Summary August 6, 2014

I am so close to finishing my paper. I have like two things to change and then I can send it to Dr. Wheeler to be approved. 

Today we met with the office of admissions and financial aid. I think Amber and I were the only ones who asked the important questions considering we are seniors and already have a pretty good idea of what we want to do and where we want to go. Not all of my questions were answered due to the fact that I didn't ask them, so I have set up a meeting with Philip on Friday. He's going to answer the questions I have about applying to Duquesne, the major that I want to study, and possibly what I can do with a minor in music therapy. I also have a campus tour set up on Friday at 1! Phil went ahead and made the meeting for me since I had mentioned something about touring while we were in the meeting earlier. It was so nice of him. 

Until tomorrow, SEED!

I'm a little behind on blog summaries..

I haven't posted a blog summary in a while. The only things i've been working on since the last summary are my ACS poster and my paper. I am almost completely finished with the paper but my poster need a lot of work. It needs to be finished before noon tomorrow so I am most definitely going to be working on it tonight and tomorrow morning.

Summary July 30th, 2014

Today I finished up what i needed to before my meeting with Dr. Wheeler. It wasn't as bad as I thought it was going to be. He gave me a list of things to change and add and a way to create more space by two categories.
I also am planning activities for our trip to San Francisco! I found an open-top bus tour for only $45. It shows us everything, from downtown, the golden gate bridge, the "Painted Ladies", everything. I'm so excited.
So, I'm going to make the changes to my poster and start my paper!
Until tomorrow, SEED!

Summary July 29th, 2014

Yesterday I couldn't do very much. I spent the morning putting my data in graphs and finding room for all of it on my ACS poster. I ran out of room though, so when I meet with Dr. Wheeler today, I hope he tells me that I can take some background information off of it. It is comprised of, give or take, 75% background information, and 15% data. I did research on the Arrhenius equation during the afternoon, something I should have done a long time ago, but neglected to because I didn't think I needed to know it. I was wrong. Today I'm going to hopefully start my paper and have my poster finished by this afternoon.

Summary July 28th, 2014

I was so busy today.
I spent nearly all day acquiring correct data and putting it into graphs. I'm going to put everything on my ACS poster tomorrow because I have a meeting with Dr. Wheeler to discuss the poster and what I'm presenting on Wednesday. Technically, I finished my project today. I'm not going to be calculating the activation energy.
Until tomorrow, SEED.

2014 URP Symposium Experience- Melissa

Hi guys!
Friday was the Undergraduate Research Program's symposium. It was a chance for undergraduate students (and SEED students, too!) to display what they have accomplished during the duration of their respective programs. The morning began with a breakfast and the keynote which was given by Dr. Yoosuf Picard from Carnegie Mellon University. He talked about lasers and using them to make micro and nanoscale tools. After that was the plenary session where specific undergraduates who were chosen before hand to give their talks were able to. After these presentations was the picnic lunch. This gave me time to be with my family and calm myself down before my half of the two-hour presentation window was to begin. This summer's symposium went a lot smoother than last year and my poster had a lot more traffic than last year as well. Even the keynote speaker came to my poster, and he told me that I did a great job despite only being in high school.
There wasn't anything I didn't enjoy about friday, but a man came up to my poster and asked me if I knew what D0 stood for in the Arrhenius equation. I did, but due to nerves, I was unable to properly relay to him what it is the equation does and what the prefactor (or D0) means. This lead him to give me a 10 minute lecture on an equation that I had already known about, but I appreciated it nonetheless.
Dr. Wheeler came to my poster, too. He congratulated me for what I had accomplished and told me we weren't finished yet. There is much more still needed to be done before I depart for San Francisco and the ACS fall meeting. He also told me that if I ever needed a recommendation letter, he would be more than happy to write me a very strong recommendation. Upon hearing this, I teared up. The visiting Duquesne Alumnus didn't lie, networking is very important.
Everyone did a wonderful job on Friday, and I'm very upset that this was my last symposium at Duquesne. Unfortunately my SEED experience is almost over, and I cherish everything I've been taught and everyone I've met along the way. I wish I had more time here.

