User:Brian P. Josey/Notebook/2009/10/08

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Amylose, Passivation and Robots
Where to begin?

Robots
Anthony is getting the optical tweezers set up to his liking so that he can start running his experiments in a couple of weeks. He would like to have everything be set up and within reach of his position behind the computer. Because of the layout of the optical table, the laser is farther away from him than he can reach without going around, the long way, the table. Currently he is using a rod to slide the razor blades that we use to block the laser back and forth. While this works, he would like to have the controls for everything within arms reach, or better yet on the computer. This is where I come in.

As a fun project, I am going to make an automated system that will move the razor blades back and forth to shield and unshield the laser beam. To do this I am using a Lego Mindstorms NXT system. It's cool, I am hoping to understand how to make it do everything that we want it to do. So on Tuesday I built up a simple driving robot and I am programming it to move around and respond to the environment. As soon as I learn how to use all of the features, from the necessary like moving to the random, like detecting a change in color, I am going to design and build a series of gears that will move the razors back and forth. Later we can use this to automate whatever we want and to do more than move somethings around.

Luckily, the programing software is a very, very simplified version of LabVIEW, so by programming the robot and building up some systems to automate our processes I will be getting my feet wet in programing and gain at least a basic understanding of how LabVIEW works. If I want to, I imagine that I could use this as a jumping point for getting more serious in programing. Who knows, we might include more sophisticated systems later. I think that it would be unlikely, but you never know.

Amylose and Passivation
The more meatier thing that I have going on is that I am looking into using amylose for Andy's passivation experiments. Essentially, the root question is: why do we use Casein as in passivation and could we use other things to do the same thing as Casein? To do this Andy has come up with a couple of ideas. I'm going to summarize them here and brainstorm a little bit past what we've done so far.

Silica nanoparticles. Andy has a really good notebook page that describes his idea for this here. Andy is concerned about what happens when the kinesin comes in contact with the surface of the glass slides, and believes that without a rigid structure the kinesin will fall over and bind to the glass, they have an affinity for the glass. This is opposed to the idea that they denature when they come in contact with the glass. The idea is silica beads, which essentially are glass, will provide a structure and rough terrain for the kinesin to stand up properly. If they work, it will indicate that the surface of the glass is what is important for keeping the kinesin erect.

Carbohydrates, especially Amylose. This is an idea that we have talked about before. Andy is curious to find out what effect the use of lipids or starches would be on the passivation of the slides. The one that I am going to look into shortly is the use of amylose as a coating for the slides. Amylose is a polysaccharide, formed out of glucose molecules linearly with alpha carbon 1 to carbon 4 bonds. We were wondering if we could have it coat the glass and if kinesin would bind to it. I am concerned about the mass of the casein or starch that we would use. I came up with the idea that because casein has a lower molar mass (~19000 g/mol) it could easily go into solution, but not be washed away when we put more substances into the flow cells. An amylose chain of three hundred glucose molecules would have a molar mass of ~54000 g/mol, this might prevent it from going into solution, but it would not be washed away. However, Andy pointed out that affinity is more important to processivity, because if the weight alone determined whether it worked or not, casein wouldn't work and it would be washed away every time we added something to the flow cells.

I am going to hit the books on this one and see what I can turn up.


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