Yesterday (Sunday) I switched the theme of my lab from building large massive objects to building more molecular-cellular type objects. Actually, I had told myself that I was going to take time off from building, to rest. I managed to do it for most of the day. But then at around 8pm, the itch started again and I worked from 8pm to about midnight. The first thing I decided to build was a millipore filter. This is the beginning of my "Cells on Pores" project in SL. I will have to explain the Cells on Pores project later on...there is a brief description of the RL Cells on Pores project in my website...Xinyuan Zhang is the grad student working on this. But, I also want to model cells on pores in SL. Actually, I started building a millipore filter in SL on Saturday, but I followed a wrong building strategy that ended exhausting me and the whole thing never looked good and actually fell apart at the end. I deleted this first try without even documenting it, but Jason stopped by lab and took a peek at it. If you ask him, he will tell you how horrible it looked :-.( The second time, I began building the millipore filter with a new building strategy. This one worked really well. The strategy is to embed a hollow cyllinder inside a hollow block. This, way each pore is embedded in a square, and the squares can be easily assebled and the spaces between squares filled in with blocks. So, I finished the filter and painted it pink.
Interestingly, I decided to build the filter really big. As big as I could. So, in SL, it floats far above my lab, in the sky. The filter is NonPhysical in nature. I decided to build it NonPHysical, because we would need space in the main floor of my lab to put a physical struture down --the only way I can build it up in space is to keep it Nonphysical. But, it could be easily translated into a physical object. Now, the existence of this "millipore filter" in SL makes me wonder: What size are the pores? I guess I could make them any size. As they are, they are bigger than an avatar, so as to let an avatar fly through the pore. But, if I am going to be building a virtual cell, should these pores be 1, 10, 100 nanometers or micrometers big? This issue of scale in SL is important. I am not sure I really know the right answer, but it will definitely affect the work we do in the future. As far as buildling goes, it is much easier to build big. But then, if the objects are phyiscal, one needs land to put them on. So, there are issues. Also, building a millipore filter is one things. But then, if one is going to build cells on top of those millipore filters, the bigger the filters the more work it will take to build the cells. And if one would want molecular detail in the cells (ie. atom resoultion) the pores would need to be bigger. It would be nice to know if one could rescale objects easily. That would obviate the problem. But as things stand, I don't know if rescaling things in SL is easy or not....I wished someone could answer these questions for me.
Nevertheless, Millipore filters are just one step away from doing a size exclusion cromatography experiment in SL. I want to be the first to do this...It will be fun and a nice experiment, and it will give me some time to think about the macromolecular crowding expeirments I was doing in graduate school with Joel Swanson. Will the size exclusion cromatography experiment work? My plan is to construct a size exclusion chromatography column phyiscally. I will build the column with a stack of hollow cyllinders. I will fill up the column with rigid balls. Then I will pour a mixture of small balls and big balls into the top of the column. To facilitate diffusion, I will add some "heat": physically shaking the column. If the column is vertical, the balls should fall down based on their gravity, thus simulating flow. I expect the small balls to separate from the big balls.But maybe there are other better ways to build columns. I can build it out of plates...millipore tube like plates. In fact, this is more in line with how I was taught how a chromatography column works: theoretical plates. So, maybe instead of balls, I will fill it up with theoretical plates... Easier to go back and forth between theory and simulation expeirment that way. But, filling it with balls may be more akin to a RL chromatography column. Anyway, it is an experiment...Maybe I am getting the theory wrong and it will take some time before I get some size spearatation. So, I will do both: a plate/filter based size exclusion column, and a bead-based size exclusion column.
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