Wednesday, July 23, 2014

Squiggles!

I averaged all of the ICP runs from the past two weeks and compiled them onto one Excel spreadsheet. I then began looking at the Na/Co ion competition more thoroughly using the article Prof. Andresen and John Giannini collaborated on a few summers ago, "Ion Competition in Condensed DNA Arrays in the Attractive Regime" as a guide. I tried to use the ion binding model used in the article to analyze the relationship between the number of ions near the DNA arrays and the solution's ion concentrations. This involved finding a constant, ξ, to relate the two sets of numbers (aka. the squiggle). After rearranging the formula given for a simplified ion binding model, I found a ξ for each data point. I took a rough average and an actual average and compared the values found using the ξ against the data from the ICP (shown below).
As you can see, the model only fits the middle three points. This could be due to my own error in calculating each point, the assumptions I made when using the model, the interactions due to Cl- that I neglected, or the model might not accurately represent this data. 

Tuesday, July 22, 2014

The Long Post

I haven't been blogging lately because I broke the USB wifi adapter on the computer I've been working on. I accidentally stepped on it. So, here's a run down of everything I've been doing lately, with pictures. Also, the magnetic tweezers are almost finished, minus a working flow cell.

As of today, this is what the Tweezers look like:


As you can see, the lab is not as much of a mess as it has been in the past. Besides that, let's take a tour of each part of the MT, now that it is completed (more or less).

In general, MT is actually an inverted microscope with magnets jammed into it. It is inverted because in a normal microscope, the light source comes from the bottom. However, in MT, the light source comes from the top down. 


This is the light source. It is a red Thorlabs LED with a wavelength of 625nm. The LED has been collimated by an aspheric condenser lens, f=20mm. In MT, it is important to have a collimated light source with a low coherence length, as this allows for a better generation of diffraction rings around the beads, which is essential in taking measurements. The long, ventilated part on top of the LED is the heat sink. The LED is being held by a kinematic mount attached to our rail system. This allows for greater control over the positioning of the LED and direction of the light source.


Directly under the light source are two motors and the magnet setup. Here you see the rotary motor, which has been coupled to a sled moved by a stepper motor, which in turn has been mounted on the rails. The rotary motor holds the magnet holder, and allows for rotation of the magnets. By rotating the magnets, we can apply a torque to the magnetic beads, and thus, the DNA (or whatever is attached to the bead). The stepper motor that controls the sled allows for moving the rotary motor up and down in space, and therefore controls the strength of the force being applied to the beads (magnet closer to the bead, stronger force).


This is the magnet holder, and attached to the magnet holder are the magnets. They are two Neodymium magnets.


Here we can see the full-middle setup of the MT. Underneath the rotary motor is the XY table. We will couple our flow cell (still in production) to the top of this. The XY table allows manual movement of the flow cell in X and Y directions (i.e. horizontal to this picture.


This is the view underneath the XY stage. Not shown here is the microscope objective, which is a Nikon 100X oil-immersion objective. The objective attaches to the objective holder, which has been coupled to another sled controlled by a stepper motor. This stepper motor allows for control of the focus of the magnified image of the sample cell. By moving the objective closer or further away from the sample, we can change the focus of the image.


Light exiting the objective is reflected by this 45 degree mirror. I have momentarily removed it from the MT setup in order to make access to the underside of the MT easier. The mirror reflects the light to the camera setup.






And this is the camera setup. It consists of a lens tube, a 100mm aspheric focusing lens, and a JAI-Pulnix CCD camera. The light collected in the tube is focused onto the CCD, which then transmits black and white images of the sample to the computer.

This is the entirety of the MT setup. So, how does it work, and what is it's purpose? You'll just have to wait for another blog post...


 


Monday, July 21, 2014

Last Week...

Today, I tried to normalize the cobalt-only data several ways. I'm still not sure if I did it right or if WinLab did it correctly on the computer. Both ways I normalized it lead to larger error bars (not by much but still). Overall they all look pretty much the same. Because of this, I made a PowerPoint of my overall results for this set of data off of the original data instead of the reprocessed. A few days ago I thought my error bars were great overall, then today I realized I forgot to multiply one set by three so now they are not that good. Hopefully they are good enough when I add a few more runs of samples onto it in the next three days that have the extra buffer.
All three of the ways I tried to look at my data. All pretty much the same except for slightly different error bars.

Thursday, July 17, 2014

Tie dye Thursday

This morning I created new calibrations that included 0- 2.5 ppm Na to see if there are any effects due to sodium in the cobalt- only samples. I then diluted another set of sample solutions to run. This afternoon, I attempted to run the samples with the new calibration solutions but the sodium was very very off. I used a new stock solution of Na to make the solutions so tomorrow I am going to use the old and see if that fixes the problem. If not, I might have to scrap the new calibrations and simply use the old without sodium. The rest of the afternoon, the physics department tie dyed behind the science center.

Wednesday, July 16, 2014

Week 8: Wednesday

This morning, I ran the remaining samples from the other dilution of the cobalt- only series. They had concentrations similar to the runs I have made this week so I must have made a mistake a month ago when I ran them. This afternoon, I made more samples to run and ran a combination of all the samples I have made this past week. The last run had an overall trend of lower concentrations for Co, P and the internal standard Sr. Hopefully I can use the standard to correct for this tomorrow.
Steve and Prof. Andresen are super excited about making the motors move!! (and other stuff probably but I wasn't paying attention)

Tuesday, July 15, 2014

Week 8: Tuesday

I recreated a 30x dilution set of the cobalt-only samples and got the same result as yesterday. Although the ion concentrations are about a factor of 10 lower than the previous data, the charge ratio of cobalt for both dilutions are within each other's uncertainties. Tomorrow I'm going to play with the old samples to see if the factor of 10 still exists in the samples and then possible make new samples of that dilution and run it to compare to the old results.  

Monday, July 14, 2014

Monday Funday

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. 

Wednesday, July 9, 2014

Week 7: Wednesday

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.

Tuesday, July 8, 2014

Week 7: Tuesday

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.

Monday, July 7, 2014

Week 7 Day 1

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.

7/7

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.

Thursday, July 3, 2014

The Third of July

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. 
As you can see from the graph above, the sodium was all over the place for each run. There is a slight increase of sodium with higher sodium amounts (shocker) but it is not as smooth by any means as the other dilutions.

Wednesday, July 2, 2014

Week Six: Wednesday

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. 

Tuesday, July 1, 2014

Week Six: Tuesday

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. 

United States vs. Belgium: Week 6 Day 2

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.

Monday, June 30, 2014

Week Six: Lunes

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.