| 14-12-2020 |
Mathematical and computational modelling of embryonic development, continuation
This iPre is part of an interdisciplinary project that will study a self-organizing collective of two cell types in the early embryo of annual killifish (see image). We will utilize advanced methods from developmental biology, microscopy, image analysis, and microfabrication to track the behaviour of cells in embryos and in vitro culture, and construct mathematical and computational models of their interactions. Our aim is to understand the principle mechanisms that give rise to self-organized emergent behaviour at multiple scales from molecular, through cellular, tissue and ultimately to whole embryo structure. The aim of the iPre project is to develop mathematical and computational models using: Python, C++ and other programming languages Differential equations and partial differential equations Finite elements Computational geometry
Prerequisites:
None.
Evaluation method: Nota 1-7, with 0/1 available vacants |
Mentor(s): Open in the plataform |
| 24-07-2020 |
Development of hybrid model for protein folding simulations
Protein folding is a biological phenomenon with a timescale in the order of milliseconds to seconds. Thus, it is challenging to explore these processes in molecular dynamics simulations. However, recent years have witnessed the development of models rigorously footed in the energy landscape theory of protein folding that enable simulating these phenomena with low computational costs. This is the case of the SMOG2 software, that generates both all-atom and single-bead coarse-grained modelos for simulations in GROMACS. However, it has been recently determined that hybrid double-bead (alpha + beta carbon) or pseudo-empiric models are useful to simulate protein folding processed that incorporate sequence-dependent information (electrostatics, hydrophobic). In this research, SMOG2-dependent hybrid models will be developed for protein folding simulations in GROMACS.
Prerequisites:
None.
Evaluation method: Nota 1-7, with 0/1 available vacants |
Mentor(s): Open in the plataform |