Pierre de Buyl · @pdebuyl
70 followers · 34 posts · Server fediscience.org

That's it, I finally updated tidynamics to use pyproject.toml (+GitHub actions to replace travis + + + update) This means that version 1.1.2 does not support Python 2 anymore.

tidynamics is a library to compute correlations and mean-square displacements for and simulations.

See lab.pdebuyl.be/tidynamics/ pypi.org/project/tidynamics/

#moleculardynamics #stochastic #python #numpy #sphinx #condaforge #pypi

Last updated 1 year ago

Sachin Rawat · @sachinxr
395 followers · 65 posts · Server mas.to

🔬 In recent years, scientists have developed sophisticated tools to look inside living cells in ever-finer detail. However, these images are generally frozen in time and capture only a slice of the dynamic and messy reality.

📸 Kyoto University researchers have developed a method to visualize cellular dynamics down to the level of single molecules.

✍️ I write for the Asian Scientist Magazine asianscientist.com/2023/07/in-

#molecularBiology #cellbiology #moleculardynamics

Last updated 1 year ago

Enthalpiste · @Bibobu
245 followers · 452 posts · Server mastodon.xyz


(copie d'un post twitter)
Je suis les séminaires de recherche reproductible et cette conf de @arnaudlegrand17
sur Org mode et les cahiers de labo est très cool: videos.univ-grenoble-alpes.fr/

Bon moi je suis sur neovim mais les remarques sur jupyter, RStudio et l'apparition des normes sont (très) pertinentes.

#theochem #moleculardynamics #research #recherche

Last updated 1 year ago

Andrew Plested · @andrewplested
245 followers · 806 posts · Server mstdn.science

Important work to unite simulation and experimental data from Kolloff and Olsson. Also, a beautifully written and illustrated manuscript.

biorxiv.org/content/10.1101/20

#biophysics #moleculardynamics #NMR #proteins #disulfides

Last updated 1 year ago

Santiago · @santiago
2802 followers · 11744 posts · Server mastodon.uy

Cuando vas a actualizar un software y no compila, falla una librerĂ­a. Voy a compilar la librerĂ­a y no compila, falla el CMake, voy a compilar el CMake, si falla voy derecho a compilar un nuevo kernel

#moleculardynamics #cmake #gcc #fortran #programming #programacion

Last updated 2 years ago

Andrew Plested · @andrewplested
241 followers · 707 posts · Server mstdn.science

Molecular dynamics simulations of the dimer of AMPA-type glutamate receptor binding domains from DE Shaw and colleagues. Seems to confirm some of our earlier functional work on desensitization (including one of the first mutants we published in 2012!), and also the transient encounters of glutamate on its way to the binding site. 190 µs of simulations!
sciencedirect.com/science/arti

#IonChannels #glutamate #moleculardynamics #electrophysiology #receptors

Last updated 2 years ago

Andrew Plested · @andrewplested
237 followers · 668 posts · Server mstdn.science

Quantum mechanics of hydrated calcium in GluA2! Fun Collaboration as part of the @dfg_public research group.

Mechanism of Calcium Permeation in a Receptor

pubs.acs.org/doi/10.1021/acs.j

Vol63 Issue4

#dynion #glutamate #IonChannel #moleculardynamics #QMMM #jcim #compchem #biophysics

Last updated 2 years ago

Miranda Lynch · @MirandaLynchPhD
290 followers · 279 posts · Server mathstodon.xyz

For those here at in Seattle for , I hope you had the pleasure of catching two of the most outstanding sessions on and organized by Celia Schiffer and Rommie Amaro. Both were fantastic!

#mlinstructuralbiology #moleculardynamics #compchem #aiinchem #asbmb #discoverbmb

Last updated 2 years ago

Andrew Plested · @andrewplested
231 followers · 632 posts · Server mstdn.science

Compare with simulations on AMPARs (using the multisite model) where we readily see Ca2+ permeation, and confirmed water statistics and polarisation effects with QM/MM.

