Ashutosh Kumar
@mudgal17.bsky.social
PhD student at UniFr Switzerland | Phase separation | Computational Bio-physics/chemistry
Reposted by Ashutosh Kumar
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!
October 13, 2025 at 2:17 PM
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!
Reposted by Ashutosh Kumar
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...
August 7, 2025 at 8:45 AM
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...
Reposted by Ashutosh Kumar
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
Tons of open slots, invited and selected speakers all get 20 mins ❤️
#EESNucleus
July 23, 2025 at 10:49 AM
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
Tons of open slots, invited and selected speakers all get 20 mins ❤️
#EESNucleus
Reposted by Ashutosh Kumar
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)
July 23, 2025 at 11:55 AM
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)
Reposted by Ashutosh Kumar
When observed closely, lipid mixing looks like classic hemifusion-like intermediates with exposed lipid-tails (but stabilized within protein rings here). (10/13)
July 23, 2025 at 11:51 AM
When observed closely, lipid mixing looks like classic hemifusion-like intermediates with exposed lipid-tails (but stabilized within protein rings here). (10/13)
Reposted by Ashutosh Kumar
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)
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)
July 23, 2025 at 11:40 AM
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)
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)
Reposted by Ashutosh Kumar
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".
July 22, 2025 at 2:13 PM
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".
Reposted by Ashutosh Kumar
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!
April 15, 2025 at 4:06 PM
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!
Reposted by Ashutosh Kumar
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....
pubs.acs.org/doi/full/10....
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 ...
pubs.acs.org
March 19, 2025 at 3:21 PM
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....
pubs.acs.org/doi/full/10....
Reposted by Ashutosh Kumar
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
buff.ly/4b3E0xy
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
buff.ly
March 19, 2025 at 3:26 PM
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
buff.ly/4b3E0xy
Reposted by Ashutosh Kumar
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/...
rupress.org/jcb/article/...
Any1 is a phospholipid scramblase involved in endosome biogenesis | Journal of Cell Biology | Rockefeller University Press
This study identifies Any1 as a lipid scramblase, which cycles between Golgi and endosome and is involved in MVB biogenesis. To do so, Any1 cooperates with
rupress.org
March 19, 2025 at 3:30 PM
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/...
rupress.org/jcb/article/...
Reposted by Ashutosh Kumar
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
March 19, 2025 at 3:34 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Ashutosh Kumar
Finally, a couple of nice preprints from younger members of the lab. Pre-doc Mira Mors (now PhD student in Stuttgart) contributed to this thorough screening of amphipathic helices by @shoken-lee.bsky.social from the @bahmanyarlab.bsky.social lab! (1/2)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Amphipathic helices sense the inner nuclear membrane environment through lipid packing defects
Amphipathic helices (AHs) are ubiquitous protein motifs that modulate targeting to organellar membranes by sensing differences in bulk membrane properties. However, the adaptation between membrane-tar...
www.biorxiv.org
March 19, 2025 at 3:34 PM
Finally, a couple of nice preprints from younger members of the lab. Pre-doc Mira Mors (now PhD student in Stuttgart) contributed to this thorough screening of amphipathic helices by @shoken-lee.bsky.social from the @bahmanyarlab.bsky.social lab! (1/2)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Ashutosh Kumar
Amino Acid Transfer Free Energies Reveal Thermodynamic Driving Forces in Biomolecular Condensate Formation https://www.biorxiv.org/content/10.1101/2024.12.01.625774v1
Amino Acid Transfer Free Energies Reveal Thermodynamic Driving Forces in Biomolecular Condensate Formation https://www.biorxiv.org/content/10.1101/2024.12.01.625774v1
The self-assembly of intrinsically disordered proteins into biomolecular condensates shows a depende
www.biorxiv.org
December 5, 2024 at 5:49 PM
Amino Acid Transfer Free Energies Reveal Thermodynamic Driving Forces in Biomolecular Condensate Formation https://www.biorxiv.org/content/10.1101/2024.12.01.625774v1
Reposted by Ashutosh Kumar
Meet the CALVADOS RNA model
Ikki Yasuda, Sören von Bülow & Giulio Tesei have parameterized a simple model for disordered RNA. Despite it's simplicity (no sequence, no base pairing) we find that it captures several phenomena that depend on the charge, stickiness and polymer properties of RNA 🧬🧶🧪
Ikki Yasuda, Sören von Bülow & Giulio Tesei have parameterized a simple model for disordered RNA. Despite it's simplicity (no sequence, no base pairing) we find that it captures several phenomena that depend on the charge, stickiness and polymer properties of RNA 🧬🧶🧪
November 29, 2024 at 8:25 AM
Meet the CALVADOS RNA model
Ikki Yasuda, Sören von Bülow & Giulio Tesei have parameterized a simple model for disordered RNA. Despite it's simplicity (no sequence, no base pairing) we find that it captures several phenomena that depend on the charge, stickiness and polymer properties of RNA 🧬🧶🧪
Ikki Yasuda, Sören von Bülow & Giulio Tesei have parameterized a simple model for disordered RNA. Despite it's simplicity (no sequence, no base pairing) we find that it captures several phenomena that depend on the charge, stickiness and polymer properties of RNA 🧬🧶🧪
Reposted by Ashutosh Kumar
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???
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Stereochemistry in the disorder–order continuum of protein interactions - Nature
Studies on protein–protein interactions using proteins containing d- or l-amino acids show that stereoselectivity of binding varies with the degree of disorder within the complex.
www.nature.com
November 27, 2024 at 8:31 PM
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???
