Countdown

Only 13 more days until Project SEED starts up again. Can't wait to meet the new students!

Tag Team Blog Challenge

Hey guys, this is Ian and Mary and we're gonna rock your socks. We decided to combine our posts into one awesome post filled with magical adventures in the realms of chemistry.

This is Mary. She is a senior at North Catholic High School and is working with Dr. Jeffry Madura in his computational chemistry lab. On an average day, she is running jobs on the National Science Foundation's TeraGrid super computer. Although, it took a lot of trials and errors... especially a lot of errors, to get to where she is now. Throughout the past 8 weeks, Mary has started over approximately 17 times (we lost count). Her project is to model the effects of sodium and potassium chloride on glutamic acid. The reason for doing such a wonderful project is to study how proteins made up of glutamic acid will be effected by sodium and potassium chloride. As you can see in the picture, she loves to decorate her cubicle..and everyone else's for that matter. Now that Mary finally has everything working properly, she is analyzing data 24/7. In this particular picture, she is analyzing her 2.0M NaCl salt box after 30 nanoseconds of molecular dynamics.

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This is Ian. He is also going to be a senior but he goes to Sewickley Academy. He is working with Ben Mogesa and Dr. Basu making synthetic bio-mimetic compounds. He is seen here making his copper (I) complex with dithione ligands. He is working in the glove box to be able to prevent oxygen from reacting with his compounds because it is filled with nitrogen. After making the compound, he dries it using a vacuum to suck out the liquid solvent and then can use the dried product. He can put it into different solvents and then analyze it using UV-Vis and Cyclic Voltammetry or he can use it dry to analyze it using IR. Ian also used copper (II) in his complex to study a different form of the complex.

Dr. Jeffry Madura's Academic Career

(Click here to view the video of this interview)

Growing up in Transfer, Pennsylvania. Jeffry D. Madura had no idea what he wanted to be when he grew up. Then, in the fifth grade, he started testing soil and the sparks started to fly- he had instantly developed an interest in science. It wasn't long before he dumped the soil to move on to bigger and better things.

As a high school student Jeffry was your average jock, spending his time on the basketball court and the football field at Reynolds High School. "Because there were no computers at the time, it was hard to be a nerd." Jeffry explains, even though he loved biology, chemistry, and physics.

After four years of being a star athlete, Jeffry moved on to Thiel college, where he declared a major of chemistry. He gave up being a star athlete and quit athletics to become a star pupil. There were 4 good faculty members that gave him the love of chemistry he still has today.

Knowing he wanted to continue his education, he tried out Purdue University to get his Ph.D in chemistry. His thesis was on gas phase reactions. Although it may be hard to believe, Jeffry did struggle to pass his qualifying exams. He was given 4 hours to answer 8 questions, an almost impossible task when the subject is physical chemistry. The only thing he regrets is not going as a Post Doc.

It wasn't long before he took on the challenging role as Chair of Duquesne University's Department of Chemistry and Biochemistry. "It was a real learning experience learning to juggle." He explains. It was most rewarding seeing his faculty becoming successful. After 10 years, he stepped down. His philosophy is to get new ideas, new new energy. Now, his goal is to train as many students as possible. He continues to share his gifts and touch almost every student he meets.

Field Trips Galore!

This week, we had two field trips back to back. On Thursday, we went to PPG's Monroeville branch. We were able to see some of the projects they are working on, such as photochromics and Teslin paper. Later, a chemical engineer came to talk to us about different jobs you can have with a chemistry degree, something very helpful to all of us SEED students. It was such a wonderful experience.




On Friday, all of the senior SEED students took a trip to Washington and Jefferson College. One of the admissions counselors talked to us about applying for student aid, and what colleges look for. This is very helpful, as all of us will be applying to colleges in just a few short months. From there, we had a tour guide take us on a walking tour of campus. Sydney and I immediately fell in love with it. Next was our amazing lunch, and finally a tour of the brand new science building, fully equipped with all the newest technology. The trip was great. I now have a new college to consider! and to think I would have never known about Washington and Jefferson if it wern't for Project Seed!

Trial and Error

Last week, I found out that all my data was wrong, because I did not check the concentration of my salt box. I later found out that I was adding the wrong number of ions to my salt box. My equation gave me the number 16...there was confusion whether that meant 16 anions and 16 cations, or 8 anions and 8 cations to add to the box. We later found out that it meant 16 of each. Now, I'm back on track. I've equilibrated and minimized 4 boxes, NaCl and KCl 0.2 and 2.0M. Now all we have to do is run them on our super, TeraGrid computer, and I'll finally have some results. (:

It's Crunch Time!

There are so many things planned for this week, it's hard to keep up! We have everything from our abstracts being due tomorrow, to seminars and guest speakers. Not to mention only 2 and a half weeks til the symposium! I can't wait to see how this week unfolds.

Learning the Ropes

Today, I started to learn how to use Assisted Model Building with Energy Refinement, or AMBER for short. It's the program I will use to build my salt box for my project. It's amazing how you can do research like this entirely on the computer. I'm all set up now on Visual Molecular Dynamics. This program was once like reading a foreign language but is now second nature to me. Most of all, I can't wait to see what is for lunch today (:

Amazing Technology

This would be my computer- the iMac. It's a lot different than a PC, and i'm still learning the ropes on how to use it. This is my one and only piece of equipment for this summer. The capabilities of this computer are endless. It's amazing all the research one can do with the programs. There are several unique programs this computer is capable of running. The one I am learning to use right now is called Visual Molecular Dynamics, or VMD for short. With this program, you can upload proteins from the online protein database, and see what they look like in 3D. You are also able to physically see the difference between two proteins, something that is very important for my project. The graduate students are using this program to find the area between the spaces in the protein. As of right now, I am still running through the training for this program. I still have many similar programs like it to learn, like the Nanoscale Molecular Dynamics, and Assisted Model Building with Energy Refinement. It has been such a learning experience so far with all of these programs. It is amazing to see the technology out there.This is a picture of a molecule I was using to get to know the program. It is known as Bovine. I still have yet to get a scale of the amino acid I will be using for my project, K2SO4 and NA2SO4. That is something I will attempt this afternoon.

First Day! (:

Today's first day was very exciting. I met tons of new people and learned how to use a MAC computer....or at least attempted to do so. Now, all I have to do is read up and learn more about the characteristics my specific amino acid. I'm so grateful for this experience, and I can't wait to see what this summer has in store (: