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Mathieu Linares

@mathieulinares.bsky.social

35 followers 56 following 14 posts

Application Expert at PDC @KTH Working on the interoperability of #compchem tools. Active developer of @veloxchem.bsky.social and @viamd.bsky.social

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Materials science 44%

Engineering 21%

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Mathieu Linares @mathieulinares.bsky.social · Jun 2

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

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Reposted by Mathieu Linares

FX Coudert @nanoporous.net · Sep 4

“CrystalNets: a web app for topology determination of crystalline structures” — our latest preprint on @chemrxiv.org doi.org/10.26434/che...

User interface of the CrystalNets web app

Architecture of the CrystalNets web app, showing client-side and server-side tasks.

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Mathieu Linares @mathieulinares.bsky.social · Sep 3

Looking forward to the flat earth model. 🤪

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Mathieu Linares @mathieulinares.bsky.social · Sep 2

Kamoulox !

Reposted by Mathieu Linares

VeloxChem @veloxchem.bsky.social · Aug 7

Check out our latest paper! #compchem You will find descriptions and short examples of how VeloxChem integrates quantum chemistry with classical methods.
doi.org/10.1021/acs....

VeloxChem Quantum–Classical Interoperability for Modeling of Complex Molecular Systems

Being a program written primarily in Python that strictly adheres to modern object-oriented software engineering and parallel programming practices, VeloxChem is shown to be suitable for the development of (semi)automatized workflows that extend its scope from first-principles quantum chemical purism to hybrid quantum–classical interoperability and some degree of semiempiricism. Methods are presented for building complex systems such as metal–organic frameworks, constructing molecular mechanics and interpolation mechanics force fields, conformer searches, system solvation, determining free energies of solvation, and determining free energy profiles of reaction pathways using the empirical valence bond method. The implementations are made intuitive with opportunities for interactive plotting and 3D molecular structure illustrations through the use of Jupyter notebooks.

doi.org

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Reposted by Mathieu Linares

BioExcel CoE @bioexcelcoe.bsky.social · Aug 6

🤝 Our collaboration with other leading EU #HPC Centres of Excellence has resulted a white paper providing guidance and best practices for CoEs aiming to build their #innovation and #commercialisation capabilities

Read more: bioexcel.eu/k7b9
DOI: dx.doi.org/10.13140/RG....

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Mathieu Linares @mathieulinares.bsky.social · Jul 2

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

Reposted by Mathieu Linares

VIAMD @viamd.bsky.social · Jul 1

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

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Mathieu Linares @mathieulinares.bsky.social · Jun 22

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

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Mathieu Linares @mathieulinares.bsky.social · Jun 21

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

Reposted by Mathieu Linares

VeloxChem @veloxchem.bsky.social · Jun 21

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

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Reposted by Mathieu Linares

Jean-Philip Piquemal @jppiquem.bsky.social · Jun 21

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

#WATOC #CompChemSky #ChemSky

www.watoc2025.no

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Mathieu Linares @mathieulinares.bsky.social · Jun 18

I am sorry but the otter is the goat skogsduva.

Mathieu Linares @mathieulinares.bsky.social · Jun 18

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

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Reposted by Mathieu Linares

Élise Duboué-Dijon @elisedd.bsky.social · Jun 13

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

Signez la pétition

Sauvons le Palais de la découverte

chng.it

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Reposted by Mathieu Linares

Matthieu Montes @matthieumontes.bsky.social · Jun 9

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

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

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Reposted by Mathieu Linares

Wojciech Kopec @wojciechkopec.bsky.social · Jun 5

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

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

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Mathieu Linares @mathieulinares.bsky.social · Jun 4

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

Reposted by Mathieu Linares

Xin@QuantumChem @xinquantum.bsky.social · Jun 4

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

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Reposted by Mathieu Linares

Royal Society of Chemistry @rsc.org · Jun 4

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

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Mathieu Linares @mathieulinares.bsky.social · Jun 4

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

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.

pubs.acs.org

Reposted by Mathieu Linares

Jean-Philip Piquemal @jppiquem.bsky.social · Jun 3

#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/...

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...

pubs.acs.org

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Reposted by Mathieu Linares

Siewert-Jan Marrink @cg-martini.bsky.social · Jun 3

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....

pubs.acs.org

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Mathieu Linares @mathieulinares.bsky.social · May 28

Thanks. Looking forward to your feedback.

Reposted by Mathieu Linares

VeloxChem @veloxchem.bsky.social · May 27

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

veloxchem.org

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Reposted by Mathieu Linares

Matthieu Montes @matthieumontes.bsky.social · May 14

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

GitHub - VTX-Molecular-Visualization/VTX

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

github.com

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Reposted by Mathieu Linares

Jan H. Jensen @janhjensen.bsky.social · Apr 28

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

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Mathieu Linares @mathieulinares.bsky.social · Apr 25

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

LUMIhpc @lumi-supercomputer.eu · Apr 25

🔬 Into quantum chemistry + HPC?
Join the VeloxChem on LUMI Workshop — 26–27 May 2025 in Espoo, Finland!
💡 Learn to:
Run VeloxChem via Jupyter
Scale jobs on LUMI's GPUs with Slurm
Analyze results with VIAMD

Info + signup 👉 lumi-supercomputer.eu/events/velox...
lumi-supercomputer.eu/events/velox...

Mathieu Linares @mathieulinares.bsky.social · Apr 25

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

Reposted by Mathieu Linares

LUMIhpc @lumi-supercomputer.eu · Apr 25

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