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Cake day: July 10th, 2023

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  • Here is an AI based summary of top breakthroughs:

    Here are some of the biggest breakthroughs mentioned in the provided references:

    1. Exascale Simulations for SARS-CoV-2:

      • Conducted exascale simulations of SARS-CoV-2 spike protein, revealing dramatic spike opening and cryptic pockets, which have implications for drug design and understanding viral infectivity (Zimmerman et al., 2021) .
    2. Ab Initio Protein Folding Simulations:

      • Achieved molecular simulations of ab initio protein folding for the NTL9 protein, providing insights into the protein folding process (Voelz et al., 2010) .
    3. Markov State Models for Protein Dynamics:

      • Developed Markov State Models (MSMs) to study protein folding kinetics and dynamics, providing a framework to understand protein conformational changes over long timescales (Bowman et al., 2009; Lane et al., 2011) .
    4. RNA Polymerase II Dynamics:

      • Investigated the dynamics of RNA polymerase II translocation at atomic resolution, elucidating mechanisms of transcription elongation (Silva et al., 2014) .
    5. Ligand Modulation of GPCR Activation:

      • Used cloud-based simulations to reveal how ligands modulate G protein-coupled receptor (GPCR) activation pathways, advancing the understanding of GPCR function and drug targeting (Kohlhoff et al., 2014) .
    6. Nanotube Confinement Effects on Proteins:

      • Demonstrated that nanotube confinement can denature protein helices, providing insights into the effects of nanoscale environments on protein structure (Sorin & Pande, 2006) .
    7. Simulation and Experiment in Protein Folding:

      • Combined simulation and experimental approaches to reveal slow unfolded-state structuring in acyl-CoA binding protein folding, highlighting the interplay between simulations and experiments (Voelz et al., 2012) .
    8. Advances in Markov State Models:

      • Improved coarse-graining and adaptive sampling techniques in MSMs, enhancing the modeling of biomolecular dynamics (Bowman, 2012; Zimmerman et al., 2018) .
    9. Insights into Allosteric Sites:

      • Identified potential cryptic allosteric sites within folded proteins using equilibrium fluctuation analysis, suggesting new targets for drug discovery (Bowman & Geissler, 2012) .
    10. GPCR Activation Pathways:

      • Revealed ligand modulation of GPCR activation pathways through extensive simulations, providing insights into receptor function (Kohlhoff et al., 2014) .



  • The fact that you made this post shows you are not a bad person. It shows you care about yourself to set a standard and measure yourself against it. You are just like everyone else in that regard and that is pretty special.

    I say you are not bad. I say you are amazing. To quote: “What a piece of work is a man, How noble in reason, how infinite in faculty, In form and moving how express and admirable, In action how like an Angel, In apprehension how like a god, The beauty of the world, The paragon of animals.“

    Now that is a pretty high bar. We strive for it and we measure ourselves against it. Does the fact we do not achieve it makes us bad? No, it makes us human.


  • This is what is called a shame spiral. How do you get out of it? As this reply said give yourself a pass. Being able to identify negative self-talk is the first step to being able to lift yourself out of it. For me learning to identify and exit the spiral of shame has had a huge positive effect on my mental health and made existence more tolerable.