Do you want to learn Finite Element Analysis in the context of biomechanics in life science?


If you want to learn Finite Element Analysis in the context of biomechanics in life science, a new Transmitting Science course is launched for the next July in Catalonia: FINITE ELEMENT ANALYSIS APPLIED TO LIFE SCIENCES

In the course, there is an introduction to the Finite Element in order to model biological structures and understand how they worked. It will cover all the steps involved in FEA except the creation or reconstruction of the model, which it is covered in the previous course Introduction to 3D Imaging Technologies: Photogrammetry, Laser, CT-scan and (µ)CT-scan for Life Sciences by my colleague and teacher of the FEA course, Josep Fortuny. And, I know, sometimes is where we are spending most of our time and efforts!

In the course you will learn how to define the material properties of biological structures, the use of a consistent Mesh Generation Methods, and the proper definition of biomechanical boundary conditions and finally, how understand and analyse the results obtained in plane models (the wrong-called 2D) and in the fancy 3D models created from CT-data. But, the limitation of time is always a problem and, in the course, we are just covering static analysis and linear materials. Which it is enough for an starting course because most of the works published in life sciences are covering this part and creates and open window for everybody in the course to learn more in the future.

You can enroll in the website and ask me questions if you have doubts!


Using statistics in the post-process of FEA results

When we are solving a model using Finite Element Analysis, the results are obtained via a distribution map. These internal distributions of the forces  ̶ called stress ̶  appear in the inner regions of the models due to the action of external forces. To model how different forces act on a biological structure, as a bone for example, computational models are created. These models are subdivided in small pieces called “elements” using a mesh. Then, theoretical forces are applied to the model and the stress values of each element are recorded and mapped in a coloured map called stress distribution which enables a qualitative comparison between different models. Of course, this “coloured map” is related with values. Specifically,. with the values obtained from the solving in each element of the mesh.

Screenshot 2016-09-05 11.32.23.png

To analyse these stress values in a quantitative framework could be complicated, as these elements have different size in the same mesh. for this reason, we published recently the work: ” Accounting for differences in element size and homogeneity when comparing Finite Element models: Armadillos as a case study” in Palaeontologia Electronica. In this work we propose a method to obtain the average mean and median of the distribution of these stresses in a Finite Element model weighting for the differences in elements size. On the other hand we propose a procedure to check whether the meshes used to generate the elements provide accurate results to be used later in statistical analysis. Therefore the stress values can be used as a proxy of the relative strength of vertebrate structures in a comparative framework and allow comparing the obtained mechanical results of different models.

This figure is an example: Box-plots of Von Mises stress distributions when Quasi-Ideal Meshes (QUIM) are assumed for the 20 Cingulata mandibles analysed in the work enabling a qualitative comparison between species and diets.


Citation: Marcé-Nogué, J., Esteban-Trivigno, S. de, Escrig, C., & Gil, L. (2016). Accounting for differences in element size and homogeneity when comparing Finite Element models: Armadillos as a case study. Palaeontologia Electronica, 19(2), 1–22

Read more:


Crocodile or salamander? The role of the giant amphibians in the Triassic ecosystems

A new study published in Scientific Reports journal analyze the biomechanics of the skull in Temnospondyls – a group of extinct amphibians of huge sizes- to elucidate the role of these animals in the ecosystems about 250 million years ago. The results show an ecological position different from the extant salamanders but also different from crocodiles – being those resembling in size and appearance. 

Comparison between the models of bilateral bite in different animals. From left to right, the extant giant salamander of California, two extinct temnospondyls and an alligator. In red, the areas that present more stress during the biting (Josep Fortuny / ICP)

The study closes a historical debate about the role that played the temnospondyls in the Triassic ecosystems. This group of amphibians dominates the freshwater aquatic environments (rivers, lakes, swamps…) and some members of this group tended to gigantism, reaching 5-6 meters long. Although the relationship of temnospondyls with salamanders and newts, the scientists debated –though to the external appearance and its huge sizes more similar to crocodiles – if the biology of these animals was similar to the living giant salamanders (as from China or California), or was more similar to crocodiles, although there were still 25 million years for the appearance of crocodiles.

“Nor as crocodiles, neither as salamanders”, explains Josep Fortuny, head of the Virtual Paleontology research group of the ICP that heads the study. “The biomechanical analysis of the temnospondyl skulls and its comparison with crocodiles and salamanders shows that these extant amphibians occupied a peculiar ecological position, very different to the position that occupies the extant animals”, explains Fortuny. In some issues – as the skull shape- these extinct amphibians resembles the crocodiles, but its amphibian nature determined its flat morphology of the skull and difficult the apparition of a secondary palate, a character present in crocodiles that also allows them to breathe with the mouth full of water. The two temnospondyl species analyzed are Edingerella madagascariensis and Stanocephalosaurus birdi.

