INTERNATIONAL WINTER SCHOOL - New Challenges in the Physics of the Brain: From Cells to Organs, February 2016, Ecole de Physique des Houches, France.

Latest News:

IBMTL Co-Director, Prof Alain Goriely, has written a piece for the Oxford Science Blog highlighting the maths of the brain.

A new publication from IBMTL member Fatiha Nothias on the use of biomaterials based on the use of chitosan alone for spinal cord injury repair.

‘We Are All Soft In The Head’ – according to IBMTL member Professor Michel Destrade

Dr Subra Suresh, president of Carnegie Mellon University, USA, elected to an Honorary Fellowship at St Hugh’s College, Oxford. Dr Suresh spoke at the 2015 Oxford Brain Mechanics Workshop held at St Hugh’s.

Les Houches Winter School attendees – Feb 2016

Key Publications

D. Garcia-Gonzalez, J. Jayamohan, S.N. Sotiropoulos, S.-H. Yoon, J. Cook, C.R. Siviour, A. Arias, A. Jérusalem. On the mechanical behaviour of PEEK and HA cranial implants under impact loading. Journal of the Mechanical Behavior of Biomedical Materials, Volume 69, May 2017, Pages 342–354.

David E Koser, Amelia J Thompson, Sarah K Foster, Asha Dwivedy, Eva K Pillai, Graham K Sheridan, Hanno Svoboda, Matheus Viana, Luciano da F Costa, Jochen Guck, Christine E Holt and Kristian Franze. Mechanosensing is critical for axon growth in the developing brain. Nature Neuroscience 19, 1592–1598 (2016) doi:10.1038/nn.4394

Alain Goriely, Johannes Weickenmeier, and Ellen Kuhl. Stress Singularities in Swelling Soft Solids. Phys. Rev. Lett. Vol. 117, Iss. 13. DOI:

S. Song, N. S. Race, A. Kim, T. Zhang, R. Shi and Ziaie. A Wireless Intracranial Brain Deformation Sensing System for Blast-Induced Traumatic Brain Injury Blast. Scientific Reports 5, Article number: 16595, DOI: 10.1038/srep16959.

A. Goriely, J.A.W. van Dommelen, M.G.D. Geers, G.A. Holzapfel, J. Jayamohan, A. Jérusalem, S. Sivaloganathan, W. Squier, S. Waters and E. Kuhl. Mechanics of the brain: perspectives, challenges, and opportunities. Biomechanics and Modeling in Mechanobiology (online): DOI:10.1007/s10237-015-0662-4


About the Lab

The International Brain Mechanics and Trauma Lab (IBMTL) is a new international initiative created at the beginning of 2013. It involves the collaboration of (as of today) 18 main sites for 33 academics. All 33 academics are currently involved in direct collaborations on projects related to brain mechanics and trauma. This interaction (and the choice of each one of the members) is motivated by the need to gather the following necessary multidisciplinary expertise for the study of the relation between brain cell/tissue mechanics and brain functions/diseases/trauma:

  • Biology: stem cells, tissue engineering, physiopathology
  • Computing: supercomputing, neuroinformatics, image processing, big data analytics
  • Engineering: materials engineering, biomechanics, computational mechanics of materials, mechanobiology, systems engineering
  • Mathematics: mathematical modelling, computational statistics, continuum mechanics, data mining
  • Medical/Clinical: neurology, neuropathology, neuroimaging, veterinary medicine, neurosurgery, psychiatry
  • Neuroscience: translational neuroscience, functional connectivity and brain network architecture, brain plasticity computational modelling
  • Physics: nanoscience, cells/tissues nanomechanics, cell rheology, shockwave/ultrasound physics, biophysics

This initiative is built around the complementary collaboration of experts of different disciplines around the study of the brain cell and tissue mechanics and its relation with brain functions, diseases or trauma.