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ashutosh Kumar
An Intermediate Resolution Model of RNA Dynamics and Phase Separation with Explicit Mg2+ https://www.biorxiv.org/content/10.1101/2024.11.17.624048v1
An Intermediate Resolution Model of RNA Dynamics and Phase Separation with Explicit Mg2+ https://www.biorxiv.org/content/10.1101/2024.11.17.624048v1
RNAs are major drivers of phase separation in the formation of biomolecular condensates. They can al
www.biorxiv.org
November 19, 2024 at 12:50 AM
An Intermediate Resolution Model of RNA Dynamics and Phase Separation with Explicit Mg2+ https://www.biorxiv.org/content/10.1101/2024.11.17.624048v1
Reposted by Ashutosh Kumar
New collaborative work in collaboration with the labs of Robert Best & Tanja Mittag driven by Ben Schuler.
Identifying Sequence Effects on Chain Dimensions of Disordered Proteins by Integrating Experiments and Simulations.
pubs.acs.org/doi/10.1021/...
Identifying Sequence Effects on Chain Dimensions of Disordered Proteins by Integrating Experiments and Simulations.
pubs.acs.org/doi/10.1021/...
Identifying Sequence Effects on Chain Dimensions of Disordered Proteins by Integrating Experiments and Simulations
It has become increasingly evident that the conformational distributions of intrinsically disordered proteins or regions are strongly dependent on their amino acid compositions and sequence. To facili...
pubs.acs.org
November 15, 2024 at 4:56 PM
New collaborative work in collaboration with the labs of Robert Best & Tanja Mittag driven by Ben Schuler.
Identifying Sequence Effects on Chain Dimensions of Disordered Proteins by Integrating Experiments and Simulations.
pubs.acs.org/doi/10.1021/...
Identifying Sequence Effects on Chain Dimensions of Disordered Proteins by Integrating Experiments and Simulations.
pubs.acs.org/doi/10.1021/...
Reposted by Ashutosh Kumar
We have a 2-year #postdoc position in my lab supported by a fellowship from the Carl Trygger foundation. Intrinsically disordered regions, modular domains, protein-protein interactions, phage display and more. More info here: www.nature.com/naturecareer...
Postdoctoral fellow - Uppsala (Stad) (SE) job with Uppsala University, Department of Chemistry - BMC | 12832275
The laboratory of Prof. Ylva Ivarsson is seeking a highly motived candidate for a two-year postdoctoral fellowship on a project focused on short li...
www.nature.com
November 18, 2024 at 11:37 AM
We have a 2-year #postdoc position in my lab supported by a fellowship from the Carl Trygger foundation. Intrinsically disordered regions, modular domains, protein-protein interactions, phage display and more. More info here: www.nature.com/naturecareer...
Reposted by Ashutosh Kumar
Hello Bluesky! We're thrilled to announce an open PhD position on exploring controlling condensate membrane attachment and exocytosis! Collaborate across Europe in the ComeInCell EU network. Apply now! Details: www.comeincell.org & www.ru.nl/en/working-a...
ComeInCell – Doctoral Network on Integrative Synthetic Cell Design
www.comeincell.org
November 18, 2024 at 10:31 AM
Hello Bluesky! We're thrilled to announce an open PhD position on exploring controlling condensate membrane attachment and exocytosis! Collaborate across Europe in the ComeInCell EU network. Apply now! Details: www.comeincell.org & www.ru.nl/en/working-a...
Reposted by Ashutosh Kumar
Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!
November 17, 2024 at 4:20 PM
Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!
Reposted by Ashutosh Kumar
You try a "universal" machine learning force field and wonder why the wheels start falling off your simulations. A scroll through "homonuclear diatomics" on huggingface.co/spaces/atomi... is informative! #CompChem #CompChemSky
November 17, 2024 at 9:53 AM
You try a "universal" machine learning force field and wonder why the wheels start falling off your simulations. A scroll through "homonuclear diatomics" on huggingface.co/spaces/atomi... is informative! #CompChem #CompChemSky
Reposted by Ashutosh Kumar
Even though Newton's laws are deterministic, the behavior of many interacting bodies is so chaotic that it looks essentially "random."
Statistical mechanics effectively says: why bother with all those complex trajectories? Just go ahead and replace them with truly random motion.
Statistical mechanics effectively says: why bother with all those complex trajectories? Just go ahead and replace them with truly random motion.
November 18, 2024 at 10:52 PM
Even though Newton's laws are deterministic, the behavior of many interacting bodies is so chaotic that it looks essentially "random."
Statistical mechanics effectively says: why bother with all those complex trajectories? Just go ahead and replace them with truly random motion.
Statistical mechanics effectively says: why bother with all those complex trajectories? Just go ahead and replace them with truly random motion.
Reposted by Ashutosh Kumar
I’m excited to share my most recent manuscript describing an approach to assess local conformational sampling in simulations of intrinsically disordered proteins. This one’s for my computational biophysics aficionados www.biorxiv.org/content/10.1... a 🧵
Disentangling folding from energetic traps in simulations of disordered proteins
Protein conformational heterogeneity plays an essential role in a myriad of different biological processes. Extensive conformational heterogeneity is especially characteristic of intrinsically disorde...
www.biorxiv.org
November 12, 2024 at 5:48 PM
I’m excited to share my most recent manuscript describing an approach to assess local conformational sampling in simulations of intrinsically disordered proteins. This one’s for my computational biophysics aficionados www.biorxiv.org/content/10.1... a 🧵