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Journal of Mathematical Biology

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https://www.readbyqxmd.com/read/27921151/free-boundary-problem-for-cell-protrusion-formations-theoretical-and-numerical-aspects
#1
Olivier Gallinato, Masahito Ohta, Clair Poignard, Takashi Suzuki
In this paper, a free boundary problem for cell protrusion formation is studied theoretically and numerically. The cell membrane is precisely described thanks to a level set function, whose motion is due to specific signalling pathways. The aim is to model the chemical interactions between the cell and its environment, in the process of invadopodia or pseudopodia formation. The model consists of Laplace equation with Dirichlet condition inside the cell coupled to Laplace equation with Neumann condition in the outer domain...
December 5, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27915430/protection-zone-in-a-diffusive-predator-prey-model-with-beddington-deangelis-functional-response
#2
Xiao He, Sining Zheng
In any reaction-diffusion system of predator-prey models, the population densities of species are determined by the interactions between them, together with the influences from the spatial environments surrounding them. Generally, the prey species would die out when their birth rate is too low, the habitat size is too small, the predator grows too fast, or the predation pressure is too high. To save the endangered prey species, some human interference is useful, such as creating a protection zone where the prey could cross the boundary freely but the predator is prohibited from entering...
December 3, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27904954/the-mathematics-of-xenology-di-cographs-symbolic-ultrametrics-2-structures-and-tree-representable-systems-of-binary-relations
#3
Marc Hellmuth, Peter F Stadler, Nicolas Wieseke
The concepts of orthology, paralogy, and xenology play a key role in molecular evolution. Orthology and paralogy distinguish whether a pair of genes originated by speciation or duplication. The corresponding binary relations on a set of genes form complementary cographs. Allowing more than two types of ancestral event types leads to symmetric symbolic ultrametrics. Horizontal gene transfer, which leads to xenologous gene pairs, however, is inherent asymmetric since one offspring copy "jumps" into another genome, while the other continues to be inherited vertically...
November 30, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27896438/survival-of-a-recessive-allele-in-a-mendelian-diploid-model
#4
Rebecca Neukirch, Anton Bovier
In this paper we analyse the genetic evolution of a diploid hermaphroditic population, which is modelled by a three-type nonlinear birth-and-death process with competition and Mendelian reproduction. In a recent paper, Collet et al. (J Math Biol 67(3):569-607, 2013) have shown that, on the mutation time-scale, the process converges to the Trait-Substitution Sequence of adaptive dynamics, stepping from one homozygotic state to another with higher fitness. We prove that, under the assumption that a dominant allele is also the fittest one, the recessive allele survives for a time of order at least [Formula: see text], where K is the size of the population and [Formula: see text]...
November 28, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27866238/topological-horseshoe-and-its-uniform-hyperbolicity-in-the-hp-model
#5
Lei Wang, Xiao-Song Yang
A famous food-chain model proposed by Hastings and Powell is numerically restudied. The existence and uniform hyperbolicity of chaotic invariant sets are demonstrated by means of the topological horseshoe theory and the Conley-Moser conditions, indicating that, for a fixed cross section, the second return Poincaré map of the model possesses a closed uniformly hyperbolic chaotic invariant set, on which it is topologically conjugate to the 2-shift map.
November 19, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27853820/antiparallel-d-stable-traces-and-a-stronger-version-of-ore-problem
#6
Jernej Rus
In 2013 a novel self-assembly strategy for polypeptide nanostructure design which could lead to significant developments in biotechnology was presented in Gradišar et al. (Nat Chem Bio 9:362-366, 2013). It was since observed that a polyhedron P can be realized by interlocking pairs of polypeptide chains if its corresponding graph G(P) admits a strong trace. It was since also demonstrated that a similar strategy can also be expanded to self-assembly of designed DNA (Kočar, Nat commun 7:1-8, 2016). In this direction, in the present paper we characterize graphs which admit closed walk which traverses every edge exactly once in each direction and for every vertex v, there is no subset N of its neighbors, with [Formula: see text], such that every time the walk enters v from N, it also exits to a vertex in N...
