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

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

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

🔬 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. #MolecularDynamics #CellBiology #MolecularBiology

✍️ I write for the Asian Scientist Magazine https://www.asianscientist.com/2023/07/in-the-lab/a-new-ultrafast-camera-captures-molecular-dynamics-in-cells/

#theochem #moleculardynamics #research #recherche
(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: https://videos.univ-grenoble-alpes.fr/video/27179-a_legrand_01_06_23_orgmodemp4/

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

Important work to unite simulation and experimental data from Kolloff and Olsson. Also, a beautifully written and illustrated manuscript. #biophysics #MolecularDynamics #NMR #proteins #disulfides

https://www.biorxiv.org/content/10.1101/2023.05.23.541878v1?rss=1

Cuando vas a actualizar un software y no compila, falla una librería. Voy a compilar la librería y no compila, falla el CMake, voy a compilar el CMake, si falla voy derecho a compilar un nuevo kernel #programación #programming #fortran #gcc #cmake #moleculardynamics

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!
https://www.sciencedirect.com/science/article/pii/S0969212623000965

#ionchannels #glutamate #MolecularDynamics #electrophysiology #receptors

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

Mechanism of Calcium Permeation in a #Glutamate Receptor #IonChannel #MolecularDynamics #QMMM

https://pubs.acs.org/doi/10.1021/acs.jcim.2c01494

Vol63 Issue4 #JCIM #compchem
#biophysics

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

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: https://www.nature.com/articles/s41467-020-14573-w). In contrast, the multisite model is accurate in energy and validated in hydration statistics.

https://chemrxiv.org/engage/chemrxiv/article-details/631f1665faf4a4165e0f0d5f

#biophysics #GlutamateReceptors #MolecularDynamics #dynion #Electrophysiology #ionchannels #calcium

Free link (50 days) to the final version of our paper about monovalent ion permeation in NaK mutants emulating glutamate receptor selectivity filters https://authors.elsevier.com/a/1gYpQ54HFRkZC

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

https://www.biorxiv.org/content/10.1101/2022.08.08.502946v2

#biophysics #ionchannels #selectivity #Crystallography #MolecularDynamics #Electrophysiology

#compchem #simulation #moleculardynamics #materialmechanics

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): https://sciencedirect.com/science/article/pii/S001046552300019X?via%3Dihub
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.

@academicjobs

#Job offer: #PostDoc Position “#Stress transmission and #fracture in #collagen #networks” in Univ Grenoble Alpes 🥾⛰️ ⛷️ 👩‍🔬 👨‍🔬 🇫🇷

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

https://academicpositions.com/ad/universite-grenoble-alpes/2023/post-doctoral-position-project-stress-transmission-and-fracture-in-collagen-networks-12-months/193208

#Job offer: #PostDoc Position “#Stress transmission and #fracture in #collagen #networks” in Univ Grenoble Alpes 🥾⛰️ ⛷️ 👩‍🔬 👨‍🔬 🇫🇷

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

https://euraxess.ec.europa.eu/jobs/64194

Our article on the asymmetry of hybrid selectivity filters is online. Unfortunately access to this version is restricted. https://www.sciencedirect.com/science/article/abs/pii/S0022283623000268

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

https://www.biorxiv.org/content/10.1101/2022.08.08.502946v2

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

Gabriel Pérez is talking about #DepletionForces in #colloids and numerical #MolecularDynamics simulations. #Physics #StatisticalPhysics.

For all things Molecular Dynamics tutorial and best practices, go here: https://livecomsjournal.org/index.php/livecoms/index
#compchem #moleculardynamics #computationalchemistry #science

#deeplearning -assisted sampling for #moleculardynamics
https://pubs.acs.org/doi/10.1021/acs.jcim.2c01213?utm_source=SendGrid_ealert&utm_medium=ealert&utm_campaign=ASAP_jcisd8_v0_i0

Excited to share our latest #preprint from a collab with the Dodani group at #UTDallas - discovery supported by #moleculardynamics of a #FluorescentProteins #sulfate #sensor https://chemrxiv.org/engage/chemrxiv/article-details/63a223bab9c5f65de5da502f . Second paper from our group and the first as a collaboration!

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 #iteachphysics or #MolecularDynamics or #Biophysics folks, but really anyone!

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 #iteachphysics or #MolecularDynamics or #Biophysics folks, but really anyone!