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Ioana M. ILIE

@biosim-lab.bsky.social
1.2K followers 194 following 20 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 - Assistant Professor Network Netherlands @apnet.bsky.social · 19/06/2026
Congratulations to former APNet president, Ioana Ilie (@biosim-lab.bsky.social) on winning the NextGenChem Award of NEXTGENCHEM@NL. Ioana is awarded not only for her excellent research and teaching, but also for her unwavering commitment to supporting the community.
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Stephan Hacker @stephanhacker2.bsky.social · 19/06/2026
Exciting news that Ioana Ilie (@biosim-lab.bsky.social) was awarded the inaugural NextGenChem Award by NextGenChem@NL. Ioana's commitment to excellent research and teaching and her engagement to build and support a community of young group leaders in NL is truly exemplary. Huge Congratulations!
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Ioana M. ILIE @biosim-lab.bsky.social · 01/03/2026
We uncover the physical mechanisms governing nanoparticle–membrane interactions using coarse-grained simulations, mapping distinct regimes from adhesion to wrapping. A step toward predictive design rules for nanomedicine & adaptive materials pubs.aip.org/aip/jcp/arti...
pubs.aip.org
Physical mechanisms of nanoparticle–membrane interactions: A coarse-grained study
Nanoparticles are promising drug carriers for targeted therapies, diagnostic imaging, and advanced vaccines. However, their clinical translation is limited by c
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Reposted by Ioana M. ILIE
Ioana M. ILIE @biosim-lab.bsky.social · 22/09/2025
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...
eye-openers.nl
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.
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Reposted by Ioana M. ILIE
APNet - Assistant Professor Network Netherlands @apnet.bsky.social · 03/12/2025
Today we had the ceremonial handover of the keys to APNet from our previous president, Ioana Ilie (@biosim-lab.bsky.social), to our new president, @stephanhacker2.bsky.social! (1/3) #AssistantProfessor #Network #Keys
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Stephan Hacker @stephanhacker2.bsky.social · 03/12/2025
Thank you so much, Ioana Ilie (@biosim-lab.bsky.social), for coming up with this cool tradition of handing over the keys to APNet. I will do my best to follow the great example that you set for the engagement and excitement of president of @apnet.bsky.social and will keep this amazing new tradition.
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Stephan Hacker @stephanhacker2.bsky.social · 03/12/2025
#NWOCHAINS comes to an end with the closing ceremony led by Ioana Ilie (@biosim-lab.bsky.social)! I had two days of exciting science and learned a lot. Thank you to everyone, who was involved in organizing and who contributed to the program. Congratulations to all winners of the poster prizes!
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Stephan Hacker @stephanhacker2.bsky.social · 02/12/2025
The scientific program of #NWOCHAINS starts with the opening words by Sandra de Keijzer, head of NWO Chemistry and Physics, and Ioana Ilie (@biosim-lab.bsky.social), chair of the programme committee of CHAINS. #ChemSky #ChemBio #Conferencing
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APNet - Assistant Professor Network Netherlands @apnet.bsky.social · 29/10/2025
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)
ap-net.nl
Register – ap-net.nl
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APNet - Assistant Professor Network Netherlands @apnet.bsky.social · 29/10/2025
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)
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APNet - Assistant Professor Network Netherlands @apnet.bsky.social · 06/10/2025
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
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Ioana M. ILIE @biosim-lab.bsky.social · 22/09/2025
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...
eye-openers.nl
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.
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Reposted by Ioana M. ILIE
Stephan Hacker @stephanhacker2.bsky.social · 21/09/2025
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
eye-openers.nl
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.
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Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 27/08/2025
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!
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Elizabeth Wood, PhD @lizbwood.bsky.social · 24/07/2025
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!
efzu.fa.em2.oraclecloud.com
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 ...
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Stephan Hacker @stephanhacker2.bsky.social · 09/07/2025
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
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Dr. Martin Skrodzki @msmathcomp.bsky.social · 08/07/2025
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
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Materials Advances @materialsadvances.rsc.org · 13/05/2025
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...
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Materials Advances @materialsadvances.rsc.org · 02/05/2025
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...
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APNet - Assistant Professor Network Netherlands @apnet.bsky.social · 30/04/2025
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...
utoday.nl
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...
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Diego del Alamo @delalamo.xyz · 04/04/2025
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
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Ioana M. ILIE @biosim-lab.bsky.social · 01/04/2025
🚨 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
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Ioana M. ILIE @biosim-lab.bsky.social · 10/03/2025
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
tinyurl.com
Computational design of Bax-inhibiting peptides - Materials Advances (RSC Publishing) DOI:10.1039/D4MA01142B
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Ioana M. ILIE @biosim-lab.bsky.social · 10/03/2025
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
tinyurl.com
Computational design of Bax-inhibiting peptides - Materials Advances (RSC Publishing) DOI:10.1039/D4MA01142B
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Fabio Lolicato @fabiololicato.com · 06/03/2025
🚨 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
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Massimiliano Paesani @m-paesani.bsky.social · 04/02/2025
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
pubs.aip.org
Tuning and modeling nanoparticles with flexible cores
Tunable and responsive coarse-grained models enable accurate simulations of flexible nanoparticles, especially significant in biomedical applications
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Ioana M. ILIE @biosim-lab.bsky.social · 24/01/2025
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
pubs.aip.org
Tuning and modeling nanoparticles with flexible cores
Tunable and responsive coarse-grained models enable accurate simulations of flexible nanoparticles, especially significant in biomedical applications
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Massimiliano Paesani @m-paesani.bsky.social · 24/01/2025
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
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Martin Vögele @martinvoegele.bsky.social · 14/01/2025
Obituary for computational chemistry pioneer Martin Karplus in the New York Times (gift link). #CompChem #ChemSky 🧪 www.nytimes.com/2025/01/13/s...
nytimes.com
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.
