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Biomat 2023: Multiscale Methods at the Frontier Between Data and Mathematical Models

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Advanced course / School
From June 12, 2023
to June 16, 2023
Registration deadline 24 / 05 / 2023



The eighteenth edition of the Biomat International Summer School is based on the relationship between Biochemistry and Biomechanics, and their possible applications in neuroscience. The determination of the chemical interactions that govern the genesis, growth and renewal of different types of tissues is an emerging research problem in which advances have begun to be made with important implications. To some extent, it may be surprising to understand that the mechanical interactions that take place during the mentioned processes can also condition the functioning of a whole series of chemical reactions that take place in the tissue itself. The proper understanding of this type of relationship requires approaches that combine physical-mathematical foundations, analysis of experimental data, and computational simulation of models.

That is why the lines of teaching and research that this summer school addresses are found at the interface between Physics, Mathematics, Biology, Computer Science and the aforementioned Life Sciences and Social Sciences. The speakers have extensive experience in multidisciplinary research, which, from the point of view of training young scientists, will allow them to integrate various research sensibilities: mathematical modeling from micro to macro, complexity, data analysis, developmental biology , biomechanics, tumor dynamics, cell mechanics, social dynamics, numerical simulation, Deep learning… In turn, students will be able to make contact with the new frontiers of knowledge that are opening up as a result of the combination of the mentioned aspects, allowing them to acquire a privileged position to address cutting-edge lines of research with wide repercussions on society.

It is a fact that these types of topics are framed in an international context that is increasingly conducive to collaborations between scientists and specialists from different disciplines. For the reasons mentioned, this type of multidisciplinary school is growing.



4 sessions, the first of which is devoted to a general introduction to the subject matter dealt within the course, and from there more specific/technical aspects are developed

Keynote talks

2-session talks by specialists of recognized prestige in their areas

Short half-hour talks

reserved for young speakers to present your work


Mathematical modelling of self-organisation during embryonic development

Dagmar Iber

ETH Zurich

Dagmar Iber studied mathematics and biochemistry in Regensburg, Cambridge, and Oxford. She holds Master degrees and PhDs in both disciplines. After three years as a Junior Research Fellow in St John’s College, Oxford, Dagmar became a lecturer in Applied Mathematics at Imperial College London. Dagmar has joined ETH Zurich in 2008 after returning from an investment bank where she worked as an oil option trader for one year.



Reproduction of complex life hinges on the reliable translation of the linear information that is contained in our DNA into complex 3D shapes and functions. In this course, I will present chemical and biophysical principles that enable this reliable self-organisation. While there is only a limited number of candidate mechanisms and at times it may be difficult to uncover any candidate mechanism, often more than one mechanism can, in principle, explain the same biological phenomenon. Careful data-based mathematical modelling is therefore important to distinguish between candidate mechanisms. In the last part, I will discuss approaches for data-based modelling and model selection.

Collective cell motility

Jean-François Joanny

College de France

After physics studies at Ecole Normale Supérieure de Paris (ENS ULM), Jean-François obtained his Thèse de 3e cycle in 1978 on polymer demixing and Thèse d’Etat in 1985 on wetting phenomena under the supervision of Pierre-Gilles de Gennes.  Since January 2019, he is Professor at Collège de France, where he holds the chair of soft-matter and biophysics. Jean-François Joanny has received several distinctions: silver and bronze medals from the CNRS or the Ampère prize from the Académie des sciences. He was a junior and senior member of the Institut Universitaire de France (IUF).



The course discusses some aspects of cell motility both at the individual cell level and at the collective level. The presentation is theoretical but the problems studied will be motivated by biological questions. One of the main aspects of the course is to treat the cell itself and at a larger cell an assembly of cells as active matter and to discuss cell motility within the framework of active matter theory.

