Ioana M. ILIE

PhD scholarship in Machine Learning for Molecules - DTU Chemistry Advance large scale data generation for chemical and biological AI in a 3 year PhD. Work on the frontier of active learning, and develop novel probabilistic machine learning techniques for experiment ...

Want to work at the frontier of active learning and AI-guided experimentation? @eliweinstein.bsky.social is hiring PhD students at @dtu.dk DTU Chemistry.

Full job link: efzu.fa.em2.oraclecloud.com/hcmUI/Candid...

Thanks for re-sharing widely!

Great discussion today at #NextGenChemLeaders by #KNCV led by Ioana Ilie (@biosim-lab.bsky.social) on building scientific partnerships that last! The focus: creating powerful, long-term consortia.

#ScientificCollaboration #ChemSky #Academia #Leadership #SciComm

Looking forward to seeing a lot of #AssistantProfessor in the Netherlands join for this event. If you're an @apnet.bsky.social member, this is a free #leadership course! Spread the word! #AcademicSky

Honored to be featured! Thank you.

Meet Ioana M. Ilie (@biosim-lab.bsky.social) #NewPrincipalInvestigator at University of Amsterdam. Learn about her current research interests and advice for those seeking to start their own group in our latest blog post: blogs.rsc.org/jm/2025/04/1...

Check out the front cover of issue 7 of @materialsadvances.rsc.org!
'Computational design of Bax-inhibiting peptides' by Ioana M. Ilie et al. @biosim-lab.bsky.social
doi.org/10.1039/D4MA...

Universitair hoofddocenten UT krijgen promotierecht Universitair hoofddocenten in vaste dienst mogen vanaf nu doctorstitels uitreiken aan promovendi. Dat maakte het College voor Promoties vandaag bekend. De verruiming in het beleid zorgt voor minder we...

Associate Professors (UHDs) and certain Assistant Professors (UDs) will get the promotion right at the University of Twente. Another step for #iedereenprofessor that strives for promotion right for all group leaders including UDs and UHDs at all Dutch universities. www.utoday.nl/news/75510/u...

Screencap from the homepage showing various structural similarity metrics between a pose and a reference structure

A single python package for calculation of quality metrics like DockQ, LDDT, RMSD, & others

peppr.vant.ai

🚨 New paper out — and it made the cover! @materialsadvances.rsc.org
We designed peptide inhibitors that bind to Bax, modulating apoptosis via MD simulations & rational design.
🧬 Check it out: tinyurl.com/BaxPep
Paving the way for ML-powered peptide design! #PeptideDesign #CompChem
tinyurl.com/BaxPep

Computational design of Bax-inhibiting peptides
Tom & Bernadette
🧩 Designed cyclic peptides to bind Bax
💡 Optimized via molecular dynamics
🖥️ Validated high-affinity binders
@materialsadvances.rsc.org

Paving the way for ML-powered peptide design! #PeptideDesign #CompChem
tinyurl.com/BaxPep

Computational design of Bax-inhibiting peptides
Tom & Bernadette
🧩 Designed cyclic peptides to bind Bax
💡 Optimized via molecular dynamics
🖥️ Validated high-affinity binders
@materialsadvances.rsc.org

Paving the way for ML-powered peptide design! #PeptideDesign #CompChem
tinyurl.com/BaxPep

🚨 Postdoc Opportunity #2 🚨

We are looking for candidates with a strong background in molecular dynamics simulations of membrane protein interactions to unravel the role of lipids in CD95 oligomerization and signaling!

Please apply by March 28!

#LipidTime @bzh-hd.bsky.social

Could you please add me?

Tuning and modeling nanoparticles with flexible cores Tunable and responsive coarse-grained models enable accurate simulations of flexible nanoparticles, especially significant in biomedical applications

Read about our MetaParticles in the recent #Scilight
pubs.aip.org/aip/sci/article/2025/4/041101/3332086

You can find my and Ioana's (@biosim-lab.bsky.social) full paper at pubs.aip.org/aip/jcp/article/161/24/244905/3328202

@justinlemkulvt.bsky.social something for you?

