Miłosz Wieczór
@milosz-wieczor.bsky.social
Comp bio postdoc @ IRB Barcelona. The voice behind Phase Space Invaders, the keystrokes behind Gromologist, the molecular cameraman behind Molywood. 🇵🇱❤️🇺🇦
Episode 29 of the Phase Space Invaders #podcast features Jérôme Hénin @jerome-henin.bsky.social! Give it a listen on Spotify or other podcasting platforms: open.spotify.com/episode/23q9...
Episode 29 - Jérôme Hénin: Free energy methods, building useful software, and human learning from biomolecular systems
Phase Space Invaders (ψ) · Episode
open.spotify.com
April 22, 2025 at 1:32 PM
Episode 29 of the Phase Space Invaders #podcast features Jérôme Hénin @jerome-henin.bsky.social! Give it a listen on Spotify or other podcasting platforms: open.spotify.com/episode/23q9...
Another episode of Phase Space Invaders is out, and today, my guest number 28 is Yuji Sugita! You can find the #podcast on all platforms, including Spotify and Apple Podcasts: buzzsprout.com/2313153
In the conversation, we cover the birth of replica exchange simulations, ...
In the conversation, we cover the birth of replica exchange simulations, ...
Phase Space Invaders (ψ)
With the convergence of data, computing power, and new methods, computational biology is at its most exciting moment. At PSI, we're asking the leading researchers in the field to discover where we're ...
buzzsprout.com
April 15, 2025 at 8:54 AM
Another episode of Phase Space Invaders is out, and today, my guest number 28 is Yuji Sugita! You can find the #podcast on all platforms, including Spotify and Apple Podcasts: buzzsprout.com/2313153
In the conversation, we cover the birth of replica exchange simulations, ...
In the conversation, we cover the birth of replica exchange simulations, ...
Phase Space Invaders' episode 27 is now online, featuring Kresten Lindorff-Larsen @lindorfflarsen.bsky.social! Listen to it on Spotify or other platforms: www.buzzsprout.com/2313153
Phase Space Invaders (ψ)
With the convergence of data, computing power, and new methods, computational biology is at its most exciting moment. At PSI, we're asking the leading researchers in the field to discover where we're headed for, and which exciting pathways will ta...
www.buzzsprout.com
March 25, 2025 at 11:25 AM
Phase Space Invaders' episode 27 is now online, featuring Kresten Lindorff-Larsen @lindorfflarsen.bsky.social! Listen to it on Spotify or other platforms: www.buzzsprout.com/2313153
Phase Space Invaders episode 26 is here, and this week I'm talking to Pratyush Tiwary! Listen to the podcast on Spotify or your favorite app: www.buzzsprout.com/2313153
Phase Space Invaders (ψ)
With the convergence of data, computing power, and new methods, computational biology is at its most exciting moment. At PSI, we're asking the leading researchers in the field to discover where we're ...
www.buzzsprout.com
March 18, 2025 at 11:33 AM
Phase Space Invaders episode 26 is here, and this week I'm talking to Pratyush Tiwary! Listen to the podcast on Spotify or your favorite app: www.buzzsprout.com/2313153
Reposted by Miłosz Wieczór
#PCBCommunity |🍰 Aquest matí, els #PCBakers han celebrat l’ #Endorfest en suport de la investigació per l’ #endometriosi, una malaltia ginecològica que afecta el 10% de les dones en edat fèrtil a Espanya🌸. Els fons recaptats es destinaran a la recerca que porta a terme @hospitalclinic.bsky.social 🤝
March 11, 2025 at 11:20 AM
#PCBCommunity |🍰 Aquest matí, els #PCBakers han celebrat l’ #Endorfest en suport de la investigació per l’ #endometriosi, una malaltia ginecològica que afecta el 10% de les dones en edat fèrtil a Espanya🌸. Els fons recaptats es destinaran a la recerca que porta a terme @hospitalclinic.bsky.social 🤝
It took a while, but... the podcast is back! In episode 25, and opening season 4 of Phase Space Invaders, my guest is Ivet Bahar - find our conversation on Spotify, or check for other platforms on Buzzsprout: www.buzzsprout.com/2313153
Phase Space Invaders (ψ)
With the convergence of data, computing power, and new methods, computational biology is at its most exciting moment. At PSI, we're asking the leading researchers in the field to discover where we're ...
www.buzzsprout.com
March 11, 2025 at 11:37 AM
It took a while, but... the podcast is back! In episode 25, and opening season 4 of Phase Space Invaders, my guest is Ivet Bahar - find our conversation on Spotify, or check for other platforms on Buzzsprout: www.buzzsprout.com/2313153
This is a great tool for blind exploration of chemical/conformational space, try it out!
