PhD in mechanistic modelling of chondrocyte-mediated destruction of hyaline cartilage in relation with subchondral bone morphology and inflammation – UPF, Barcelona

PhD in mechanistic modelling of chondrocyte-mediated destruction of hyaline cartilage in relation with subchondral bone morphology and inflammation in osteoarthritis and intervertebral disc degeneration



Universitat Pompeu Fabra, Dept. of Information & Communication Technologies, DTIC-UPF


The Department of Information and Communication Technologies (DTIC) of Universitat Pompeu Fabra covers a broad range of research topics: Computation and Intelligent Systems; Multimedia Technologies; Networks and Communications; Computational Biology and Biomedical Systems; and the Center of Brain and Cognition (CBC). This broad spectrum of topics reflects the current interdisciplinary reality of cutting edge research in ICT. The DTIC is now running a Maria de Maeztu Strategic Research Program on data-driven knowledge extraction, boosting synergistic research initiatives across our different research areas.

The DTIC consistently ranks among the top computer science departments in Spain (e.g. the only computer science department from an Spanish university that has even been included in the top 100 of the Shanghai Ranking).

Its PhD program offers advanced training in this interdisciplinary field, becoming an innovative and unique program in Spain. The DTIC PhD program has been growing steadily and currently hosts about 140 PhD students and 40 supervisors. The program received a Mention of Excellence award from the Ministry of Science and Innovation in 2011.

The UPF university was awarded in 2010 the distinction of International Excellence Campus by the Spanish Ministry of Education and it is widely considered to be one of the best universities in Spain (e.g. is the top Spanish university according to 2013 Times Higher Education Ranking).

The UPF is located in Barcelona. Its excellent location on the shores of the Mediterranean, its gentle climate, its open, cosmopolitan character, its gastronomy and architecture make Barcelona an extraordinary place to live. The DTIC is sited in UPF’s Communication Campus, which was opened in 2009 and is located within the vibrant 22@ technological district of Barcelona.


  • Research incomes: 15.6 M€ / year
  • 67 FP7 projects participated and coordinated by 26 staff members (> 60% UPF EU funds) including 13 prestigious ERC Grants, the Human Brain Project
  • Leader in Spain with  > 5% of all the competitive funds obtained by Spanish Universities, Maria de Maeztu Strategic Program.
  • Consolidated scientific productivity ~200 articles/year, > 75% Q1 international journals
  • 50% scientific papers and articles with at least one international collaborator

Roc Boronat, 138 – edifici Tànger, 08018 Barcelona, Barcelona


Physical Sciences, Mathematics and Engineering Panel


Dr.Jerôme Noailly

-Research Project / Research Group Description:

The proposed PhD will involve the Biomechanics and Mechanobiology (BMMB) and the Machine Learning for Personalised Medicine areas of BCN MedTech. BCN MedTech focuses on biomedical integrative research, including mathematical and computational models, algorithms and systems for computer-aided diagnosis and treatment of health problems. It has 60 full time researchers working on computational simulations, image analyses, signal processing, machine learning, and biomedical electronics.

Early cartilage degradation in osteochondral systems is poorly understood. In early osteoarthritis (OA), new theories point out the involvement of subchondral bone structural and mechanical changes [1]. In the IVD, the hyaline cartilage adjacent to the subchondral bone shows the first signs of ageing [2], and numerical explorations by the BMMB team have pointed out that specific subchondral bone structures induce above-average fluid velocities in the adjacent cartilage [3]. Thanks to the coupling of continuum tissue models and cell biology models, the BMMB team has recently demonstrated that early degradation of the IVD osteochondral layer is likely to result in the propagation of degenerative changes in the organ [4].

Accordingly, this project will explore new common paradigms of early OA and IVD degeneration processes through mechanistic modelling of the relationships among tissue interstitial fluid flow, chondrocyte mechanostimulation, inflammation and cartilage extracellular matrix turnover. It will involve finite element poromechanical models, and agent-based models of chondrocyte biological activity in different physical and biochemical environments. Model assessment will be achieved through experimental data on articular cartilage biology and multiphysics in OA patients, though an ongoing collaborative project with the Hospital del Mar, and though collaborations with the Universites of Zaragoza and Liège. Simulation results will be analysed through interpretable machine learning techniques.

-Job position description:

The successful candidate will work in a highly international environment in interaction with biomechanicians, biologists and computer scientists. He/She will be in charge of developing an intracellular network model for the simulation of chondrocyte mechanosensitivity in different inflammatory and nutritional environments, based on generic systems biology Boolean models. He/She will also handle multiphysics poromechanical models of the cartilage tissue matrix available at UPF to simulate the mechanical environment of the chondrocytes, simulated as agents. Sensitivity analyses, model evaluation and result interpretation will involve state-of-the-art techniques for model uncertainty evaluation and parameter/result classifications through in-house interpretable machine learning theories. He/She will actively participate to internal research seminars and international conferences in fields related with biomedical engineering, biomechanics, systems biology and rheumatology.

Candidates are expected to have a bachelor and master degrees in biomedical engineering, physics, applied mathematics or any related fields. They should be able to work in a team environment and have good communication skills. Proficient English is mandatory. For any inquiry, please contact Dr Jerome Noailly:

[1] Li, G. et al, 2013. Arthritis Res. Ther. 15, 223. doi:10.1186/ar4405
[2] Benneker, L.M., et al, 2005. Eur. Spine J. 14, 27–35. doi:10.1007/s00586-004-0759-4
[3] Malandrino, A., et al, 2014. Osteoarthritis Cartilage 22, 1053–60. doi:10.1016/j.joca.2014.05.005
[4] Baumgartner L., et al, 2017. Altered cell activity in the intervertebral disc transition zone due to early cartilage endplate degeneration. 23rd Congress of the European Society of Biomechanics, 2-3 July 2017, Seville, Spain

Application (through “La Caixa” Foundation online system)

Contact for inquiries and support:

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