🪨 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/

#AtomProbeTomography #MolecularDynamics #Biophysics #ProteinStructure #Nanotech #ComputationalBiology #StructuralBiology #Biomaterials #ProteinScience

Engineering Supercomputing Platforms for Biomolecular Applications

#CUDA #ROCm #Biology #Biomolecules #MolecularDynamics #HPC #Physics #Package

https://hgpu.org/?p=29954

🤯 Oh joy, another "primer" that's supposed to demystify molecular dynamics by regurgitating a 7.8k-word #snoozefest. If you've got 36 minutes and a desperate need to feel like you barely skimmed the surface while your brain melts into goo, this one's for you! 😂🔬
https://www.owlposting.com/p/a-primer-on-molecular-dynamics #moleculardynamics #scienceprimer #brainmeltdown #skimmingknowledge #humor #HackerNews #ngated

A Primer on Molecular Dynamics

https://www.owlposting.com/p/a-primer-on-molecular-dynamics

#HackerNews #MolecularDynamics #Science #Education #Research #Simulation

🧬 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 🙏

#science #amyloids #MolecularDynamics

🐦🧭 How do migratory birds sense Earth’s magnetic field? Quantum biology might hold the answer.

🔗 Cryptochrome magnetoreception: Time course of photoactivation from non-equilibrium coarse-grained molecular dynamics. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.11.001

📚 CSBJ Quantum Biology and Biophotonics: https://www.csbj.org/qbio

#Biophysics #QuantumBiology #Magnetoreception #MolecularDynamics #BirdNavigation #ComputationalBiology #Cryptochrome

#attomicroscopy #bioengineering #chemicalreactions #electronmicroscopy #MaterialsScience #MohammedHassan #moleculardynamics #nanotechnology #PierreAgostini #quantumphysics #realtimeimaging #UniversityofArizona #UVlight

https://miltonmarketing.com/news/time-stopped-attomicroscopy-quantum-revolution/

🛠️ Is it possible to rewire cellular energy control by targeting a single protein domain?

🔗 Disrupting the network of co-evolving amino terminal domain residues relieves mitochondrial calcium uptake inhibition by MCUb. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.12.007

📚 CSBJ: https://www.csbj.org/

#Mitochondria #CellBiology #CalciumSignaling #ProteinEngineering #ProteinScience #StructuralBiology #Bioenergetics #MolecularDynamics #Biophysics #MCU #MCUb #NMR

🧪 How can customized molecular simulations reshape the search for new therapeutics?

🔗 Predicting fragment binding modes using customized Lennard-Jones potentials in short molecular dynamics simulations. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.12.017

📚 CSBJ: https://www.csbj.org/

#DrugDiscovery #ComputationalChemistry #MolecularDynamics #FragmentBasedDesign #Biophysics #StructuralBiology #PharmaInnovation #ProteinLigandBinding

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).

https://codeberg.org/amartya/MolDyn_Rust

#rustlang #rust #c #moldyn #moleculardynamics #learning #programming #cpp #llm

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.

#MolecularDynamics #ProteinScience

With advancements in computational power and algorithms, Molecular Dynamics is unlocking new possibilities in chemistry, biology, and materials science.

In our latest blog, we explore how Molecular Dynamics simulations work, their real-world applications, and the future direction of this field.

Read more: https://www.redoakconsulting.co.uk/blog/molecular-dynamics/

#MolecularDynamics #ComputationalScience #MachineLearning

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.

#simulation #compchem #molecularDynamics #MolecularModeling

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, …

#UM25 #EuropeanXFEL

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

Okay, who snuck in a #Tricky quote into #GROMACS ?!

https://youtu.be/nDYeb6PeixQ

#triphop #moleculardynamics #scientificcomputing

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.

#proteins #structuralbiology #moleculardynamics

The D. E. Shaw Research DNA/RNA #moleculardynamics force-fields look great.

These non-canonical DNA structures are beautiful. Observing B-DNA <-> Z-DNA inter-conversion during simulation is so cool.

G-quadruplexes are such neat compact bundles.

The deficiencies are in nucleic acid-protein interactions -- getting values from different force-fields to play nice and be consistent is hard.

• Paper: https://pubs.acs.org/doi/10.1021/acs.jpcb.1c10971
• Force-field code: https://github.com/DEShawResearch/viparr-ffpublic

#structuralbiology