New CCH highlight: GOAT: A Global Optimization Algorithm for Molecules and Atomic Clusters
www.compchemhighlights.org/2025/02/goat... #compchem
www.compchemhighlights.org/2025/02/goat... #compchem
GOAT: A Global Optimization Algorithm for Molecules and Atomic Clusters
Bernardo de Souza (2025) Highlighted by Jan Jensen If you want to predict accurate reaction energies and barrier heights of typical organic ...
www.compchemhighlights.org
March 1, 2025 at 8:50 AM
This is a great tool for blind exploration of chemical/conformational space, try it out!
Reposted by Miłosz Wieczór
Unveiling the Complete Spectrum of SARS-CoV-2 Fusion Stages by In Situ Cryo-ET https://www.biorxiv.org/content/10.1101/2025.02.25.640151v1
February 28, 2025 at 2:21 AM
Unveiling the Complete Spectrum of SARS-CoV-2 Fusion Stages by In Situ Cryo-ET https://www.biorxiv.org/content/10.1101/2025.02.25.640151v1
Impressive scaling of Gromacs!
Quite notably though, there's almost a hard performance limit at small systems sizes. With a 4fs time step, 1-1.5 microsecond/day seems to be the new standard, at which point it only makes sense to invest in more replicas
Quite notably though, there's almost a hard performance limit at small systems sizes. With a 4fs time step, 1-1.5 microsecond/day seems to be the new standard, at which point it only makes sense to invest in more replicas
🤩 Highly optimized software running on a SOA #HPC cluster provides sufficient #computing power to #simulate #biomolecular systems at the mesoscale of viruses and organelles, and potentially small cells in the near future... Want to know more? Check out our paper 📑 in #JCC 🔗 doi.org/10.1002/jcc....
February 19, 2025 at 11:28 AM
Impressive scaling of Gromacs!
Quite notably though, there's almost a hard performance limit at small systems sizes. With a 4fs time step, 1-1.5 microsecond/day seems to be the new standard, at which point it only makes sense to invest in more replicas
Quite notably though, there's almost a hard performance limit at small systems sizes. With a 4fs time step, 1-1.5 microsecond/day seems to be the new standard, at which point it only makes sense to invest in more replicas
Reposted by Miłosz Wieczór
The paper on ORCA 6’s Global Optimization Algorithm GOAT is finally published at Angewandte Chemie! Feel free to try Bernardo's (@bernadsz.bsky.social) algorithm to generate conformer ensembles and much more.
doi.org/10.1002/anie...
Tutorial on GOAT: www.faccts.de/docs/orca/6....
#ORCAqc #ChemSky
doi.org/10.1002/anie...
Tutorial on GOAT: www.faccts.de/docs/orca/6....
#ORCAqc #ChemSky
GOAT: A Global Optimization Algorithm for Molecules and Atomic Clusters
In this work, we propose a new Global Optimization Algorithm (GOAT) for molecules and clusters of atoms and show how it can find the global energy minima for both systems without resorting to molecul...
doi.org
February 19, 2025 at 9:24 AM
The paper on ORCA 6’s Global Optimization Algorithm GOAT is finally published at Angewandte Chemie! Feel free to try Bernardo's (@bernadsz.bsky.social) algorithm to generate conformer ensembles and much more.
doi.org/10.1002/anie...
Tutorial on GOAT: www.faccts.de/docs/orca/6....
#ORCAqc #ChemSky
doi.org/10.1002/anie...
Tutorial on GOAT: www.faccts.de/docs/orca/6....
#ORCAqc #ChemSky
Reposted by Miłosz Wieczór
Although barely discussed outside neurology, cerebral small vessel disease is a major aging-related driver of stroke, dementia, and disability🧠
It is a major public health concern without an available treatment📈
Huge unmet clinical need❗️
It is a major public health concern without an available treatment📈
Huge unmet clinical need❗️
February 17, 2025 at 6:33 PM
Although barely discussed outside neurology, cerebral small vessel disease is a major aging-related driver of stroke, dementia, and disability🧠
It is a major public health concern without an available treatment📈
Huge unmet clinical need❗️
It is a major public health concern without an available treatment📈
Huge unmet clinical need❗️
Incredible that whenever an otherwise user-friendly service gets taken over by @microsoft.com, it turns into hell on Earth. And it's literally every single one of them - that takes dedication! 🧐
February 12, 2025 at 8:50 PM
Incredible that whenever an otherwise user-friendly service gets taken over by @microsoft.com, it turns into hell on Earth. And it's literally every single one of them - that takes dedication! 🧐
Reposted by Miłosz Wieczór
This isn't a surprising but it is devastating.
The great betrayal of Ukraine begins.
We, in Europe, are in a place of danger.
