Digital Twins for Neural Tissue – Data Assimilation in large-scale neural network models

A multidisciplinary, bleeding edge neurotech PhD position at the Erasmus Medical Center (Rotterdam, The Netherlands).

Keywords:

Biophysically plausible neural networks, Data assimilation, Neurodynamics, Homeostasis.

The Project

A digital twin is a surrogate representation of a biological system that allows for the prediction and understanding of biological processes. To produce a digital twin, one combines a theoretical understanding of the cellular processes (biophysics / molecular) with measurements of the biological system into a computational model that is tuned to reproduce observable biological behavior. 

Empirical studies of biological systems produce coarse grained observations (e-phys, Optics, LFP, MEA). Systematically integrating these observables into biophysically plausible/accurate models is a mostly unsolved problem.

Biology finds parameters via homeostasis and plasticity. We take inspiration in biology to solve the problem of finding parameter sets for digital twins that reproduce coarse grained observations by invoking homeostatic constraints (on-the-fly control). In this project we would explore the feasibility of techniques ranging from systems and dynamics theory to optimization and machine learning and try to improve on this using novel results in data assimilation from hierarchical and distributed control theory.

The goal of the project is to engineer data-assimilation pipelines for efficient reconstruction of models of neuronal tissue (“Digital twin”). They will be used to produce predictions about disease pathways and the effect of pharmacology on neuronal dynamics. 

Candidate’s Profile

We are looking for one outstanding Postdoc or PhD to conduct computational neuroscience research in the neurocomputing lab in Rotterdam (www.neurocomputinglab.com). The candidate has firm theoretical background and/or interest in physics and  Systems and Control Theory and excellent command of the English language.

In addition to a solid foundation in neurobiology (particularly cells and networks), and biophysics (good understanding of Hodgkin-Huxley models and ion channel mechanisms), the candidate is expected to feel comfortable with applied mathematics and physics, and to have a penchant for the data sciences (under the many guises of supervised and unsupervised learning). 

The candidate is expected to be open, proactive, hard working, an efficient coder and a clear thinker.

The Institutions (Erasmus Medical Center and TU Delft)

Today’s urgent and complex societal challenges call for convergence; crossing boundaries between institutions and disciplines to create new perspectives and solutions. This is why TU Delft, Erasmus MC and Erasmus University Rotterdam are joining forces in what is referred to as: the Convergence. Within the Convergence theme of Health & Technology, we form new frameworks that promote scientific discoveries and technological innovation in the field of health and healthcare.

Erasmus MC stands for a healthy population and excellence in healthcare. By conducting groundbreaking work, we aim to push boundaries through leading the way in research, education and healthcare. We have access to the latest equipment and techniques in a state-of-the-art environment.

The Department of Neuroscience at Erasmus MC, Rotterdam is a dynamic and collaborative environment of about 150 people across 22 research groups. The PhD candidates will work in a motivated small team with close supervision by Dr. Mario Negrello (computational neuroscience, EMC), Dr. Daan Brinks (TUD, imaging physics)  and Dr. Matin Jafarian (TUD, systems and control theory). Wetlab data will be obtained in collaboration with Dr. Geeske Van Woerden (EMC, neurobiology).

This project is part of the Convergence program Integrative Neuromedicine, a large-scale collaborative effort from Erasmus University, Erasmus Medical Center and Delft University of Technology to develop integrated biological and computational models of the human brain. The PhD student will be part of the Badura and Schonewille labs, but interact regularly with the other project members for different aspects of the project.   

 What we offer

Following Erasmus MC policy:
– You will receive a temporary position for 4 years at Erasmus MC
– The gross monthly salary is € 2.631 ,- in the 1st year and increases to € 3.336,- in the 4th year (scale OIO).
– There are excellent fringe benefits, such as a 13th month that is already paid out in November and a personal travel budget.
– You will receive pension insurance with ABP.
– The employer covers approximately 2/3 of the monthly contribution. 
– Also included: special benefits, such as a physiotherapist and a company bicycle repairer. And there is also a sports club where you can work on your fitness after work.
– An International Office which aids you in preparing for your journey and stay.

The terms of employment are according to the Collective Bargaining Agreement for Dutch University Medical Centers (CAO UMC).

Interested candidates should contact 

Dr. Mario Negrello (m.negrello@erasmusmc.nl)

Job Category: Open PhD Positions
Job Type: Full Time
Job Location: Rotterdam

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