In classical force fields, calcium doesn't move, it just gets stuck (see: nature.com/articles/s41467-020). In contrast, the multisite model is accurate in energy and validated in hydration statistics.

chemrxiv.org/engage/chemrxiv/a

#biophysics #moleculardynamics #dynion #electrophysiology #IonChannels #calcium #GlutamateReceptors

Last updated 2 years ago

Andrew Plested · @andrewplested
231 followers · 632 posts · Server mstdn.science

Free link (50 days) to the final version of our paper about monovalent ion permeation in NaK mutants emulating glutamate receptor selectivity filters authors.elsevier.com/a/1gYpQ54

The preprint is free for the long term (and it's quite similar):

biorxiv.org/content/10.1101/20

#biophysics #IonChannels #selectivity #crystallography #moleculardynamics #electrophysiology

Last updated 2 years ago

Enthalpiste · @Bibobu
230 followers · 380 posts · Server mastodon.xyz

I am very proud of this paper which is a follow-up to some of my thesis work to which I could finally provide a framework and integrate in LAMMPS. (3y work, mostly on my spare time): sciencedirect.com/science/arti
Thanks to Aidan to kickstart the project of writing about it.

It is an extension of Lutsko's and Van Vorkum et al. works on the computation of mechanical properties.

#compchem #simulation #moleculardynamics #materialmechanics

Last updated 2 years ago

@academicjobs

offer: Position “ transmission and in ” in Univ Grenoble Alpes 🥾⛰️ ⛷️ 👩‍🔬 👨‍🔬 🇫🇷

Join Mehdi Bouzid and myself for this project involving simulations of a network and going towards deeper understanding of how they allow –cell communication.

academicpositions.com/ad/unive

#cell #biopolymer #moleculardynamics #networks #collagen #fracture #stress #postdoc #job

Last updated 2 years ago

offer: Position “ transmission and in ” in Univ Grenoble Alpes 🥾⛰️ ⛷️ 👩‍🔬 👨‍🔬 🇫🇷

Join Mehdi Bouzid and myself for this project involving simulations of a network and going towards deeper understanding of how they allow –cell communication.

euraxess.ec.europa.eu/jobs/641

#cell #biopolymer #moleculardynamics #networks #collagen #fracture #stress #postdoc #job

Last updated 2 years ago

Andrew Plested · @andrewplested
231 followers · 632 posts · Server mstdn.science

Our article on the asymmetry of hybrid selectivity filters is online. Unfortunately access to this version is restricted. sciencedirect.com/science/arti

But the preprint has been freely available on @biorxivpreprint for a while, and will continue to be.

biorxiv.org/content/10.1101/20

It's almost the same -figures in a different order, some explanations missing, no new data.

Congrats Sonja, Saeid and Sebastian!

#IonChannels #biophysics #physiology #crystallography #moleculardynamics #electrophysiology

Last updated 2 years ago

Gustavo RodrĂ­guez Liñán · @gsrdzl
41 followers · 129 posts · Server mstdn.science

Gabriel PĂ©rez is talking about in and numerical simulations. .

#depletionforces #colloids #moleculardynamics #physics #statisticalphysics

Last updated 2 years ago

Dr Anthony Nash · @acnash
8 followers · 3 posts · Server mastodon.social
alexeyorlov · @alexeyorlov
62 followers · 1 posts · Server qoto.org
Alice Walker · @arwalker_on_gpu
75 followers · 52 posts · Server fediscience.org

Excited to share our latest from a collab with the Dodani group at - discovery supported by of a chemrxiv.org/engage/chemrxiv/a . Second paper from our group and the first as a collaboration!

#sensor #sulfate #FluorescentProteins #moleculardynamics #UTDallas #preprint

Last updated 2 years ago

Michael G. Lerner · @mglerner
137 followers · 35 posts · Server mastodon.cloud

I'm giving a talk about my research to an AP physics class on Monday. I've never done that before! Any advice from anyone? I'm thinking or or folks, but really anyone!

#iteachphysics #moleculardynamics #biophysics

Last updated 2 years ago

Michael G. Lerner · @mglerner
193 followers · 64 posts · Server mastodon.cloud

I'm giving a talk about my research to an AP physics class on Monday. I've never done that before! Any advice from anyone? I'm thinking or or folks, but really anyone!

#iteachphysics #moleculardynamics #biophysics

Last updated 2 years ago