This week has been a new beginning as well as a continuance of certain concepts addressed in the past weeks of the internship. I had the great pleasure of meeting Professor Slava Bekker as well as Mr. John Dawson, two incredible people who work with Professor Igor Vorobyov in his lab to research molecular dynamics.
We were introduced to the concept of modeling changing ion channels and examining the different factors that can affect the behavior of the molecules such as the solvent that the chains are submerged in, as well as the presence of an ion located in the center of the channel.
We began the process of learning how to run a simulation using a program called “VMD,” or Visual Molecular Dynamics. Each of us students were able to at least begin running a simulation on a structure called Valinomycin, a type of carrier that binds Potassium ions. Using the program, we were able to see how the different molecules moved and changed shape over very short periods of time, commonly nanoseconds. A picture of the Valinomycin visualized using VMD is included below:
As I dive into this new field of study, I am once again overwhelmed with gratitude for the opportunity to become acquainted with people who are so incredibly knowledgeable and enthusiastic about such an important field of science. Professors Vorobyov and Bekker and Mr. Dawson have proven to be more supportive than I could ever ask for. They are always happy to take time to make sure everybody is understanding the material and able to perform the different tasks at their own pace. Everybody I have met through this internship has taught me the value of collaborators and teachers to learn from and alongside.
In my spare time this week, I have been continuing my different projects around my house as well as outside in the wilderness. One particular project that I am proud of is a honey jar I made out of clay using a pottery wheel that my parents own in our garage. I created the lid and then measured the pot to perfectly match the lid. I included an image of the greenware below:
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