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Mechanisms of Side Branching and Tip Splitting in a Model of Branching Morphogenesis  [PDF]
Yina Guo, Mingzhu Sun, Alan Garfinkel, Xin Zhao
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0102718
Abstract: Recent experimental work in lung morphogenesis has described an elegant pattern of branching phenomena. Two primary forms of branching have been identified: side branching and tip splitting. In our previous study of lung branching morphogenesis, we used a 4 variable partial differential equation (PDE), due to Meinhardt, as our mathematical model to describe the reaction and diffusion of morphogens creating those branched patterns. By altering key parameters in the model, we were able to reproduce all the branching styles and the switch between branching modes. Here, we attempt to explain the branching phenomena described above, as growing out of two fundamental instabilities, one in the longitudinal (growth) direction and the other in the transverse direction. We begin by decoupling the original branching process into two semi-independent sub-processes, 1) a classic activator/inhibitor system along the growing stalk, and 2) the spatial growth of the stalk. We then reduced the full branching model into an activator/inhibitor model that embeds growth of the stalk as a controllable parameter, to explore the mechanisms that determine different branching patterns. We found that, in this model, 1) side branching results from a pattern-formation instability of the activator/inhibitor subsystem in the longitudinal direction. This instability is far from equilibrium, requiring a large inhomogeneity in the initial conditions. It successively creates periodic activator peaks along the growing stalk, each of which later on migrates out and forms a side branch; 2) tip splitting is due to a Turing-style instability along the transversal direction, that creates the spatial splitting of the activator peak into 2 simultaneously-formed peaks at the growing tip, the occurrence of which requires the widening of the growing stalk. Tip splitting is abolished when transversal stalk widening is prevented; 3) when both instabilities are satisfied, tip bifurcation occurs together with side branching.
Almost sure convergence of vertex degree densities in the vertex-splitting model  [PDF]
Sigurdur ?rn Stefánsson,Erik Th?rnblad
Mathematics , 2015,
Abstract: We study the limiting degree distribution of the vertex splitting model introduced in \cite{DDJS:2009}. This is a model of randomly growing ordered trees, where in each time step the tree is separated into two components by splitting a vertex into two, and then inserting an edge between the two new vertices. Under some assumptions on the parameters, related to the growth of the maximal degree of the tree, we prove that the vertex degree densities converge almost surely to constants which satisfy a system of equations. Using this we are also able to strengthen and prove some previously non-rigorous results mentioned in the literature.
Research on the Evolutionary Model of A Kind of Vertex-splitting Network  [cached]
Narisa Zhao,Xiaoming Dai
Journal of Networks , 2011, DOI: 10.4304/jnw.6.6.904-906
Abstract: A problem is presented about the evolutionary process of the vertex splitting complex network. The rule of the evolution is: every newly-added vertex is the copy of or is split from the existing vertex. The analytic equation set of this network evolutionary model and arithmetic of iteration are put forward. A series of simulation calculation prove that the complex network is Scale Free Network and the power-law increases along with the increment of the splitting similarity degree of λ(t) and even approaches to +∞. When the initial degree of each new vertex is constant, the evolutionary process of the network is similar to that of the BA model.
An irreversible local Markov chain that preserves the six vertex model on a torus  [PDF]
Alexei Borodin,Alexey Bufetov
Mathematics , 2015,
Abstract: We construct an irreversible local Markov dynamics on configurations of up-right paths on a discrete two-dimensional torus, that preserves the Gibbs measures for the six vertex model. An additional feature of the dynamics is a conjecturally nontrivial drift of the height function.
A new family of Markov branching trees: the alpha-gamma model  [PDF]
Bo Chen,Daniel Ford,Matthias Winkel
Mathematics , 2008,
Abstract: We introduce a simple tree growth process that gives rise to a new two-parameter family of discrete fragmentation trees that extends Ford's alpha model to multifurcating trees and includes the trees obtained by uniform sampling from Duquesne and Le Gall's stable continuum random tree. We call these new trees the alpha-gamma trees. In this paper, we obtain their splitting rules, dislocation measures both in ranked order and in sized-biased order, and we study their limiting behaviour.