1-Introduction to cell motility: The first lecture gives a general introduction to single cell motility in two and three dimensions. It discusses the large scale motion of cells as a persistent random walk and introduces briefly taxis phenomena. The final part discusses the general physical principles of cell motion on a solid substrate

2-Keratocyte motion: Keratocytes are one of the most studied models of cell motility. They have a very flat shape containing mostly the actin-myosin cytoskeleton that can be considered as an active gel. This second lecture presents very simple models of keratocyte motions emphasizing in particular the relative roles of actin turn-over and of acto-myosin contractility. It also discusses the shape of moving cells.

3-Spontaneous cell motion in cell monolayers: The third lecture considers collective cell motion in a confluent layer of elongated cells on a solid substrate. The cell layer is considered as an active nematic fluid. The lecture introduces the hydrodynamic theory of active nematics and shows how spontaneous flows can occur in the absence of imposed pressure gradients. If the activity is very large the layer reaches an active turbulent state.

4-Collective cell migration in an elastic matrix: During metastasis cancer cells migrate collectively through conjonctive tissues that can be considered as elastic media. Experiments in particular by P. Friedl have shown that there exist several types of migration patterns. The lectures presents a hydrodynamic theory of the cells migration in an elastic medium by considering them as an active polar fluid permeating through an elastic gel, and discusss the stability of a unifomly moving pattern. It also presents a more microscopic model where the cells remodel the matrix both by secreting and degrading it.

Bridging between higher-order mechanisms and higherorder phenomena

Giovanni Petri

CENTAI Institute

I am a Principal Researcher at CENTAI Institute working on topological approaches to complex networks and their underlying geometry, with special attention to the topology of brain structure and dynamics. Previously affiliation: ISI FoundationImperial College London.


      • PhD in Complex Networks, 2012Imperial College London
      • MSc in Theoretical Physics, 2008University of Pisa
      • BSc in Physics, 2005University of Pisa



In this mini-course we will link together two sides of the recent progresses in higher-order systems.

On the one hand, we will describe recent advances in dynamical systems with interactions among groups of nodes (higher-order interactions) and the novel phenomenologies that stem from them.

On the other one, we will see how recent tools from algebraic topology and multivariate information theory characterise these behaviours in real-world data.
Finally, we will describe the current attempts to infer or reconstruct the original underlying higher-order models from data.

Topological Data Analysis for Oncology

Bernadette Stolz-Pretzer

École Polytechnique Fédérale de Lausanne
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Topological data analysis (TDA) is an emerging mathematical field that uses topological and geometric approaches to quantify the “shape” of data. Persistent Homology (PH), the most prominent method from TDA, captures topological invariants such as connected components, loops, and voids in data at multiple scales. The output from PH can be visualised in a barcode which can further be vectorised to enable integration with  statistical and machine learning tools. In recent years, PH has been successfully applied to study many biological phenomena.

In this mini course I will introduce the mathematical concepts behind TDA and PH and show applications to both experimental data from oncology and the output from mathematical models. I will in particular demonstrate how PH allows us to quantify the effect of drugs on experimental data of vascular networks of tumours and how we can use similar approaches to stratify the parameter space of a mathematical model of tumour vasculature. I will then show how we can combine TDA and mathematical models to understand the effect of structural features of vascular networks on perfusion level and response to radiotherapy. Finally, I will present how PH can give insight into spatial relations in data and how it can complement machine learning approaches for biological data.



A mechano-biological feedback between cancer organoids and the ECM initiates and sustains collective invasion

Marino Arroyo

Universitat Politécnica de Catalunya
Professor Marino Arroyo is an associate researcher at IBEC and a member of the Department of Civil and Environmental Engineering and the Institute of Mathematics of the Universitat Politècnica de Catalunya (UPC)-BarcelonaTech (IMTech) of the UPC, where he leads the Mechanics of soft and living interfaces laboratory from the Cell and Tissue Mechanobiology Research Program. His research objective is to develop mathematical and computational models to understand the mechanics of biological interfaces, cells and tissues, that is, the small-scale mechanics of biological materials and systems.


