Ashutosh Kumar

2026 has been a remarkable year for me so far (despite the current world events): opening my lab at the University of Zurich, assembling an amazing group of people in the group, and celebrating it with a fantastic lab warming party. Figured it's also time for a small profile refresh.

You are finishing your PhD and looking to continue in science?

The Martin lab @biology-unige.bsky.social has an open postdoctoral position in cell biology to study cell-cell fusion. For more information, please consult mocel.unige.ch/research-gro....

Thanks for reposting!

Physical mechanisms of nanoparticle–membrane interactions: A coarse-grained study Nanoparticles are promising drug carriers for targeted therapies, diagnostic imaging, and advanced vaccines. However, their clinical translation is limited by c

We uncover the physical mechanisms governing nanoparticle–membrane interactions using coarse-grained simulations, mapping distinct regimes from adhesion to wrapping. A step toward predictive design rules for nanomedicine & adaptive materials

pubs.aip.org/aip/jcp/arti...

Lipid scrambling: New players, new questions, new opportunities Nearly a quarter of the proteins encoded in most organisms are transmembrane proteins. Contrary to textbook description, many feature a hydrophilic gr…

Amazing PhD @cristianrocharoa.bsky.social
and I have collected our thoughts and questions (many!) on lipid scramblases in this review:
www.sciencedirect.com/science/arti...
If you are interested in lipid transport and metabolism, membrane asymmetry and membrane protein function, give it a read!

Happy to share our newest preprint on Parkin missense variants in work led by Erna Sol &
@vvouts.bsky.social in @rhp-lab.bsky.social

Using a multiplexed assay we determined the effects of 9,212 out of 9,300 single amino acid substitutions and nonsense Parkin variants. 1/n

doi.org/10.64898/202...

Pablo’s work on “condensate Deborah numbers” is now out in #JCP!! Selected as Editor’s Pick and featured as a #Scilight
pubs.aip.org/aip/jcp/arti...

Espadas, J., Souza, D. P., Hakala, M., García-Arcos, J. M., Tran, J., Kumar, A., Marcuello, C., Merino, A., ..., Toret, C. P., & Roux, A. (2025). Molecular basis for cellular compartmentalization by an ancient membrane fission mechanism. bioRxiv. #EpithelialMechanics
buff.ly/OQv9qMw

Graphical abstract of pre-print

Does targeting enzymes and substrates in a condensate lead to rate enhancement? No. Here, we investigate how the condensate environment can inhibit an enzyme reaction.

Spoiler: Mass-transport limitations. We find a strong correlation between diffusion and reaction rates.

doi.org/10.64898/202...

How does molecular valency shape condensate assembly and function? We used the CO2-fixing organelle in algae—the pyrenoid—to find out… 🧵

Preprint here!:
www.biorxiv.org/content/10.6...

@cellarchlab.com @phaips.vd.st @biologyatyork.bsky.social
#Rubisco #PhaseSeparation #Condensates #Pyrenoid

Please share!!! I am looking for a postdoctoral researcher to join us. Focus will be on exciting collaborative projects on lipids and membrane biology, pushing the boundaries of in silico "reconstitutions". Previous experience with molecular dynamics simulations of biological systems a strong plus!

Figure illustrating the role of machine learning in IDP design, showing both the training data, machine learning and applications

Looking for something to read over the weekend?

Our review on computational design of intrinsically disordered proteins is now published in final form 🍝

With @giuliotesei.bsky.social & @fpesce.bsky.social

doi.org/10.1016/j.sb...

Finally, @danialv.bsky.social used CG simulations to show that VPS13A can deliver lipids to an acceptor membrane that is bound at the C-terminal of VPS13A, and that XKR1 is proximal, but not continuous, to the delivery site. (6/7)

Happy to finally share the amazing results of our long-term collaboration with Karin Reinisch’s lab on how bridge lipid-transfer proteins (BLTPs) cooperate with partner proteins to orchestrate lipid delivery. A quick thread (1/7)
www.biorxiv.org/content/10.6...

Molecular insights into bulk lipid transport from structural studies of the bridge-like protein VPS13A complexed with the scramblase XKR1 In eukaryotes, bridge-like lipid-transfer proteins (BLTPs) are central in mediating vesicle-independent lipid transfer between organelles. BLTPs span the cytosolic space between organelles at contact ...

Molecular insights into bulk lipid transport from structural studies of the bridge-like protein VPS13A complexed with the scramblase XKR1 www.biorxiv.org/content/10.6...

Biomolecular condensate architecture of an autophagic cargo at molecular resolution in situ https://www.biorxiv.org/content/10.64898/2026.01.07.698105v1

LAMMPS-ANI: Large Scale Molecular Dynamics Simulations with ANI Neural Network Potential Machine Learning Interatomic Potentials (MLIPs), trained with Quantum Mechanics data, can model potential energy surfaces for molecular systems with very high accuracy and extreme speedups compared to...

