Kelly Stellmacher, Molecular Dynamics: Modeling and Analyzing Changes in Biological Structures, Week 5

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Here, after another amazing week with an amazing group of people, I have arrived at another transition point. I am not sure what will become of my last week interning at UC Davis, but what I am sure of is the weeks that have led up to this point. 

This past week, we have spent time each day learning about varying components of the research field of molecular dynamics. We used Visual Molecular Dynamics (VMD), a program we were introduced to last week, as a tool for visualizing and simulating the process of a channel or protein changing shape over time. We learned how to use the program to change the visualization of the molecules, how to display the ions that passed through, and how to select certain chains in certain components. Below is an image of an ion channel visualized with VMD from Professor Vorobyov’s simulation that features the voltage-sensing domain inside the channel:

We were also able to utilize our knowledge of equations used in physics including Ohm’s Law in order to derive the resistance of the ions as they passed through the channels. Throughout this process, we were given both clear and directed instruction and the ability to communicate and collaborate with our fellow students in breakout rooms to assist one another along the way. 

I must once again rave about the incredibility of each of our instructors. Professor Vorobyov would send us all an email after a meeting to thank us for attending as well as ask us if we had any questions or sought any additional assistance. He worked so incredibly hard to ensure that each of us were able to learn as much as we could in the limited amount of time that we had. Professor Bekker and Mr. Dawson each devoted their time to guiding and teaching us throughout the week as well, attending meetings and giving their experienced insight into different topics to which we students are still very new.

I’m once again crestfallen to hear that we are ending this phase of our internship to work with another professor at UC Davis, especially after so little time spent with these amazing people. And yet, if I have learned anything about collaboration and connection from the teachers and fellow students I have met during this internship, it is that if I am open-minded and willing to learn all that others are willing to offer, then I am able to connect with and appreciate everybody whom I will meet in the world of academics and research. 

With this mindset, I will face my final week of internship with positivity and enthusiasm to meet a new mentor and absorb all that I can in the time which remains of this incredible experience. 

On a different note, I have been mostly knitting, woodcarving, and creating other forms of practical art to fill the rest of my time. The blanket I told you about a few weeks ago is coming along and I decided to begin a new project. I am taking long stalks of feather grass and making Asian-style hats using some duct tape and the segments of bamboo-like stalks. Here is my first finished product that features a hexagonal-pyramid structure:

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