Mathieu Linares

C'est le problème des pauvres, ils sont pas suffisamment disrupteur pour trouver des solutions contre le changement climatique.

You can now save Ultra HD (8k) resolution screenshot in VIAMD, with or without the GUI. Here illustrated on a visualization of a Moebius ring calculated with @veloxchem.bsky.social. #compchem

Come and visit us at the @veloxchem.bsky.social booth at #watoc #compchem.

Road trip to #watoc! See you there. #compchem

Hi Jean-Philip. Long time no see. Pass by the @veloxchem.bsky.social booth if you have time.

On my way to the World Association of Theoretical and Computational Chemists (WATOC) meeting in Olso.

#WATOC #CompChemSky #ChemSky

www.watoc2025.no

I am sorry but the otter is the goat skogsduva.

See you there. I'll be at the @veloxchem.bsky.social booth. Presenting our QM software as well as @viamd.bsky.social. #WATOC #compchem

Signez la pétition Sauvons le Palais de la découverte

Pour la réouverture du palais de la découverte ! chng.it/gncnBRZnTc

Frontiers | Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model VTX is an open-source molecular visualization software designed to overcome the scaling limitations of existing real-time molecular visualization software wh...

www.frontiersin.org/journals/bio...

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...

MscL channel opens up asymmetrically! Check out our latest story, spearheaded by my brilliant postdoc Olga

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

Happy #pride month! We believe that chemistry is for everyone. In the face of opposition that threatens the progress we've made, it's never been more important for us to promote equality of opportunities and make chemistry as open, inclusive and diverse as it should be: buff.ly/1dShs0l #ChemSky

See you there. I will be at the @veloxchem.bsky.social booth.

Surprisingly, the UMA (by meta) model captures the bond-breaking process in the carbon nanotube stretching test, similar to GFN2-xTB. I hadn't expected deep learning models to extrapolate over bond lengths.
#compchemsky #chemsky

Get inside a bacterial cell with this cool combination of @cg-martini.bsky.social and @viamd.bsky.social

Also check out our recent webinars on each:

🎬 Whole cell simulation with Martini ▶️ youtu.be/fvFaPgSoM90

🎬 Visual analysis of #moleculardynamics with VIAMD ▶️ youtu.be/wVENzcx0XmQ

PolyPal: A Python Package for Molecular Dynamics Simulation of Amorphous Polymers Easily tunable and processable, porous organic polymers (POPs) have found increasing utility in various applications. Molecular modeling and simulations are invaluable tools in polymer science but remain under-reported in the POP literature. Accurate modeling and simulation of these materials could boost the discovery of high-performance POPs and allow for a more thorough contribution to big data. These polymers contain free volume-promoting structural units, such as iptycenes, and exhibit high glass-transition temperatures, excellent thermal stability, and tunable functionality. However, popular transferable force fields utilized in all-atomistic molecular dynamics (MD) simulations are not fully parametrized for intrinsically porous thermoplastic materials. We present a streamlined workflow for all-atomistic MD simulations of nonporous and porous amorphous polymer materials. In conjunction with the programs ORCA, Q-Force, Assemble!, and GROMACS, a highly accessible methodology is established for force field (FF) parametrization, creation of initial configurations, and simulation of various nonporous and porous polymers. This protocol can reproduce experimental bulk densities and fractional free volume values for amorphous polymeric materials with excellent accuracy and has been made available as a Python package, called PolyPal. As an example, we present our results using PolyPal on a series of nonporous and porous polymers that were previously synthesized and experimentally characterized. FF accuracy was also validated through solid-state NMR studies. These simulations will not only open new avenues for the rational design of high-performance POPs through the contribution of improved insight but also provide a streamlined pathway for simulating previously unexplored porous polymeric materials.

Very interesting #compchem article: pubs.acs.org/doi/10.1021/...

The Q-AMOEBA (CF) Polarizable Potential We present Q-AMOEBA (CF), an enhanced version of the Q-AMOEBA polarizable model that integrates a geometry-dependent charge flux (CF) term while designed for an explicit treatment of nuclear quantum e...

#compchem New paper in J. Phys. Chem. Lett.
: "The Q-AMOEBA (CF) Polarizable Potential".
Enhanced version of the Q-AMOEBA polarizable model integrating a geometry-dependent charge flux term while designed for an explicit treatment of nuclear quantum effects.
pubs.acs.org/doi/10.1021/...

MA(R/S)TINI 3: An Enhanced Coarse-Grained Force Field for Accurate Modeling of Cyclic Peptide Self-Assembly and Membrane Interactions | Journal of Chemical Theory and Computation pubs.acs.org/doi/full/10....

Interactive visualization of @cg-martini.bsky.social bacterial cell with @viamd.bsky.social. #compchem @gromacs.bsky.social

Thanks. Looking forward to your feedback.

In addition to our website veloxchem.org, we are now opening the discussion on github, this is the place to exchange and ask questions about veloxchem (github.com/orgs/VeloxCh...). #compchem

GitHub - VTX-Molecular-Visualization/VTX Contribute to VTX-Molecular-Visualization/VTX development by creating an account on GitHub.

New publication out!
doi.org/10.1093/bioi...

VTX is open source and freely accessible for non commercial use! github.com/VTX-Molecula...

Builds available at vtx.drugdesign.fr

Happy to see ChemRxiv now has a Bluesky button! #chemsky

#compchem, I will be teaching in this workshop. Join if you want to learn about @viamd.bsky.social and @veloxchem.bsky.social

@viamd.bsky.social @veloxchem.bsky.social

New feature! You can now visualize trajectories with bond formation and breaking by checking the Recalc Bonds option. #compchem

Machine learning workflows beyond linear models in low-data regimes Data-driven methodologies are transforming chemical research by providing chemists with digital tools that accelerate discovery and promote sustainability. In this context, non-linear machine learning...

#compchem Good read: Machine learning workflows beyond linear models in low-data regimes #compchemsky doi.org/10.1039/D5SC...

The problem with most machine-based random number generators is that they’re not TRULY random, so if you need genuine randomness it is sometimes necessary to link your code to an external random process like a physical noise source or the current rate of US tariffs on a given country.

A schematic of the functioning of a ML/QM hybrid framework

When you combine #machinelearning and #compchem, you need to start worrying at the QM details within your ML architecture. We use our indirect Hamiltonian framework and pySCFAD to explore the enormous design space arxiv.org/abs/2504.01187

In the center: "ML-guided exploration of chemical & synthesis space". Around it, three axes of work: "High-throughput synthesis & analysis", "Data analysis, curation & storage", "Bayesian model".

📢 PhD offer in my group: “Active learning to accelerate discovery of multi-variate MOFs” — I'm very excited about this new project, #compchem with a strong collaboration with experimental group of Christian Serre / IMAP #chemsky

🔗 www.coudert.name/tmp/PhD_posi...