Babak Vajdi Hokmabad

Thank you, Saverio! It was a fun experiment, indeed, and there's so much more to explore :)

Excited to see this paper out @pnas.org

Microbial self-organization in response to self-made oxygen gradients! 🦠 🔄 🍥

PhD or Master's position available for Fall 2026!

Interested in how actin drives cell crawling, eating, dividing, or osmoregulation? What about pathogenesis of a brain-eating amoeba? Or eukaryotic evolution? If so, apply through my website: katrinavelle.wixsite.com/science/cont...
Please share!

We have a postdoc opening for a protistologist with biophysics inclinations to join our @hfspo.bsky.social project! (focus will be on characterising the morphology, ultrastructure and behaviour of excavates) #protistsonsky

Apply by Sept 17th (RTs appreciated!)
jobs.exeter.ac.uk/hrpr_webrecr...

Excited to release our latest work:
doi.org/10.1101/2025...

Here, we describe how confined bacterial suspensions self-organize into structured domains of different motilities, in response to oxygen limitations🦠🍥

Bluetorial follows! [1/8]

Genome duplication in a long-term multicellularity evolution experiment - Nature In the Multicellularity Long Term Evolution Experiment, diploid yeast evolve to be tetraploid under selection for larger multicellular size, revealing how whole-genome duplication can arise due to its...

1/46 Hey folks, we have a new paper out on the MuLTEE. Strap in and I’ll tell you the story of how this “little paper on polyploidy” turned into the most data rich paper our lab has produced, largely thanks to the leadership and work ethic of @kaitong25.bsky.social.

www.nature.com/articles/s41...

It was fun to uncover this story—bridging microbial physiology, biological pattern formation, & active matter physics. The results may even have implications for controlling microbes in applications. We'd love your feedback. Please report/share with whoever might be interested! [8/8]

Many biological fluids are polymer solutions, whose viscoelasticity can enhance cell swimming and promote large-scale mixing.
We showed that the core-shell organization also arises in polymer solutions, but with fascinating additional flow fluctuations. [7/8]

We then developed a biophysical model describing this interplay quantitatively. The model recapitulates the experiments, and also yields criteria for predicting the different ways in which confined bacterial populations self-organize under different conditions. [6/8]

Cells consume O2, creating a gradient that alters motility: (i) They move up the gradient toward the droplet boundary via aerotaxis, & (ii) They stop swimming in the anoxic droplet core and accumulate. These motility variations in turn reshape O2 fluxes. A feedback loop! [5/8]

By simultaneously measuring cell distributions, oxygen concentration, and swimming-generated fluid flow, we figured out that this spatial organization is driven by the interplay between cell metabolism-generated oxygen gradients and collective motility. [4/8]

Surprisingly, when the droplets are big and concentrated, the cells self-organize into a concentrated inner "core" of immotile cells surrounded by a more dilute outer "shell" of highly motile cells. (See movie in 1st tweet.) In some cases, the core shrinks and disappears. [3/8]

Bacteria often inhabit confined spaces, such as biological tissues/gels & soils/sediments, where metabolites are scarce. What influence does confinement have on a population of motile bacteria?
We addressed this question by studying quasi 2D droplets of swimming E. coli. [2/8]

Excited to release our latest work:
doi.org/10.1101/2025...

Here, we describe how confined bacterial suspensions self-organize into structured domains of different motilities, in response to oxygen limitations🦠🍥

Bluetorial follows! [1/8]

Intracellular competition shapes plasmid population dynamics Conflicts between levels of biological organization are central to evolution, from populations of multicellular organisms to selfish genetic elements in microbes. Plasmids are extrachromosomal, self-r...

I'm so happy that I can finally share the results of my first postdoc paper with @baym.lol!!! Turns out plasmids are an amazing system to study multi-scale evolution and we can track within-cell and between-cell dynamics!
(1/n) www.biorxiv.org/content/earl...

The 🪱 mania continues!
In our latest study, led by Rosa, we explored the locomotion and dynamics of living worms—acting as active polymers—navigating a porous environment made of 3D-printed pillar arrays. And we found something surprising...

Spatial population dynamics of bacterial colonies with social antibiotic resistance

#PNAS by @marlis.bsky.social and late Kevin B. Wood

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

Stickiness matters! From powder handling to geophysical flows, cohesion in granular material plays a crucial role. We review in Soft Matter @roysocchem.bsky.social experimental approaches to create and control inter-particle adhesion pubs.rsc.org/en/content/a...

🄱🄸🄾🄵🄸🄻🄼
🄱🄸🄾🄿🄷🅈🅂🄸🄲🅂

Fascinating work from Sebastian Gonzalez La Corte, Sujit Data, et al at CalTech on polymer-induced entropic attractions that hinder diffusion and lead bacteria to form long spaghetti-like cables within mucus and biofilms

Paper in Science Advances: www.science.org/doi/10.1126/...

Fresh off the press, our work on wing deployment in Drosophila 🪰:
www.nature.com/articles/s41...
Work by: Simon Hadjaje, Ignacio Andrade-Silva, Marie-Julie Dalbe and Raphaël Clément

Can I please be added here?

This is a beautiful work Nico! Congrats!

Starter Pack: Collective #CellMigration /Dynamics is growing. Looking at related emergent phenomena eg. #intercallation, dorsal closure or branching #morphogenesis? Reach out! Also modelers, soft-matter physicists & YOUNG scientists etc etc!

go.bsky.app/DLUDYX3
#cellbio #SoftMatterPhysics #science

Can I please be added here?

Can I please be added here?

Can I please be added here?

Can I please be added here?

Yeah, right 😅

💥Beyond happy 💥 Our work is now published in PNAS!
www.pnas.org/doi/10.1073/...

With Gloria Canales & @mazi1.bsky.social we studied how the single celled alga Pyrocystis lunula 🌙 move their chloroplast in response to strong light.

Get ready for some fun mechanics, signals and organelle motion! 🧵