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Reinier de Vries

@reinierdevries.bsky.social
106 followers 170 following 4 posts

PhD student in the Computational Biomolecular Dynamics group at the Max Planck Institute for Multidisciplinary Sciences | Molecular Dynamics | Potassium Channels

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Reposted by Reinier de Vries
Reinier de Vries @reinierdevries.bsky.social · 19/08/2025
New preprint: www.biorxiv.org/content/10.1... We used molecular dynamics simulations and solid-state NMR (@fmp-berlin.de) to look at calcium binding to the pore domain of the calcium-gated K+ channel MthK. @wojciechkopec.bsky.social @compbiophys.bsky.social
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Reinier de Vries @reinierdevries.bsky.social · 19/08/2025
New preprint: www.biorxiv.org/content/10.1... We used molecular dynamics simulations and solid-state NMR (@fmp-berlin.de) to look at calcium binding to the pore domain of the calcium-gated K+ channel MthK. @wojciechkopec.bsky.social @compbiophys.bsky.social
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Reposted by Reinier de Vries
Chenggong惠成功 @chenggonghui.bsky.social · 17/08/2025
Come to my talk on ACS Fall 2025 about K+ channel ECC force field on 19 Aug😏 We also have our new developed GCMC FEP with benchmark.😉 #acsfall2025
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Reposted by Reinier de Vries
Wojciech Kopec @wojciechkopec.bsky.social · 05/06/2025
MscL channel opens up asymmetrically! Check out our latest story, spearheaded by my brilliant postdoc Olga pubs.acs.org/doi/10.1021/...
pubs.acs.org
Asymmetric Nature of MscL Opening Revealed by Molecular Dynamics Simulations
The bacterial mechanosensitive channel, MscL, opens in response to elevated membrane tension during osmotic shock. Some mutations, like L17A and V21A, can reduce the activation tension threshold, thus...
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Reposted by Reinier de Vries
Maxim Igaev @maxotubule.bsky.social · 03/06/2025
Excited to share our latest work in @pnas.org! Combining simulations and cryo-ET, we reveal how microtubules decide between growth and shortening. doi.org/10.1073/pnas... @maksimkalutskii.bsky.social @vladimirvolkov.bsky.social @compbiophys.bsky.social @mpi-nat.bsky.social @qmul.ac.uk @dundee.ac.uk.
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Reposted by Reinier de Vries
MPI for Multidisciplinary Sciences @mpi-nat.bsky.social · 21/05/2025
Bert de Groot, @chenggonghui.bsky.social‬, & colleagues @compbiophys.bsky.social used molecular dynamics simulations to visualize how potassium ions pass through a potassium ion channel at atomic resolution for the first time. This could help understand ion channel regulation and drug interactions.⬇️
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Reposted by Reinier de Vries
Chenggong惠成功 @chenggonghui.bsky.social · 20/05/2025
Our K+ channel force field paper is now online on PNAS www.pnas.org/doi/epub/10.... It has been a great time working with @reinierdevries.bsky.social @wojciechkopec.bsky.social , Bert de Groot here at @mpi-nat.bsky.social @compbiophys.bsky.social
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Reinier de Vries @reinierdevries.bsky.social · 20/05/2025
Happy that this is now out in @pnas.org www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Reposted by Reinier de Vries
Wojciech Kopec @wojciechkopec.bsky.social · 20/05/2025
Very happy that this story found its home at @pnas.org www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Reposted by Reinier de Vries
Weria Pezeshkian @weria-lab.bsky.social · 17/04/2025
New preprint: TS2CG version 2, building and simulating membranes with any shape and lateral organisation. We got Martini Globe, Martini Möbius strip and again mitochondrion. www.biorxiv.org/content/10.1... @cg-martini.bsky.social @janstevens.bsky.social @fabianschuhmann.bsky.social
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Reposted by Reinier de Vries
Sara Gabrielli 💻🧬 @saragabrielli.bsky.social · 15/02/2025
Recharging batteries in Sta Monica with @compbiophys.bsky.social. Come and reach us in #bps2025! (Contributions listed in the comments) @reinierdevries.bsky.social @larsvbock.bsky.social @steschuu.bsky.social @oberend.bsky.social
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Reposted by Reinier de Vries
CompBioPhys @compbiophys.bsky.social · 14/02/2025
Poster Session #bps2025 on Sunday, February 16 starting at 1:45 pm in the West Exhibit Hall including posters of Aaron, Sara @saragabrielli.bsky.social, Ole, Bartosz, Chen, Reinier plan.core-apps.com/bpsam2025/ev...
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Reposted by Reinier de Vries
CompBioPhys @compbiophys.bsky.social · 14/02/2025
We proudly present a selection of research projects from @compbiophys.bsky.social at this year's #bps2025 meeting in LA! Don't miss the oral presentations or posters being presented and find us in the program biophysics.cld.bz/BPS2025-Full...
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Reposted by Reinier de Vries
Wojciech Kopec @wojciechkopec.bsky.social · 13/02/2025
An updated version is now available, we added some Kv1.2-2.1 and KcsA simulations (in the SI), because why not :) [IV curves close to experimental ones once again] and expanded the method section quite a bit. Hopefully soon it finds its home!
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Reposted by Reinier de Vries
Wojciech Kopec @wojciechkopec.bsky.social · 12/02/2025
New preprint! My postdoc Olga looked in detail into the mechanism, energetics and kinetics of the MscL channel opening! It's asymmetric and harder than you think ;) www.biorxiv.org/content/10.1...
biorxiv.org
Asymmetric nature of MscL opening revealed by molecular dynamics simulations
We employed all-atom unbiased molecular dynamics to simulate the L17A, V21A mutant of MscL. Under a tension of 30 mN/m, the closed state adopts a funnel-like conformation. Subsequently, five chains of...
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Reposted by Reinier de Vries
Reinier de Vries @reinierdevries.bsky.social · 28/11/2024
Side by side comparison of K+ permeation in MthK using standard Charmm36m and our ECC version.
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Reinier de Vries @reinierdevries.bsky.social · 28/11/2024
Side by side comparison of K+ permeation in MthK using standard Charmm36m and our ECC version.
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Reposted by Reinier de Vries
CompBioPhys @compbiophys.bsky.social · 25/11/2024
Happy to be part of the bluesky researcher's community now! Just moved over... Looking forward to the news and views shared here! 😀
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Reposted by Reinier de Vries
Eliane Briand @ebriand.bsky.social · 22/11/2024
cup of TIP3P
3d render of a ceramic cup full of very much not to scale water molecule (space filling sphere), nearby a protein in ribbon representation, over a science paper as table.
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Reposted by Reinier de Vries
Wojciech Kopec @wojciechkopec.bsky.social · 21/11/2024
MD simulations of K+ ions permeation through the MthK potassium channel, done at +150 mV. We developed and applied optimized ion parameters within the Electronic Continuum Correction (ECC) framework. The simulated current quantitatively matches the experimental one. www.biorxiv.org/content/10.1...
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