Previous studies analyzed the ecological diversity of temnospondyls: while some species used suction to feed as many extant salamanders, other species hunted its preys by active direct biting, as used nowadays by the crocodiles. Precisely, the descent of temnospondyls during the Early Jurassic coincides with the appearance of the first crocodile members. “The cause of the descent of these giant amphibians is still an open question, but, with the current information, it cannot be discarded that the appearance of the first crocodiles members could be correlated with its descent.”, explains Fortuny

The results from this study have been obtained thanks to computational biomechanics, a powerful research tool to study and understand different ecological issues from living and extinct animals. It consists in 3D simulations of a biological structure to understand its function based on its morphology. Thanks to these models, it can be simulated the bite of an animal and analyze the force generated by the jaws, just to cite one example. From the obtained results is it possible to make an approach on its diet, hunt mode, etc. Also, the computational biomechanics is a powerful tool to deep in the biology of species scarcely known or endangered, as the case of the giant Chinese Salamander.

Video animation that shows the stress areas present during a bilateral bite in the different species analyzed.  

The journal Scientific Reports where the study has been published is member of the Nature publishing group. The research has been performed in collaboration with researchers from Institut Català de Paleontologia Miquel Crusafont (ICP) (Barcelona, Catalonia), the Muséum National d’Histoire Naturelle of Paris, the Centrum fur Naturkunde (University of Hamburg), de Geological Department of the Universitat Autònoma de Barcelona and the Universitat Politècnica de Catalunya.

Seize the crisis

The disappearance at the end Permian up to 90% of the species meant a great opportunity for different groups during the Triassic to evolve, as the case of the turtles, and to reach until nowadays. This great mass extinction occurred about 250 million years ago – less known than the biotic crisis that caused the disappearance of the dinosaurs, but more sever – also was a great opportunity for the temnospondyls to re-radiate and dominate most of the freshwater ecosystems. Other groups, as the dinosaurs, first appeared also during the Triassic (Late Triassic, about 200 million years ago) and dominated the terrestrial ecosystems until the end of the Cretaceous.

+ info: Fortuny, J. et al. Comparative 3D analyses and palaeoecology of giant early amphibians (Temnospondyli: Stereospondyli). Sci. Rep. 6, 30387; doi: 10.1038/srep30387 (2016).

Text: Pere Figuerola – ICP

Picture in the front: Reconstruction of Calmasuchus acri, a capitosaur temnospondyl that lived in Catalonia, Spain (Mauricio Antón / ICP)

FEA Summer Tour

Summer is the season of most of the conferences and I presented my work in two of them. At the end of June I attended the International Conference of Vertebrate Morphology (ICVM) in Washington and the next week I attended the XIV Annual Meeting of the European Association of Vertebrate Palaeontologists in Haarlem (the Netherlands). I presented different works from different collaborations in temnospondylis, carnivora, cingulata or primates. The connexion between all of them was the study of the biomechanics and the use of Finite Element Analysis. In the ICVM this is the list of the works I presented:

  •  Fortuny, J. et al. “Hunting in the Late Triassic: insights on the ambush strategy of the metoposaurs (Temnospondyli: Stereospondyli)”.
  • Luján, À. et al. “Feeding in Testudines: A Finite Element and parametric analysis of a tortoise skull”.
  • Tambuso, S. et al. “3D finite element analysis of lower jaws in glyptodonts”.
  • Marcé-Nogué, J. et al. “Primate chewing biomechanics revisited using Finite Element Analysis of the mandible”.
  • De Esteban-Trivigno, S. et al.”Early dietary, jaw shape and biomechanical performance differentiation in the evolution of armadillos (Xenarthra: Cingulata)”.
Whereas in the EAVP the works I presented were focalized to the addition od extinct species:
  • Marcé-Nogué, J. et al. “Biomechanical traits of carnivorous jaws with Finite Element Methods”.
  • Marcé-Nogué, J. et al. “Biomechanics as a predictor of enamel thickness in extinct primates”.
  • Gruntmejer, K. et al. “Comparative of histology and three-dimensional computer analysis of Metoposaurus krasiejowensis (Amphibia, Temnospondyli) skull biomechanics”.
  • De Esteban-Trivigno, S. et al. “Exploring shape change and biomechanics in Carnivora jaw: preliminary results”.
Most of the works presented there are based in the idea that biomechanics and forces as well as properties of teeth are demonstrated to be crucial to understand diet, dental functional traits and evolution and, we are trying to develop new methods and new ideas to shed light in all of this. The meetings were great, I could attend a lot of talks to learn what other researchers are doing to learn new methods and have new ideas. I could also met old friends, know what they are doing and in which field they are now working, and I made news, which is always another good reason to attend conferences. And I had few time (but enough!) to take me a picture in the most knowns places around the venue!
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Virtual Paleontology meets China

L’investigador de l’Institut Català de Paleontologia Miquel Crusafont, Josep Fortuny, juntament amb Jordi Marcé-Nogué, investigador de la Universitat d’Hamburg, han estat convidats durant la primera setmana d’abril a la Guilin University of Electronic Technology (ciutat de la Regió Autònoma de Guangxi) a impartir xerrades i treballar conjuntament amb l’equip liderat pel Dr. Zupeng Zhou en l’àmbit de la biomecànica computacional.

