Reinier de Vries
@reinierdevries.bsky.social
PhD student in the Computational Biomolecular Dynamics group at the Max Planck Institute for Multidisciplinary Sciences | Molecular Dynamics | Potassium Channels
Reposted by Reinier de Vries
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
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
August 19, 2025 at 7:42 AM
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
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
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
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
August 19, 2025 at 7:42 AM
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
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
Reposted by Reinier de Vries
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
We also have our new developed GCMC FEP with benchmark.😉
#acsfall2025
August 17, 2025 at 5:03 PM
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
We also have our new developed GCMC FEP with benchmark.😉
#acsfall2025
Reposted by Reinier de Vries
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/doi/10.1021/...
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...
pubs.acs.org
June 5, 2025 at 4:07 PM
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/doi/10.1021/...
Reposted by Reinier de Vries
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.
June 3, 2025 at 9:08 AM
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.
Reposted by Reinier de Vries
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.⬇️
May 21, 2025 at 7:32 AM
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.⬇️
Reposted by Reinier de Vries
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
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
May 20, 2025 at 7:34 PM
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
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
May 20, 2025 at 6:29 PM
Reposted by Reinier de Vries
May 20, 2025 at 6:23 PM
Reposted by Reinier de Vries
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
www.biorxiv.org/content/10.1...
@cg-martini.bsky.social @janstevens.bsky.social @fabianschuhmann.bsky.social
April 17, 2025 at 5:57 PM
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
www.biorxiv.org/content/10.1...
@cg-martini.bsky.social @janstevens.bsky.social @fabianschuhmann.bsky.social
Reposted by Reinier de Vries
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
@reinierdevries.bsky.social
@larsvbock.bsky.social
@steschuu.bsky.social @oberend.bsky.social
February 15, 2025 at 2:59 AM
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
@reinierdevries.bsky.social
@larsvbock.bsky.social
@steschuu.bsky.social @oberend.bsky.social
Reposted by Reinier de Vries
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...
plan.core-apps.com/bpsam2025/ev...
February 14, 2025 at 2:09 PM
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...
plan.core-apps.com/bpsam2025/ev...
Reposted by Reinier de Vries
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...
February 14, 2025 at 2:09 PM
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...
Reposted by Reinier de Vries
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!
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...
www.biorxiv.org/content/10.1...
February 13, 2025 at 1:55 PM
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!
Reposted by Reinier de Vries
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
February 12, 2025 at 6:28 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Reinier de Vries
Side by side comparison of K+ permeation in MthK using standard Charmm36m and our ECC version.
November 28, 2024 at 4:34 PM
Side by side comparison of K+ permeation in MthK using standard Charmm36m and our ECC version.
Side by side comparison of K+ permeation in MthK using standard Charmm36m and our ECC version.
November 28, 2024 at 4:34 PM
Side by side comparison of K+ permeation in MthK using standard Charmm36m and our ECC version.
Reposted by Reinier de Vries
Happy to be part of the bluesky researcher's community now! Just moved over... Looking forward to the news and views shared here! 😀
November 25, 2024 at 10:25 AM
Happy to be part of the bluesky researcher's community now! Just moved over... Looking forward to the news and views shared here! 😀
Reposted by Reinier de Vries
Reposted by Reinier de Vries
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...
www.biorxiv.org/content/10.1...
November 21, 2024 at 8:12 AM
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...
www.biorxiv.org/content/10.1...