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Ashutosh Kumar

@mudgal17.bsky.social
590 followers 303 following 5 posts

PhD student at UniFr Switzerland | Phase separation | Computational Bio-physics/chemistry

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Reposted by Ashutosh Kumar
Maksim Kalutskii @maksimkalutskii.bsky.social · 23/09/2026
Excited to share our new preprint! 📜 Here, we used CALVADOS and ultra-CG models to show how the kinetochore establishes a robust attachment to the dynamic microtubule end. Spoiler: IDRs 🧵 1/n www.biorxiv.org/content/10.6...
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Reposted by Ashutosh Kumar
bioRxivpreprint @biorxivpreprint.bsky.social · 13/09/2026
A new class of lipid transfer proteins is required for the recycling of lipids from the P. falciparum digestive vacuole www.biorxiv.org/content/10.64898/20…
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Reposted by Ashutosh Kumar
Molecular Cell @cp-molcell.bsky.social · 04/09/2026
The dystonia-associated Torsin1A sustains CLCC1 function in membrane fusion of the nuclear envelope for NPC biogenesis
dlvr.it
The dystonia-associated Torsin1A sustains CLCC1 function in membrane fusion of the nuclear envelope for NPC biogenesis
Maslennikova et al. identify the ER membrane protein CLCC1 as an interaction partner of the dystonia-linked AAA+ ATPase Torsin1A. Torsin1A sustains the function of CLCC1, which is proposed to facilitate fusion of the nuclear envelope during NPC biogenesis by forming an oligomer that promotes lipid bilayer approach and remodeling.
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Journal of Cell Biology @jcb.org · 04/09/2026
Any1 is a #phospholipid scramblase involved in #endosome biogenesis. From Jieqiong Gao, @labvanni.bsky.social, Christian Ungermann and colleagues: rupress.org/jcb/article/... 📕 From our #Lipid and #Membrane collection: rupress.org/jcb/collecti... #EMBOLipidCode
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Reposted by Ashutosh Kumar
mareikejordan.bsky.social @mareikejordan.bsky.social · 04/09/2026
Check out our preprint on the structural mechanisms of how LEM2 and ESCRTs seal the nuclear envelope. Awesome collaboration with @karenpalacior.bsky.social who brought my structures to life 💃🔬❄️🌀 @hummerlab.bsky.social www.biorxiv.org/content/10.6...
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Molecular Cell @cp-molcell.bsky.social · 03/09/2026
A conserved mechanism of membrane fusion in nuclear pore complex assembly
dlvr.it
A conserved mechanism of membrane fusion in nuclear pore complex assembly
Fischer et al. uncover a fundamental mechanism of membrane fusion during nuclear pore complex (NPC) assembly. Brl1 and Brr6 form ring-shaped, membrane-remodeling complexes that interact and bridge the nuclear envelope at NPC-assembly sites to mediate fusion. This pathway is conserved in humans via the metazoan fusogen CLCC1.
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Reposted by Ashutosh Kumar
Chelsea Brown @chelseabrown.bsky.social · 01/09/2026
Delighted to share my first author paper on how the MIC10 protein complex generates curvature in mitochondrial crista out now in Science Advances!! 🥳🥳 www.science.org/doi/10.1126/... See below for a run through of why we were interested and what we found 👇
science.org
The molecular basis of mitochondrial crista formation by the MIC10 complex
Mitochondrial cristae are essential for respiration, yet the molecular basis of how the high curvature of these membrane folds is maintained remains unclear. Using structure prediction tools and multi...
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Reposted by Ashutosh Kumar
Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 30/08/2026
Preprint with work led by Fran Toplek in Tatiana Morozova's recently established lab in Lyon on refining and testing the Martini models ability to capture properties of IDR condensates including structural and dynamical properties, and ion partitioning. doi.org/10.64898/202...
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MRC-LMB Cell Biology Division @cellbiol-mrclmb.bsky.social · 28/08/2026
Great tribute to the discovery by Barbara Pearce of clathrin, the first protein found to act in membrane traffic, along with her mentoring and support of the pioneers (many of whom were other women) who revealed the workings of this key player in cellular function.