We all owe Ukraine & its people a debt of gratitude for its extraordinary courage. 😢
The great betrayal of Ukraine begins.
We, in Europe, are in a place of danger.
We all owe Ukraine & its people a debt of gratitude for its extraordinary courage. 😢
February 12, 2025 at 5:45 PM
This isn't a surprising but it is devastating.
The great betrayal of Ukraine begins.
We, in Europe, are in a place of danger.
We all owe Ukraine & its people a debt of gratitude for its extraordinary courage. 😢
The great betrayal of Ukraine begins.
We, in Europe, are in a place of danger.
We all owe Ukraine & its people a debt of gratitude for its extraordinary courage. 😢
Reposted by Miłosz Wieczór
Who's going to #BPS2025?
Please join us at the MGO Symposium @mgo-bps.bsky.social on Saturday 1:30 pm Room 511ABC
Featuring experiments, simulations, and all the scales by
@serenasanulli.bsky.social @melikel.bsky.social
@maristizabal.bsky.social @janhuemar.bsky.social and more
Please repost! 🚀✨
Please join us at the MGO Symposium @mgo-bps.bsky.social on Saturday 1:30 pm Room 511ABC
Featuring experiments, simulations, and all the scales by
@serenasanulli.bsky.social @melikel.bsky.social
@maristizabal.bsky.social @janhuemar.bsky.social and more
Please repost! 🚀✨
February 7, 2025 at 10:33 AM
Who's going to #BPS2025?
Please join us at the MGO Symposium @mgo-bps.bsky.social on Saturday 1:30 pm Room 511ABC
Featuring experiments, simulations, and all the scales by
@serenasanulli.bsky.social @melikel.bsky.social
@maristizabal.bsky.social @janhuemar.bsky.social and more
Please repost! 🚀✨
Please join us at the MGO Symposium @mgo-bps.bsky.social on Saturday 1:30 pm Room 511ABC
Featuring experiments, simulations, and all the scales by
@serenasanulli.bsky.social @melikel.bsky.social
@maristizabal.bsky.social @janhuemar.bsky.social and more
Please repost! 🚀✨
I got DeepSeek to give a decent and objective summary of the various takes on Taiwan's legal status, and when it finished, it immediately switched to "Sorry, that's beyond my current scope. Let’s talk about something else." Looks like a cheap censorship patch added at post-inference 🙃
January 28, 2025 at 11:46 AM
I got DeepSeek to give a decent and objective summary of the various takes on Taiwan's legal status, and when it finished, it immediately switched to "Sorry, that's beyond my current scope. Let’s talk about something else." Looks like a cheap censorship patch added at post-inference 🙃
In my latest podcast commentary, I was arguing our field needs initiatives like this one: journalclub.io
It's harder and harder to catch up with the literature, and AI summaries are still not good enough, but I'd genuinely pay a small fee to have a weekly review of coolest papers in biophysics 🙌
It's harder and harder to catch up with the literature, and AI summaries are still not good enough, but I'd genuinely pay a small fee to have a weekly review of coolest papers in biophysics 🙌
Journal Club: The latest academic research explained in plain English.
Journal Club is a premium daily newsletter and podcast authored and hosted by Malcolm Diggs. Each episode is lovingly crafted by hand, and delivered to your inbox every morning in text and audio form.
journalclub.io
January 18, 2025 at 1:36 PM
In my latest podcast commentary, I was arguing our field needs initiatives like this one: journalclub.io
It's harder and harder to catch up with the literature, and AI summaries are still not good enough, but I'd genuinely pay a small fee to have a weekly review of coolest papers in biophysics 🙌
It's harder and harder to catch up with the literature, and AI summaries are still not good enough, but I'd genuinely pay a small fee to have a weekly review of coolest papers in biophysics 🙌
Reposted by Miłosz Wieczór
📢 Our new paper in #SciAdv on #Bayesian electron density determination from single-molecule #X-ray scattering is out! 🧐 High resolutions can be achieved from #XFEL exp at low S/N ratios using less than 50 #photons per image! 🔗https://www.science.org/doi/10.1126/sciadv.adp4425 @mpi-nat.bsky.social
January 10, 2025 at 12:10 PM
Reposted by Miłosz Wieczór
Looking to curate your own private feed that also helps you discover new voices? I highly recommend the DISCOVER feed. You can mark what kind of posts you like and don't like by clicking on 3 dots at bottom right. Thanks @why.bsky.team!
More: publish.obsidian.md/debbieohi/cu...
#BlueSkyTips
More: publish.obsidian.md/debbieohi/cu...
#BlueSkyTips
January 7, 2025 at 2:35 PM
Looking to curate your own private feed that also helps you discover new voices? I highly recommend the DISCOVER feed. You can mark what kind of posts you like and don't like by clicking on 3 dots at bottom right. Thanks @why.bsky.team!
