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#moleculardynamics — Public Fediverse posts

Live and recent posts from across the Fediverse tagged #moleculardynamics, aggregated by home.social.

  1. ⚛️ 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: doi.org/10.34133/csbj.0024

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

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

  2. 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.

  3. 🚀 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: doi.org/10.1016/j.csbj.2025.11

    📚 CSBJ: csbj.org/

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

  4. 🔬 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: doi.org/10.1016/j.csbj.2025.10

    📚 CSBJ: csbj.org/

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

  5. 🧬 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: doi.org/10.1016/j.csbj.2025.07

    📚 CSBJ: csbj.org/

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

  6. 🧬 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: doi.org/10.1016/j.csbj.2025.07

    📚 CSBJ: csbj.org/

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

  7. 🧬 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: doi.org/10.1016/j.csbj.2025.07

    📚 CSBJ: csbj.org/

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

  8. 🧬 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: doi.org/10.1016/j.csbj.2025.07

    📚 CSBJ: csbj.org/

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

  9. 🧬 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: doi.org/10.1016/j.csbj.2025.07

    📚 CSBJ: csbj.org/

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

  10. Sat my butt down, drank too much ​:neofox_cofe:​ coffee, and wrote an introductory blog post exploring the amazing world of molecular dynamics. Bewhold! Check it out and do let me know what you think! ​:neofox_uwu:​ ❤️ Thank yoooou!
    https://bugwhisperer.dev/blog/exploring-the-world-of-molecular-dynamics/
    gemini://capsule.bugwhisperer.dev/posts/exploring-the-world-of-molecular-dynamics.gmi
    #molecularDynamics #biophysics #blogging #scienceRules #computationalBiology

  11. 🧬 Can entropy help us decode how hormone receptors make real-time decisions?

    🔗 Temporal complexity of LVV-hemorphin-7 allosterism at the angiotensin II type 1 receptor assessed using entropy-based approaches. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.csbj.2025.10

    📚 CSBJ: csbj.org/

    #StructuralBiology #Biophysics #GPCR #Entropy #MolecularPharmacology #AllostericModulation #DrugDiscovery #MolecularDynamics

  12. My PhD research proposal is nearly done after over a month of working on it full tilt. Been an incredible (re)learning experience! Feel so much more comfortable with producing academic style writing again. Had some mega size cobwebs to dust off there. 🕸 Helps to have had to read so many journal articles to grok it all and connect the dots.

    Excited to start reaching out to programs and lab heads!
    ​:neofox_glasses:​ If you happen know folks here on mastodon that are involved in Computational Biology or Biophysics program please drop names in replies or boost for reach. Looking to connect!

    Now to treat myself to a much needed rest day and massage for my keyboard-warped back and tired eyed.
    ♨️
    #research #compBio #proteinStructure #molecularDynamics #bioPhysics

  13. My PhD research proposal is nearly done after over a month of working on it full tilt. Been an incredible (re)learning experience! Feel so much more comfortable with producing academic style writing again. Had some mega size cobwebs to dust off there. 🕸 Helps to have had to read so many journal articles to grok it all and connect the dots.

    Excited to start reaching out to programs and lab heads!
    ​:neofox_glasses:​ If you happen know folks here on mastodon that are involved in Computational Biology or Biophysics program please drop names in replies or boost for reach. Looking to connect!

    Now to treat myself to a much needed rest day and massage for my keyboard-warped back and tired eyed.
    ♨️
    #research #compBio #proteinStructure #molecularDynamics #bioPhysics

  14. My PhD research proposal is nearly done after over a month of working on it full tilt. Been an incredible (re)learning experience! Feel so much more comfortable with producing academic style writing again. Had some mega size cobwebs to dust off there. 🕸 Helps to have had to read so many journal articles to grok it all and connect the dots.

    Excited to start reaching out to programs and lab heads!
    ​:neofox_glasses:​ If you happen know folks here on mastodon that are involved in Computational Biology or Biophysics program please drop names in replies or boost for reach. Looking to connect!