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Reposted by Ashutosh Kumar
Martin Vögele @martinvoegele.bsky.social · 26/08/2026
Interesting coarse-graining trick: Simply scaling the mass of water particles in the Martini model speeds up the simulation without affecting equilibrium properties. www.biorxiv.org/content/10.6...
biorxiv.org
Light Martini water accelerates sampling in coarse-grained molecular dynamics simulations
Molecular dynamics (MD) simulations of slow biomolecular processes, such as exploration of the conformational ensembles of intrinsically disordered proteins (IDPs), are computationally demanding. Alth...
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Reposted by Ashutosh Kumar
Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 25/08/2026
Predicting RNA structure is hard, and predicting RNA dynamics is even harder We combined extensive NMR data with MD simulations to study the dynamics of RNA tetraloops By projecting onto the universe of tetraloop structures, we show how NMR+MD captures structures not seen by prediction methods
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Evdokiia Potolitsyna @evdokiiap.bsky.social · 26/08/2026
1/ Do cells use phase separation to adapt biosynthetic output to changing demands? In our new preprint, we show that under nutrient limitation, the nucleolus enters a reversible ‘hibernation’ state that slows ribosome biogenesis. See doi.org/10.64898/202...
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Kutay lab @kutaylab.bsky.social · 09/08/2026
We are excited by the publication of our work on Torsin1A, its interaction partner CLCC1, and their role in membrane fusion during NPC biogenesis! A fantastic collaboration with @jagannathan-lab.bsky.social @labvanni.bsky.social @gautamdey.bsky.social and the Korkhov and Antonin labs!
cell.com
The dystonia-associated Torsin1A sustains CLCC1 function in membrane fusion of the nuclear envelope for NPC biogenesis
Maslennikova et al. identify the ER membrane protein CLCC1 as an interaction partner of the dystonia-linked AAA+ ATPase Torsin1A. Torsin1A sustains the function of CLCC1, which is proposed to facilitate fusion of the nuclear envelope during NPC biogenesis by forming an oligomer that promotes lipid bilayer approach and remodeling.
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Reposted by Ashutosh Kumar
Molecular Cell @cp-molcell.bsky.social · 04/08/2026
Online Now: The dystonia-associated Torsin1A sustains CLCC1 function in membrane fusion of the nuclear envelope for NPC biogenesis Online now:
dlvr.it
The dystonia-associated Torsin1A sustains CLCC1 function in membrane fusion of the nuclear envelope for NPC biogenesis
Maslennikova et al. identify the ER membrane protein CLCC1 as an interaction partner of the dystonia-linked AAA+ ATPase Torsin1A. Torsin1A sustains the function of CLCC1, which is proposed to facilitate fusion of the nuclear envelope during NPC biogenesis by forming an oligomer that promotes lipid bilayer approach and remodeling.
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Reposted by Ashutosh Kumar
Joris Sprakel @jorissprakel.bsky.social · 25/07/2026
How do transcription factors bind DNA strongly, and in a switch like manner, while remaining sequence specific? Our new paper on a canonical plant TF suggests the answer is a previously underappreciated assembly state: transcription factor nanoclusters. www.science.org/doi/10.1126/...
science.org
Nanoclustering of a plant transcription factor enables strong yet specific DNA binding
Transcription factor nanoclusters balance the DNA binding trade-off between weakly binding oligomers and nonspecific condensates.
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 19/07/2026
It’s time for the World Cup final with one of the greatest footballers that may be playing his last cup So time for a short thread on a link between Messi and an intrinsically disordered protein. 1/n
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Pedro Beltrao @pedrobeltrao.bsky.social · 14/07/2026
Team science preprint, exploring the capabilities and limitations of Alphafold3 across different application areas, including protein-RNA, protein-lipid, ubiquitination,TCR and antibody recognition with @ninjani.bsky.social @labvanni.bsky.social @dgfeller.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
Capabilities, specificity gaps and training-data dependence of AlphaFold3 across diverse application areas
Structure prediction models have moved from single proteins to assemblies that include diverse biomolecules and their modifications. AlphaFold3 (AF3) and related models extended structural modelling v...
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Mittal Group @ TAMU @mittalgrouptamu.bsky.social · 10/07/2026
We are hiring postdoctoral researchers. Please share!