Previous Events

Second Oxford Brain Mechanics Workshop,
Mathematical Institute, Oxford,
Monday 13th and Tuesday 14th January, 2014


IBMTL Directors

Prof. Alain Goriely

Position: Professor of Mathematical Modelling / IBMTL Co-Director
Research interests: Mathematics: Mathematical modelling
Publications: Main list
Home institution webpage

Prof. Antoine Jérusalem

Position: Associate Professor / IBMTL Co-Director
Research interests: Engineering: Computational mechanics of materials
Publications: Google Scholar
Home institution webpage

University of Oxford

Prof. Robin Cleveland

Position: Professor of Engineering Science
Research interests: Engineering: Shock wave/ultrasound physics
Publications: ResearcherID
Home institution webpage

Prof. Sonia Contera

Position: Associate Professor
Research interests: Physics: Nanoscience in medicine, biological physics, scanning probe microscopy
Publications: ResearcherID, Google Scholar
Home institution webpage

Mr. Jayaratnam Jayamohan

Position: Neurosurgeon
Research interests: Clinical: Paediatric neurosurgery, craniofacial surgery
Home institution webpage

Dr. Damian Jenkins

Position: Fellow in Medicine, St Hugh’s and Army TBI Research Fellow
Research interests: Neurodegeneration in brain injury and dementia, cognitive neuroscience
Home institution webpage

Mr. Tim Lawrence

Position: Consultant Neurosurgeon and Clinical Research Fellow
Research interests: Imaging biomarkers in acute traumatic brain injury
Home institution webpage

Prof. Stam Sotiropoulos

Position: Honorary Research Fellow, FMRIB Analysis (Associate Professor, University of Nottingham)
Research interests: Neuroimaging, Brain connectivity/Connectome estimation, Diffusion MRI analysis, Functional MRI analysis, Brain microstructure & Biophysical modelling, Bayesian inference, Machine learning, Numerical Methods, Image processing & analysis
Home institution webpage

Prof. Mark Thompson

Position: Associate Professor
Research interests: Engineering: Biomechanics
Publications: Main list, ResearcherID
Home institution webpage

Dr. Natalie Voets

Position: Research Fellow
Research interests: Cognitive Neuroscience, Neuroimaging approaches to monitor brain injury and repair following trauma and neurosurgery
Publications: Main list
Home institution webpage

Prof. Cathy (Hua) Ye

Position: Associate Professor
Research interests: Engineering: Tissue engineering / stem cells
Publications: Main list
Home institution webpage

BIOTEC Dresden

Prof. Dr Jochen Guck

Position: Alexander-von-Humboldt Professor and Professor of Cellular Machines
Research interests: Biophysics, Cell Mechanics, CNS Tissue Mechanics, Mechanosensing, Spinal Cord Repair
Home institution webpage

Boston University

Prof. Lee Goldstein

Position: Associate Professor
Research interests: Medicine/Engineering: Psychiatry, neurology, biomedical engineering
Publications: Main list
Home institution webpage

Carnegie Mellon University

Prof. K. Jimmy Hsia

Position: Professor of Biomedical and Mechanical Engineering
Research interests: Solid Mechanics & Materials
Home institution webpage

Prof. Philip R. LeDuc

Position: William J. Brown Professor, Mechanical Engineering
Research interests: Cell mechanics, micro-/nano-technology, systems engineering
Publications: Main list
Home institution webpage

Cognitive Neuroscience Research Unit

Prof. Morten Overgaard

Position: Professor
Research interests: Cognitive Neuroscience
Publications: Main list
Home institution webpage

Dublin City University

Dr. Jeremiah Murphy

Position: Lecturer
Research interests: Mathematics: Mathematical modelling
Publications: Main list
Home institution webpage

Graz University of Technology

Prof. Gerhard Holzapfel

Position: Professor
Research interests: Biomechanics: Solid/continuum mechanics
Publications: Main list
Home institution webpage

Massachusetts Institute of Technology

Dr. Ming Dao

Position: Principal Research Scientist
Research interests: Materials Science: Cell mechanics
Publications: Main list
Home institution webpage

National University of Ireland, Galway

Prof. Michel Destrade

Position: Professor
Research interests: Mathematics: Mathematical modelling
Publications: Main list, Google Scholar
Home institution webpage

Purdue University

Prof. Riyi Shi

Position: Professor of Neuroscience and Biomedical Engineering
Research interests: Veterinary Medicine/Bioengineering: Translational neuroscience
Publications: Main list
Home institution webpage

Stanford University

Prof. Ellen Kuhl

Position: Associate Professor
Research interests: Engineering: Computational biomechanics
Publications: Main list
Home institution webpage

