331 research outputs found
Comparison of relativistic bound-state calculations in Front-Form and Instant-Form Dynamics
Using the Wick-Cutkosky model and an extended version (massive exchange) of
it, we have calculated the bound states in a quantum field theoretical
approach. In the light-front formalism we have calculated the bound-state mass
spectrum and wave functions. Using the Terent'ev transformation we can write
down an approximation for the angular dependence of the wave function. After
calculating the bound-state spectra we characterized all states found.
Similarly, we have calculated the bound-state spectrum and wave functions in
the instant-form formalism. We compare the spectra found in both forms of
dynamics in the ladder approximation and show that in both forms of dynamics
the O(4) symmetry is broken.Comment: 22 pages Latex, 7 figures, style file amssymb use
Relativistic bound-state calculations in Light Front Dynamics
We calculated bound states in the quantum field theoretical approach. Using
the Wick-Cutkosky model and an extended version of this model (in which a
particle with finite mass is exchanged) we have calculated the bound states in
the scalar case.Comment: 3 pages, proceedings of the Light Cone Meeting Trento 2001, to be
published in Nucl. Phys. B - Proceedings Supplement
Techniques for solving bound state problems
We have used different methods to obtain the bound states of a Hamiltonian of a relativistic two scalar particle system in a local potential. The potentials we are interested in are binding and confining potentials, that are associated with particle exchange. The issues we concentrate on when comparing the different methods are ease of numerical implementation, accuracy and stability. To check our codes we have made use of several potentials for which the bound states are known in the nonrelativistic situation. Finally we calculate the bound states for the Yukawa potential in the relativistic situation and look at the collapse of the wave functions in this situation
Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets
Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set T of binary binets or trinets over a taxon set X, and constructing such a network whenever it exists. We show that this is NP-hard for trinets but polynomial-time solvable for binets. Moreover, we show that the problem is still polynomial-time solvable for inputs consisting of binets and trinets as long as the cycles in the trinets have size three. Finally, we present an O(3^{|X|} poly(|X|)) time algorithm for general sets of binets and trinets. The latter two algorithms generalise to instances containing level-1 networks with arbitrarily many leaves, and thus provide some of the first supernetwork algorithms for computing networks from a set of rooted 1 phylogenetic networks
A Note on Encodings of Phylogenetic Networks of Bounded Level
Driven by the need for better models that allow one to shed light into the
question how life's diversity has evolved, phylogenetic networks have now
joined phylogenetic trees in the center of phylogenetics research. Like
phylogenetic trees, such networks canonically induce collections of
phylogenetic trees, clusters, and triplets, respectively. Thus it is not
surprising that many network approaches aim to reconstruct a phylogenetic
network from such collections. Related to the well-studied perfect phylogeny
problem, the following question is of fundamental importance in this context:
When does one of the above collections encode (i.e. uniquely describe) the
network that induces it? In this note, we present a complete answer to this
question for the special case of a level-1 (phylogenetic) network by
characterizing those level-1 networks for which an encoding in terms of one (or
equivalently all) of the above collections exists. Given that this type of
network forms the first layer of the rich hierarchy of level-k networks, k a
non-negative integer, it is natural to wonder whether our arguments could be
extended to members of that hierarchy for higher values for k. By giving
examples, we show that this is not the case
Folding and unfolding phylogenetic trees and networks
Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any phylogenetic network can be "unfolded" to obtain a MUL-tree and, conversely, a MUL-tree can in certain circumstances be "folded" to obtain a phylogenetic network that exhibits . In this paper, we study properties of the operations and in more detail. In particular, we introduce the class of stable networks, phylogenetic networks for which is isomorphic to , characterise such networks, and show that they are related to the well-known class of tree-sibling networks.We also explore how the concept of displaying a tree in a network can be related to displaying the tree in the MUL-tree . To do this, we develop a phylogenetic analogue of graph fibrations. This allows us to view as the analogue of the universal cover of a digraph, and to establish a close connection between displaying trees in and reconcilingphylogenetic trees with networks
Use of GenMAPP and MAPPFinder to analyse pathways involved in chickens infected with the protozoan parasite Eimeria
<p>Abstract</p> <p>Background</p> <p>Microarrays allow genome-wide assays of gene expression. There is a need for user-friendly software to visualise and analyse these data. Analysing microarray data in the context of biological pathways is now common, and several tools exist.</p> <p>Results</p> <p>We describe the use of MAPPFinder, a component of GenMAPP to characterise the biological pathways affected in chickens infected with the protozoan parasite <it>Eimeria. </it>Several pathways were significantly affected based on the unadjusted p-value, including several immune-system pathways.</p> <p>Conclusion</p> <p>GenMAPP/MAPPFinder provides a means to rapidly visualise pathways affected in microarray studies. However, it relies on good genome annotation and having genes reliably linked to pathway objects. We show that GenMAPP/MAPPFinder can produce useful results, and as the annotation of the chicken genome improves, so will the level of information gained.</p
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