Multi-Channel Scheduling for Fast Convergecast in Wireless Sensor Networks

We explore the following fundamental question - how fast can information be collected from a wireless sensor network? We consider a number of design parameters such as, power control, time and frequency scheduling, and routing. There are essentially two factors that hinder efficient data collection - interference and the half-duplex single-transceiver radios. We show that while power control helps in reducing the number of transmission slots to complete a convergecast under a single frequency channel, scheduling transmissions on different frequency channels is more efficient in mitigating the effects of interference (empirically, 6 channels suffice for most 100-node networks). With these observations, we define a receiver-based channel assignment problem, and prove it to be NP-complete on general graphs. We then introduce a greedy channel assignment algorithm that efficiently eliminates interference, and compare its performance with other existing schemes via simulations. Once the interference is completely eliminated, we show that with half-duplex single-transceiver radios the achievable schedule length is lower-bounded by max(2nk − 1,N), where nk is the maximum number of nodes on any subtree and N is the number of nodes in the network. We modify an existing distributed time slot assignment algorithm to achieve this bound when a suitable balanced routing scheme is employed. Through extensive simulations, we demonstrate that convergecast can be completed within up to 50% less time slots, in 100-node networks, using multiple channels as compared to that with single-channel communication. Finally, we also demonstrate further improvements that are possible when the sink is equipped with multiple transceivers or when there are multiple sinks to collect data

Algorithms for Fast Aggregated Convergecast in Sensor Networks

Fast and periodic collection of aggregated data is of considerable interest for mission-critical and continuous monitoring applications in sensor networks. In the many-to-one communication paradigm, referred to as convergecast, we focus on applications wherein data packets are aggregated at each hop en-route to the sink along a tree-based routing topology, and address the problem of minimizing the convergecast schedule length by utilizing multiple frequency channels. The primary hindrance in minimizing the schedule length is the presence of interfering links. We prove that it is NP-complete to determine whether all the interfering links in an arbitrary network can be removed using at most a constant number of frequencies. We give a sufficient condition on the number of frequencies for which all the interfering links can be removed, and propose a polynomial time algorithm that minimizes the schedule length in this case. We also prove that minimizing the schedule length for a given number of frequencies on an arbitrary network is NP-complete, and describe a greedy scheme that gives a constant factor approximation on unit disk graphs. When the routing tree is not given as an input to the problem, we prove that a constant factor approximation is still achievable for degree-bounded trees. Finally, we evaluate our algorithms through simulations and compare their performance under different network parameters

Riboswitch Detection Using Profile Hidden Markov Models

<p>Abstract</p> <p>Background</p> <p>Riboswitches are a type of noncoding RNA that regulate gene expression by switching from one structural conformation to another on ligand binding. The various classes of riboswitches discovered so far are differentiated by the ligand, which on binding induces a conformational switch. Every class of riboswitch is characterized by an aptamer domain, which provides the site for ligand binding, and an expression platform that undergoes conformational change on ligand binding. The sequence and structure of the aptamer domain is highly conserved in riboswitches belonging to the same class. We propose a method for fast and accurate identification of riboswitches using profile Hidden Markov Models (pHMM). Our method exploits the high degree of sequence conservation that characterizes the aptamer domain.</p> <p>Results</p> <p>Our method can detect riboswitches in genomic databases rapidly and accurately. Its sensitivity is comparable to the method based on the Covariance Model (CM). For six out of ten riboswitch classes, our method detects more than 99.5% of the candidates identified by the much slower CM method while being several hundred times faster. For three riboswitch classes, our method detects 97-99% of the candidates relative to the CM method. Our method works very well for those classes of riboswitches that are characterized by distinct and conserved sequence motifs.</p> <p>Conclusion</p> <p>Riboswitches play a crucial role in controlling the expression of several prokaryotic genes involved in metabolism and transport processes. As more and more new classes of riboswitches are being discovered, it is important to understand the patterns of their intra and inter genomic distribution. Understanding such patterns will enable us to better understand the evolutionary history of these genetic regulatory elements. However, a complete picture of the distribution pattern of riboswitches will emerge only after accurate identification of riboswitches across genomes. We believe that the riboswitch detection method developed in this paper will aid in that process. The significant advantage in terms of speed, of our pHMM-based approach over the method based on CM allows us to scan entire databases (rather than 5'UTRs only) in a relatively short period of time in order to accurately identify riboswitch candidates.</p

Interferometric measurement of complex-field changes in transient detection imaging

We report an experimental method that combines nonlinear-crystal-based transient detection imaging (TDI) with interferometric complex-field retrieval. The system allows measuring both phase and amplitude of a dynamic scene while suppressing stationary background. Theoretical and experimental results prove the linear relation existing between input and output phases, as well as the benefits of phase analysis for both detection and measurement with high resolutions of λ/30, even under noisy conditions. Additionally, we present experimental evidence of the remarkable ability of the technique to detect phase sign changes in the scene what we call differential-phase TDI showing great detection sensitivity and no calibration requirements

Atomic step motion during the dewetting of ultra-thin films

We report on three key processes involving atomic step motion during the dewetting of thin solid films: (i) the growth of an isolated island nucleated far from a hole, (ii) the spreading of a monolayer rim, and (iii) the zipping of a monolayer island along a straight dewetting front. Kinetic Monte Carlo results are in good agreement with simple analytical models assuming diffusion-limited dynamics.Comment: 7 pages, 5 figure