Ph.D student at @LabVanni || Computational Bio-physics/chemistry || Intrinsically disordered proteins || Biomolecular Phase separation.
Fribourg, Switzerland
Joined April 2020
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Ashutosh Kumar retweeted
huuuum comparing AlphaFold to this is a complete breakdown of scientific literacy, alphafld learned physical representations to predict 200M+ real protein structures, published its weights & gave the tool to humanity
openAI didn’t solve the Millennium Prize…. theyused 10 000 agents in lean to autoformalize a forced edge case (f(x,t)) whose theoretical map was already drawn by human scholars then hid the model behind an API for pre-IPO PR
one is open computational biology; the other is automated proof checking over a loophole, closed behind a corporate paywall
conflating open scientific revolution with closed computational brute force is how silicon valley tricks people into worshipping PR over physics…
Ashutosh Kumar retweeted
To fuse, or not to fuse: Closing in on the nuclear envelope fusion machinery dlvr.it/TVMm0c
Ashutosh Kumar retweeted
Two new CALVADOS preprints:
Coarse-grained models for simulations of double-stranded nucleic acids for mixed protein-nucleic acid condensates
doi.org/10.64898/2026.08.14.…
MEM-CALVADOS: A Residue-Level Model for Flexible Proteins at Membrane Interfaces
doi.org/10.64898/2026.08.12.…
Ashutosh Kumar retweeted
New preprint in which we built and simulated full-length models of α-Synuclein fibrils to reveal how the fuzzy coat mediates selective binding of peptides to amyloid fibrils
Work led by Carlos Pintado-Grima in a nice collaboration with Salvador Ventura's lab
Full-Length Molecular Models of Brain-Derived α-Synuclein Fibrils Reveal a Fuzzy-Coat-Mediated Mechanism for Selective Peptide Binding biorxiv.org/content/10.64898… #biorxiv_bioinfo
Ashutosh Kumar retweeted
Can we design mutations that predictably bias proteins towards desired conformational states?
Today in @ScienceMagazine, we introduce Conformational Biasing (CB), a simple and scalable computational method that uses contrastive scoring by inverse folding models to identify conformation-biasing mutations.
science.org/doi/10.1126/scie…
Ashutosh Kumar retweeted
(Part 1/2) Excited to share that our work, led by PhD student Keerthivasan Muthukumar (@kvasan452) and postdoc Dr. Dinesh S. Devarajan (@Dsundara993), is now published in PNAS (pnas.org/doi/10.1073/pnas.25…).
Ashutosh Kumar retweeted
Dystonia-associated Torsins sustain CLCC1 function to promote membrane fusion of the nuclear envelope for NPC biogenesis biorxiv.org/content/10.1101/… #biorxiv_cellbio
Ashutosh Kumar retweeted
I am hiring at the PhD or Postdoc level. I am looking for motivated candidates willing to work on a challenging project at the frontiers of what we understand of protein colloidal stability.
Ashutosh Kumar retweeted
Our collaborative work "The #Martini3 #Lipidome: Expanded and Refined Parameters Improve Lipid Phase Behavior" is now published in #ACSCentralScience! 🎉
📄 Read: pubs.acs.org/doi/10.1021/acs…
💾 GitHub: github.com/Martini-Force-Fie…
#MolecularDynamics #Biophysics #Simulations #Lipids
Ashutosh Kumar retweeted
If heterochromatin is really a liquid-like condensate, why is it not spherical?
We investigated whether mechanical interactions between a condensate and a fiber network can explain the variety of morphologies seen in phase-separated nuclear compartments.
biorxiv.org/content/10.1101/…
Ashutosh Kumar retweeted
Excited to share the new work from the Carvalho lab
@Dunn_School! 🎉This was part of my PhD & a collaboration with the @LabVanni
& Ernst labs!
Big thanks to everyone involved! 🙌
Read more: doi.org/10.1083/jcb.20240903… (1/2)
Ashutosh Kumar retweeted
Join our interdisciplinary team developing computational approaches to understand and engineer biomolecular condensates. We’re looking for a postdoc—please apply or share with interested persons! 👩🏽💻💧🧬 puwebp.princeton.edu/AcadHir…
Ashutosh Kumar retweeted
Nature research paper: Structural basis of lipid transfer by a bridge-like lipid-transfer protein
go.nature.com/4itODM4
Ashutosh Kumar retweeted
Martini 3 - IDP is out! Improved parameters for disordered proteins, great work from Liguo Wang: nature.com/articles/s41467-0…
Ashutosh Kumar retweeted
ABHD17 enzymes remove fatty acids from #membrane proteins like NRas. New work from Holme, Sapia, @LabVanni, Conibear @UBC et al. show that their activity depends on two mobile regions: an S-acylated N-terminal helix and a loop. hubs.la/Q036MbQS0
Ashutosh Kumar retweeted
After some work, we’ve now made the @github for our #Martini3 #LNP models and protocols publicly available: github.com/Martini-Force-Fie…
We also have a new @ChemRxiv with some minor updates: chemrxiv.org/engage/chemrxiv…
#LipidNanoparticles #MD #DrugDelivery #mRNA #Simulation
Ashutosh Kumar retweeted
In collaboration with @BanerjeeLab_UB, we dive a little deeper into the microscopic interactions and sequence patterns shaping condensate activation energies pubs.acs.org/doi/10.1021/acs…. For more context, see also our prior work science.org/doi/10.1126/scia…
Ashutosh Kumar retweeted
Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @MSFTResearch AI for Science.
#ML #AI #NeuralNetworks #Biology #AI4Science
biorxiv.org/content/10.1101/…
Ashutosh Kumar retweeted
We did this crazy project where we tried to see if proteins could interact with their mirror image ligand. Seems impossible when proteins need to form 3D structures to interact. But what about if the interaction remains disordered???
nature.com/articles/s41586-0…
