Blog Archives

PhD position on crumbling reefs: simulation based monitoring of coral reefs @Heriot-Watt University

The project aims to develop computational models to analyse the impact of ocean acidification on cold-water coral reefs. Our vision is to facilitate rapid monitoring strategies that can help to preserve some of the most vulnerable ecosystems. To realise this, we aim to develop fast and effective multiscale in silico models from coral skeleton to reef length scale to predict the ocean acidification induced decay of cold-water coral reef systems. A major challenge is the ability to such complex systems, and we aim to overcome this by combining the power of multiscale models based on physical knowledge with the speed of artificial neural networks.

More information can be found here:

PhD position on fast and effective personalised multiscale modelling for precision medicine in musculoskeletal diseases @Heriot-Watt University

Motivated by the pressing need for treatment optimisation in musculoskeletal diseases, our vision is to create a clinical point-of-care test that uses X-rays to visualise mechanical analyses of long bones such as the femur to illustrate potential therapeutic success in a couple of minutes, without adding significant time to patient consultations or training needs for clinicians. To realise this, we aim to develop fast and effective patient-specific in silico models to predict the multiscale mechanical behaviour of long bones. These combine the power of multiscale models based on physical knowledge with the speed of artificial neural networks.

More information can be found here:

2 PhD positions to advance integrated computational simulations of intervertebral disc degeneration

Lower back pain (LBP) is the largest cause of morbidity worldwide, yet there remains controversy as to the specific cause leading to poor treatment options and prognosis. Intervertebral disc degeneration (LDD) is reported to account for 50% of LBP in young adults, but the interplay of factors such as genetics, environmental, cellular responses, social and psychological is poorly understood. Unfortunately, the integration of such data into a holistic and rational map of degenerative processes and risk factors has not been achieved, requiring the creation of professional cross-competencies, which current training programmes in biomedicine, biomedical engineering and translational medicine fail to address, individually.

Disc4All aims to tackle this issue through collaborative expertise of clinicians; computational physicists and biologists; geneticists; computer scientists; cell and molecular biologists; microbiologists; bioinformaticians; and industrial partners. It provides interdisciplinary training in data curation and integration; experimental and theoretical/computational modelling; computer algorithm development; tool generation; and model and simulation platforms to transparently integrate primary data for enhanced clinical interpretations through models and simulations. Complementary training is offered in dissemination; project management; responsible research and innovation; ethics; regulation; policy; business strategy; public and patient engagement. Disc4All will train a new generation of internationally mobile professionals with unique skill sets for the development of thriving careers in translational research applied to multifactorial disorders.

Position 1:

Topic: Multiscale modelling of IVD cell activity & potential tissue turnover

Description: The successful candidate will work on the multiscale modelling of the mechanisms of intervertebral disc regulation. Specifically, the work will target the modelling and simulation of bottomup processes of tissue regulation, through which the dynamics of cell activity contributes to disc tissue turnover in specific regions of interest, in response to multifactorial cell stimulations. Different types of intervertebral disc network models will be used and combined to successively incorporate cell culture experimental data, proteomics measurements and eventually gene variant effects. Interplays of biochemical, mechanical and nutritional cell stimulation will be modelled in representative volume elements through agent-based modelling. Eventually, collective cell activity will be linked with heterogeneous cell environments predictable through finite element simulations of disc tissue and organ multiphysics.

Supervision: Jérôme Noailly (UPF)

More information:

Position 2:

Topic: Bottom-up simulations of spatio-temporal degenerative events in the IVD & biological LDD stratification

Description: The successful candidate will work on the systematization of multiscale modelling of the intervertebral disc regulation for improved LDD stratification. Existing regulatory network and multiphysics models, at the molecular/cell and tissue/organ scales will be locally integrated in relevant regions of interest of the IVD. Such integration will be coupled with different disc model morphologies and molecular signature inputs, from the Twins UK and Northern Finland Birth cohorts. A smart atlas of simulated data will be generated, to eventually enable efficient calculations through metamodeling. Metamodeling will further allow the mining of simulated and real word data altogether, to establish different fingerprints of LDD and the spatio-temporal evolution thereof, characterised by specific hierarchies of risk factors and exploitable clinically.

Supervision: Jérôme Noailly (UPF)

More information:

3 Marie Sklodowska-Curie Early Stage Researchers (PhD positions) in Medical Engineering

Do you want to be part of a globally leading research network comprising institutions across Europe? Would you like to learn new skills in medical engineering with a focus on implant design and biotribology? Could you be a future research leader in providing solutions to some of Europe’s most pressing healthcare problems? Do you want to further your career and attain a PhD at one of the UK’s leading research intensive universities? To complete one of these exciting projects you will be based in the Institute of Functional Surfaces and have access to world leading equipment including advanced simulators and other devices for both the tribological / corrosion testing of implants and the characterisation of the surfaces both coated and uncoated.  You will join a recently funded European Training Network (ETN) BioTrib (project ID 956004, call H2020-MSCA-ITN-2020). BioTrib offers high-level doctoral training to a total of 15 Early Stage Researchers (ESRs) of which 3 will be employed at the University of Leeds. The project lead is Prof Richard M Hall at the University of Leeds.  This projects will be supervised by Prof Richard M Hall and Dr Michael Bryant.

Important eligibility rules for this position:

There are no restrictions on the nationality, but applicants must, at the time of recruitment,

(1) have not yet been awarded a doctorate degree and be in the first 4 years (full-time equivalent) of their research careers. This is measured from the date that you obtained the degree which would entitle you to embark on a PhD.

