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Dr. Ph.D. Cesar Lopez Pastrana

Offered Bachelor’s or Master’s Theses Topics

Computational model for the growth of closed shells: how can self-assembled shapes be conserved during growth?
The aim of this Master thesis is to use computer simulations as a tool to explore possible growth mechanisms for closed shells that form by self-assembly via out-of-equilibrium mechanisms. These shells could be the envelope of biological cells or of engineered biosynthetic containers made, e.g. of DNA or proteins. This thesis will focus on the conceptual kinetic mechanisms, on a coarse-grained level, rather than the detailed molecular implementation. 
suitable as
  • Master’s Thesis Applied and Engineering Physics
Supervisor: Ulrich Gerland
Growing shapes: Kinetics of integrating cell wall material into the envelope of a growing cell
The aim of this Master thesis is to explore different modes of cell wall growth, which is locally controlled by enzymes but has a global effect on the shape of the cell. Which schemes of enzymatic action permit stably growing cell shapes? And which ones can mimick the observed growth behavior of different bacterial species? These fundamental questions are surpisingly largely open, partially due to the difficulty of experimentally determining which local properties of the cell wall affect the enzymatic activity. In light of this experimental barrier, conceptual theoretical models can classify different plausible schemes by their large-scale behavior, which is more easily observed experimentally. This thesis will combine simulations of stochastic models for growing shapes with simple analytical toy models to address some of the open questions.
suitable as
  • Master’s Thesis Biophysics
Supervisor: Ulrich Gerland
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