Introducing myself - Kiheon Baek

Cyberteams TRECIS
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I’m Kiheon Baek, a postdoctoral fellow at the University of Texas at Dallas. Thanks for managing Europa and letting me join this system.

My research is focusing on designing and analyzing molecular structures of biomolecules for developing bioengineering tools. I’ve spent my time for studying about self-assembling peptides and protein engineering during my Master and PhD. My works are mixture of experimental and computational content, and in the case of computational part, I’m usually running the molecular dynamics (MD) simulations, analyzing those simulation data, and investigating protein structure database.

I have an experience in using Linux, some MD simulation and analysis tools (GROMACS, AMBER, NAMD), and Python about 8 years. I used TACC and servers in some labs for several years for simulating molecular structures in atomistic scale.

My challenges are

  1. building proper systems for running MD simulation of proteins. I think I can get help about these from colleagues using Europa.
  2. studying the basic of HPC. I may know how to run programs, set paths and variables, and allocate works to nodes, but I only know few basics about HPC. I’m hoping to have an opportunity to learn these in here.

Thanks.

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Welcome Kiheon !

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Hey Kiheon,

I’m very familiar with GROMACS, Amber and NAMD. My Ph.D. is actually in chemical physics and I’m a computational chemist by training.

GROMACS and NAMD we can get on the system in the next week or two. Amber is a commercial program but a PI on campus recently got Amber20 which we can install on our systems as well (I think; need to double check the license).

We will let you know when the software is available.

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Hi Chris,

This is really exciting! Thanks for managing the system and software again (+ letting me know about your background, too!).

My PI (Dr. Sheel Dodani) and I are planning several computational projects, and I guess she already mentioned some of those to you. I’ll update you with more details soon if that is okay for you.

Thanks again!