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FJ

@farzanejp

Postdoc @data science and AI division #compchem/Molecular Dynamics/Protein Simulation #GROMACS #AI4science #chemsky #compchemsky

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17.11.2024
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Latest posts by FJ @farzanejp

A pre-print based on Nils, Francisco, and Farzaneh's work is available on the ChemRxiv: doi.org/10.26434/che...

02.06.2025 08:21 πŸ‘ 2 πŸ” 1 πŸ’¬ 0 πŸ“Œ 0
Farzaneh, Nils, Francisco, and RocΓ­o after Nils and Francisco successfully defended their MSc thesis at Chalmers.

Farzaneh, Nils, Francisco, and RocΓ­o after Nils and Francisco successfully defended their MSc thesis at Chalmers.

Congratulations to Nils and Francisco on a successful defense of their MSc thesis today at Chalmers, as well as to @farzanejp.bsky.social for the excellent supervision!

02.06.2025 08:21 πŸ‘ 8 πŸ” 1 πŸ’¬ 1 πŸ“Œ 0
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πŸ”œ Almost 1 month to go!

Join the @eurohpc-ju.bsky.social at #EuroHPCSummit2025 (18-20 March) in KrakΓ³w for 3 days of #HPC thought-provoking conversations & networking!

Register now πŸ‘‰ www.eurohpcsummit.eu

03.02.2025 11:34 πŸ‘ 10 πŸ” 4 πŸ’¬ 0 πŸ“Œ 0

We've finally defeated cancel culture. Now people only get fired for criticizing the government

23.01.2025 15:35 πŸ‘ 16910 πŸ” 2887 πŸ’¬ 82 πŸ“Œ 24
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β€˜Never seen anything like this’: Trump’s team halts NIH meetings and travel In an unprecedented move, research-grant reviews have been suspended indefinitely at the world’s largest public funder of biomedical research.

β€˜Never seen anything like this’: Trump’s team halts NIH meetings and travel www.nature.com/articles/d41...

"The uncertainty caused by the pause will be 'devastating for the scientific community', particularly for early-career researchers..."

23.01.2025 23:18 πŸ‘ 100 πŸ” 31 πŸ’¬ 5 πŸ“Œ 6
x.com

We have just moved here, and trying to get settled. Let's start with the good news of the day: Our manuscript on 'Ranking Single Fluorescent Protein-Based Calcium Biosensor Performance by Molecular Dynamics Simulations' was the #HighlightOfTheWeek by @JCIM_JCTC. x.com/JCIM_JCTC/st...

23.01.2025 18:12 πŸ‘ 8 πŸ” 3 πŸ’¬ 1 πŸ“Œ 0
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Hello EuroHPC Community!πŸ‘‹

As of today, the EuroHPC Joint Undertaking is officially on #BlueSky! πŸ¦‹

We look forward to sharing updates and insights with you here.

Follow us to stay informed on #EuroHPC developments! πŸ’»βš‘

21.01.2025 09:32 πŸ‘ 36 πŸ” 10 πŸ’¬ 7 πŸ“Œ 2
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Talking about how being #WASP postdoc and PhD feels.…
And here is the #WASP lucky ducky.

> WASP – Wallenberg AI, Autonomous Systems and Software Program #cimpchem #AI #ML #Sweden

15.01.2025 15:58 πŸ‘ 3 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
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China releases Top 100 supercomputer list for 2024: No ExaFLOPS systems mentioned, obfuscation continues Just like last year.

#China releases Top 100 #supercomputer list for 2024 with NO new systems and a minor increase in aggregate performance

No #Exascale systems mentioned, obfuscation continues

www.tomshardware.com/tech-industr...

#HPC #AI

29.12.2024 01:57 πŸ‘ 12 πŸ” 1 πŸ’¬ 1 πŸ“Œ 0
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GitHub - bytedance/Protenix: A trainable PyTorch reproduction of AlphaFold 3. A trainable PyTorch reproduction of AlphaFold 3. Contribute to bytedance/Protenix development by creating an account on GitHub.

Protenix, the AF3 reproduction made by TikTok's parent company ByteDance, is now available for commercial use with an Apache 2.0 license

13.12.2024 16:48 πŸ‘ 44 πŸ” 8 πŸ’¬ 0 πŸ“Œ 3
Vacancy ID 11821

Please repost: We have THREE open #PhD positions in theoretical #chemistry Deadline Jan 6th

Topic: Ion #transport in atomically thin #membranes made of 2D #polymers and #graphene derivatives

www.verw.tu-dresden.de/StellAus/ste...

#phdjobs #chemsky #chemjobs #phdlife #PhDposition #science #physics

11.12.2024 09:48 πŸ‘ 28 πŸ” 13 πŸ’¬ 2 πŸ“Œ 2
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From the Damnthatsinteresting community on Reddit: Google’s Willow Quantum Chip: With 105 qubits and real-time error correction, Willow solved a task in 5 minutes that would take classical supercomput... Explore this post and more from the Damnthatsinteresting community

www.reddit.com/r/Damnthatsi...

11.12.2024 10:05 πŸ‘ 1 πŸ” 1 πŸ’¬ 0 πŸ“Œ 0

Alive X πŸ˜‚πŸ˜‚πŸ˜‚πŸ˜‚ they are playing with him…

05.12.2024 14:29 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
A schematic representation of the main building blocks that are contained inside a Calculator of a range-separated architecture, that combines an evaluation of the short-range part of the potential  based on local interatomic distance information with the evaluation of the long-range part  using grids via a MeshInterpolator and a KSpaceFilter.

