Can sand-like molecules help us map the secrets of protein structure?
Adsorption of silica oligomers on biomolecules: Structural and dynamical insights for atom probe tomography via classic molecular dynamics simulations. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.06.004
CSBJ: https://www.csbj.org/
Engineering Supercomputing Platforms for Biomolecular Applications
#CUDA #ROCm #Biology #Biomolecules #MolecularDynamics #HPC #Physics #Package
Our new paper "Allosteric amyloid catalysis by coiled coil fibrils" published in *Nat Commun*! https://doi.org/10.1038/s41467-025-60379-z
We studied amyloids facilitating β-lactam antibiotic hydrolysis - work done at BGU during wartime. I remember stopping mid-working to run to shelters.
Thanks to the amazing team: Elad Arad, Sisira Mambram Kunnath, Ran Zalk, Anat Shahar, Albert Batushansky, Hanna Rapaport & Raz Jelinek 
Rewrote the existing C code for a simple molecular dynamics simulation in Rust.
What a brilliant language. So clean and clear.
Fun experience. Took me 3 days. (No LLM help haha).
A great paper (https://rdcu.be/ecxKI) from the group of Prof. Buckle explaining why Ab can recognize GAD65 but does not recognize GAD67. Also, this highlight (again) that upon brigand-binding, proteins become more stable.
In addition, this paper is a beautiful example of how to combine experimental and theoretical methods for the use of proteins function or dysfunction.
Running 16 simulations in parallel is a very efficient way of making simulations.
It sucks however, that they all crash if one of them crashes.
Young Scientist Award:
Petrick Heighway
for his pivotal role in the DiPOLE-100x Community Proposals measuring #XRay #diffraction at extreme pressures and temperatures at the HED-HiBEF instrument.
Combines experimental data with #MolecularDynamics simulations to provide critical insight into the nature of release pathways of shock compressed materials, kinematics of plastisticy, …
I am shamefully copying this post from Linkedin but if you happen to know any candidate, do not hesitate to reach:
It's on. To my #ComputationalChemistry network, I am calling on you. 
The PM2E team in the CIMAP laboratory (www.cimap.ensicaen.fr) is looking for a #PhD hashtag#candidate. The goal of the project is to understand key parameters in #semiconductor defects stability and physics (both vacancies and color centers, see for example: https://doi.org/10.1016/j.nimb.2022.12.025) through the use of
#DFT and #MolecularModeling. The end goals of the project is concerned with application for #QuantumComputing through the making of stable #qubit. Collaboration and communication with experimentalists will be part of the project.
If you're interested in #MolecularDynamics, #MonteCarlo simulations, or DFT and quantum calculations, we are waiting for you. We are using codes such as #Lammps and #QuantumEspresso. We are looking for a candidate finishing or already having a master degree (or equivalent diploma) with training in #physics/ #MaterialsScience / #TheoreticalChemistry. Any experience in programming using #Python, #C and the #Linux environment would be considered a plus.
The position is located in Alençon (Orne) between Caen and Le Mans. Founding is assured for relevant candidates.
Link to the offer (in french, you can ask for an english version): https://www.abg.asso.fr/en/candidatOffres/show/id_offre/127985/job/simulation-atomistique-de-defauts-crees-par-irradiation-dans-les-semiconducteurs
Trying to get back in the #moleculardynamics bandwagon. Found a #NMR structure for a relatively small neurotoxin protein bound to a small peptide that neutralizes it. No one seems to have done any MD simulations yet. Started some sims. Maybe I’ll observe something interesting worth publishing.
Thrilled to share our new paper in PROTEINS! "Similar but Distinct-Biochemical Characterization of Staphylococcus aureus Serine Hydrolases FphH and FphI" (https://doi.org/10.1002/prot.26785) reveals key structural features of these enzymes, including flexible lids and distinct active sites. My MD simulations contributed to this work, led by Matthias Fellner. This research advances our understanding of S. aureus biofilm formation and could lead to targeted therapies.
#ProteinScience
#MolecularDynamics
Is anyone doing structure prediction with #AlphaFold3 figured out an easy way to do the relaxation step that Colabfold did? I'm looking into OpenMM and Amber, and making some progress, but it seems like it will be very difficult to make it work when phosphoresidues, ions, or anything else besides standard amino acid residues are included.
In-Situ Techniques on GPU-Accelerated Data-Intensive Applications
RBMD: A molecular dynamics package enabling to simulate 10 million all-atom particles in a single graphics processing unit
Para los que estuvieron en mi charla en la FLISoL sobre clústers de cálculo numérico, hoy largamos 729 simulaciones de 3000 partículas al clúster de una, más o menos esperamos que el mismo complete 10 corridas por día, por lo que en unos 73 días tendríamos los resultados #hpc #cluster #ciencia #md #dinamicamolecular #moleculardynamics #science #fisica #physics
Gaining Cross-Platform Parallelism for HAL’s Molecular Dynamics Package using SYCL
J'ai fait une petite simulations rigolote pour vérifier numériquement un vieux truc que j'ai trouvé dans un article de Boltzmann. Si on met une particule dans un plan avec deux ressorts qui ont des constantes de forces k1 et k2, la trajectoire est périodique si k1/k2 est un nombre rationnel: https://youtu.be/keGGbb2uiB8
Évidemment si c'est pas un nombre rationnel (genre pi), c'est pas périodique: https://youtu.be/Tty0jFWKkv8
Voilà, c'est tout pour moi.
GROMACS on AMD GPU-Based HPC Platforms: Using SYCL for Performance and Portability
#Physics #MolecularDynamics #HPC #Performance #SYCL #Package