Stevens Institute of Technology

Prof. Mehmet Kurt

Position: Assistant Professor of Mechanical Engineering
Research interests: Brain biomechanics, mechanical neuroimaging, preventive equipment design in contact sports
Publications: Main list Google Scholar
Home institution webpage

Technical University of Madrid

Prof. Fernando Maestú

Position: Professor in Cognitive and Computational Neuroscience
Research interests: Cognitive Psychology: MEG/EEG recording for TBI treatment surveillance and prediction
Publications: Google Scholar
Home institution webpage

Prof. José-Maria Peña

Position: Associate Professor in Computer Science
Research interests: Computer Science: Supercomputing, data mining, neuroinformatics, image processing
Publications: Google Scholar
Home institution webpage

University College London

Prof. Yiannis Ventikos

Position: Kennedy Professor of Mechanical Engineering and Head of Department
Research interests: Transport Phenomena & Computational Modelling in Biomechanics, Energy, Processes and the Environment
Home institution webpage

University of California, Santa Barbara

Prof. Robert McMeeking

Position: Professor of Mechanical Engineering & Materials
Research interests: Engineering: Solid mechanics
Publications: Main list
Home institution webpage

University of Cambridge

Prof. Vikram Deshpande

Position: Professor of Materials Engineering
Research interests: Engineering: Materials engineering
Publications: Main list
Home institution webpage

Dr. Kristian Franze

Position: Lecturer, MRC Fellow
Research interests: Mechanobiology: Developmental Neuroscience, Neuronal Regeneration
Publications: Main list
Home institution webpage

University of Glasgow

Dr. Peter Stewart

Position: Lecturer
Research interests: Mathematics: Continuum mechanics
Publications: Main list
Home institution webpage

University Pierre & Marie Curie

Fatiha Nothias

Position: Research Director at CNRS
Research interests: Neuroscience: Axon regeneration and growth
Publications: Main list
Home institution webpage

Dr Jean-Michel Peyrin

Position: Research Director at CNRS
Research interests: Microtechnologies, Microfluidics, Neuronal Networks Collapse, Axonal Degeneration
Publications: Main list
Home institution webpage

Research Assistants

Dr. Julian Andres Garcia Grajales

Position: Post-doctoral Researcher, Oxford Centre for Collaborative Applied Mathematics (OCCAM), Mathematical Institute, University of Oxford
Project: Mathematical and Computational Modelling for neuron growth

Dr. Antonio LaTorre

Position: Post-doctoral Fellow [JdC, Cajal Blue Brain], UPM, CeSViMa
Project: Image processing and heuristic optimization

Dr. Majid Malboubi

Position: Post-doctoral Researcher, Solid Mechanics Group, University of Oxford
Project: Experimental cell mechanics

Dr. Jesus Montes

Position: Post-doctoral Fellow [Cajal Blue Brain], UPM, CeSViMa
Project: Image processing, simulation and data analysis

Dr. Pierre Recho

Position: Post-doctoral Researcher, Mathematical Institute, University of Oxford
Project: Electrophysiological mechanical coupling modelling in neurons

Dr. Pablo Saez

Position: Post-doctoral researcher, Mathematical Institute, University of Oxford
Project: Theoretical and computational models for brain surgery

Dr. Lili Zhang

Position: Post-doctoral Researcher, Solid Mechanics Group, University of Oxford
Project: Multiscale cell mechanics modeling

Emily Kwong

Position: Ph.D. Student, Solid Mechanics Group, University of Oxford
Project: Electrophysiological mechanical coupling modelling in neurons

Dongli Li

Position: Ph.D. Student, Healthcare Innovation CDT, University of Oxford
Project: Numerical model of shock wave interactions with cells


Biomimetic, nanomechanically designed materials for 3-D cell culture and tissue regeneration

Biological systems exploit the physical chemistry of nm-sized biomolecules (proteins, DNA…) to create complex functional, dynamical composite structures with detailed mechanical properties and tailored interfaces with a hierarchical organization (from nm to micron to mm scales), e.g. in the extracellular matrix. These functional structures enable biological function e.g. cell division, morphogenesis and the organization of tissues, and they are altered by disease/trauma. We have concentrated in the fundamental science: we have developed techniques based on the atomic force microscope (AFM) that enable us to study interfaces with sub-nm resolution and to develop techniques based on multifrequency-AFM for mapping mechanical properties of living cells with unprecedented speed and accuracy. Currently we exploit this knowledge to design hybrid bio inspired nanostructures (nanocomposites of biopolymers such as chitosan with nanotubes) for 3-D cell culture and tissue regeneration that enable selectivity and biocompatibility using nanotechnology to design structure, mechanics and interfaces.