Random tree growth by vertex splitting  [PDF]
Francois David,Mark Dukes,Thordur Jonsson,Sigurdur Orn Stefansson
Mathematics , 2008, DOI: 10.1088/1742-5468/2009/04/P04009
Abstract: We study a model of growing planar tree graphs where in each time step we separate the tree into two components by splitting a vertex and then connect the two pieces by inserting a new link between the daughter vertices. This model generalises the preferential attachment model and Ford's $\alpha$-model for phylogenetic trees. We develop a mean field theory for the vertex degree distribution, prove that the mean field theory is exact in some special cases and check that it agrees with numerical simulations in general. We calculate various correlation functions and show that the intrinsic Hausdorff dimension can vary from one to infinity, depending on the parameters of the model.
Recurrence for branching Markov chains  [PDF]
Sebastian Müller
Mathematics , 2007,
Abstract: The question of recurrence and transience of branching Markov chains is more subtle than for ordinary Markov chains; they can be classified in transience, weak recurrence, and strong recurrence. We review criteria for transience and weak recurrence and give several new conditions for weak recurrence and strong recurrence. These conditions make a unified treatment of known and new examples possible and provide enough information to distinguish between weak and strong recurrence. This represents a step towards a general classification of branching Markov chains. In particular, we show that in \emph{homogeneous} cases weak recurrence and strong recurrence coincide. Furthermore, we discuss the generalization of positive and null recurrence to branching Markov chains and show that branching random walks on $\Z$ are either transient or positive recurrent.
The algebra of the general Markov model on phylogenetic trees and networks  [PDF]
J. G. Sumner,B. H. Holland,P. D. Jarvis
Quantitative Biology , 2010, DOI: 10.1007/s11538-011-9691-z
Abstract: It is known that the Kimura 3ST model of sequence evolution on phylogenetic trees can be extended quite naturally to arbitrary split systems. However, this extension relies heavily on mathematical peculiarities of the K3ST model, and providing an analogous augmentation of the general Markov model has thus far been elusive. In this paper we rectify this shortcoming by showing how to extend the general Markov model on trees to to include arbitrary splits; and even further to more general network models. This is achieved by exploring the algebra of the generators of the continuous-time Markov chain together with the "splitting" operator that generates the branching process on phylogenetic trees. For simplicity we proceed by discussing the two state case and note that our results are easily extended to more states with little complication. Intriguingly, upon restriction of the two state general Markov model to the parameter space of the binary symmetric model, our extension is indistinguishable from the previous approach only on trees; as soon as any incompatible splits are introduced the two approaches give rise to differing probability distributions with disparate structure. Through exploration of a simple example, we give a tentative argument that our approach to extending to more general networks has desirable properties that the previous approaches do not share. In particular, our construction allows for the possibility of convergent evolution of previously divergent lineages; a property that is of significant interest for biological applications.
Ancestral lineages and limit theorems for branching Markov chains  [PDF]
Vincent Bansaye
Mathematics , 2013,
Abstract: We consider a branching model in discrete time where each individual has a trait in some general state space. Both the reproduction law and the trait inherited by the offsprings may depend on the trait of the mother and the environment. We study the long time behavior of the population and the ancestral lineage of typical individuals under general assumptions, which we specify for applications to some models motivated by biology. Our results focus on the growth rate, the trait distribution among the population for large time, so as local densities and the position of extremal individuals. The approach consists in comparing the branching Markov chain to a well chosen (possibly non-homogeneous) Markov chain.
Enhancement of Loop Induced $H^\pm W^\mp Z^0$ Vertex in Two Higgs-doublet Model  [PDF]
Shinya Kanemura
Physics , 1997, DOI: 10.1103/PhysRevD.61.095001
Abstract: The non-decoupling effects of heavy Higgs bosons as well as fermions on the loop-induced $H^\pm W^\mp Z^0$ vertex are discussed in the general two Higgs doublet model. The decay width of the process $H^+ \to W^+ Z^0$ is calculated at one-loop level and the possibility of its enhancement is explored both analytically and numerically. We find that the novel enhancement of the decay width can be realized by the Higgs non-decoupling effects with large mass-splitting between the charged Higgs boson and the CP-odd one. This is due to the large breakdown of the custodial $SU(2)_V$ invariance in the Higgs sector. The branching ratio can amount to $10^{-2} \sim 10^{-1}$ for $m_{H^\pm} = 300$ GeV within the constraint from the present experimental data. Hence this mode may be detectable at LHC or future $e^+e^-$ linear colliders.
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