The shoot apical meristem (SAM) is a stem cell niche acting as a main

regulator of above-ground plant development. The maintenance of stem

cells in the SAM, and the initiation of organs at the periphery are

dependent on genetic regulation, hormone signaling, and mechanical

anisotropies resulting in a complex dynamical system regulating

organized differentiation and growth. Mathematical modeling has proven

to be a useful tool to understand SAM development at a systems level,

and the use of live microscopy has increased our knowledge of details

in the protein dynamics associated with SAM development. This allow

for creating computational models where microscopy data provides

experimental templates for optimizing the models, and the models can

introduce experimentally verifiable predictions.

In this talk I will discuss models for stem cell regulation and

primordia formation in the SAM. I will give examples of models where

hormone signaling and transport are combined with mechanical models

for generating phyllotactic patterns as well as models for stem cell

regulation focusing on the CLAVATA WUSCHEL feedback. I will further

discuss how we use model optimization to fit the models to templates

where expression regions are marked in spatial regions relating to

confocal images, and how this is used to make model predictions for

the molecular networks.