People: Prof. S. Contera
Sponsor: Oxford Martin School through Programme on Nanotechnology

Cajal Blue Brain

The Computational Mechanics of Materials group of Prof. Jérusalem, is working on a research new line in collaboration with Prof. Peña of the Computer Science Department of the UPM, within the framework of the Cajal Blue Brain project. The ongoing projects in collaboration with medical and biological communities, and in synergy with de Cajal Blue Brain project´s goals, aim at bringing new simulation tools to the study of brain disease either due to sudden changes in the mechanical properties of the neurons (e.g. TBI) or to slowly evolving dysfunctions (e.g. Alzheimer or Huntington diseases).

People: Prof. J.M. Peña, Antonio LaTorre, Jesus Montes
Sponsor: Spanish Ministry of Science (Special Activities)

Computational multiscale neuron mechanics (COMUNEM)

The last few years have seen a growing interest in computational cell mechanics. This field encompasses different scales ranging from individual monomers, cytoskeleton constituents, up to the full cell. Its focus, fuelled by the development of interdisciplinary collaborative efforts between engineering, computer science and biology, until recently relatively isolated, has allowed for important breakthroughs in bio-medicine/engineering or even neurology. However, the natural "knowledge barrier" between fields often leads to the use of one numerical tool for one bioengineering application with a limited understanding of either the tool or the field of application itself. Few groups, to date, have the knowledge and expertise to properly avoid both pits. Within the computational mechanics realm, new methods aim at bridging scales and modelling techniques; from density functional theory up to continuum modelling on large scale parallel supercomputers. To the best of the knowledge of the author, a thorough and comprehensive research campaign aimed at bridging scales from proteins to the cell level while including its interaction with its surrounding media/stimulus is yet to be done. Among all cells, neurons are at the heart of tremendous medical challenges, and an increased understanding of the intrinsic coupling between mechanical and chemical mechanisms in such cell is of drastic relevance. I thus propose here the development of a neuron model constituted of length-scale dedicated numerical techniques, adequately bridged together. The model will be used for two specific applications: neuron migration/growth and electrophysiological-mechanical coupling in neurons. Upon completion of the project, this multiscale computational framework will be made available to the bioengineering and medical communities to enhance their knowledge on neuron deformation, growth, electro-signaling and thus, on slowly evolving damaging diseases (Alzheimer's disease, epilepsy), as well as more direct damages such as traumatic brain injuries.

People: Prof. A. Jérusalem, Lili Zhang, Majid Malboubi, Emily Kwong
Sponsor: ERC Starting Grant

Engineering human neural networks

The creation of an in-vitro model of the human brain will involve a 'bottom-up' approach by engineering and assembly of 'elements' (synapses), 'units' (neural networks) and 'domains' (structured compartments). The proposed project focuses on the formation of a biological neural network (bNN), capable of learning, initially from NT2.D1 cultures and then human stem cells.

Specifically we will differentiate human stem and NT2.D1 cells into functional neurons, selecting specific scaffolds and optimising culture conditions to direct their growth into 3-D architectures, so facilitating synaptic connection formation. Such screening and optimisation studies will involve multiple parallel perfused microbioreactors. The NT2.D1s will be transfected with channelrhodopsin 2 capability, facilitating axon stimulation through digital light processing.

The bNN's will be formed using guided cell self-assembly and tissue engineering and will involve a blue-light stimulated input layer, (473 nm), followed by an output layer (monitored with Ca2+ imaging). A middle layer will be created using collagen-based constructs. Functional measurement through electrophysiological and optogenetic approaches will monitor action potentials in individual neurons, and synaptic currents will be detected with grid electrodes to observe spiking at the output layer, and 2-photon microscopy will record Ca2+ transients as a measure of net activity.