The concurrence of structure and function in developing networks: An explanation for synaptic pruning

Ana Paula Millán

Universidad de Granada
In 2014 she obtained a degree in Physics from the University of Granada and in 2015 she completed a Master’s Degree in Physics and Mathematics at the University of Granada and the University of Castilla-la Mancha, specializing in biomathematics. She obtained here PhD in the Department of Electromagnetism and Physics of Matter at the University of Granada under the co-direction of Joaquín J. Torres and Joaquín Marro, studying statistical physics phenomena in complex networks, and their possible application in neuroscience. She is a member of the research group on Statistical Physics and Complex Systems, at the University of Granada.

A fundamental question in neuroscience is how structure and function of neural systems are related. We study this interplay by combining a familiar auto-associative neural network with an evolving mechanism for the birth and death of synapses. A feedback loop then arises leading to two qualitatively different behaviours. In one, the network structure becomes heterogeneous and dissasortative and the system displays good memory performance. In the other, the structure remains homogeneous and incapable of pattern retrieval. These findings are compatible with experimental results on early brain development, and provide an explanation for the existence of synaptic pruning. Other evolving networks, such as those of protein interaction, might share the basic ingredients for this feedback loop, and indeed many of their structural features are as predicted by our model.


Epithelial mechanobiology from the bottom up

Xavier Trepat

Institute for Bioengineering of Catalonia
Xavier Trepat received a BSc in Physics in 2000 and a B.Sc in Engineering in 2001. In 2004 he obtained his PhD from the Medical School at the University of Barcelona. He then joined the Program in Molecular and Integrative Physiological Sciences at Harvard University as a postdoctoral researcher. In 2008 he became a Ramon y Cajal researcher at the University of Barcelona and the Institute for Bioengineering of Catalonia (IBEC), and in January 2011 he became an ICREA Research Professor. His research at IBEC focuses on integrative tissue dynamics and cytoskeletal mechanics.

Epithelial sheets form specialized 3D structures suited to their physiological roles, such as branched alveoli in the lungs, tubes in the kidney, and villi in the intestine. To generate and maintain these structures, epithelia must undergo complex 3D deformations across length and time scales. How epithelial shape arises from active stresses, viscoelasticity and luminal pressure remains poorly understood. I will present different approaches to study the mechanobiology of epithelial shape from the bottom up. I will discuss new technologies to design epithelia of arbitrary size and geometry and to subject them to controlled mechanical deformations in 3D. I will show that monolayers exhibit superelastic behavior when stretch is applied and that they readily buckle when tension is released. We use this phenomenology and a 3D vertex model to rationally direct spontaneous pattern formation, and hence engineer tissue folding. I will also present our recent advances to understand the mechanobiology of intestinal organoids. We show that these organoids exhibit a non-monotonic stress distribution that defines mechanical and functional compartments. From these experiments we conclude that the stem cell compartment folds through apical constriction and that cells are pulled out of the crypt along a gradient of increasing tension, rather than pushed by a compressive stress downstream of mitotic pressure as previously assumed. This experimental and theoretical work unveils how patterned forces enable folding and collective migration in the intestinal crypt.



Alfonso Valencia

Centro Nacional de Supercomputación de Barcelona

Alfonso Valencia is the director of the Spanish National Bioinformatics Institute (INB-ISCIII). The INB represents the Spanish node of the European Bioinformatics infrastructure ELIXIR, and is committed to generating and supplying bioinformatics solutions in the context of national and international activities and consortia. His research group is dedicated to the application of machine learning and artificial intelligence to Personalized Medicine, and exhibits ample experience in the development of software platforms for the extraction, integration and representation of big data for large-scale genome projects. 