A schematic representation of the main building blocks that are contained inside a Calculator of a range-separated architecture, that combines an evaluation of the short-range part of the potential based on local interatomic distance information with the evaluation of the long-range part using grids via a MeshInterpolator and a KSpaceFilter.

TLDR; this is a torch implementation of Ewald, PME, P3M that is tested, accurate, versatile and reasonably fast (jax implementation underway for those who crave fast & furious). Emphasis is on the modular design.

05.12.2024 11:27 πŸ‘ 3 πŸ” 2 πŸ’¬ 1 πŸ“Œ 0
Header and author section of the preprint accompanying the release of torch-pme. Authors are 
Philip Loche
Kevin K. Huguenin-Dumittan
Melika Honarmand
Qianjun Xu
Egor Rumiantsev
Wei Bin How
Marcel F. Langer
Michele Ceriotti

Header and author section of the preprint accompanying the release of torch-pme. Authors are Philip Loche Kevin K. Huguenin-Dumittan Melika Honarmand Qianjun Xu Egor Rumiantsev Wei Bin How Marcel F. Langer Michele Ceriotti

There is a pre-print to read on the #arxiv arxiv.org/html/2412.03..., a repo to try it github.com/lab-cosmo/to..., and a wonder team to thank for it (most not yet on πŸ¦‹ sadly).

05.12.2024 11:27 πŸ‘ 6 πŸ” 2 πŸ’¬ 1 πŸ“Œ 0

Does it also include aptamers?

03.12.2024 18:00 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

The word is new to me! There are so many terms invented to describe a woman! 😐 For many people, English isn’t their first language. I know plenty of Swedish words that sound really bad in my two other languagesβ€”but it’s all fine and fun! :)

03.12.2024 17:56 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Would like to read the paper if it out.

03.12.2024 17:51 πŸ‘ 2 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
GitHub - microsoft/mattersim: MatterSim: A deep learning atomistic model across elements, temperatures and pressures. MatterSim: A deep learning atomistic model across elements, temperatures and pressures. - microsoft/mattersim

🚨Our Machine Learning Force Field Mattersim is now available! 🚨

Check it out here πŸ‘‡
msft.it/6013oBZLt

The force field is designed to be used on a vast range of temperatures and pressures, try it yourself :)

Feedback and suggestions are very welcome!

03.12.2024 17:11 πŸ‘ 81 πŸ” 25 πŸ’¬ 5 πŸ“Œ 2

It is scary! And too many dead bodies… not fun at all!

01.12.2024 01:50 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
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Cozy Christmas in DSAI division
@ chalmers uni…
researchers are training the models in peace :) #compchem #datascience

29.11.2024 21:48 πŸ‘ 4 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
Release 2.8.0 of MDAnalysis Β· MDAnalysis

We released MDAnalysis 2.8.0 πŸš€ See the blog post www.mdanalysis.org/2024/11/22/r... . Highlights: (1) all code under the GNU Lesser General Public License, (2) new Guesser API, (3) general parallelization for analysis tools, (3) DSSP analysis class, (4) more MDAKits.

27.11.2024 17:33 πŸ‘ 58 πŸ” 17 πŸ’¬ 0 πŸ“Œ 1

And why?!?!

28.11.2024 11:25 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
Chai-1 is released under an Apache 2.0 License, which means it can be used for both academic and commerical purposes, including for drug discovery.

Chai-1 is released under an Apache 2.0 License, which means it can be used for both academic and commerical purposes, including for drug discovery.

Chai-1, the open source AF3 clone, is now available with an Apache 2 license github.com/chaidiscover...

27.11.2024 16:58 πŸ‘ 77 πŸ” 23 πŸ’¬ 0 πŸ“Œ 2

The field is growing so fast!

28.11.2024 11:23 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

I still miss our Beskow(Swedish HPC at PDC) replaced by Dardel. I used it a lot for great projects πŸ˜ƒ

28.11.2024 11:22 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
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The Bigger the Better? Accurate Molecular Potential Energy Surfaces from Minimalist Neural Networks Atomistic simulations are a powerful tool for studying the dynamics of molecules, proteins, and materials on wide time and length scales. Their reliability and predictiveness, however, depend directly...

The Bigger the Better? Accurate Molecular Potential Energy Surfaces from Minimalist Neural Networks
arxiv.org/abs/2411.18121 #compchem

28.11.2024 09:45 πŸ‘ 15 πŸ” 3 πŸ’¬ 0 πŸ“Œ 0
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Had my last lecture of the semester. I’m going to miss all my students! #DataScience

28.11.2024 11:18 πŸ‘ 8 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
Two mirror imaged pictures of Samuel Jackson labelled Samuel-L-Jackson and Samuel-D-Jackson

Two mirror imaged pictures of Samuel Jackson labelled Samuel-L-Jackson and Samuel-D-Jackson

Do you know the difference between left and right?

If not, don't worry, some proteins don't either.

Check out ultra cool work from my colleagues in which they compared binding of L- and D-peptides to a series of proteins and found something interesting ... 🧬🧢πŸ§ͺ

26.02.2024 20:17 πŸ‘ 70 πŸ” 10 πŸ’¬ 2 πŸ“Œ 6
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Looks like the EFMC (@euromedchem.bsky.social) and the EFMC Young Scientist Network (@youngscinet.bsky.social) are also now joining us over here. Welcome them and give them a follow, if you want to hear about their exciting activities.

28.11.2024 09:42 πŸ‘ 8 πŸ” 4 πŸ’¬ 1 πŸ“Œ 0