Summary July 24th, 2014

Yesterday I worked on my ACS poster all day. I got it down to the point where I only need to add data and draw conclusions, get it approved by Dr. Wheeler, and it can be printed. We don't plan to get in printed until it is absolutely needed to be because I haven't even began to touch on any of my specific aims let alone get adequate data. That's the problem with doing something no one else has.. it takes time to set the calculations up and right when you think everything worked, you discover that it hasn't. That is what happened in our case.
Today I plan on getting my symposium posted approved, printed, and on construction paper for the symposium tomorrow.

Summary July 22nd, 2014

These summaries are honestly the last thing on my mind at the end of the day.

On Tuesday I met with Travis to discuss my poster for the ACS meeting. It has to be printed, so I needed to know what to include on it. Dr. Wheeler took our lab and Dr. Burba out for lunch at the Cafe Fifth. It was nice, I'm going to miss everyone at the end of the program. After we came back, I spent the remainder of the afternoon designing my poster and finishing some things up on my panel poster. I have to add conclusions and more references and I'll be ready to present.

Summary July 21st, 2014

I was pretty busy all day yesterday.
I put all of my data that I've gathered so far into graphs and Travis reviewed it and decided that my MD simulations haven't reached equilibrium yet, and there is major energy fluctuations, so he's going to be tweaking our input files to see what helps. He and Dr. Burba, Luther's professor from Oklahoma, think that our box has to bigger than what it was initially, so hopefully I can get these calculations running before Thursday, pull the data Friday morning, and put it on my powerpoint before the symposium.
Since he is finally home from New York, my physics lessons are going to continue tomorrow after Dr. Wheeler takes our lab out for lunch.
Until tomorrow, SEED!

Summary July 18th, 2014

Today was wasted.

Luther told me yesterday to rerun all of my calculations because I didn't rename my output files in the script. I was almost done with that today when he told me to delete all of my data because he had developed an all encompassing script so that I didn't have to run 12 calculations. The script is temperature annealing my system. This means that it is heating up the box, decreasing the pressure, increasing the pressure, lowering the temperature again, and then decreasing the pressure to its initial pressure. From this calculation, I will get the density, MSDs, and total energy of the IL.

I'm running a calculation right now as a test run and I'm going to check it later tonight to see if it is finished.

See you Monday, SEED.

ALSO: My blog challenge will be done on Monday. Shakasia was busy this afternoon, so I didn't get the chance to interview her.

Blog Challenge #3- Melissa Fowkes

For this blog challenge, we were told to take pictures of the other SEED student in action in their labs and then interview one other student about their project.

Katie is separating her ligand using a separation funnel.

Rob is labeling his samples.

Steven is checking step 5 of his process. 

Cheyeanne is examining recombinant DNA that is being iced.

Amber is washing out the mortar and pestle with aqua regina solution.

Shakasia is examining her oxidized fuel using the ROTOVAP

Jisca is measuring out NaOH using a beaker. 

The SEED student I chose to interview is Shakasia Pierce. Shakasia is a 17 year old soon-to-be senior at West Mifflin Area High School. At school, she loves math and considers herself to be a math geek. Shakasia doesn't only focus on academics, though. Volleyball is a passion of hers, and she is currently the captain of her volleyball team. SEED isn't a program that she had heard of before or even want to apply to at first. One of her teachers pushed her to apply because she thought Shakasia would fit in here. College applications were also taken into consideration when she applied; she thought it would look good on them.
This summer at Duquesne University, Shakasia is studying diesel fuel and how it oxidizes. This project is significant because updated engine systems can't handle diesel fuel. The fuel causes problems in the engine when it reaches a certain temperature and was giving off admissions that are harmful to the environment. She is developing a new method that would lessen the amount of fuel oxidation. By using the SMORS methodology she is examining how much the fuel has oxidized and using dodecane to lessen the fuel oxidation.

Summary July 17th, 2014

I presented my PowerPoint to the group today and it went a lot smoother than the first time. The only thing I need to work on is the Einstein Equation slide, which I don't really know much about yet, but I'll have it before next Friday.

After the theory group meeting, I met with Luther to talk about my results. It turns out I DID ALL OF THE 12 CALCULATIONS WRONG and now I have to do them all again.Well, I did them right, but I didn't rename the MSD file as an output for every restart, so it rewrote after ever termination. They take at least an hour to complete, so I'm going to run them at home tonight and tomorrow so that I can potentially get data by tomorrow afternoon. 