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Reposted by Ashutosh Kumar
Vanni Lab at UNIFR, Switzerland @labvanni.bsky.social · 10/07/2026
Happy to share that this beautiful work by @mudgal17.bsky.social in collaboration with the Weis lab @eth-dbiol.bsky.social, discovering a new membrane fusion mechanism in eukaryotes, is finally out in peer-reviewed form at @cp-molcell.bsky.social. www.cell.com/molecular-ce...
cell.com
A conserved mechanism of membrane fusion in nuclear pore complex assembly
Fischer et al. uncover a fundamental mechanism of membrane fusion during nuclear pore complex (NPC) assembly. Brl1 and Brr6 form ring-shaped, membrane-remodeling complexes that interact and bridge the...
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Reposted by Ashutosh Kumar
Gregor Weiss @weiss-lab.bsky.social · 10/07/2026
Some bacteria do not live as individuals. They build multicellular filaments and connect neighboring cells through tiny cell-cell junctions. Cyanobacteria are among the most beautiful examples 😍 In our new paper, we reveal first molecuar insights on the cyanobacterial septal junction architecture 🧵
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Armando Rubio Ramos @bioarm.bsky.social · 10/07/2026
Not everyday a friend is able to define a new organelle!!! If you like membrane compartimentalization and are interested in how cells responde to stress in membrane tension, check this out!👇👇 Congrats to Elda and co!! www.biorxiv.org/content/10.6...
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Ashutosh Kumar @mudgal17.bsky.social · 10/07/2026
Our work on identifying membrane fusion mechanism prior to NPC assembly is now out in peer reviewed form at @cp-molcell.bsky.social Have a look if you are interested in NPC biogenesis and membrane fusion.
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Reposted by Ashutosh Kumar
Vanni Lab at UNIFR, Switzerland @labvanni.bsky.social · 12/06/2026
This amazing work by @danialv.bsky.social and Bodan Hu is now out in peer-reviewed form at @cp-cell.bsky.social with a lot of new simulations! Check it out if interested in lipid transport!
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Reposted by Ashutosh Kumar
André Nadler @nadlerlab.bsky.social · 15/06/2026
This story by the Reinisch, Vanni & De Camilli is among the most important membrane biology papers this year. Amazing work, Congratulations everyone!!!
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Vanni Lab at UNIFR, Switzerland @labvanni.bsky.social · 15/06/2026
Beautiful cover on our Atg2-Atg18 work (with @ungermannlab.bsky.social, @arnemoeller.bsky.social and reggiori lab) by lab PhD student @yarasayed1.bsky.social. Congrats Yara! #lipidtime
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ungermannlab.bsky.social @ungermannlab.bsky.social · 19/05/2026
Three PhD positions available to work on yeast lysosome biogenesis and reconstitution of membrane fusion as of July or September 2026. Details can be found here: myshare.uni-osnabrueck.de/f/76c16d1fcc...
myshare.uni-osnabrueck.de
260508_PhD positions available.pdf
Share link for 260508_PhD positions available.pdf.
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Reposted by Ashutosh Kumar
Mir Lab @mirlab.bsky.social · 07/06/2026
1/🧵 Can transcription factor condensate formation be explained without phase separation? Our new preprint introduces SPARK, a simulation tool that reproduces condensate behavior (clustering, fusion, FRAP) from diffusion & binding kinetics alone. Movie: 60 sec FRAP sim www.biorxiv.org/content/10.6...
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Vanni Lab at UNIFR, Switzerland @labvanni.bsky.social · 21/05/2026
Happy to share our latest work on bridge lipid transfer proteins, by PhD student @yarasayed1.bsky.social. A great collaboration with @ungermannlab.bsky.social @arnemoeller.bsky.social and Reggiori lab!
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The EMBO Journal @embojournal.org · 20/05/2026
Atg18 interaction positions Atg2 for efficient lipid transfer into phagophore elongation Sabrina Chumpen Ramirez, @dmitryshvarev.bsky.social  et al link.springer.com/article/10.1...
link.springer.com
Atg18 interaction positions Atg2 for efficient lipid transfer into phagophore elongation - The EMBO Journal
During macroautophagy, the de novo formation of the autophagosome at a membrane contact site (MCS) with the endoplasmic reticulum requires directional lipid flux for the growth of the initial phagopho...
