We describe the identification and characterization of novel homing endonucleases using genome database mining to identify putative target sites, followed by high throughput activity screening in a bacterial selection system. We characterized the substrate specificity and kinetics of these endonucleases by monitoring DNA cleavage events with deep sequencing. The endonuclease specificities revea...

Mobile agents operating in networked environments face threats from other agents as well as from the hosts (i.e., network sites) they visit. A black hole is a harmful host that destroys incoming agents without leaving any trace. To determine the location of such a harmful host is a dangerous but crucial task, called black hole search. The most important parameter for a solution strategy is the ...

In this paper, we prove the global asymptotic stability of a class of mass action futile cycle networks which includes a model of processive multisite phosphorylation networks. The proof consists of two parts. In the first part, we prove that there is a unique equilibrium in every positive compatibility class. In the second part, we make use of a piecewise linear in rates Lyapunov function in o...

We analyze the computational complexity of various rolling cube puzzles.

A partial orthomorphism of a group G (with additive notation) is an injection π : S → G for some S ⊆ G such that π(x) − x 6= π(y) − y for all distinct x, y ∈ S. We refer to |S| as the size of π, and if S = G, then π is an orthomorphism. Despite receiving a fair amount of attention in the research literature, many basic questions remain concerning the number of orthomorphisms of a given group, a...

Research so far has provided little evidence that benthic biogeochemical cycling is affected by ocean acidification under realistic climate change scenarios. We measured nutrient exchange and sediment community oxygen consumption (SCOC) rates to estimate nitrification in natural coastal permeable and fine sandy sediments under pre-phytoplankton bloom and bloom conditions. Ocean acidification, a...

In this paper, we study pattern matching conditions in the cycle structures of permutations. We develop methods to find the joint distribution of the number of cycles and the number of cycle descents over the set of permutations in the symmetric group Sn which have no cycle occurrences or no consecutive cycle occurrences of a given pattern or set of patterns. Our methods also allow us to refine...

The hierarchical hypercube network is suitable for massively parallel systems. The number of links in the hierarchical hypercube network forms a compromise between those of the hypercube and the cube-connected cycles. Recently, some interesting properties of the hierarchical hypercube network were investigated. Since the hierarchical hypercube is bipartite. A bipartite graph is bipancyclic if i...

[This corrects the article DOI: 10.1371/journal.pone.0152611.].

Let Γ denote a Q-polynomial distance-regular graph with diameter D ≥ 4. Assume that the intersection numbers of Γ satisfy ai = 0 for 0 ≤ i ≤ D − 1 and aD 6= 0. We show that Γ is a polygon, a folded cube, or an Odd graph.