November 16, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27853819/sur-les-processus-lin%C3%A3-aires-de-naissance-et-de-mort-sous-critiques-dans-un-environnement-al%C3%A3-atoire
#7
Nicolas Bacaër
An explicit formula is found for the rate of extinction of subcritical linear birth-and-death processes in a random environment. The formula is illustrated by numerical computations of the eigenvalue with largest real part of the truncated matrix for the master equation. The generating function of the corresponding eigenvector satisfies a Fuchsian system of singular differential equations. A particular attention is set on the case of two environments, which leads to Riemann's differential equation.
November 16, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27853818/statistics-of-topological-rna-structures
#8
Thomas J X Li, Christian M Reidys
In this paper we study properties of topological RNA structures, i.e. RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological structures having genus zero. We derive a new bivariate generating function whose singular expansion allows us to analyze the distributions of arcs, stacks, hairpin- , interior- and multi-loops. We then extend this analysis to H-type pseudoknots, kissing hairpins as well as 3-knots and compute their respective expectation values...
November 16, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27837260/the-optimal-treatment-of-an-infectious-disease-with-two-strains
#9
Robert Rowthorn, Selma Walther
This paper explores the optimal treatment of an infectious disease in a Susceptible-Infected-Susceptible model, where there are two strains of the disease and one strain is more infectious than the other. The strains are perfectly distinguishable, instantly diagnosed and equally costly in terms of social welfare. Treatment is equally costly and effective for both strains. Eradication is not possible, and there is no superinfection. In this model, we characterise two types of fixed points: coexistence equilibria, where both strains prevail, and boundary equilibria, where one strain is asymptotically eradicated and the other prevails at a positive level...
November 11, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27832321/a-mathematical-analysis-of-rebound-in-a-target-mediated-drug-disposition-model-ii-with-feedback
#10
Philip J Aston, Gianne Derks, Balaji M Agoram, Piet H van der Graaf
We consider the possibility of free receptor (antigen/cytokine) levels rebounding to higher than the baseline level after the application of an antibody drug using a target-mediated drug disposition model. It is assumed that the receptor synthesis rate experiences homeostatic feedback from the receptor levels. It is shown for a very fast feedback response, that the occurrence of rebound is determined by the ratio of the elimination rates, in a very similar way as for no feedback. However, for a slow feedback response, there will always be rebound...
November 10, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27826736/a-mathematical-model-for-the-simulation-of-the-contraction-of-burns
#11
Daniël C Koppenol, Fred J Vermolen, Gabriela V Koppenol-Gonzalez, Frank B Niessen, Paul P M van Zuijlen, Kees Vuik
A continuum hypothesis-based model is developed for the simulation of the contraction of burns in order to gain new insights into which elements of the healing response might have a substantial influence on this process. Tissue is modeled as a neo-Hookean solid. Furthermore, (myo)fibroblasts, collagen molecules, and a generic signaling molecule are selected as model components. An overview of the custom-made numerical algorithm is presented. Subsequently, good agreement is demonstrated with respect to variability in the evolution of the surface area of burns over time between the outcomes of computer simulations and measurements obtained in an experimental study...
November 8, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27800561/on-the-challenge-of-reconstructing-level-1-phylogenetic-networks-from-triplets-and-clusters
#12
Philippe Gambette, K T Huber, S Kelk
Phylogenetic networks have gained prominence over the years due to their ability to represent complex non-treelike evolutionary events such as recombination or hybridization. Popular combinatorial objects used to construct them are triplet systems and cluster systems, the motivation being that any network N induces a triplet system [Formula: see text] and a softwired cluster system [Formula: see text]. Since in real-world studies it cannot be guaranteed that all triplets/softwired clusters induced by a network are available, it is of particular interest to understand whether subsets of [Formula: see text] or [Formula: see text] allow one to uniquely reconstruct the underlying network N...
October 31, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27796478/continuous-and-discrete-sir-models-with-spatial-distributions
#13
Seong-Hun Paeng, Jonggul Lee
The SIR-model is a basic epidemic model that classifies a population into three subgroups: susceptible S, infected I and removed R. This model does not take into consideration the spatial distribution of each subgroup, but considers the total number of individuals belonging to each subgroup. There are many variants of the SIR-model. For studying the spatial distribution, stochastic processes have often been introduced to describe the dispersion of individuals. Such assumptions do not seem to be applicable to humans, because almost everyone moves within a small fixed radius in practice...
