Ioana M. ILIE
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biosim-lab.bsky.social
Ioana M. ILIE
@biosim-lab.bsky.social
1.1K followers 190 following 19 posts
Assistant Prof. @UvA | amyloids, multiscale soft matter, computational peptide design, smart (adaptable) biomaterials, CompChem
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Reposted by Ioana M. ILIE
apnet.bsky.social
If you are interested in APNet's activities, join us by becoming a member: www.ap-net.nl/register

We are looking forward to a great year for APNet and to hopefully welcoming you to our next in-person event next year. (10/10)
Register – ap-net.nl
www.ap-net.nl
October 29, 2025 at 5:53 AM
Reposted by Ioana M. ILIE
apnet.bsky.social
We opened with our General Assembly, in which our president Ioana Ilie (@biosim-lab.bsky.social) gave an overview of APNet's mission and activities in the last year. (2/10)
October 29, 2025 at 5:53 AM
Reposted by Ioana M. ILIE
apnet.bsky.social
Ready to be a voice for Assistant Professors?

Join the APNet board! We're looking for new members e.g. in the role of secretary, community lead, social media lead, union liaison or website manager.

Make an impact with a great team. DM us or email info@ap-net.nl to learn more! #Academia #Leadership
October 6, 2025 at 2:18 PM
Reposted by Ioana M. ILIE
biosim-lab.bsky.social
Every 3 seconds, someone develops dementia.
Here, I explain how we use AI and molecular simulations to understand what happens at the nanoscale in the brain, and how that can open new avenues for prevention and treatment of Parkinson’s and other dementias.
www.eye-openers.nl/en/seethecas...
Ioana M. Ilie - When the brain forgets itself
Ioana Ilie seeks to understand and develop novel therapies against dementia-related diseases such as Parkinson’s and Alzheimer’s by using computer simulations and AI to study the proteins involved.
www.eye-openers.nl
September 22, 2025 at 7:37 AM
biosim-lab.bsky.social
Every 3 seconds, someone develops dementia.
Here, I explain how we use AI and molecular simulations to understand what happens at the nanoscale in the brain, and how that can open new avenues for prevention and treatment of Parkinson’s and other dementias.
www.eye-openers.nl/en/seethecas...
Ioana M. Ilie - When the brain forgets itself
Ioana Ilie seeks to understand and develop novel therapies against dementia-related diseases such as Parkinson’s and Alzheimer’s by using computer simulations and AI to study the proteins involved.
www.eye-openers.nl
September 22, 2025 at 7:37 AM
Reposted by Ioana M. ILIE
stephanhacker2.bsky.social
Great 1-minute eye-opener pitch by Ioana Ilie (@biosim-lab.bsky.social, video in English) on the importance of her group's research into addressing neurodegenerative diseases like #ParkinsonsDisease and #Alzheimer using computational technologies and AI!
www.eye-openers.nl/nl/seethecas...
#Chemsky
Ioana M. Ilie - Wanneer de hersenen zichzelf vergeten
Ioana Ilie probeert grip te krijgen op ziektes als dementie door gerelateerde eiwitten te bestuderen met computersimulaties en AI.
www.eye-openers.nl
September 21, 2025 at 11:26 AM
Reposted by Ioana M. ILIE
carolynbertozzi.bskyverified.social
Spread the word - we at @stanford-chemh.bsky.social are searching to fill a new junior faculty at the interface of molecular and computational science. See link below!
stanford-chemh.bsky.social Sarafan ChEM-H @stanford-chemh.bsky.social · Aug 26
Open faculty position!
We're seeking applicants for a tenure-track faculty position at the junior level (Assistant or untenured Associate Professor) with research programs that exist at the interface between molecular science and computation. Apply here: stanford.io/45MF3Qa
Open Faculty Position: Assistant or Associate (Untenured) Professor Application deadline: 11:55 PM on Wednesday, October 15, 2025 Sarafan ChEM-H is seeking candidates with research programs that exist at the interface between molecular science and computation. Click the link above to learn more & apply!
August 27, 2025 at 3:27 AM
Reposted by Ioana M. ILIE
lizbwood.bsky.social
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!
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 ...
efzu.fa.em2.oraclecloud.com
July 24, 2025 at 5:39 PM
Reposted by Ioana M. ILIE
stephanhacker2.bsky.social
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
July 9, 2025 at 9:57 AM
Reposted by Ioana M. ILIE
msmathcomp.bsky.social
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
apnet.bsky.social APNet - Assistant Professor Network Netherlands @apnet.bsky.social · Jul 7
Shape your academic future at our career development workshop for Assistant Professors (Utrecht, October 28th)

Craft a personalized career path and maximize your professional impact

Free for APNet members; €30 for external participants: docs.google.com/form...
#AssistantProfessor #AcademicChatter
July 8, 2025 at 8:21 PM
Reposted by Ioana M. ILIE
materialsadvances.rsc.org
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...
May 13, 2025 at 9:29 AM
Reposted by Ioana M. ILIE
materialsadvances.rsc.org
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...
May 2, 2025 at 9:06 AM
Reposted by Ioana M. ILIE
apnet.bsky.social
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...
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...
www.utoday.nl
April 30, 2025 at 10:48 AM
Reposted by Ioana M. ILIE
delalamo.xyz
A single python package for calculation of quality metrics like DockQ, LDDT, RMSD, & others

peppr.vant.ai
Screencap from the homepage showing various structural similarity metrics between a pose and a reference structure
April 4, 2025 at 6:32 AM
biosim-lab.bsky.social
🚨 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
April 1, 2025 at 11:57 AM
Reposted by Ioana M. ILIE
biosim-lab.bsky.social
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 - Materials Advances (RSC Publishing) DOI:10.1039/D4MA01142B
tinyurl.com
March 10, 2025 at 8:05 AM
biosim-lab.bsky.social
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 - Materials Advances (RSC Publishing) DOI:10.1039/D4MA01142B
tinyurl.com
March 10, 2025 at 8:05 AM
Reposted by Ioana M. ILIE
fabiololicato.com
🚨 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
March 6, 2025 at 3:43 PM
Reposted by Ioana M. ILIE
m-paesani.bsky.social
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
Tuning and modeling nanoparticles with flexible cores
Tunable and responsive coarse-grained models enable accurate simulations of flexible nanoparticles, especially significant in biomedical applications
pubs.aip.org
February 4, 2025 at 9:24 AM
biosim-lab.bsky.social
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
Tuning and modeling nanoparticles with flexible cores
Tunable and responsive coarse-grained models enable accurate simulations of flexible nanoparticles, especially significant in biomedical applications
pubs.aip.org
January 24, 2025 at 2:18 PM
Reposted by Ioana M. ILIE
m-paesani.bsky.social
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
January 24, 2025 at 9:33 AM
Reposted by Ioana M. ILIE
martinvoegele.bsky.social
Obituary for computational chemistry pioneer Martin Karplus in the New York Times (gift link).
#CompChem #ChemSky 🧪
www.nytimes.com/2025/01/13/s...
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.
www.nytimes.com
January 14, 2025 at 2:57 AM
biosim-lab.bsky.social
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
January 8, 2025 at 1:42 PM
Reposted by Ioana M. ILIE
rolanddunbrack.bsky.social
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...
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
January 3, 2025 at 5:39 PM
Reposted by Ioana M. ILIE
martinvoegele.bsky.social
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....
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...
pubs.acs.org
December 16, 2024 at 3:12 AM