Dagmar Iber & CoBi
@iberd.bsky.social
380 followers 370 following 41 posts
Computational Biology @ETH: data-driven modeling & simulation of emerging phenomena in development & disease https://bsse.ethz.ch/cobi https://youtube.com/@cobi-ethz
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iberd.bsky.social
Are you a C++ expert and interested in making 3D cell-based tissue simulations with #SimuCell3D ever more powerful? Please apply and join us as #Master student, #PhD student or #Post-Doc!!

jobs.ethz.ch/job/view/JOP...

jobs.ethz.ch/job/view/JOP...

x.com/DagmarIber/s...
PhD Position - 3D Cell-Based Tissue Simulation Framework
jobs.ethz.ch
Reposted by Dagmar Iber & CoBi
sib.swiss
"Within the competition to bring this field to a new level, SimuCell3D is remarkable and will mark a clear evolution of the topic."
🥁That’s what the committee said about this #SIBRemarkableOutputs 2024
👉Discover the output: tinyurl.com/53arz2rz
@iberd.bsky.social
iberd.bsky.social
The goal: make it easier for others to reproduce and extend these models within COMSOL.

We hope this serves as a generalizable reference for simulating collective cell behavior and pattern formation.

arxiv.org/pdf/2509.08930
arxiv.org
iberd.bsky.social
This complements our earlier work introducing the DCM model 👉 bsky.app/profile/iber...

That previous paper focused on the biological questions and mathematical framework.

Here, we focus on the practical COMSOL #PIDE implementation: setup, BCs, 1D–3D, and Lagrangian reformulation for growth.
iberd.bsky.social
How can cells self-organize rapidly into complex patterns during development?

Let’s explore a powerful and underappreciated mechanism: Directed Cell Migration (DCM).

Preprint @biorxivpreprint.bsky.social : doi.org/10.1101/2025...

👇Thread 🧵(1/11)
iberd.bsky.social
Out now: Simulating Organogenesis in #COMSOL: Tissue Patterning with Directed Cell Migration

We provide a detailed walkthrough of how to implement #DCM partial integro-differential equation models - enabling accessible simulations of tissue patterning and morphogenesis.

arxiv.org/pdf/2509.08930
iberd.bsky.social
Our paper "Morphogen gradients can convey position and time in growing tissues" is now out in Newton ‪@cp-newton.bsky.social‬

Quite fitting to see this novel idea that morphogen gradients not only encode position, but can also time & synchronise development over long distances out in a new journal.
iberd.bsky.social
📌 Summary:

#DCM is a rapid, robust mechanism for developmental pattern formation
• COMSOL FEM implementation makes DCM models numerically accessible
#DCM patterning parameter ranges and timeframes
• Pattern Orientation via attraction anisotropy or directed tissue growth

👇Thread 🧵(10/11)
iberd.bsky.social
2. Dynamic #attraction #zones

Spatially varying cell attraction that changes with tissue growth can guide migrating cells, leading to precise large-scale patterning.

This mimics how tissues form rings, bands, or layered structures in vivo.

👇Thread 🧵(9/11)
iberd.bsky.social
We identify two mechanisms for guiding pattern orientation:

1. #Anisotropic #attraction
Cells pulling or migrating more strongly in one direction form aligned stripe-like patterns—e.g., during directional tissue growth.

👇Thread 🧵(8/11)
iberd.bsky.social
#DCM naturally leads to unoriented patterns—spots, labyrinths—similar to Turing-like systems.

But biological tissues often require oriented patterns to fulfill specific functions.

Can DCM produce stripes, too?

👇Thread 🧵(7/11)
iberd.bsky.social
Three key parameters drive the emergence and morphology of patterns:

• Initial density of motile cells
• Intercellular attraction strength
• Cell sensing radius

👇Thread 🧵(6/11)
iberd.bsky.social
Simulations and linear stability analysis allowed us to find #critical #conditions for pattern formation and predict #patterning #speed.

We show under which conditions #DCM can realistically pattern tissues in development.

👇Thread 🧵(5/11)
iberd.bsky.social
We developed a mathematical framework that represents a wide range of #DCM cues, e.g., chemotaxis, durotaxis, haptotaxis & a general Finite Element Method #FEM:

👉 1D, 2D, 3D
👉 arbitrary geometries & boundary conditions
👉 isotropic & anisotropic interactions
👉 fast, large-scale simulations

🧵(4/11)
iberd.bsky.social
To study #DCM, both discrete and continuum models have been used.

But:
👉 Discrete models are computationally expensive.

👉 Continuum models have required custom Finite Volume Method #FVM implementations—until now.

👇Thread 🧵(3/11)
iberd.bsky.social
During embryonic development, cellular tissues transition from uniform starting conditions into robust spatial patterns.

#DCM offers a particularly fast and versatile route to spontaneously symmetry breaks and pattern formation without tissue buckling.

🧵(2/11)
iberd.bsky.social
How can cells self-organize rapidly into complex patterns during development?

Let’s explore a powerful and underappreciated mechanism: Directed Cell Migration (DCM).

Preprint @biorxivpreprint.bsky.social : doi.org/10.1101/2025...

👇Thread 🧵(1/11)
iberd.bsky.social
Let me add our paper to this review of mechanical drivers of NT folding.

We showed that mammalian spinal #neuraltube folding is primarily driven by #mesoderm expansion and #zippering. #Hingepoints emerge as a result of these extrinsic forces.

www.pnas.org/doi/10.1073/...

x.com/DagmarIber/s...
Reposted by Dagmar Iber & CoBi
epimechfc.bsky.social
Epithelial tissues are well-known to invade free space and stop proliferation at confluency.

Do we know what regulates cell proliferation spatially and temporally?

🧵by @dedenonmathieu.bsky.social
iberd.bsky.social
Are you a C++ expert and interested in making 3D cell-based tissue simulations with #SimuCell3D ever more powerful? Please apply and join us as #Master student, #PhD student or #Post-Doc!!

jobs.ethz.ch/job/view/JOP...

jobs.ethz.ch/job/view/JOP...

x.com/DagmarIber/s...
PhD Position - 3D Cell-Based Tissue Simulation Framework
jobs.ethz.ch
Reposted by Dagmar Iber & CoBi
epimechfc.bsky.social
SimuCell3D … for simulating tissue mechanics with cell polarization. @iberd.bsky.social

Dimension: 3D
Software language: C++
Download: git.bsse.ethz.ch/iber/Publica...

bsky.app/profile/epim...
iberd.bsky.social
👩💻 Want to try it? Just a few extra lines of code vs. classic PINNs!
Code & details: git.bsse.ethz.ch/iber/Publica...

Retweet 🔄 if you’d use this for your inverse problems! #OpenScience
iber / Publications / 2025_almanstoetter_pinnverse · GitLab
GitLab Community Edition
git.bsse.ethz.ch
iberd.bsky.social
⚡ No plateaus here!
Classical PINNs stall. PINNverse keeps improving physics loss ∼ epoch^(-1.4) for Fisher’s equation.
Algebraic decay >> stagnation!
iberd.bsky.social
📉 #PINNverse crushes parameter error — even with:
- High noise
- Terrible initial guesses

Stable & accurate where others fail (e.g., Fisher-KPP).