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Ioana M. ILIE @biosim-lab.bsky.social · 08/01/2025
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
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 03/01/2025
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 portraitMartin Karplus receiving the Nobel Prize in Chemistry, December 2013
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Martin Vögele @martinvoegele.bsky.social · 16/12/2024
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....
pubs.acs.org
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...
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APNet - Assistant Professor Network Netherlands @apnet.bsky.social · 01/01/2025
@apnet.bsky.social wishes all of you a happy and successful 2025. Let's make it an amazing year together!
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Ioana M. ILIE @biosim-lab.bsky.social · 31/12/2024
Wrapping up the year with MetaParticles on and off the cover of @JChemPhys pubs.aip.org/aip/jcp/arti... #chemsky #metaparticles
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Alex MacKerell @alexmackerell.bsky.social · 30/12/2024
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...
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Ioana M. ILIE @biosim-lab.bsky.social · 25/12/2024
Seems like we’ve been nice. Santa brought us MetaParticles right on Christmas Eve! #compchem pubs.aip.org/aip/jcp/arti...
pubs.aip.org
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
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APNet - Assistant Professor Network Netherlands @apnet.bsky.social · 23/12/2024
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)
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Olexandr Isayev 🇺🇦 🇺🇸 @olexandr.bsky.social · 16/12/2024
Here are 35 Taylor series for Taylor Swift's 35th birthday 😸 [stolen from the other platform] #scisky #mathsky #chemsky
35 Taylor series for Taylor Swift's 35th birthday
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Ioana M. ILIE @biosim-lab.bsky.social · 07/12/2024
Does anyone have recommendations for a good scientific illustrator? #compchem
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Ioana M. ILIE @biosim-lab.bsky.social · 29/11/2024
Congratulations! Well deserved, Liesbeth!
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Peter Kenny @pwk2024.bsky.social · 27/11/2024
Opportunity in chemical biology & #proteomics at Pfizer (Groton CT USA) ref: 4924293 | closing: 06-Dec-2024 #ChemBiol #biochem #chemsky 🧪 pfizer.wd1.myworkdayjobs.com/PfizerCareer...
pfizer.wd1.myworkdayjobs.com
Senior Scientist, Chemical Biology and Proteomics
Would you like to discover the medicines of the future? At Pfizer we deliver Breakthroughs That Change Patients Lives. In the Chemical Biology and Proteomics group, we play a vital role in this missio...
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Ioana M. ILIE @biosim-lab.bsky.social · 27/11/2024
Love it every time!
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APNet - Assistant Professor Network Netherlands @apnet.bsky.social · 26/11/2024
Yesterday, >20,000 students, researchers and staff protested against the devastating cuts to higher education and research in the Netherlands: No innovation without education. No progress without knowledge! To the House of Representatives and the government: DOE.HET.NIET! 🟥
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Ioana M. ILIE @biosim-lab.bsky.social · 19/11/2024
I’ve started a starter pack on peptide design. Please suggest more colleagues to be added or let me know if you want to be added. Peptides rock! go.bsky.app/QL4rSPE
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Raluca Groza @ralucag.bsky.social · 21/11/2024
great talk today here at @ethzurich.bsky.social by @biosim-lab.bsky.social about her work on alpha-synuclein aggregation modeling and cyclic peptide design for apoptosis inhibition. Always great to see fellow Romanian expats doing great science!
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Stephan Hacker @stephanhacker2.bsky.social · 21/11/2024
Great to see the community of Assistant Professors in the Netherlands growing. Check out the Starter Pack, if you want to connect, and reply to the below post, if you want to be added to the list.
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bioRxiv Bioengineering @biorxiv-bioeng.bsky.social · 31/10/2024
Computational design of Bax-inhibiting peptides www.biorxiv.org/content/10.1101/202…
biorxiv.org
Computational design of Bax-inhibiting peptides https://www.biorxiv.org/content/10.1101/2024.10.28.617283v1
The proteins in the Bcl-2 family play crucial roles in regulating apoptosis. In particular, Bax is a
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Ioana M. ILIE @biosim-lab.bsky.social · 19/11/2024
I’ve started a starter pack on peptide design. Please suggest more colleagues to be added or let me know if you want to be added. Peptides rock! go.bsky.app/QL4rSPE
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Stephan Hacker @stephanhacker2.bsky.social · 18/11/2024
If you are an Assistant Professor (or equivalent) in the Netherlands, check out @apnet.bsky.social and help us to build a strong network of Assistant professors by following our bluesky account and ideally becoming a member: ap-net.nl/register/
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APNet - Assistant Professor Network Netherlands @apnet.bsky.social · 18/11/2024
We made a (far from complete) Starter Pack of Assistant Professors in the Netherlands across all scientific disciplines: go.bsky.app/AYBAKDp If you want to be added (or removed), please reply to this post. And while you are at it, consider joining APNet: ap-net.nl/register/
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