    Now to treat myself to a much needed rest day and massage for my keyboard-warped back and tired eyed.
    ♨️
    #research #compBio #proteinStructure #molecularDynamics #bioPhysics

  15. My PhD research proposal is nearly done after over a month of working on it full tilt. Been an incredible (re)learning experience! Feel so much more comfortable with producing academic style writing again. Had some mega size cobwebs to dust off there. 🕸 Helps to have had to read so many journal articles to grok it all and connect the dots.

    Excited to start reaching out to programs and lab heads!
    ​:neofox_glasses:​ If you happen know folks here on mastodon that are involved in Computational Biology or Biophysics program please drop names in replies or boost for reach. Looking to connect!

    Now to treat myself to a much needed rest day and massage for my keyboard-warped back and tired eyed.
    ♨️
    #research #compBio #proteinStructure #molecularDynamics #bioPhysics

  16. Nuestro pequeño cluster para cálculos de dinámica molecular en el CURE. Configurar este cluster fue una gran experiencia que amplió notablemente mis conocimientos previos de sysadmin con Undernet. Le saco poco cartel #cluster #moleculardynamics #cure #udelar #diy #physics #debian #slurm #openmpi

  17. 💊 Can understanding receptor bias help us design safer, more selective GPCR drugs?

    🔗 Biased activation of the vasopressin V2 receptor probed by molecular dynamics simulations, NMR and pharmacological studies. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.csbj.2024.10

    📚 CSBJ: csbj.org/

    #GPCR #StructuralBiology #MolecularDynamics #NMR #Pharmacology #ProteinStructure #DrugDiscovery #ComputationalBiology #CellSignaling

  18. 💊 Can understanding receptor bias help us design safer, more selective GPCR drugs?

    🔗 Biased activation of the vasopressin V2 receptor probed by molecular dynamics simulations, NMR and pharmacological studies. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.csbj.2024.10

    📚 CSBJ: csbj.org/

    #GPCR #StructuralBiology #MolecularDynamics #NMR #Pharmacology #ProteinStructure #DrugDiscovery #ComputationalBiology #CellSignaling

  19. 🧬 Can salt levels change how cell-penetrating peptides behave at membranes?

    🔗 Molecular dynamics simulations unveil the aggregation patterns and salting out of polyarginines at zwitterionic POPC bilayers in solutions of various ionic strengths. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.csbj.2024.11

    📚 CSBJ: csbj.org/

    #MolecularDynamics #PeptideAggregation #MembraneProtein #Biophysics #StructuralBiology #ProteinFolding #MembraneBiology

  20. 🧬 Can molecular simulations transform the future of long-acting diabetes treatments?

    🔗 In silico investigations of albumin-GLP-1 receptor agonist complexes for diabetes drug delivery applications. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.csbj.2025.11

    📚 CSBJ: csbj.org/

    #MolecularDynamics #DiabetesResearch #Biotherapeutics #GLP1 #Albumin #DrugDelivery #Biomaterials #ComputationalBiology #ProteinEngineering

  21. 🧫 What secret molecular choreograph helps bacteria stay resilient against antibiotics and detergents?

    🔗 Coordinated subdomain movements of MlaC regulate ligand binding and transport. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.csbj.2025.05

    📚 CSBJ: csbj.org/

    #Microbiology #AntibioticResistance #MembraneBiology #StructuralBiology #ComputationalChemistry #MolecularDynamics #ComputationalBiology #Biophysics #ProteinStructure #DrugDiscovery #MolecularDocking

  22. 🧫 What secret molecular choreograph helps bacteria stay resilient against antibiotics and detergents?

    🔗 Coordinated subdomain movements of MlaC regulate ligand binding and transport. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.csbj.2025.05

    📚 CSBJ: csbj.org/

    #Microbiology #AntibioticResistance #MembraneBiology #StructuralBiology #ComputationalChemistry #MolecularDynamics #ComputationalBiology #Biophysics #ProteinStructure #DrugDiscovery #MolecularDocking

  23. 🧫 What secret molecular choreograph helps bacteria stay resilient against antibiotics and detergents?

