The Reticulation of a Universal Algebra

The reticulation of an algebra $A$ is a bounded distributive lattice ${\cal L}(A)$ whose prime spectrum of filters or ideals is homeomorphic to the prime spectrum of congruences of $A$, endowed with the Stone topologies. We have obtained a construction for the reticulation of any algebra $A$ from a semi-degenerate congruence-modular variety ${\cal C}$ in the case when the commutator of $A$, applied to compact congruences of $A$, produces compact congruences, in particular when ${\cal C}$ has principal commutators; furthermore, it turns out that weaker conditions than the fact that $A$ belongs to a congruence-modular variety are sufficient for $A$ to have a reticulation. This construction generalizes the reticulation of a commutative unitary ring, as well as that of a residuated lattice, which in turn generalizes the reticulation of a BL-algebra and that of an MV-algebra. The purpose of constructing the reticulation for the algebras from ${\cal C}$ is that of transferring algebraic and topological properties between the variety of bounded distributive lattices and ${\cal C}$, and a reticulation functor is particularily useful for this transfer. We have defined and studied a reticulation functor for our construction of the reticulation in this context of universal algebra.Comment: 29 page

Online fabrication and characterization of capsule populations with a flow-focusing microfluidic system

This paper was presented at the 3rd Micro and Nano Flows Conference (MNF2011), which was held at the Makedonia Palace Hotel, Thessaloniki in Greece. The conference was organised by Brunel University and supported by the Italian Union of Thermofluiddynamics, Aristotle University of Thessaloniki, University of Thessaly, IPEM, the Process Intensification Network, the Institution of Mechanical Engineers, the Heat Transfer Society, HEXAG - the Heat Exchange Action Group, and the Energy Institute.We have designed a microfluidic system that combines a double flow-focusing setup for calibrated capsule fabrication with a microchannel for the characterization of their mechanical properties. The double flow-focusing system consists of a first Y junction to create the microdroplets and of a second Y junction to introduce the cross-linking agent allowing the membrane formation. The human serum albumin (HSA) aqueous solution for the dispersed solution, hydrophobic phase for the continuous solution and cross-linking agent solution are introduced by means of syringe pumps. A wavy channel after the second junction allows to control the reticulation time. A cylindrical microchannel then enables to deform and characterize the capsules formed. The mechanical properties of the capsule membrane are obtained by inverse analysis (Chu et al. 2011). The results show that the drop size increases with the flow rate ratio between the central and lateral channels and does not change much regardless of the flow rate of the reticulation phase. The mean shear modulus of the capsules fabricated after 23 s of reticulation is of the order of the surface tension of HSA solution with Dragoxat indicating that the reticulation time is too short to form an elastic membrane around the droplet. When the reticulation time is increased to 60 s, the membrane shear modulus is multiplied by a factor of 3 confirming that a solid membrane has formed around the drop

Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters

Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees are obtained for several data sets (e.g. for different genes), then their clusters are often contradicting. Consequently, the set of all clusters of such a data set cannot be combined into a single phylogenetic tree. Phylogenetic networks are a generalization of phylogenetic trees that can be used to display more complex evolutionary histories, including reticulate events such as hybridizations, recombinations and horizontal gene transfers. Here we present the new CASS algorithm that can combine any set of clusters into a phylogenetic network. We show that the networks constructed by CASS are usually simpler than networks constructed by other available methods. Moreover, we show that CASS is guaranteed to produce a network with at most two reticulations per biconnected component, whenever such a network exists. We have implemented CASS and integrated it in the freely available Dendroscope software

On unrooted and root-uncertain variants of several well-known phylogenetic network problems

The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view accurately inferring the root location in a phylogenetic tree is notoriously difficult and poor root placement can artificially inflate the hybridization number. To this end we study a number of relaxed variants of this problem. We start by showing that the fundamental problem of determining whether an \emph{unrooted} phylogenetic network displays (i.e. embeds) an \emph{unrooted} phylogenetic tree, is NP-hard. On the positive side we show that this problem is FPT in reticulation number. In the rooted case the corresponding FPT result is trivial, but here we require more subtle argumentation. Next we show that the hybridization number problem for unrooted networks (when given two unrooted trees) is equivalent to the problem of computing the Tree Bisection and Reconnect (TBR) distance of the two unrooted trees. In the third part of the paper we consider the "root uncertain" variant of hybridization number. Here we are free to choose the root location in each of a set of unrooted input trees such that the hybridization number of the resulting rooted trees is minimized. On the negative side we show that this problem is APX-hard. On the positive side, we show that the problem is FPT in the hybridization number, via kernelization, for any number of input trees.Comment: 28 pages, 8 Figure