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Reposted by Ashutosh Kumar
Miro Astore @miroastore.bsky.social · 24/04/2026
We just preprinted one of my favorite studies @FlatironInst . I was lucky to be part of an amazing team studying the effects of rapid cooling to preserve samples in cryoEM. Read on to learn about the limits of cryoEM for biophysics and how to overcome them www.biorxiv.org/content/10.6...
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Marintia Nava-García @marintianava.bsky.social · 14/04/2026
Beyond proteins and DNA, #lipids are emerging as key players in nuclear biology - shaping nuclear envelope dynamics, mechanosensing, gene regulation and genome stability. Our new Perspective highlights recent advances, open questions, and future directions 👉 journals.biologists.com/jcs/article/...
journals.biologists.com
Emerging roles of lipids in nuclear function and homeostasis
Summary: Lipids are increasingly recognized as essential regulators of nuclear homeostasis, membrane dynamics, mechanotransduction and genome stability, opening new frontiers for understanding nuclear...
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Jelle van den Ameele @jellevda.bsky.social · 05/04/2026
Wonderful and honoured to write a perspective with @prudentlab.bsky.social @mrc-mbu.bsky.social on such an intriguing and cool observation of beautiful mitochondrial biology! Amazing work on how pearling allows mitochondrial genome organisation by @jclandoni.bsky.social @sulianamanley.bsky.social!
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Molecular Cell @cp-molcell.bsky.social · 05/04/2026
Mechanosensory channels mediate ER Ca2+ transients to trigger assembly of autophagosome initiation sites for degradation of ER subdomains
dlvr.it
Mechanosensory channels mediate ER Ca2+ transients to trigger assembly of autophagosome initiation sites for degradation of ER subdomains
Ma et al. show that stress-induced, high-luminal Ca2+ ER sheets are selectively degraded by autophagy (ER-phagy), which requires the concerted actions of FAM134B and lipidated LC3. The ER-localized channels PIEZO1 and TRPV1 mediate Ca2+ release from these ER subdomains, triggering the formation of FIP200 puncta to initiate autophagosome assembly.
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Martin Pacesa @martinpacesa.bsky.social · 03/03/2026
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.
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Sophie G Martin @sophiemartinlab.bsky.social · 03/03/2026
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!
mocel.unige.ch
Contact/Job - Department of Molecular and Cellular Biology - UNIGE
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Ioana M. ILIE @biosim-lab.bsky.social · 01/03/2026
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...
pubs.aip.org
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
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Vanni Lab at UNIFR, Switzerland @labvanni.bsky.social · 24/02/2026
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!
sciencedirect.com
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…
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 16/02/2026
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...
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Jerelle Joseph @jerelleaj.bsky.social · 13/02/2026
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...
pubs.aip.org
Molecular origins of viscoelasticity in biomolecular condensates
Biomolecular condensates are membraneless organelles that compartmentalize functions in living cells. Formed by the phase separation of biomolecules, condensate
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epithelial mechanics fan club @epimechfc.bsky.social · 06/02/2026
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
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Magnus Kjærgaard @proteinmagnus.bsky.social · 02/02/2026
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...
Graphical abstract of pre-print
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James Barrett @james-r-barrett.bsky.social · 30/01/2026
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
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Vanni Lab at UNIFR, Switzerland @labvanni.bsky.social · 30/01/2026
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!
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 23/01/2026
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...
Figure illustrating the role of machine learning in IDP design, showing both the training data, machine learning and applications
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Vanni Lab at UNIFR, Switzerland @labvanni.bsky.social · 12/01/2026
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)
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Vanni Lab at UNIFR, Switzerland @labvanni.bsky.social · 12/01/2026
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...
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Cell Biology J-Club @cellclub.bsky.social · 09/01/2026
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...
biorxiv.org
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 ...
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bioRxiv Cell Biology @biorxiv-cellbio.bsky.social · 08/01/2026
Biomolecular condensate architecture of an autophagic cargo at molecular resolution in situ www.biorxiv.org/content/10.64898/20…
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Adrian Roitberg @adrianroitberg.bsky.social · 05/01/2026
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...
chemrxiv.org
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...
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Javier Espadas @javierespadas.bsky.social · 01/12/2025
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.
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