Durant aquesta estada, els investigadors catalans i xinesos compartiran coneixements i experiències en una disciplina, la biomecànica computacional, que té el seu origen en l’enginyeria, però que traslladada al camp de la biologia o la paleontologia permet realitzar simulacions biomecàniques tridimensionals en estructures biològiques complexes, tals com cranis o dents, que són difícils o impossibles de dur a terme amb organismes vius.

Aquesta nova col·laboració persegueix obrir aquest camp al continent asiàtic, on fins al moment no hi ha cap equip que uneixi la vessant paleobiològica i d’enginyeria. Gràcies al treball conjunt d’aquests equips de recerca es podran obtenir noves dades molt rellevants, tant sobre els diversos grups d’animals tetràpodes amb els que així com pels nous mitjans tècnics que es desenvoluparan arran d’aquesta nova col·laboració.

L’objectiu de la biomecànica computacional és reproduir el moviment i les tensions que es produeixen en una determinada estructura d’una forma no invasiva. Aquestes anàlisi són d’especial utilitat en especies extingides on no es poden observar aquests comportaments en viu, així com també per conèixer la biologia i ecologia d’espècies poc conegudes o bé en perill d’extinció. En aquests casos, conèixer la seva biologia pot ser de gran utilitat per establir mesures correctores.

El Departament de Paleontologia Virtual de l’ICP fa anys que treballa en aquest camp, unint paleontologia, biologia i enginyeria i col·laborant amb altres institucions com la universitat Politècnica de Catalunya o la Universitat d’Hamburg. Es tracta d’una unitat transversal als altres grups de recerca del centre que utilitza tecnologies no invasives en l’estudi dels fòssils per tal d’explorar i quantificar estructures habitualment no visibles. Les tècniques inclouen modelització 3D, tomografia computada industrial i mèdica, escaneig làser i fotogrametria així com tècniques d’enginyeria com l’Anàlisi d’Elements Finits.


(text: Pere Figuerola, ICP)

Primate chewing biomechanics revisited

The Meeting of the german Working Group in Vertebrate Paleontology has been held during the weekend of the 12th and 13th of March in the nice fortress Burg Lichtenberg. The castle was built around 1200 and has a length of 425m and is the biggest castle ruin in Germany. It is located near Thallichtenberg in the district of Kusel in Rhineland-Palatinate. 


I presented the first and preliminary results about the biomechanics of primate jaw analysed using a classical two-dimensional lever approach together with a Finite Element Model. The motivation of this work is because  Biomechanics and forces as well as properties of teeth are demonstrated to be crucial to understand diet, dental functional traits and evolution in primates in general. My presentation was entitled “Primate chewing biomechanics revisited” because I´m revisiting a known knowledge and a known approach but through my point of view. Let´s see if it works! 

Classical biomechanics rocks!

This January I have been teaching the theoretical background of classical biomechanics in the workshop “Introduction to Functional Morphology and Biomechanics” (4th Ed) in Catalonia (Premises of Sabadell of the Institut Català de Paleontologia Miquel Crusafont (ICP)). My colleagues Dr. Richard Fariña, Dr. Pere Ibáñez-Gimeno and Dr. Soledad de Esteban-Trivingno are showing simple models based on the basic principles of classical physics to infer the life history of extinct vertebrates. My duty in this workshop is introduce the physics of the problems: Static equations, Newton laws, Beam theory and tools such as Free Body Diagram or Moment and Force Diagrams to the attendants.

The three laws of motion were first compiled by Isaac Newton in his Philosophiæ Naturalis Principia Mathematica (Mathematical Principles of Natural Philosophy), first published in 1687 and the Beam Theory for bending was first enunciated circa 1750 by Leonhard Euler and Daniel Bernoulli. In spite of being quite old theories they are nowadays used in biomechanics to solve lots of problems related with the chewing mechanism of vertebrates or the behaviour of bones.

Some recent examples from 2015 and 2016 are the three dimensional free body analysis that describe the relationship between the orientation and position of the jaw elevator muscles, the position of the jaw articulation relative to the bite point, the joint reaction forces and the bite force in the lower jaw of the non-mammalian cynodont Probainognathus: or the work of my colleagues Varela & Fariña where the moment arms of jaw muscles and the hypsodonty index (HI) have been used in Artiodactyla in a research done last year:

This examples are giving us the perspective that, in spite of being old theories, biomechanics are still rocking and we can use in our new brand research.


More information of the course:…/funct-mo…/biomechanics/