Author: Prof. Andresen

On Friday I created a new calibration set to run more cobalt-only samples. In those and the samples I made today to run, I included an internal standard (Sr). The standard worked well in all the calibration solutions on Friday, but I must have made the samples less precisely this morning because the concentration of Sr was no where near the value it should have been, so the internal standard was dropped. The samples I ran today were a factor of 10 lower than the cobalt-only samples I ran more than a month ago. I am still unsure if this is a calculation mistake or a trend that actually exists in the data. 

I read several articles while making sure Steve did not harm himself in the machine shop. The first article I read will be discussed on Friday during the lab’s journal club and was about the effects of different salts on DNA elasticity using magnetic tweezers. If you have been reading this blog, it is obvious that this article includes aspects of both our projects. Funnily enough, Prof. Andresen contributed to two of the articles in the reference section of this article. The other articles I read further explained the compaction of DNA and the protocol we can utilize in my project using the ICP-OES. I also reviewed all of my notes thus far to condense the method I’ve used this summer.

Today, I completely finished analyzing the data I have so far! Hopefully I can start the cobalt only samples tomorrow and finish them up by next week.

Today, I machined.I finished the taps for the piece that I made last Thursday, which connects a stepper motor to the 95mm rail mount, thus allowing us to attach the stepper motor to the rails. I also drew up plans and began to machine parts to allow us to connect the rotary motor to the stepper motor. The rotary motor will have the magnet holder (which we have yet to machine) attached to it.

Today, I worked on the data from the last two dilution sets. I averaged them together two different ways and then had to decide which way to display the data in a rough results explanation. The weighted average gave an odd shape for sodium similar to a wave. Now we are trying to fix the odd graphs by analyzing the data in different ways.

This morning, I ran the second set of samples twice. The calibrations for the second run were a little funky but overall it mostly affected the wavelengths that we do not use in data analysis. This afternoon I have been organizing the four runs, averaging them together and creating graphs that match the ones for the 100x and 20x dilutions. 

Because we have only taken data for a high and low dilution, today I made and ran samples at a dilution between the previous samples. I created two sample sets along with new calibration solutions. This afternoon, I ran the first set of samples twice. Taking a quick glance at the data, I noticed that the concentrations for the different elements are not a steady increase or decrease as it was previously. Hopefully once I begin analyzing the data, these strange data points will not significantly affect the overall trends. 

Today I got to run all of my samples! First I ran 10 samples of 20x buffer solution twice to get smaller standard error. The error was reduced from about 0.14 to 0.04. I also ran a sixth run of the 20x samples for varied sodium by combining the left over solution from the other 4 runs. Unfortunately, this run measured sodium much lower than the other runs so I am not sure if we should include this data or not. 

Yesterday and today, I machined and fixed a rail that will be used to hold our XY stage. I also spent some time figuring out the step size for our motors. That is all.

I continued researching articles about the various parts of my experiment from ion competition to the different techniques used to investigate DNA compaction and aggregation including the ICP, tweezers, AFM, SAXS and different types of crystallography. This afternoon, the argon gas was replaced and the ICP began to warm up for the numerous runs that will hopefully take place the rest of the week. The first run will be with the 10 buffer solutions I just made at 20x dilution to decrease error bars. In the previous four runs at 20x, the concentration of sodium in the buffer solutions steadily decreased each run. Hopefully running ten more samples will even out the averaged concentration.