New Preprint dropped. LAMMPS + ANI, a super fast implementation of MLIPs. Highly parallel (> 1000 GPUS) and much faster than anything else out there ! Work done by the amazing @ignaciopickering.bsky.social, @nickterrel.bsky.social , and Jinze (Richard) Xue. chemrxiv.org/engage/chemr...

Meet Hofund, the N-terminal amphipathic helix of 15 aa in Heimdall ESCRT-IIIA (named after Heimdall’s sword).
How do we know Hofund is the molecular trigger for fission?
Remove Hofund → ESCRT-IIIA loses fission activity.
Add Hofund alone → uncontrolled fission.

Molecular basis for cellular compartmentalization by an ancient membrane fission mechanism The emergence of cell compartmentalization depends on membrane fission to create the endomembrane compartments. In eukaryotes, membrane fission is commonly executed by ESCRT-III, a protein complex con...

New preprint from the lab!!🎉
We show that Asgard archaea ESCRT-III proteins can trigger membrane fission and reveal its molecular mechanism, offering clues to how these cells may have built internal compartments. But do these organisms even have these compartments?
www.biorxiv.org/content/10.1...

Thanks to @snsf.ch, we are hiring two PhD students to investigate frontier topics in lipid biology using a combination of MD simulations and experiments. Preferred starting date: ASAP. Fribourg - and Switzerland - are quite nice, for both work and private life! Please spread the word!

Happy to share the latest from the lab, led by Daniel Alvarez, in collaboration with @lizconibear.bsky.social‬. In this AA-MD tour-de-force, we delve deep into the mechanism and energetics of lipid uptake by bridge-like lipid transfer proteins, and we learn a few interesting things along the way...

1 month to abstract deadline for the first cell biology of the nucleus meeting at @embl.org in many years - organised by the stellar @luskinglab.bsky.social @sarawickstrom.bsky.social Tom Quail & Simone Koehler

Tons of open slots, invited and selected speakers all get 20 mins ❤️

#EESNucleus

Altogether, we think that the mechanism of membrane fusion described in the context of NPC assembly here is different from what known for other fusion machineries (e.g. SNAREs, dynamin-like GTPases,…). More details in the manuscript—let us know your thoughts! (13/13)

When observed closely, lipid mixing looks like classic hemifusion-like intermediates with exposed lipid-tails (but stabilized within protein rings here). (10/13)

Happy to share the latest work from the lab, led by @mudgal17.bsky.social‬, in collaboration with the Weis lab @ethzurich.bsky.social.
How do nuclear membranes fuse during NPC assembly? We answer this question in our latest work, where we identify a new mechanism for membrane fusion… (1/13)

Unexpectedly, @jurgjn.bsky.social found that running Alphafold3 predictions for protein interactions can yield ipTM scores that are more predictive of true interactions when run in pools of proteins instead of pairwise predictions. Presumably, this reflects some sort of "competition effect".

Our lab is hiring 1 PhD and 1 Postdoc to study the mechanism of lipid transport using computational methods (Molecular Dynamics, AI). Fully funded by @snsf-ch.bsky.social for 4 years, with amazing collaborators and excellent life and working conditions. Apply by email. Please share and repost!

RNA Order Regulates Its Interactions with Zwitterionic Lipid Bilayers RNA–lipid interactions directly influence RNA activity, which plays a crucial role in the development of new applications in medicine and biotechnology. However, while specific preferential behaviors ...

Talented postdoc Akhil Singh (with help from recent graduate Janak Prabhu) provided a thorough investigation of RNA-membrane interactions using AA simulations, finding that RNA order regulates its interactions with zwitterionic bilayers (1/2)
pubs.acs.org/doi/full/10....

An S-acylated N-terminus and a conserved loop regulate the activity of the ABHD17 deacylase ABHD17 enzymes remove fatty acids from membrane proteins like NRas. This study shows that their activity depends on two mobile regions: an S-acylated N-ter

The work of “soon-to-be” (we will miss her!) graduate Jennifer Sapia on the S-acylase ABHD17 (in collaboration with the lab of @lizconibear.bsky.social and grad student Sydney Holme) is also out! (1/3)
buff.ly/4b3E0xy

Star PhD student Cristian Rocha Roa, in collaboration with Jieqiong Gao and the Ungermann lab, identified endosomal protein Any1 in yeast, and SLC66A2 in human, as novel lipid scramblases. (1/2)
rupress.org/jcb/article/...

Pex30-dependent membrane contacts sites maintain ER lipid homeostasis In eukaryotic cells, communication between organelles and the coordination of their activities depend on membrane contact sites (MCS). How MCS are regulated under the dynamic cellular environment rema...

While, in a nice collaboration with the Carvalho lab and @joanavferreira.bsky.social, PhD student Yara Ahmed used MD simulations to characterize the binding mechanism of the Dysferlin domain of Pex30 to phosphatidic acid. Anyone interested in a novel PA-sensor? (2/2)
www.biorxiv.org/content/10.1...