'Training' of bNNs in pattern recognition by inducing targeted synaptic plasticity will be by repetitive stimulation, so showing ability to distinguish between stimuli. Once self-organized, the bNN's will respond to inputs (supervised learning). Functional bNNs will be monitored in neural plasticity during aging and degeneration. Ultimately, we will create 'functional 'domains', i.e., a large cluster of inter-connected multi-compartment clusters of bNNs, which is effectively artificial human brain tissue.

People: Prof. H. Ye
Sponsor: BBSRC (BB/H008527/1)

Quantitative nanomechanical mapping of live cells with atomic force microscopy

We have recently developed a method based on atomic force microscopy (AFM) (Raman & Trigueros et al Nature Nanotech 2011) that uses the multifrequency response of cantilever as it is scanned over live cell surfaces in physiological conditions to produce a fast quantitative mapping of the properties (stiffness, viscoelasticity) of live cells and tissues that is orders of magnitude faster than previous methods, with a resolution (~ 10nm) sufficient to detail the subcellular and cytoskeletal structures directly involved in mechanotransduction. However this technique is experimentally difficult and data analysis is relatively complex. We are currently developing a method by vibrating the cells at ultrasonic frequencies in the AFM experiment to extend this technique and develop new ones that are more stable and easier to use and analyse in order to map the mechanical properties/rheology of cells in tissues, including subsurface imaging in projects ranging from drug delivery, to tissue regeneration and plant biology.

People: Prof. S. Contera
Sponsors: EPSRC for ECRs grant and Oxford Martin School through Programme on Nanotechnology

Mathematical and computational modelling for neuron growth

The project aims at developing mathematical and computational models of the mechanics, growth, and remodelling of neurones. In this project, we build new microscopic and macroscopic models for axonal growth and implement them by developing numerical methods for evolving continuum bodies. This work is done in collaboration with the Mathematical Institute and the Department of Engineering Sciences.

People: Dr. J.A.G. Grajales, Prof. A. Jérusalem, Prof. A Goriely
Sponsor: King Abdullah University of Science and Technology (KAUST) Global Research Partnership

Numerical modelling of shockwave interaction with kidney cells

Shock waves have been used medically in lithotripsy (i.e. fragmenting kidney stones) and the treatment for musculoskeletal indications. However, the shock waves can result in undesired damage to healthy tissue. Shock waves also show great potential in cancer therapy by mechanically destroying tumour cells or enhancing sonoporation to effect therapeutic drug delivery. However, the efficacy of these applications and the involved mechanisms are poorly understood. Our numerical work is aimed at understanding the interaction of shock waves and tissue at the cellular level.

In lithotripsy the goal is to minimise soft-tissue injury—an unwanted side-effect from the procedure. For the other therapeutic applications to focus is on understanding the mechanisms of action and optimising the therapeutic effect on the target cells whilst minimising the impact on healthy cells. This work focuses initially on kidney tissue which has both lithotripsy and cancer applications. However, the model can be extended to others organs.

People: Prof. A. Jérusalem, Prof. R. Cleveland, Dongli Li
Sponsor: Healthcare Innovation CDT

Theoretical and computational models for brain surgery

This project aims at improving predictive preoperative and postoperative plans in brain surgery. We characterize the brain as a complex mechano-chemical tissue to bring micro- and macrostructural information of the brain mechanics into theoretical models. One specific application studied here is the ablation of brain tumour and its effect on post-surgery radiotherapy.

People: Pablo Saez, Stamatios Sotiropoulos
Sponsor: CMU-Oxford alliance


The following resources and facilities are currently available to members of the group:

  • Oxford Supercomputing Centre (OSC)
  • Supercomputing and Visualization Center of Madrid (CeSViMa)
  • Multiphoton microscope
  • Fluorescent microscope
  • Electrospinning apparatus
  • Oxygen plasma system
  • Cell/Tissue culture facilities
  • FTIR
  • HPLC
  • 3D CAVE (5-wall cave automated virtual environment)
  • State-of-the-art scanning probe microscopy
  • SEM, cell and biological specimen preparation lab for in vitro experiments



Prof. Antoine Jérusalem
Associate Professor
Department of Engineering Science
University of Oxford
Parks Road
Oxford, OX1 3PJ - UK
Tel: +44 (0) 1865 2 83302
Email: antoine.jerusalem AT