Alex Grigas

Excited to highlight a new preprint about mechanical contributions to tissue homeostasis, from the Manning group in collaboration with the amazing Carien Niessen and Sara Wickstrom @sarawickstrom.bsky.social labs, spearheaded by Dr. Somiealo Azote: www.biorxiv.org/content/10.6...

9/ We end by doing some mean-field theory to explain the numerical results. We’re very excited to go hunting for the molecular mechanisms in vivo guided by our modeling and to add new details to the models guided by new experiments.

8/ We also developed a second model of CIL where instead of crawling away from neighbors, cells reach out and grab new neighbors away from their current neighbors. This pulling model also results in a fluid under tension.

7/ Next, we figured the simplest way to fight the clumping instability is to direct that motion not randomly, but away from a cell’s neighbors, like contact inhibition of locomotion. This generates a tensioned fluid network of cells that, while directed, still flows diffusively.

6/ We first tried maintaining the cell network by letting the cells move with a random self-propelled walk commonly used to model cell motion. However, no set of parameters could generate the kind of material we see in experiments. It always clumps!

5/ But how can a network be under tension and flowing at the same time? Breaking one bond would cause a cell to be pulled towards its remaining neighbors. To model this, we use a simple but effective model of hysteretic sticking between cells.

4/ However, those stellate appendages made us wonder, is there tension across those arms? By ablating the PSM with a laser, we measure a significant retraction velocity, suggesting yes, the cellular network is under tension!

3/ We confirm that, just like in many other systems of body-axis elongation, when we track the relative motion of the cells in the avian PSM, they move diffusively like a fluid.

2/ First, notice how different the cell architecture in the avian presomitic mesoderm (PSM) is from confluent and bubble-like cells seen in other tissues. It looks more like a network of cells attached by stellate arms.

Sparse mesenchymal cell networks as a fluid under tension Sparse mesenchymal cellular networks are ubiquitous across animals, shaping both embryonic and adult structures through dynamic interactions with epithelia. Yet, the physical principles underlying the...

How do sparse mesenchymal cells, with unique stellate arms spanning large gaps between cells, maintain their network while still flowing during development? In our new preprint we describe the avian PSM as a fluid under tension and develop new theory to explain it: www.biorxiv.org/content/10.6...

GitHub - agrigas115/HS-HP: HS+HP all-atom protein model HS+HP all-atom protein model. Contribute to agrigas115/HS-HP development by creating an account on GitHub.

All the code to run the all-atom protein model is available on my GitHub. All you need is a protein PDB file with the hydrogens added using the Reduce software. Please let me know if you want to use it and have any trouble!
github.com/agrigas115/H...

We first review the jamming transition, show how it applies to polymer collapse and then develop a new all-atom protein model that captures just the complex shapes of amino acids plus their hydrophobic interactions.

Protein Folding as a Jamming Transition Densely packed protein cores have the same interior packing density irrespective of overall fold, arising from a jamming transition where amino acids reach a critical, incompressible density, as expla...

Our new paper relating protein folding and jamming is out in PRX Life! All protein cores are densely packed irrespective of overall fold, and we show this arises from a jamming transition where amino acids reach a critical, incompressible density.
journals.aps.org/prxlife/abst...