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) .

Ah yes, Ubuntu, African for “I can’t figure out how to install Debian.”

Saturday morning cartoons. This was a sacred ritual that we looked forward to every weekend.

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.