Progress:Yonghui

Checked
To be checked
In progress

20160803

1. After obtain the number of lipids vs. time using the COM definition, calculation hill coefficient from this relationship, summarize in a table and compare old and new ones.
2. g(r) calculation: bin size 2A, two layers separately, and then take the average, plot three curves in one plot for each system
3. Animations of new simulations

20160802

1. run 2 sets of simulations for 6 types of lipids asap, we need the data in 2 weeks and submit the paper by the end of this month.
2. BN manuscript figures
   • calculate Hill coefficient for two simulations, summarize it in a table
   • calculate No. of lipids using COM of each lipid rather than P atom
   • g(r) calculation using last 50ns rather than last 10 ns, also for BN-lipid interaction energy, Scd
   • Why Scd of POPS changed a lot, compare new and old simulations, re-check the calculation.
   • Name of lipids are all in capital letters.
3. Questions
   • Interaction Energy between lipids are only in the same layer or all lipids? Please re-calculate it for the same layer and between different layers, and re-compare.
   • views of lipids on different layers, how do you define layers, based on g(y) or g(r)?
   • How long are the simulations of 295 and 300K pure DMPC membrane ? Which time period are used for Scd calculation?
   • Why energy between lipids are the same (old and new) on your slide 9 of 8/1?
4. About the Scd comparison slide
   • Please answer 3 comments on the slide in red

20160727

1. BN manuscript figure
   • Fig.1 simulation snapshots
   • Fig.2 TEM results (Exp)
   • Fig.3 Extract time
   • Fig.4 Energy
   • Fig.5 EDS results (Exp)
   • Fig.5 Ordering
2. BN manuscript SI figure
   • move the COM, Energy evolution profile to SI
3. Check the Tm of POPE (298K)

20160721

1. BN manuscript

20160714

1. DMPC Scd data
   • calculate with gromacs
   • value of each tailed carbon
2. DMPC RDF data
   • check the data of 295k and 300k
3. Rerun data analysis
   • for 7 bilayer membrane
4. Movie of DMPC Mem