Organizing and Scientific Committee

Tomás Alarcon | ICREA-CRM
Juan Calvo | Universidad de Granada
David Poyato | Universidad de Granada
Juan Soler | Universidad de Granada


Participants have the option to contribute with a 30 min talk presentation if they wish to do so. To apply, please select the relevant option during the registration process.
    • Contributions deadline: May 2nd, 2023
    • Decisions will be communicated by May 9th, 2023


In order to increase the number of young researchers participating in this activity, the CRM offers registration grants and lodging on-campus. To apply, you must complete the registration process. Please go to SIGN IN, indicate in the OTHERS section that you wish to apply for a registration grant, you will be asked to attach your CV. Please click on the Reservation option before finishing the process.
  • Application deadline for grants: May 2nd, 2023
  • Grantees will be notified  by May 9th, 2023


To register for this event, please click on the Sign in button located at the top of this page. You will be asked to create a CRM web user account (if you already have an account, please log in) before registering to the activity through the following link:


Please note that it will be necessary to fill in both the personal and academic requested information in the web user intranet. Once your web user is created, you may register for the activity through the following link.


list of participants

Name Institution
Silvia Bordel Vozmediano Universidad de Castilla-La Mancha
Lucía Benito Barca Universidad de Castilla-La Mancha
Sébastien Tran Tien Université Lyon 1
Dagmar Iber Francis Crick Institute & King’s College, London
Jean-François Joanny College de France, París
Giovanni Petri CENTAI Institute
Bernadette Stolz-Pretzer École Polytechnique Fédérale de Lausanne
Xavier Trepat Institut de Bioenginyeria de Catalunya (IBEC)
Alfonso Valencia Barcelona Supercomputing Center (BSC)
Júlia Folguera Profitós Universitat Autònoma de Barcelona
Marino Arroyo Universitat Politècnica de Catalunya
Ahmad Khan Universitat Politècnica de Catalunya
Adam Ouzeri Universitat Politècnica de Catalunya
Marta Casanellas Rius Universitat Politècnica de Catalunya
Jose Muñoz Universitat Politècnica de Catalunya
Juan Campos Universidad de Granada
Juan Soler Universidad de Granada
Elena Torres Lozano Universidad de Granada
Alexis Béjar López Universidad de Granada
Carlos Borja Pulido Garcia Universidad de Granada
Jesús David Poyato Sánchez Universidad de Granada
Juan Calvo Yagüe Universidad de Granada
Oscar Sanchez Universidad de Granada
Simon Bonnal Universidad de Granada
Felipe Guerrero Barba Universidad de Granada
Angel Franco Rodriguez Universidad de Granada
Blanca A. López Ríos Universidad de Granada
Juan Manuel Montes López Universidad de Granada
Cristóbal Vázquez García Universidad de Granada
Julián Cabrera Linares Universidad de Granada
Beatriz Blanco Besteiro Universidad de Granada
Daniel Téllez Calle Universidad de Granada
Ana Paula Millan Universidad de Granada
Benjamin Tirado Heras Universidad de Granada
Allan García Universidad de Castilla La Mancha
Pilar Guerrero Universidad Carlos III de Madrid
Charlotte Dugourd Claude Bernard University Lyon 1
Manish Gupta Dresden University of Technology
Josep Sardanyés Centre de Recerca Matemàtica
Isaac Salazar-Ciudad Centre de Recerca Matemàtica
Juan Arellano Tintó Centre de Recerca Matemàtica
Alvaro Corral Centre de Recerca Matemàtica
Roser Homs Pons Centre de Recerca Matemàtica
Kevin Martínez Añón Centre de Recerca Matemàtica
Angélica Torres Centre de Recerca Matemàtica
Giovanni Dalmasso Centre de Recerca Matemàtica
Tomas Alarcon Centre de Recerca Matemàtica


IF YOUR INSTITUTION COVERS YOUR REGISTRATION FEE: Please note that, in case your institution is paying for the registration via bank transfer, you will have to indicate your institution details and choose “Transfer” as the payment method at the end of the process.


*If the paying institution is the UPF / UB/ UPC / UAB, after registering, please send an email to with your name and the institution internal reference number that we will need to issue the electronic invoice. Please, send us the Project code covering the registration if needed.

Paying by credit card

IF YOU PAY VIA CREDIT CARD but you need to provide the invoice to your institution to be reimbursed, please note that we will also need you to send an email to providing the internal reference number given by your institution and the code of the Project covering the registration (if necessary).

lodging information





For inquiries about this event please contact the Scientific Events Coordinator Ms. Núria Hernández at​​