(2) At the time of recruitment, applicants must not have resided or carried out their main activity (work, studies, etc…) in the UK for more than 12 months in the 3 years immediately prior to their recruitment under the BioTrib project. Compulsory national service and/or short stays such as holidays are not taken into account.


The Marie Skłodowska-Curie Early Stage Researcher living allowance is fixed at €62,057 per annum including the mobility allowance. This figure is before employer’s and employee’s deductions for national insurance and taxes per year, which will be paid in Sterling using an appropriate conversion rate.

Further details on each of these posts please refer to the applications website for the background, job description and person specification.

To explore the posts further or for any queries you may have, please contact:

Prof Richard M Hall, School of Mechanical Engineering


PhD position on computational modeling of mechanically-driven sprouting angiogenesis @Charité

Background and scope of the work

Angiogenesis, the growth of new blood vessels from pre-existing vessels, constitutes a fundamental physiological process during the regeneration of many tissues, including bone. In a DFG-funded collaborative project, we are using a combined experimental/computational approach to investigate how mechanical forces mediate angiogenesis during bone repair. As part of this project, a PhD position is available to investigate the role of mechanical strains on the growth of new blood vessels using mechano-biological computational models.  


You will develop computer models of sprouting angiogenesis taking into account the role played by chemical and mechanical signals in vessel patterning. You will work in close collaboration with project partners working in in vitro and in vivo models to inform and validate the computer models.

Your profile

  • Master Degree in Mechanical Engineering, Computational Biomechanics, Computational Biology or a related discipline
  • Strong programming skills
  • Knowledge of finite element analysis
  • High motivation, curiosity and commitment to scientific excellence
  • Team player skills and enthusiasm to work in a multi-disciplinary, collaborative environment
  • Excellent command in written and spoken English
  • Independent and responsible attitude, collaborative spirit

What we provide

This position is available for a period of three years with the possibility to be extended if new funding is available. You will work in a friendly team and in a unique research environment. As a PhD student, you will be associated to the Berlin-Brandenburg School of Regenerative Therapies ( and benefit from the interaction with international scientists.

Starting date: as soon as possible.


If you are interested, please send your CV, motivation letter and two references to: Prof. Sara Checa (

Computational modelling for personalised treatment of osteoarthritis @University of Edinburgh

The primary aim of the study is to establish the inter-relationship of initial cartilage quality, subchondral bone stiffness and loading scenarios (due to different physiological activies which result in loads with varying magnitudes, frequencies and strain rates) by using computational models to optimise osteoarthritis treatment.

Outline: The research will be conducted by using data from mechanical testing and imaging of testing clinical samples in conjunction with available physiological loading data. Novel computational simulations using the finite element method will be employed. A range of cartilage properties will be considered; variation of properties from normal to cartilage weakened by infection or inflammation will be considered. Similarly the material properties of the subchondral bone will be varied to represent subchondral sclerosis. The findings of this project will enable the interplay of bone and cartilage properties and loading to be considered in different patients. This will indicate the leading mechanism of joint failure in different patients, which will allow us to personalize the treatment inline with the principles of precision medicine

Project supervisors: Professor Pankaj Pankaj and Professor Hamish Simpson, The University of Edinburgh
Project description:
To apply:
Application deadline: 7 January 2021
Applicants are encouraged to contact Prof Pankaj Pankaj ( with their CV prior to applying.

PhD student position at Lund University

We are looking for a PhD student to explore the potential of Neutron scattering for studying soft musculoskeletal tissues and their structural and mechanical changes due to osteoarthritis. The student will be supervised by Prof Hanna Isaksson and Prof Martin Englund and be part of SwedNESS – the Swedish national graduate school for neutron research. 

More information can be found here:

Post-doc position in the Computational Biomechanics Research Group at University of Glasgow

A one-year postdoc position is available in the Computational Biomechanics Research Group at University of Glasgow. The project is aimed at combining image segmentation with biomechanical calculations and requires experience in scientific code development and nonlinear biomechanics.

For more information on the position, please check


More information on my research group can be found at


If you have any questions about the position, please email:

ESB webinar on ITK-SNAP: Open-Source Software for Medical Image Segmentation

October 27th 2020

15:00 – 16:00 CET

Click here to register for the webinar.

The objective of this webinar is to introduce ITK-SNAP and provide an overview of its capabilities for medical image navigation and segmentation.

In this webinar, attendees will learn some of the core capabilities of ITK-SNAP:

  • Visualization of 3D medical image data
  • Labeling of anatomical structures in 3D images both manually and semi-automatically
  • Loading, editing, and saving segmentation files
  • Rotating and landmarking 3D images
  • Using the ITK-SNAP distributed segmentation service

The webinar will be Led by Dr. Paul Yushkevich (creator of ITK-SNAP) and by Dr. Alison Pouch from the Penn Image Computing and Science Laboratory.

The seminar will last 45 minutes followed by 15 minutes of Q/A from the audience. You will have the chance to ask your questions which will be addressed by the speaker at the end of the webinar. However, it would be great if you could send your question in advance while filling the registration form or by sending to and/or  before the start of the webinar.

Click here to register for the webinar.

The webinar will be on the GoToWebinar Platform and will be uploaded to our YouTube channel afterwards. The information to join the webinar will be sent to you after your registration.

Please subscribe to our YouTube channel! ( )

Looking forward to your attendance.

ESB Student Committee