Journal of Theoretical Biology
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A relaxed modification of the Rappaport model for cytokinesis.
COStar: A D-star Lite-based dynamic search algorithm for codon optimization.
We introduce COStar, a D-star Lite-based dynamic search algorithm for codon optimization. The algorithm first maps the codon optimization problem into a weighted directed acyclic graph using a sliding window approach. Then, the D-star Lite algorithm is used to compute the shortest path from the star...
Investigating the link between epithelial-mesenchymal transition and the cancer stem cell phenotype: A mathematical approach.
We mathematically investigate the nature of this increase in stem cell activity. A stochastic model is used when small number of cells are under consideration, namely in simulating the mammosphere assay, while a related continuous model is used to probe the dynamics of larger cell populations. Two s...
On the dynamics of the growth plate in primary ossification.
We show that the size of the Proliferative Zone in the growth plate is rather insensitive to variations in the flux coefficients for Ihh and PTHrP at their boundaries. Besides, we also show that the model is also insensitive to large changes in the (comparatively small) critical value of the PTHrP c...
Adhesion induced by mobile cross-bridges: steady state peeling of conjugated cell pairs.
We introduce a specific adhesion model to investigate the complex interaction between rate of peeling, lateral diffusivity and the rate of detachment of bonds. Our analysis show that adhesive energy density increases with the rate of peeling and with lateral diffusivity of the bonds but decreases wi...
The cost of departure from optimal radii in microvascular networks.
We have previously had no expressions for evaluating the apparent energy cost for departures from the optimal junction exponent of 3. Such expressions are derived here. They show that junction exponents, from about 1.5 to large positive values, are within 5% of the energy minimum. With the new equat...
Evolutionarily stable strategies for a finite population and a variable contest size.
This paper presents a generalization of Maynard Smith's concept of an evolutionarily stable strategy (ESS) to cover the cases of a finite population and a variable contest size. Both equilibrium and stability conditions are analysed. The standard Maynard Smith ESS with an infinite po...
Algebraic expressions for the waveforms of sea urchin sperm flagella.
The waveforms of live sea urchin sperm flagella were digitized with video-digitizing apparatus. The flagellar waveforms were expressed by the coordinates of 20 points spaced 2 micron apart along the flagella. The waveforms were condensed into simple algebraic expression with four parameters. Each of...
Minimum dynamic core in consciousness.
Putative anticodons in mitochondrial tRNA sidearm loops: Pocketknife tRNAs?
The hypothesis that tRNA sidearm loops bear anticodons assumes crossovers between anticodon and sidearms, or translation by expressed aminoacylated tRNA halves forming single stem-loops. Only the latter might require ribosomal adaptations. Drosophila mitochondrial codon usages coevolve with sidearm...