Danny Krizanc

Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics

The central questions of bacterial ecology and evolution require a method to consistently demarcate, from the vast and diverse set of bacterial cells within a natural community, the groups playing ecologically distinct roles (ecotypes). Because of a lack of theory-based guidelines, current methods in bacterial systematics fail to divide the bacterial domain of life into meaningful units of ecology and evolution. We introduce a sequence-based approach (“ecotype simulation”) to model the evolutionary dynamics of bacterial populations and to identify ecotypes within a natural community, focusing here on two Bacillus clades surveyed from the “Evolution Canyons” of Israel. This approach has identified multiple ecotypes within traditional species, with each predicted to be an ecologically distinct lineage; many such ecotypes were confirmed to be ecologically distinct, with specialization to different canyon slopes with different solar exposures. Ecotype simulation provides a long-needed natural foundation for microbial ecology and systematics.

Asynchronous deterministic rendezvous in graphs

Two mobile agents (robots) having distinct labels and located in nodes of an unknown anonymous connected graph have to meet. We consider the asynchronous version of this well-studied rendezvous problem and we seek fast deterministic algorithms for it. Since in the asynchronous setting, meeting at a node, which is normally required in rendezvous, is in general impossible, we relax the demand by allowing meeting of the agents inside an edge as well. The measure of performance of a rendezvous algorithm is its cost: for a given initial location of agents in a graph, this is the number of edge traversals of both agents until rendezvous is achieved. If agents are initially situated at a distance D in an infinite line, we show a rendezvous algorithm with cost O(D|Lmin|2) when D is known and O((D + |Lmax|)3) if D is unknown, where |Lmin| and |Lmax| are the lengths of the shorter and longer label of the agents, respectively. These results still hold for the case of the ring of unknown size, but then we also give an optimal algorithm of cost O(n|Lmin|), if the size n of the ring is known, and of cost O(n|Lmax|), if it is unknown. For arbitrary graphs, we show that rendezvous is feasible if an upper bound on the size of the graph is known and we give an optimal algorithm of cost O(D|Lmin|) if the topology of the graph and the initial positions are known to agents.

Ecology of Speciation in the Genus Bacillus

ABSTRACT Microbial ecologists and systematists are challenged to discover the early ecological changes that drive the splitting of one bacterial population into two ecologically distinct populations. We have aimed to identify newly divergent lineages (“ecotypes”) bearing the dynamic properties attributed to species, with the rationale that discovering their ecological differences would reveal the ecological dimensions of speciation. To this end, we have sampled bacteria from the Bacillus subtilis-Bacillus licheniformis clade from sites differing in solar exposure and soil texture within a Death Valley canyon. Within this clade, we hypothesized ecotype demarcations based on DNA sequence diversity, through analysis of the clades evolutionary history by Ecotype Simulation (ES) and AdaptML. Ecotypes so demarcated were found to be significantly different in their associations with solar exposure and soil texture, suggesting that these and covarying environmental parameters are among the dimensions of ecological divergence for newly divergent Bacillus ecotypes. Fatty acid composition appeared to contribute to ecotype differences in temperature adaptation, since those ecotypes with more warm-adapting fatty acids were isolated more frequently from sites with greater solar exposure. The recognized species and subspecies of the B. subtilis-B. licheniformis clade were found to be nearly identical to the ecotypes demarcated by ES, with a few exceptions where a recognized taxon is split at most into three putative ecotypes. Nevertheless, the taxa recognized do not appear to encompass the full ecological diversity of the B. subtilis-B. licheniformis clade: ES and AdaptML identified several newly discovered clades as ecotypes that are distinct from any recognized taxon.

Range mode and range median queries on lists and trees

We consider algorithms for preprocessing labelled lists and trees so that, for any two nodes u and v we can answer queries of the form: What is the mode or median label in the sequence of labels on the path from u to v.

Multiple Mobile Agent Rendezvous in a Ring

We study the rendezvous search problem for k > 2 mobile agents in an n node ring. Rather than using randomized algorithms or different deterministic algorithms to break the symmetry that often arises in this problem, we investigate how the mobile agents can use identical stationary tokens to break symmetry and solve the rendezvous problem. After deriving the conditions under which identical stationary tokens can be used to break symmetry, we present several solutions to the rendezvous search problem. We derive the lower bounds of the memory required for mobile agent rendezvous and discuss the relationship between rendezvous and leader election for mobile agents.

On minimizing the sum ofensor movements for barrier coverage of a line segment

A set of sensors establishes barrier coverage of a given line segment if every point of the segment is within the sensing range of a sensor. Given a line segment I, n mobile sensors in arbitrary initial positions on the line (not necessarily inside I) and the sensing ranges of the sensors, we are interested in finding final positions of sensors which establish a barrier coverage of I so that the sum of the distances traveled by all sensors from initial to final positions is minimized. It is shown that the problem is NP complete even to approximate up to constant factor when the sensors may have different sensing ranges. When the sensors have an identical sensing range we give several efficient algorithms to calculate the final destinations so that the sensors either establish a barrier coverage or maximize the coverage of the segment if complete coverage is not feasible while at the same time the sum of the distances traveled by all sensors is minimized. Some open problems are also mentioned.

Mobile agent rendezvous: a survey

Recent results on the problem of mobile agent rendezvous on distributed networks are surveyed with an emphasis on outlining the various approaches taken by researchers in the theoretical computer science community

Revitalizing computing education through free and open source software for humanity

The humanitarian focus of socially useful projects promises to motivate community-minded undergrads in and out of CS.

Directional versus omnidirectional antennas for energy consumption and k -connectivity of networks of sensors

A network is k-connected if it remains connected after the removal of any k–1 of its nodes. Assume that n sensors, modeled here as (omni)directional antennas, are dropped randomly and independently with the uniform distribution on the interior of a unit length segment or a unit square. We derive sufficient conditions on the beam width of directional antennas so that the energy consumption required to maintain k-connectivity of the resulting network of sensors is lower when using directional than when using omnidirectional antennas. Our theoretical bounds are shown by experiment to be accurate under most circumstances. For the case of directional antennae, we provide simple algorithms for setting up a k-connected network requiring low energy.

Communication in wireless networks with directional antennas

We study the problem of maintaining connectivity in a wireless network where the network nodes are equipped with directional antennas. Nodes correspond to points on the plane and each uses a directional antenna modeled by a sector with a given angle and radius. The connectivity problem is to decide whether or not it is possible to orient the antennas so that the directed graph induced by the node transmissions is strongly connected. We present algorithms for simple polynomial-time-solvable cases of the problem, show that the problem is NP-complete in the