#molecular-dynamics — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #molecular-dynamics, aggregated by home.social.
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⚛️ 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
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Funded PhD - multiscale electrochemical modeling
University College DublinSee 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.
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🚀 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
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🔬 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
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🧬 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
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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 -
🧬 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: https://doi.org/10.1016/j.csbj.2025.10.024
📚 CSBJ: https://www.csbj.org/
#StructuralBiology #Biophysics #GPCR #Entropy #MolecularPharmacology #AllostericModulation #DrugDiscovery #MolecularDynamics
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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 -
💊 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: https://doi.org/10.1016/j.csbj.2024.10.039
📚 CSBJ: https://www.csbj.org/
#GPCR #StructuralBiology #MolecularDynamics #NMR #Pharmacology #ProteinStructure #DrugDiscovery #ComputationalBiology #CellSignaling
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🧬 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: https://doi.org/10.1016/j.csbj.2024.11.004
📚 CSBJ: https://www.csbj.org/
#MolecularDynamics #PeptideAggregation #MembraneProtein #Biophysics #StructuralBiology #ProteinFolding #MembraneBiology
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💧 Is your MD simulation lying to you because of the water model you picked?
🔗 Impact of water models on the structure and dynamics of enzyme tunnels. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2024.10.051
📚 CSBJ: https://www.csbj.org/
#ComputationalBiology #MolecularDynamics #Enzymology #StructuralBiology #ProteinEngineering #Biophysics #WaterModels #EnzymeTunnels #MolecularSimulation #ProteinDynamics
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🧬 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: https://doi.org/10.1016/j.csbj.2025.11.007
📚 CSBJ: https://www.csbj.org/
#MolecularDynamics #DiabetesResearch #Biotherapeutics #GLP1 #Albumin #DrugDelivery #Biomaterials #ComputationalBiology #ProteinEngineering
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🧫 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: https://doi.org/10.1016/j.csbj.2025.05.031
📚 CSBJ: https://www.csbj.org/
#Microbiology #AntibioticResistance #MembraneBiology #StructuralBiology #ComputationalChemistry #MolecularDynamics #ComputationalBiology #Biophysics #ProteinStructure #DrugDiscovery #MolecularDocking
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🔬 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: https://doi.org/10.1016/j.csbj.2025.10.064
📚 CSBJ: https://www.csbj.org/
#DrugResistance #MolecularDynamics #StructuralBiology #MembraneProteins #CancerResearch #Pharmacology #DrugDiscovery #ChemotherapyResistance #ProteinDynamics #Pgp #ABCB1 #Biophysics
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⚡️ 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: https://doi.org/10.1016/j.csbj.2025.10.021
📚 CSBJ: https://www.csbj.org/
#Biophysics #ProtonChannel #MolecularDynamics #StructuralBiology #HydrogenBonding #IonChannels #ProtonTransport #Hv1
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🧬 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: https://doi.org/10.1016/j.csbj.2025.10.045
📚 CSBJ: https://www.csbj.org/
#MonoclonalAntibodies #mAbs #Immunology #ComputationalBiology #MolecularDynamics #Bioinformatics #ProteinStability #StructuralBiology
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💪 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: https://doi.org/10.1016/j.csbj.2025.02.010
📚 CSBJ: https://www.csbj.org/
#ComputationalBiology #MolecularDynamics #ProteinScience #Actin #RareDiseases #PrecisionMedicine #Biophysics #CryoEM #Bioinformatics #DrugDiscovery #VisceralMyopathy #AorticAneurysm
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🧬 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: https://doi.org/10.1016/j.csbj.2025.02.032
📚 CSBJ: https://www.csbj.org/
#StructuralBiology #PeptideTherapeutics #RoseTTAFold #ProteinEngineering #MolecularDynamics #AIinDrugDiscovery #AntioxidantResearch #DrugDesign #Bioinformatics #ComputationalBiology
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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
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⚛️ 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: https://doi.org/10.1016/j.csbj.2025.02.005
📚 CSBJ: https://www.csbj.org/
#RareEarths #Lanmodulin #ComputationalBiology #Sustainability #CircularEconomy #RareEarthElements #MolecularDynamics #ProteinEngineering #MolecularModeling #MolecularSimulation
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🧬 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: https://doi.org/10.1016/j.csbj.2024.11.047
📚 CSBJ: https://www.csbj.org/
#Biophysics #ProteinDynamics #AlphaFold #CABSflex #StructuralBiology #ComputationalBiology #MolecularModeling #Bioinformatics #MolecularDynamics #ProteinFlexibility
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🧬 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: https://doi.org/10.1016/j.csbj.2025.10.018
📚 CSBJ: https://www.csbj.org/
#AntibodyEngineering #StructuralBiology #ComputationalBiology #ProteinModeling #Biophysics #Diagnostics #MolecularDynamics #MolecularSimulation #InfraredSpectroscopy #FTIR
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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?
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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 🔁
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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
