Phd Position in Multiscale Modelling of Endothelial Cell Monolayers in Health and Disease
3 weken geleden
What are you going to do
?The aims of your project are:
To develop and implement a sub-cellular model of the RhoA/RhoB pathways using lumped parameter ODE based models. Next, to develop and implement a spatiotemporal model of signalling in the sub cellular space in a single EC, using compartmentalised models. And finally, to develop and implement a model of an EC monolayer, using cellular Potts models and integrate the earlier mentioned spatiotemporal models of signalling in a single EC. To parameterize and validate your models based on the experimental results. And vice-versa, to inform new experiments based on your simulations. To study the dynamical properties of the sub-cellular model, e.g. its stable states, or bistability, and hysteresis. Also to obtain, by model fitting on experimental data, the model parameters for different types of EC to explain cell-to-cell and cell type heterogeneities. With the single cell spatiotemporal EC model you will first reproduce experimentally observed spatiotemporal oscillations of RhoB activation and then study the dynamics of quiescent EC as well as under pro-inflammatory conditions. Finally, with the EC monolayer model you will study heterogeneities in EC monolayers, fluctuations, and frequency of gap formations, and on the difference between quiescent and inflamed monolayers, explicitly including mechanics of the monolayers. Additional data obtained using plasma samples from Chronic Kidney Disease patient samples will be incorporated, to allow translation of the mathematical model to the (pre)clinical situation.For setting up the mathematical models and simulations you will rely as much as possible on existing (python based) toolkits such as PySB (pysb.org) for modelling the signalling pathways, and the Compucell3D for the EC monolayer simulations (compucell3d.org). Inclusion of blood flow modelling you will rely on Palabos (palabos.unige.ch) and our own Hemocell framework (hemocell.eu). For the multiscale coupling you will use packages such as Muscle3. Most programming will be in Python and/or C++.
Relevant URLs:
What do you have to offer?
Your experience and profile
You will have:
a first master degree or equivalent in computational science, computional biology, computational (bio)physics, applied mathematics, or an allied field; research experience in applying in-silico modelling in the life sciences, physiology, or medicine; proven programming expertise in python or c++; motivation and ambition to work in a challenging and interdisciplinary research team; a good command of English; affinity with cell biology and interested to learn wet-lab techniques.Our offer
A temporary contract for 38 hours per week for the duration of 4 years (the initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years). The preferred starting date is as soon as possible. This should lead to a dissertation (PhD thesis). We will draft an educational plan that includes attendance of courses and (international) meetings. We also expect you to assist in teaching undergraduates and master students.
The gross monthly salary, based on 38 hours per week and dependent on relevant experience, ranges between € 2, in the first year to € 3, in the last year (scale P). UvA additionally offers an extensive package of secondary benefits, including 8% holiday allowance and a year-end bonus of 8.3%. The UFO profile PhD Candidate is applicable. A favourable tax agreement, the ‘30% ruling’, may apply to non-Dutch applicants. The Collective Labour Agreement of Universities of the Netherlands is applicable.
Besides the salary and a vibrant and challenging environment at Science Park, we offer you multiple fringe benefits:
holiday hours per year (based on fulltime) and extra holidays between Christmas and 1 January; Multiple courses to follow from our Teaching and Learning Centre; A complete educational program for PhD students; Multiple courses on topics such as leadership for academic staff; Multiple courses on topics such as time management, handling stress and an online learning platform with + different courses; 7 weeks birth leave (partner leave) with % salary; Partly paid parental leave; The possibility to set up a workplace at home; A pension at ABP for which UvA pays two third part of the contribution; The possibility to follow courses to learn Dutch; Help with housing for a studio or small apartment when you’re moving from abroadAre you curious to read more about our extensive package of secondary employment benefits, take a look here.
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