Koch Lab:Meetings/Group meeting 08-10-2009
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- Talking about coarse grainng.
- Coarse graining says there are too many atoms some they get rid of some in the simulation.
- Lipids are described by 2 head groups connected by a string of beads.
- Atlas wants to start simulations with a correct potential and then coarse grain.
- A better description of coarse graining is that people make molcules pseudo molecules.
- Smart Monte Carlo uses a set of rules that dictates how a system evoles.
- Igor's stuff
- Worked on piezo stage.
- He's going to Boson to get another laser.
- Veejay's stuff
- Made a box with a bunch of molecules in it and he's trying to get out thermo quantities.
- He used different baths to see if he can get the thermo quantities.
- He settled on the Nose-Hoover bath. It's basically a thermostat.
- His box has periodic boundary conditions that changes size.
- Looking at how people parametarize an EAM potential.
- Will look at doubly ionized atoms in water with the EAM potentials.
- Andy's stuff
- Setup microscope for fluorescence studies.
- Got a camera.
- Got a motility assay to work.
- Built a spin coater.
- Larry's stuff
- Has done some Monte Carlo simulations and read lots of error analysis books.
- Did a simulation on kinesin walking based on rate constants.
- The modeling is based on "Agent based" modeling.
- Ant's stuff
- Optical tweezers calibration.
- Picture making.
- Godwin's stuff
- Working on calculations with water.
- He is using his own geometries for water and optimizing them. These aren't working too well.
- He found other geometries and used them.
- The optimizations are for specific MD calculations.
- Geometries are descriptions of how 2 molecules are positioned with respect to each other.
- Different geometries give you different energies. He's looking for minimum energy configurations.
- One has to be careful so as to not optimize local mimimums.
- Geometry changes are small tweaks and not huge changes.
- Linh's stuff
- Lab maintenance.