Tuning and modeling nanoparticles with flexible cores Tunable and responsive coarse-grained models enable accurate simulations of flexible nanoparticles, especially significant in biomedical applications

Check out the cool Metaparticles of @m-paesani.bsky.social highlighted in #Scilight
pubs.aip.org/aip/sci/arti...
Full paper: pubs.aip.org/aip/jcp/arti...
#chemsky #metaparticle #compchem #softmatter

The First paper of my PhD has been published on Journal of Chemical Physics featured on the cover of the issue, and selected for Scilight! 🤯

This research introduces MetaParticle — an adaptable, tunable model for nanoparticles.

pubs.aip.org/aip/jcp/arti...

#metaparticles

Peptides rock. Even more when they come from @olallalab.bsky.social

Martin Karplus, Chemist Who Made Early Computers a Tool, Dies at 94 (Gift Article) Proving skeptics wrong, he shared a Nobel Prize in 2013 for using computers to better understand chemical reactions and biological processes.

Obituary for computational chemistry pioneer Martin Karplus in the New York Times (gift link).
#CompChem #ChemSky 🧪
www.nytimes.com/2025/01/13/s...

To celebrate the debut of 2025, it's my pleasure to announce the next edition of our online PhD+ seminar series with talks by Clint van Hoesel from @tueindhoven.bsky.social and Fabian Lie from @utwente.bsky.social
Subscribe for the Zoom link kncv-ctc-phdplus-seminars.nl
@hybridlinn.bsky.social

Oh I was happy that my 9 am class was 80% full. I expected to be alone

Speaking with Martin Karplus on the occasion of an award to him from the Government of Austria, August 15, 2024.

Martin Karplus portrait

Martin Karplus receiving the Nobel Prize in Chemistry, December 2013

Martin Karplus died on Saturday, Dec 28 at age 94. Martin was my freshman Chem 10 professor, my undergraduate research advisor, and my PhD advisor. I will always be grateful for his true kindness to me as a mentor through some difficult times in my life. cen.acs.org/people/obitu...

Faster Sampling in Molecular Dynamics Simulations with TIP3P-F Water The need for short time steps currently limits routine atomistic molecular dynamics (MD) simulations to the microsecond time scale. For long time steps, the numerical integration of the equations of m...

José, Balázs, and Gerhard tested this idea and developed a "fast water" model that accelerates sampling by a factor of two at minimal cost in accuracy. This can save a lot of time and energy.

pubs.acs.org/doi/full/10....

@apnet.bsky.social wishes all of you a happy and successful 2025. Let's make it an amazing year together!

Wrapping up the year with MetaParticles on and off the cover of @JChemPhys
pubs.aip.org/aip/jcp/arti... #chemsky #metaparticles

SILCS-Water allows for inclusion of explicit waters during ligand docking offering improved binding affinities and poses for select systems in a computationally efficient approach. SilcsBio is hosting seminar on January 7, 2025. Please join us!

events.teams.microsoft.com/event/713bec...

Metaparticles: Computationally engineered nanomaterials with tunable and responsive properties In simulations, particles are traditionally treated as rigid platforms with variable sizes, shapes, and interaction parameters. While this representation is app

Seems like we’ve been nice. Santa brought us MetaParticles right on Christmas Eve! #compchem
pubs.aip.org/aip/jcp/arti...

APNet 2023-2024 Highlights:

New Leadership: Restructured board with @biosim-lab.bsky.social, @anouk-geologist.bsky.social, @stephanhacker2.bsky.social, @msmathcomp.bsky.social, Luisa Cortesi, @verenaseibel.bsky.social, Tessa Sinnige and Apostolos Liakopoulos. (2/7)

35 Taylor series for Taylor Swift's 35th birthday

Here are 35 Taylor series for Taylor Swift's 35th birthday 😸 [stolen from the other platform] #scisky #mathsky #chemsky

Does anyone have recommendations for a good scientific illustrator? #compchem