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- Alan C Newell, Patrick D Shipman, Zhiying Sun
- Journal of theoretical biology
- 2008

Current theories and models of the formation of phyllotactic patterns at plant apical meristems center on either transport of the growth hormone auxin or the mechanical buckling of the plant tunica. By deriving a continuum approximation of an existing discrete biochemical model and comparing it with a mechanical model, we show that the model partial… (More)

- Henry Adams, Tegan Emerson, +7 authors Lori Ziegelmeier
- Journal of Machine Learning Research
- 2017

Many data sets can be viewed as a noisy sampling of an underlying space, and tools from topological data analysis can characterize this structure for the purpose of knowledge discovery. One such tool is persistent homology, which provides a multiscale description of the homological features within a data set. A useful representation of this homological… (More)

- P D Shipman, A C Newell
- Journal of theoretical biology
- 2005

We demonstrate how phyllotaxis (the arrangement of leaves on plants) and the ribbed, hexagonal, or parallelogram planforms on plants can be understood as the energy-minimizing buckling pattern of a compressed sheet (the plant's tunica) on an elastic foundation. The key idea is that the elastic energy is minimized by configurations consisting of special… (More)

- P Shipman
- Annals of the New York Academy of Sciences
- 1981

- Sofya Chepushtanova, Tegan Emerson, +6 authors Lori Ziegelmeier
- ArXiv
- 2015

- Henry C Tuckwell, Patrick D Shipman, Alan S Perelson
- Mathematical biosciences
- 2008

We use a simple mathematical model to estimate the probability and its time dependence that one or more HIV virions successfully infect target cells. For the transfer of a given number of virions to target cells we derive expressions for the probability P(inf), of infection. Thus, in the case of needlestick transfer we determine P(inf) and an approximate… (More)

- R Mark Bradley, Patrick D Shipman
- Physical review letters
- 2010

A theory is developed that explains the genesis of the strikingly regular hexagonal arrays of nanoscale mounds that can form when a flat surface of a binary compound is subjected to normal-incidence ion bombardment. We find that the species with the higher sputter yield is concentrated at the peaks of the nanodots and that hysteretic switching between the… (More)

Pattern patterns, or phyllotaxis, the arrangements of phylla (flowers, leaves, bracts, florets) in the neighborhood of growth tips, have intrigued natural scientists for over four hundred years. Prominent amongst the observed features is the fact that phylla lie on families of alternately oriented spirals and that the numbers in these families belong to… (More)

It is not well understood why the transmission of HIV may have a small probability of occurrence despite frequent high risk exposures or ongoing contact between members of a discordant couple. We explore the possible contributions made by distributions of system parameters beginning with the standard three-component differential equation model for the… (More)

- Christopher Strickland, Gerhard Dangelmayr, Patrick D Shipman
- Journal of mathematical biology
- 2014

Mathematical models for the spread of invading plant organisms typically utilize population growth and dispersal dynamics to predict the time-evolution of a population distribution. In this paper, we revisit a particular class of deterministic contact models obtained from a stochastic birth process for invasive organisms. These models were introduced by… (More)