Novel Distances for Dollo Data

We investigate distances on binary (presence/absence) data in the context of a Dollo process, where a trait can only arise once on a phylogenetic tree but may be lost many times. We introduce a novel distance, the Additive Dollo Distance (ADD), which is consistent for data generated under a Dollo model, and show that it has some useful theoretical properties including an intriguing link to the LogDet distance. Simulations of Dollo data are used to compare a number of binary distances including ADD, LogDet, Nei Li and some simple, but to our knowledge previously unstudied, variations on common binary distances. The simulations suggest that ADD outperforms other distances on Dollo data. Interestingly, we found that the LogDet distance performs poorly in the context of a Dollo process, which may have implications for its use in connection with conditioned genome reconstruction. We apply the ADD to two Diversity Arrays Technology (DArT) datasets, one that broadly covers Eucalyptus species and one that focuses on the Eucalyptus series Adnataria. We also reanalyse gene family presence/absence data on bacteria from the COG database and compare the results to previous phylogenies estimated using the conditioned genome reconstruction approach

Representing Partitions on Trees

In evolutionary biology, biologists often face the problem of constructing a phylogenetic tree on a set X of species from a multiset Π of partitions corresponding to various attributes of these species. One approach that is used to solve this problem is to try instead to associate a tree (or even a network) to the multiset ΣΠ consisting of all those bipartitions {A,X − A} with A a part of some partition in Π. The rational behind this approach is that a phylogenetic tree with leaf set X can be uniquely represented by the set of bipartitions of X induced by its edges. Motivated by these considerations, given a multiset Σ of bipartitions corresponding to a phylogenetic tree on X, in this paper we introduce and study the set P(Σ) consisting of those multisets of partitions Π of X with ΣΠ = Σ. More specifically, we characterize when P(Σ) is non-empty, and also identify some partitions in P(Σ) that are of maximum and minimum size. We also show that it is NP-complete to decide when P(Σ) is non-empty in case Σ is an arbitrary multiset of bipartitions of X. Ultimately, we hope that by gaining a better understanding of the mapping that takes an arbitrary partition system Π to the multiset ΣΠ, we will obtain new insights into the use of median networks and, more generally, split-networks to visualize sets of partitions

Elastic cavitation, tube hollowing, and differential growth in plants and biological tissues

Elastic cavitation is a well-known physical process by which elastic materials under stress can open cavities. Usually, cavitation is induced by applied loads on the elastic body. However, growing materials may generate stresses in the absence of applied loads and could induce cavity opening. Here, we demonstrate the possibility of spontaneous growth-induced cavitation in elastic materials and consider the implications of this phenomenon to biological tissues and in particular to the problem of schizogenous aerenchyma formation

Distinct high-T transitions in underdoped Ba1−x_{1-x}Kx_{x}Fe2_{2}As2_{2}

In contrast to the simultaneous structural and magnetic first order phase transition $T_{0}$ previously reported, our detailed investigation on an underdoped Ba$_{0.84}$K$_{0.16}$Fe$_{2}$As$_{2}$ single crystal unambiguously revealed that the transitions are not concomitant. The tetragonal ($\tau$: I4/mmm) - orthorhombic ($\vartheta$: Fmmm) structural transition occurs at $T_{S}\simeq$ 110 K, followed by an adjacent antiferromagnetic (AFM) transition at $T_{N}\simeq$ 102 K. Hysteresis and coexistence of the $\tau$ and $\vartheta$ phases over a finite temperature range observed in our NMR experiments confirm the first order character of the structural transition and provide evidence that both $T_{S}$ and $T_{N}$ are strongly correlated. Our data also show that superconductivity (SC) develops in the $\vartheta$ phase below $T_{c}$ = 20 K and coexists with long range AFM. This new observation, $T_{S}\neq T_{N}$, firmly establishes another similarity between the hole-doped BaFe$_{2}$As$_{2}$ via K substitution and the electron-doped iron-arsenide superconductors.Comment: 4 pages, 3 figure

Generation of directional, coherent matter beams through dynamical instabilities in Bose-Einstein condensates

We present a theoretical analysis of a coupled, two-state Bose-Einstein condensate with non-equal scattering lengths, and show that dynamical instabilities can be excited. We demonstrate that these instabilities are exponentially amplified resulting in highly-directional, oppositely-propagating, coherent matter beams at specific momenta. To accomplish this we prove that the mean field of our system is periodic, and extend the standard Bogoliubov approach to consider a time-dependent, but cyclic, background. This allows us to use Floquet's theorem to gain analytic insight into such systems, rather than employing the usual Bogoliubov-de Gennes approach, which is usually limited to numerical solutions. We apply our theory to the metastable Helium atom laser experiment of Dall et al. [Phys. Rev. A 79, 011601(R) (2009)] and show it explains the anomalous beam profiles they observed. Finally we demonstrate the paired particle beams will be EPR-entangled on formation.Comment: Corrected reference

Evidence for Skyrmion crystallization from NMR relaxation experiments

A resistively detected NMR technique was used to probe the two-dimensional electron gas in a GaAs/AlGaAs quantum well. The spin-lattice relaxation rate $(1/T_{1})$ was extracted at near complete filling of the first Landau level by electrons. The nuclear spin of $^{75}$As is found to relax much more efficiently with $T\to 0$ and when a well developed quantum Hall state with $R_{xx}\simeq 0$ occurs. The data show a remarkable correlation between the nuclear spin relaxation and localization. This suggests that the magnetic ground state near complete filling of the first Landau level may contain a lattice of topological spin texture, i.e. a Skyrmion crystal

Low thrust propulsion in a coplanar circular restricted four body problem

This paper formulates a circular restricted four body problem (CRFBP), where the three primaries are set in the stable Lagrangian equilateral triangle configuration and the fourth body is massless. The analysis of this autonomous coplanar CRFBP is undertaken, which identies eight natural equilibria; four of which are close to the smaller body, two stable and two unstable, when considering the primaries to be the Sun and two smaller bodies of the solar system. Following this, the model incorporates `near term' low-thrust propulsion capabilities to generate surfaces of articial equilibrium points close to the smaller primary, both in and out of the plane containing the celestial bodies. A stability analysis of these points is carried out and a stable subset of them is identied. Throughout the analysis the Sun-Jupiter-Asteroid-Spacecraft system is used, for conceivable masses of a hypothetical asteroid set at the libration point L4. It is shown that eight bounded orbits exist, which can be maintained with a constant thrust less than 1:5 10􀀀4N for a 1000kg spacecraft. This illustrates that, by exploiting low-thrust technologies, it would be possible to maintain an observation point more than 66% closer to the asteroid than that of a stable natural equilibrium point. The analysis then focusses on a major Jupiter Trojan: the 624-Hektor asteroid. The thrust required to enable close asteroid observation is determined in the simplied CRFBP model. Finally, a numerical simulation of the real Sun-Jupiter-624 Hektor-Spacecraft is undertaken, which tests the validity of the stability analysis of the simplied model