    🔗 Coordinated subdomain movements of MlaC regulate ligand binding and transport. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.csbj.2025.05

    📚 CSBJ: csbj.org/

    #Microbiology #AntibioticResistance #MembraneBiology #StructuralBiology #ComputationalChemistry #MolecularDynamics #ComputationalBiology #Biophysics #ProteinStructure #DrugDiscovery #MolecularDocking

  24. 🔬 Could a tiny imbalance in ATP binding be the key to drug resistance in cancer?

    🔗 Nucleotide asymmetry and flexible linker dynamics modulate drug efflux cycle of P-glycoprotein, A computational study. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.csbj.2025.10

    📚 CSBJ: csbj.org/

    #DrugResistance #MolecularDynamics #StructuralBiology #MembraneProteins #CancerResearch #Pharmacology #DrugDiscovery #ChemotherapyResistance #ProteinDynamics #Pgp #ABCB1 #Biophysics

  25. ⚡️ How does the Hv1 proton channel conduct protons faster than diffusion should allow?

    🔗 Fluctuating hydrogen-bond network of the Hv1 ion channel. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.csbj.2025.10

    📚 CSBJ: csbj.org/

    #Biophysics #ProtonChannel #MolecularDynamics #StructuralBiology #HydrogenBonding #IonChannels #ProtonTransport #Hv1

  26. 🧬 One amino acid to stabilize them all — myth or molecular reality?

    🔗 Single-residue engineering of lambda (λ) antibody light chains reduces conformational flexibility and enhances thermal stability. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.csbj.2025.10

    📚 CSBJ: csbj.org/

    #MonoclonalAntibodies #mAbs #Immunology #ComputationalBiology #MolecularDynamics #Bioinformatics #ProteinStability #StructuralBiology

  27. 💪 Could one molecular “typo” break the balance between strength and flexibility in our muscles?

    🔗 Dynamical features of smooth muscle actin pathological mutants: The arginine-257(258)-Cysteine cases. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.csbj.2025.02

    📚 CSBJ: csbj.org/

    #ComputationalBiology #MolecularDynamics #ProteinScience #Actin #RareDiseases #PrecisionMedicine #Biophysics #CryoEM #Bioinformatics #DrugDiscovery #VisceralMyopathy #AorticAneurysm

  28. 🧬 Can AI build peptides that tell your cells to fight back against oxidative stress?

    🔗 RoseTTAFold diffusion-guided short peptide design: a case study of binders against Keap1/Nrf2. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.csbj.2025.02

    📚 CSBJ: csbj.org/

    #StructuralBiology #PeptideTherapeutics #RoseTTAFold #ProteinEngineering #MolecularDynamics #AIinDrugDiscovery #AntioxidantResearch #DrugDesign #Bioinformatics #ComputationalBiology

  29. This year’s GGMM meeting spotlighted multiscale simulations—from electron transfer in membranes to oxidative damage in nucleosomal DNA. Highlights: Aurélien de la Lande’s talk on NADPH oxidases, Natacha Gillet on ionization‑to‑repair pathways, and Mariia Avstrikova’s thesis on allosteric modulation of α7 nAChR. How do you tackle bridging such scales in your work? 🔬🧬 #MultiscaleSim #MolecularDynamics #OxidativeStress #OpenScience

    idees.moleculair.es/ggmm25-mul

  30. ⚛️ Is the secret to circular rare earth recovery hidden in molecular motion?

    🔗 Computationally derived structural insights into Rare Earth selectivity in lanmodulin and its variants. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.csbj.2025.02

    📚 CSBJ: csbj.org/

    #RareEarths #Lanmodulin #ComputationalBiology #Sustainability #CircularEconomy #RareEarthElements #MolecularDynamics #ProteinEngineering #MolecularModeling #MolecularSimulation

  31. 🧬 Can we bridge the gap between AlphaFold’s static structures and real molecular motion?