October 28, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27785559/estimation-of-under-reporting-in-epidemics-using-approximations
#14
Kokouvi Gamado, George Streftaris, Stan Zachary
Under-reporting in epidemics, when it is ignored, leads to under-estimation of the infection rate and therefore of the reproduction number. In the case of stochastic models with temporal data, a usual approach for dealing with such issues is to apply data augmentation techniques through Bayesian methodology. Departing from earlier literature approaches implemented using reversible jump Markov chain Monte Carlo (RJMCMC) techniques, we make use of approximations to obtain faster estimation with simple MCMC. Comparisons among the methods developed here, and with the RJMCMC approach, are carried out and highlight that approximation-based methodology offers useful alternative inference tools for large epidemics, with a good trade-off between time cost and accuracy...
October 26, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27785558/cooperativity-a-competition-of-definitions
#15
Melanie I Stefan
Cooperativity as a concept is easy to grasp intuitively, but surprisingly hard to define. Two recent papers shed light on the issue and continue the debate on how best to define cooperative binding.
October 26, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27783151/a-phenomenological-model-of-cell-cell-adhesion-mediated-by-cadherins
#16
Simona Mancini, René-Marc Mège, Benoit Sarels, Pierre-Olivier Strale
We present a phenomenological model intended to describe at the protein population level the formation of cell-cell junctions by the local recruitment of homophilic cadherin adhesion receptors. This modeling may have a much wider implication in biological processes since many adhesion receptors, channel proteins and other membrane-born proteins associate in clusters or oligomers at the cell surface. Mathematically, it consists in a degenerate reaction-diffusion system of two partial differential equations modeling the time-space evolution of two cadherin populations over a surface: the first one represents the diffusing cadherins and the second one concerns the fixed ones...
October 25, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27738761/robust-phase-waves-in-chains-of-half-center-oscillators
#17
Calvin Zhang, Timothy J Lewis
Many neuronal circuits driving coordinated locomotion are composed of chains of half-center oscillators (HCOs) of various lengths. The HCO is a common motif in central pattern generating circuits (CPGs); an HCO consists of two neurons, or two neuronal populations, connected by reciprocal inhibition. To maintain appropriate motor coordination for effective locomotion over a broad range of frequencies, chains of CPGs must produce approximately constant phase-differences in a robust manner. In this article, we study phase-locking in chains of nearest-neighbor coupled HCOs and examine how the circuit architecture can promote phase-constancy, i...
October 13, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27734133/an-entropy-based-technique-for-classifying-bacterial-chromosomes-according-to-synonymous-codon-usage
#18
Andrew Hart, Servet Martínez
We present a framework based on information theoretic concepts and the Dirichlet distribution for classifying chromosomes based on the degree to which they use synonymous codons uniformly or preferentially, that is, whether or not codons that code for an amino acid appear with the same relative frequency. At its core is a measure of codon usage bias we call the Kullback-Leibler codon information bias (KL-CIB or CIB for short). Being defined in terms of conditional entropy makes KL-CIB an ideal and natural quantity for expressing a chromosome's degree of departure from uniform synonymous codon usage...
October 12, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27714432/abrupt-transitions-to-tumor-extinction-a-phenotypic-quasispecies-model
#19
Josep Sardanyés, Regina Martínez, Carles Simó, Ricard Solé
The dynamics of heterogeneous tumor cell populations competing with healthy cells is an important topic in cancer research with deep implications in biomedicine. Multitude of theoretical and computational models have addressed this issue, especially focusing on the nature of the transitions governing tumor clearance as some relevant model parameters are tuned. In this contribution, we analyze a mathematical model of unstable tumor progression using the quasispecies framework. Our aim is to define a minimal model incorporating the dynamics of competition between healthy cells and a heterogeneous population of cancer cell phenotypes involving changes in replication-related genes (i...
October 6, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27714431/augmentative-biocontrol-when-natural-enemies-are-subject-to-allee-effects
#20
Nicolas Bajeux, Frédéric Grognard, Ludovic Mailleret
Intraspecific interactions such as Allee effects are key properties that can guide population management. This contribution considers component Allee effects that are elementary mechanisms leading to declines of fitness at the population scale, i.e. demographic Allee effects. It especially focuses on the consequences of such properties in predator populations, and investigates their repercussions in a biological control context. A modelling framework able to account for reproductive and/or foraging component Allee effects is proposed...
October 6, 2016: Journal of Mathematical Biology
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