Our recent paper has been published in ACS Nano. Congratulations to my PhD student, Beatrice Geiger. # FreeDTS #mesoscale #simualtions # biomembranes pubs.acs.org/doi/10.1021/...

Bimodal Mechanical Response of Membrane Necks: Implications for the Nuclear Envelope

Among the fascinating shapes that biomembranes exhibit are stomatocytes with multiple membrane necks, found for example in nuclear membranes and open autophagosomes. These morphologies, characterized ...

pubs.acs.org

the Martini Pumpkin by my PhD student Isabell Lindahl. Too much fat though! TS2CG, Martini3, Martini @cg-martini.bsky.social

The 3rd Annual Danish Workshop on Advanced Molecular Simulation. This time in Aarhus

Anna Duncan@drannaduncan.bsky.social · 11mo ago

Registration now open for the '3rd Annual Danish Workshop on Advanced Molecular Simulation' Join us in beautiful Aarhus for a 2-day workshop on biomolecular simulations! 9-10 December 2025 Link for registration: aias.au.dk/events/show/...

I am super excited to announce that we have a tenure-track faculty position in biophysics open in the Department of Physics at Carnegie Mellon! 🧪 Interfolio link: apply.interfolio.com/174360 PLEASE, share widely across the blue skies! Let me briefly explain what we're looking for: 1/10

A new preprint from my group by my PhD student Adria: No attraction between proteins, they do not induce curvature, but they cluster on membranes. One of the reasons why mesoscale modeling matters. www.biorxiv.org/content/10.1...

Martini on top of the world ! TS2CG as a Membrane Builder | Journal of Chemical Theory and Computation pubs.acs.org/doi/10.1021/...

New collaborative preprint, Helfrich Monte Carlo Flexible Fitting: physics-based, data-driven cell-scale simulations. By Valentin J. Maurer, Marc Siggel, Jan Kosinski, Julia Mahamid www.biorxiv.org/content/10.1...

New preprint: TS2CG version 2, building and simulating membranes with any shape and lateral organisation. We got Martini Globe, Martini Möbius strip and again mitochondrion. www.biorxiv.org/content/10.1... @cg-martini.bsky.social @janstevens.bsky.social @fabianschuhmann.bsky.social

interesting preprint from Weria Pezeshkian on general material properties of membranes Lateral tension can lead to membrane neck constriction at low tension & dilation at high tensions relevant to nuclear pores, ER, mitochondria, Golgi etc www.biorxiv.org/content/10.1...

A new preprint from my group by my PhD student Beatrice Geiger. The main message: increasing tension can lead to constriction of the pore in nuclear envelope like shapes, and for larger tension, the pore dilate. www.biorxiv.org/content/10.1...

Complex mechanical response of stomatocyte morphology: Implications for the nuclear envelope.

Among the fascinating shapes that biomembranes exhibit are stomatocytes, found for example in nuclear membranes and open autophagosomes. These morphologies, characterised by a high topological genus, ...

biorxiv.org

The event concluded with a workshop on FreeDTS, but I didn’t have time to take a selfie.

The final short talk by Adria Bravo Vidal my PhD student, On the sampling of simulations of membrane shape

Now active system. Dr Dmitry Fedosov (Forschungszentrum Jülich GmbH Wilhelm Johnen StraßeStraße, Jülich Germany) is talking about: Simulations of active vesicles

Short talk by Tatiana Morozova, CNRS/Institut Pasteur, Role of the sequnce length in the coil-to-globule transition of elastin-like polypeptides

Second day, exciting talk by Prof. Cecilia Clementi (@cecclementi.bsky.social) Clementi from Free University of Berlin Berlin, Germany. Navigating protein landscapes with a machine learned transferable coarse-grained model

Great first day of the workshop! Excellent participation both onsite and online. Tomorrow, we start again at 9:00 a.m. CET with a talk from Prof. Cecilia Clementi.

And the final talk (short talk) by Leonhard Starke (Aarhus University) Pore formation in complex biological membranes

Ali Asghar Hakami Zanjani from University of Southern Denmark. Advanced Sampling Methodology for Investigating Early-Stage Amyloid Aggregation Structures.

After a small break enforced by the projector, Lorena Zuzic from Aarhus University is talking about PINning down the elevator-type mechanism of auxin transport

(Short talk) Dimitrios Kolokouris from University of Copenhagen, is talking about Investigating the role of cholesterol in regulating the SLC7 family of amino acid transporters

Now we have a 4 short talks. First, Fabian Schuhmann from my group is talking about An integrative MD model reveals protein complexes and protein distribution in mitochondria

Dr. Paulo Cesar Telles de Souza's Workshop on Mastering Parameterization in Martini3 is happening right now. Absolutely one of the most insightful talks I've attended.

Now Prof. Siewert Jan Marrink from University of Groningen Groningen, The Netherlands. Simulating entire cells with Martini

and finally the first workshop by Prof. Kresten Lindorff-Larsen from University of Copenhagen. Combining experiments and simulations: theory and practical examples for disordered proteins

First short talk by Eva Smorodina from University of Oslo. Structural modeling of antibody variant epitope specificity with complementary experimental and computational techniques.

First talk by Prof. Franca Fraternali from University College London. Uncovering antibody sequences and structures, their assembly and their conformational flexibility!

"Advances in Molecular Modeling, Copenhagen 2024" Group members getting ready to welcome the participants

Can we use cross-linking mass spectrometry data to construct mesoscale simulations with predictive power? Check out our recent paper in Angewandte Chemie, and congratulations to my postdoc @fabianschuhmann.bsky.social and all the other authors onlinelibrary.wiley.com/doi/10.1002/...

Integrative Molecular Dynamics Simulations Untangle Cross‐Linking Data to Unveil Mitochondrial Protein Distributions

Cross-linking mass spectrometry (XL-MS) enables the mapping of protein-protein interactions on the cellular level. When applied to all compartments of mitochondria, the sheer number of cross-links an...

onlinelibrary.wiley.com

FreeDTS Version 2 is now available with many updates, including OpenMP multithreading support. Easily write code and add custom functions. This release is for our workshop next week. github.com/weria-pezesh...

GitHub - weria-pezeshkian/FreeDTS: a package to simulate fluid surface and biomembranes

a package to simulate fluid surface and biomembranes - weria-pezeshkian/FreeDTS

github.com

My first post here, A postdoc position in Biophysics and Developmental Biology is available in the Doubrovinski lab, at UT Southwestern Medical Center. This project will be in collaboration with my group www.utsouthwestern.edu/research/pos...