More: publish.obsidian.md/debbieohi/cu...
#BlueSkyTips
More: publish.obsidian.md/debbieohi/cu...
#BlueSkyTips
With the end of season 3, I'm summarizing the last 8 conversations at Phase Space Invaders to capture the most inspiring bits from each interview, and looking back at a whole year of recording. Listen on Spotify or any other platform: www.buzzsprout.com/2313153
Phase Space Invaders (ψ)
With the convergence of data, computing power, and new methods, computational biology is at its most exciting moment. At PSI, we're asking the leading researchers in the field to discover where we're ...
www.buzzsprout.com
January 7, 2025 at 12:04 PM
With the end of season 3, I'm summarizing the last 8 conversations at Phase Space Invaders to capture the most inspiring bits from each interview, and looking back at a whole year of recording. Listen on Spotify or any other platform: www.buzzsprout.com/2313153
Reposted by Miłosz Wieczór
Molecular simulations or AI models produce ever larger and more complex datasets. Comparing different conditions to find meaningful patterns is a bottleneck for many projects.
We address this with PENSA, a flexible open-source analysis library.
Now out in JCP:
doi.org/10.1063/5.02...
🧪 #CompChem
We address this with PENSA, a flexible open-source analysis library.
Now out in JCP:
doi.org/10.1063/5.02...
🧪 #CompChem
Systematic analysis of biomolecular conformational ensembles with PENSA
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system
doi.org
January 7, 2025 at 9:07 AM
Molecular simulations or AI models produce ever larger and more complex datasets. Comparing different conditions to find meaningful patterns is a bottleneck for many projects.
We address this with PENSA, a flexible open-source analysis library.
Now out in JCP:
doi.org/10.1063/5.02...
🧪 #CompChem
We address this with PENSA, a flexible open-source analysis library.
Now out in JCP:
doi.org/10.1063/5.02...
🧪 #CompChem
Reposted by Miłosz Wieczór
Favourite paper of 2016
"Design and synthesis of a minimal bacterial genome" by Hutchison et al. (1/3)
www.science.org/doi/10.1126/...
"Design and synthesis of a minimal bacterial genome" by Hutchison et al. (1/3)
www.science.org/doi/10.1126/...
January 7, 2025 at 11:02 AM
Favourite paper of 2016
"Design and synthesis of a minimal bacterial genome" by Hutchison et al. (1/3)
www.science.org/doi/10.1126/...
"Design and synthesis of a minimal bacterial genome" by Hutchison et al. (1/3)
www.science.org/doi/10.1126/...
Wrapping up the year 📆, and season 3, at Phase Space Invaders is my conversation with Katarzyna Marcinkiewicz, a senior editor at Nature Communications @naturecomms.bsky.social! Listen to episode 24 🎧 on Spotify and other podcasting platforms: www.buzzsprout.com/2313153
Phase Space Invaders (ψ)
With the convergence of data, computing power, and new methods, computational biology is at its most exciting moment. At PSI, we're asking the leading researchers in the field to discover where we're ...
www.buzzsprout.com
December 30, 2024 at 10:34 AM
Wrapping up the year 📆, and season 3, at Phase Space Invaders is my conversation with Katarzyna Marcinkiewicz, a senior editor at Nature Communications @naturecomms.bsky.social! Listen to episode 24 🎧 on Spotify and other podcasting platforms: www.buzzsprout.com/2313153
The best environment for tool dev is when your labmates come up with ridiculous requests like "hey I want to turn off the attractive part of LJ between these two base pairs only". Turns out that's just 5 minutes of scripting with Gromologist 🧙♂️
December 20, 2024 at 1:37 PM
The best environment for tool dev is when your labmates come up with ridiculous requests like "hey I want to turn off the attractive part of LJ between these two base pairs only". Turns out that's just 5 minutes of scripting with Gromologist 🧙♂️
Looking back at 2024, I guess no scientific achievement comes close to finally configuring the institutional VPN on Ubuntu 🧑🔧
December 19, 2024 at 6:00 PM
Looking back at 2024, I guess no scientific achievement comes close to finally configuring the institutional VPN on Ubuntu 🧑🔧
The latest episode 23 of Phase Space Invaders features Zoe Cournia as a guest! Find it on Spotify or other platforms: www.buzzsprout.com/2313153
Phase Space Invaders (ψ)
With the convergence of data, computing power, and new methods, computational biology is at its most exciting moment. At PSI, we're asking the leading researchers in the field to discover where we're ...
www.buzzsprout.com
December 17, 2024 at 10:13 AM
The latest episode 23 of Phase Space Invaders features Zoe Cournia as a guest! Find it on Spotify or other platforms: www.buzzsprout.com/2313153