device. This system is aimed at aligning pairs of proteins, using a dynamic programming algorithm. The alignment is done in parallel thanks to a pipelined approach. All functional blocks are described in detail. Experiments were done to access the performance of the system for up to pairs of 2000-amino acids-long proteins. Hardalign was compared with a similar algorithm implemented in software and running in a PC, resulting in a 1:10 speed-up ratio. Results encourage the continuity of the work, showing that reconfigurable computing can offer interesting solutions for bioinformatics problems

A graph-based genetic algorithm for the multiple sequence alignment problem

We developed a new approach for the multiple sequence alignment problem based on Genetic Algorithms (GA). A new method to represent an alignment is proposed as a multidimensional oriented graph, which dramatically decreases the storage complexity. Details of the proposed GA are explained, including new structure-preserving genetic operators. A sensitivity analysis was done for adjusting running parameters of the GA. Performance of the proposed system was evaluated using a benchmark of hand-aligned sequences (Balibase). Overall, the results obtained are comparable or better to those obtained by a well-known software (Clustal). These results are very promising and suggest more efforts for further developments.

Turbo Decoding Using the Sectionalized Minimal Trellis of the Constituent Code: Performance-Complexity Trade-Off

The performance and complexity of turbo decoding using rate k/n constituent codes are investigated. The conventional, minimal and sectionalized trellis modules of the constituent convolutional codes are utilized. The performance metric is the bit error rate (BER), while complexity is analyzed based on the number of multiplications, summations and comparisons required by the max-log-MAP decoding algorithm. Our results show that the performance depends on how the systematic bits are grouped in a trellis module. The best performance is achieved when the k systematic bits are grouped together in the same section of the module, so that the log-likelihood ratio (LLR) of the k-bit vector is calculated at once. This is a characteristic of the conventional trellis module and of some of the sectionalizations of the minimal trellis module. Moreover, we show that it is possible to considerably reduce the decoding complexity with respect to the conventional trellis if a particular sectionalization of the minimal trellis module is utilized. In some cases, this sectionalization is found within the best performing group, while in some other cases a small performance loss can be traded off for a large complexity reduction.

On the performance of network-coded cooperative communications with wireless energy transfer under a realistic power consumption model

In this work we evaluate the outage probability of a network-coded cooperative system with wireless energy transfer when a realistic power consumption model is considered, which takes into account the energy consumed by the transceiver circuitry. Our results show that there exists a tradeoff between circuit and channel outage, as well as an optimal value for the ratio of the time allocated to energy harvesting that minimizes the overall outage probability.

Network-coded secondary communication with opportunistic energy harvesting

We consider a cognitive wireless network with two energy-constrained secondary users (SUs) and a common secondary destination, where the SUs harvest energy from the transmitted signals of primary user (PU). We obtain closed-form approximations for the outage probability, the outage capacity and the optimum energy harvesting time of the proposed scheme. The analytical derivations are validated by numerical results.

Secrecy outage probability of network-coded cooperation without channel state information

We evaluate the secrecy performance of a cooperative network where the destination node is wiretapped by a malicious and passive eavesdropper. We propose the application of the network coding technique as an alternative to increase the secrecy at the destination node, in a scenario without channel state information (CSI) at the transmitter side. Network coding is leveraged by assuming that the legitimate cooperative nodes are able to perform non-binary linear combinations of different frames before the transmission. Theoretic and numerical analyses show that the secrecy can be considerably increased through the use of network coding when compared to the direct transmission and traditional cooperative techniques.

Hardalign: a parallel pairwise alignment hardware application

This paper describes the design and implementation of a hardware for parallel pairwise alignment, implemented in a FPGA device. This system is aimed at aligning pairs of proteins, using a dynamic programming algorithm. The alignment is done in parallel thanks to a pipelined approach. All functional blocks are described in detail. Experiments to evaluate the performance of the system were done for pairs of proteins with up to 2000 amino acids-long. Hardalign was compared with a similar algorithm implemented in software and running in a PC, resulting in a 1:5 speed-up ratio