    🔗 Integrating AlphaFold pLDDT Scores into CABS-flex for enhanced protein flexibility simulations. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.csbj.2024.11

    📚 CSBJ: csbj.org/

    #Biophysics #ProteinDynamics #AlphaFold #CABSflex #StructuralBiology #ComputationalBiology #MolecularModeling #Bioinformatics #MolecularDynamics #ProteinFlexibility

  32. 🧬 Could a single residue swap turn a life-saving antibody into a “dead mutant”?

    🔗 Replacement of a single residue in an antibody abolishes cognate antigen binding, as predicted by theoretical methods. Computational and Structural Biotechnology Journal, DOI: doi.org/10.1016/j.csbj.2025.10

    📚 CSBJ: csbj.org/

    #AntibodyEngineering #StructuralBiology #ComputationalBiology #ProteinModeling #Biophysics #Diagnostics #MolecularDynamics #MolecularSimulation #InfraredSpectroscopy #FTIR

  33. We reviewed the evolution of molecular visualization, from classic 3D to VR, and the challenge of clarity at scale. Where should the field go next—interaction, AI, or better narratives? 🧪🧠 Anyone else tackling massive MD datasets?

    #moleculardynamics #datavis #openscience #virtualreality

    idees.moleculair.es/mdviz

  34. Reproducing MD results is still too hard—often due to missing parameters and fuzzy protocols. Let’s normalize full documentation, robust version control, containerized environments (e.g., Guix), and well-annotated datasets in long-lived repositories (Zenodo/FigShare).

    Anyone building shared workflows or databases like MDDB? What’s working for you? #MolecularDynamics #OpenScience #Reproducibility #ComputationalBiology 🔁

    is.gd/wjXmKT

  35. Exploring ML + MD for membrane proteins: moving beyond manual inspection to detect events, change-points, and metastable states in long trajectories. Faster clustering, better patterns, fewer blind spots. Anyone pairing k-means with HELM or similar for refinement? 🤔

    #MolecularDynamics #MachineLearning #Bioinformatics #MembraneProteins

    is.gd/5Ycb2P

  36. By combining high-resolution electrostatic mapping with molecular dynamics simulations, we investigated the behavior of these surface-trapped ionic charges. We found that they spread across the surface with remarkable mobility. Their two-dimensional diffusion exceeds that of ions in bulk water, with the limiting factor being the friction between the ionic solvation shell and the solid.

    pnas.org/doi/10.1073/pnas.2505

    #PNAS #MolecularDynamics #SurfaceScience #PhysicalChemistry#ComputationalChemistry

  37. 🪨 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: doi.org/10.1016/j.csbj.2025.06

    📚 CSBJ: csbj.org/

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

  38. 🪨 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: doi.org/10.1016/j.csbj.2025.06

    📚 CSBJ: csbj.org/

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

  39. 🪨 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: doi.org/10.1016/j.csbj.2025.06

    📚 CSBJ: csbj.org/

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

  40. 🪨 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: doi.org/10.1016/j.csbj.2025.06

    📚 CSBJ: csbj.org/

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

  41. 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

  42. 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: doi.org/10.1016/j.nimb.2022.12) 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): abg.asso.fr/en/candidatOffres/

  43. 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

  44. 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: youtu.be/keGGbb2uiB8

    Évidemment si c'est pas un nombre rationnel (genre pi), c'est pas périodique: youtu.be/Tty0jFWKkv8

    Voilà, c'est tout pour moi.

    #Physics #Boltzmann #lammps #MolecularDynamics

  45. Happy to see another command I worked on merged in the LAMMPS code.

    Langevin barostat is now available to use, thanks to the dev team which is of very wise help.

    Waiting for users feedback, if any. 😊

    #science #lammps #MolecularSimulation #MolecularDynamics