A real computational tour de force by @ericneiva.bsky.social, carried out as Marie Skłodowska-Curie postdoctoral fellow in the team, now published in the Journal of Computational Physics: urlr.me/AuzK86

Congratulations, Eric!

@cnrsbiologie.bsky.social
Grateful to @ec.europa.eu for funding support

GitHub - VirtualEmbryo/VertAX: A differentiable JAX-based framework for vertex modeling and inverse design of epithelial tissues A differentiable JAX-based framework for vertex modeling and inverse design of epithelial tissues - VirtualEmbryo/VertAX

We hope VertAX can help make inverse problems & differential programming more accessible in tissue mechanics.

Thanks to @apasqui.bsky.social, Maxence Ernoult, Italian colleagues, and other members of the team for this collaboration.

Comments very welcome.

Code: github.com/VirtualEmbry... 5/5

Beyond synthetic benchmarks, we show applications to mechanical parameter inference from microscopy images and to inverse design problems in epithelial tissues. 4/5

We benchmark three strategies for bilevel optimization in vertex models: automatic differentiation, implicit differentiation, and equilibrium propagation.

This gives a practical comparison of their accuracy, speed, and memory trade-offs. 3/5

VertAX unifies forward modeling and inverse modeling in the same framework.

It lets users define custom energy functions and cost functions in pure Python, while leveraging JAX and bilevel optimization for differentiation, JIT compilation, and GPU acceleration. 2/5

How can we learn tissue mechanics directly from cell patterns and images?

In our new preprint, we introduce VertAX, a differentiable vertex-model framework in JAX for simulating epithelia, inferring parameters, and designing target tissue behaviors.

shorturl.at/PUzT0
1/5

Cell Modeling in Space and Time at CSHL - FocalPlane Cell Modeling in Space and Time at CSHL -

The abstract deadline for the CSHL Cell Modeling in Space and Time is this Friday 10 April. Don’t miss out!

Blastocoel morphogenesis: A biophysics perspective The blastocoel is a fluid-filled cavity characteristic of animal embryos at the blastula stage. Its emergence is commonly described as the result of c…

If you’re interested in the different biophysical mechanisms animal embryos use to form a blastocoel cavity, this review may also be of interest: shorturl.at/Q3LLj

A hydro-osmotic coarsening theory of biological cavity formation Author summary The formation of a single biological cavity, or lumen, in tissues and embryos has been widely studied experimentally but the collective dynamics of multiple lumens has received much les...

Extended theory in PLOS Computational Biology in 2021 shorturl.at/sgkJl.

Hydraulic fracturing and active coarsening position the lumen of the mouse blastocyst Fluid dynamics are key to lumen production and symmetry breaking in the early mammalian embryo.

Experimental study and simple modeling in Science 2019 shorturl.at/zZN2o

Break It To Make It: How Fracturing Sculpts Tissues and Organs | Quanta Magazine Growing tissues can crack, break, and dissociate to form structures that can later withstand immense forces.

Glad to see our work discussed in Quanta Magazine shorturl.at/VXa7E.

In the early embryo, building a cavity can start by “fracturing” cell-cell contacts, creating microlumens that then coarsen into a single cavity.

@cnrsbiologie.bsky.social

Excited to start a new chapter with my team’s relocation to the Pink City, at @cbitoulouse.bsky.social!

Looking forward to new scientific interactions on campus (@laas, LPT, IRIT, ANITI…) at the interface of biology, physics & computational science.

@cnrsbiologie.bsky.social @occitanie.bsky.social

How does a ball of cells become an embryo? Genes matter—but physics (forces, geometry, topology) drives self-organization. Hervé Turlier's research vision on the physics of embryogenesis👇
shorturl.at/761x9

#Embryogenesis #Biophysics #Morphogenesis
@college-de-france.fr @cnrsbiologie.bsky.social

Congratulations David !

This postdoc position is still open! Apply if you want to come work with us on asymmetric cell divisions in spiralian embryos! postdocs.stanford.edu/prospective/...

Our first paper submitted to the International Conference on Computer Vision @iccv.bsky.social has been accepted! 🎉

Huge congratulations to all co-authors — Sacha Ichbiah, Anshuman Sinha, and Fabrice Delbary — for their fantastic work.

Stay tuned… we’ll share more about deltaMic in a few days!

Job Alert! We are recruiting one postdoc to work on spiralian embryos and their crazy polar lobes. More info about this HFSP-funded position on our website baronelab.org: scroll to the end, click on "this could be you"...start your adventure!

Great time with @sugimuralab.bsky.social, Shuji Ishihara and colleagues at Tokyo University 🇯🇵. Thank you for your very kind welcome and great scientific discussions 🙂

Very excited to share a new preprint by @ericneiva.bsky.social who developed a first-of-its-kind finite element method for simulating 3D cellular dynamics with coupled surface–bulk flows and signaling. A technical tour de force with broad applications in mechanobiology & beyond tinyurl.com/bdfhfke3

First post on bsky for a very good news. Very glad to be awarded this HFSP with @chemamd.bsky.social & @baronelab.bsky.social to study the evolutionary biophysics of spiralian early asymmetric divisions !
@hfspo.bsky.social @cnrsbiologie.bsky.social @collegedefrance.bsky.social @cirbcdf.bsky.social