Brute force simulations.

"These proteins should form a pore through which RNA can pass."

Me: Manually places the RNA in the middle of the proteins on a membrane and hopes for a miracle (or a pore).

#compchem #simulation #moleculardynamics #proteinStructure #rna #protein #academicchatter #chemistry #pymol

⚛️ Could life itself be a quantum phenomenon disguised as biology?

🔗 Quantum Biology Using Ultrafast Integrative and Molecular Engineering Tools: A Perspective. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0024

📚 CSBJ Quantum Biology and Biophotonics: https://spj.science.org/journal/csbj/qbio

#QuantumBiology #QuantumPhysics #MolecularBiology #ProteinEngineering #Biophysics #Biochemistry #Bioinformatics #SystemsBiology #MolecularDynamics #Lifesciences

Our new paper published in the Computational and Structural Biotechnology Journal explains how ligands binding the exact same IL1R1 site produce opposite outcomes.

We used MD simulations and CABS-flex to show how IL1 receptor antagonists block signaling despite binding the exact same site as agonists. Instead of a static blockade, antagonists actively disrupt distal D3 domain dynamics.

Read here: https://doi.org/10.34133/csbj.0017

#MolecularDynamics #Biophysics #StructuralBiology #Allostery

Funded PhD - multiscale electrochemical modeling
University College Dublin

See the full job description on jobRxiv: https://jobrxiv.org/job/university-college-dublin-27778-funded-phd-multiscale-electrochemical-modeling/

#battery #computationalfluiddynamics #electrochemistry #moleculardynamics #quantumchemistry #ScienceJobs #hiring #research
https://jobrxiv.org/job/university-college-dublin-27778-funded-phd-multiscale-electrochemical-modeling/?fsp_sid=10273

Sometimes I imagine an LLM model trained on the #LAMMPS forum and mailing-list basically answering most #moleculardynamics related questions with:

* You should (re)read the manual.
* There are not enough information to conclude about your results.
* What do you expect in the first place?
* Garbage in, garbage out.
* As Axel Kohlmeyer said here...
* Talk to your advisor.
* This is expected and documented behavior.

In think that in this case it would actually be helpful.

Accelerating Molecular Simulations with Triton: Fused GPU Kernels for TensorNet Neural Potentials

#Triton #CUDA #MolecularDynamics #MD #MolecularSimulations #PyTorch #Chemistry #Biology

https://hgpu.org/?p=30453

🚀 What if we could precisely target the CAPON–nNOS axis — a pathway long considered undruggable?

🔗 Targeting CAPON to modulate the CAPON–NOS Axis: a computational approach. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.11.001

📚 CSBJ: https://www.csbj.org/

#DrugDiscovery #ComputationalBiology #AlzheimersResearch #Neuroscience #ProteinProteinInteractions #VirtualScreening #MolecularDynamics #AIinDrugDiscovery

🔬 Can structural shifts at the atomic level decide treatment outcomes in AML?

🔗 Understanding the characteristic behaviour of the wild-type and mutant structure of FLT3 protein by computational methods. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.023

📚 CSBJ: https://www.csbj.org/

#ComputationalBiology #MolecularDynamics #StructuralBiology #CancerResearch #AML #DrugDiscovery #PrecisionMedicine #KinaseResearch #Bioinformatics

🧬 How did changes at the atomic scale reshape viral infectivity?

🔗 Stoichiometric insights into SARS-CoV-2 spike–ACE2 binding across variants. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.07.034

📚 CSBJ: https://www.csbj.org/

#COVID19 #SARSCoV2 #SpikeProtein #ACE2 #StructuralBiology #MolecularDynamics #Virology #Biophysics #ComputationalBiology