Summary July 15th

Hi guys, sorry this is really late. I wasn't here yesterday and I left early Tuesday.

Today I did research trying to find the diffusion coefficients of 2 other IL system other than my own. Why? I have no clue, but I found one. I also finished all of my equlibration calculations, so we can begin production calculations on Thursday when I'm back. Apparently I have to present on Thursday, too. I don't have any data yet, so they're going to be getting the same presentation as last time, but hopefully I don't do as horribly this time around. 

See you thursday, SEED. 

Summary June 14th, 2014

Today I ran more calculations but at larger time steps, which means I began equilibration. This is the second step to molecular dynamics and it basically brings the system to its lowest energy by raising its temperature up really high and then lowering it again several times to see if there is any other energy barriers that it needs to overcome in order to be in its lowest energy state. Each step of the process is about an hour and a half long, so in the mean time I am doing some research on two other IL systems, [Bmim] [Cl-] & [Emim] [Cl-]. We need to have the diffusion coefficients for not only my system, but these systems, too. There is already calculated diffusion coefficients in literature for them, I just need to find them so that I can calculate mine. I also found the density per g/cm^3 and converted it into mol/L.
Until tomorrow, SEED.

Summary July 11th, 2014

Guess who actually got to run calculations today?!

It was one of the most stressful processes that I've gone through, though learning QM last year definitely beats out Molecular Dynamics. From the calcualtions ran at 290K, 300K, and 310K, I got a dumpfile that I can view in VMD of my system moving at that temperature, and the MSD's, though we aren't sure how to extract them yet.

Until tomorrow, SEED.

Summary July 10th, 2014

The morning was more productive that the afternoon.
I've been spending the last few days working on my powerpoint, and nothing else since I have nothing to do. I begin my actual project tomorrow and should have some kind of results by Monday hopefully. This way I actually know what it is I'm doing and can present a lot better than how I did on Wednesday at the symposium.
This afternoon I had a group meeting and it was pretty normal. Stephen and I left early to watch Kim Rosmus' Ph.D. defense, so I was busy all afternoon. It was interesting, being able to see everything she's done over the past 5 years. I'm so happy for her, congratulations Dr. Kim!

Abstract- Melissa Fowkes

Self-Diffusion Activation Energies of 1-methyl-3-pentylimidazolium chloride using Compensated Arrhenius Equation with Molecular Dynamics

Fowkes, Melissa; Wheeler, Ralph A.; Mackoy, Travis

Department of Chemistry and Biochemistry

Duquesne University

If ionic conductivities can be increased, ionic liquids could replace volatile electrolytes currently used in lithium ion batteries. Molecular Dynamics simulations have been performed to investigate the structure and dynamics of 1-methyl-3-pentylimidazolium chloride at different temperatures. The dynamics of the system were characterized by defining the mean squared displacement (MSD) from the dynamics trajectories. Diffusion coefficients were determined using the Einstein equation for diffusion over a distance and compared to published experimental values. A compensated Arrhenius formalism that scales out the temperature dependence of the dielectric constant in the exponential prefactor was then used to determine the activation energy for diffusion. 

Summary June 8th and 9th, 2014

On June 8th, I basically did my PowerPoint all day. I wanted to make sure that I was prepared for the meeting that was today.

Today, I reviewed my PowerPoint before the meeting and I was so ready to present. I was as confident as I could possibly be until I got in front of the group. My presentation was bad from start to finish. The main problem is I don't fully understand what is being done and this is because I'm not actually doing the calculations myself.
I had a meeting with Dr. Wheeler about my abstract, which I've submitted to the URP, and my presentation. When I told him how poorly I did and what the cause of it was, he told me that I should be running my own calculations and that he never told Travis otherwise. So, on Friday, I will be writing my own input files and trying to get calculations running in LAMMPS. I'm very excited to do this.
Until tomorrow, SEED.

Summary July 7th, 2014

Today was so stressful.
I made an attempt to write my abstract without help from either Luther or Travis. Luther says he really likes it and it's better than my first attempt, but Dr. Wheeler is still going to absolutely demolish it on Wednesday. Aside from that, I worked on my poster for most of the day. I still have so much to do to it.
Tomorrow I am probably going to be finishing what I can on it since I present to the group on Wednesday.
Until tomorrow, SEED.

Blog Challenge #2- Melissa Fowkes

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