TEACHING

Fall 2014 – Training Day “Hands-on Introduction to Protein Simulations”

• “Hands on Introduction to Protein Visualization” (pdf – required files).

• “Hands on Introduction to Protein Simulations” (pdf – required files).

Fall 2015-2016-2017-2019-2021 – Quantum Mechanics and Spectroscopy (CHEM 6510) – For more information check the OSU-CARMEN web page or contact Dr. Marcos Sotomayor.

Fall 2015 – Introduction to Electronic Structure (CHEM 6540) – For more information check the OSU-CARMEN web page or contact Dr. Marcos Sotomayor.

Spring 2014-2015-2016-2017-2018-2019-2020-2022-2023 – Physical Chemistry (CHEM 4210 / BIOCHEM 5722) – Introduction to Quantum Mechanics and Applications / Structural Biology / Statistical Thermodynamics. For more information check the OSU-CARMEN web page or contact Dr. Marcos Sotomayor.

Fall 2018-2019-2021-2022 – Early Experience in Biochemical Research (BIOCHEM 2900H) – Introduction to research in biochemistry at OSU. For more information check the OSU-CARMEN web page or contact Dr. Marcos Sotomayor.

Spring 2020 – Physical Biochemistry (BIOCHEM 6765) – Introduction to various biophysical techniques, including X-ray crystallography and small angle X-ray scattering. For more information check the OSU-CARMEN web page or contact Dr. Marcos Sotomayor / Dr. Mark Foster.

Tutorials and case studies to which M. Sotomayor contributed to while at TCBG-UIUC:

• Using VMD: http://www.ks.uiuc.edu/Training/Tutorials/vmd-index.html . Describes how to look for interesting structural properties of proteins using VMD. Tutorial works on Windows, Mac, and Unix/Linux platforms.

• NAMD Tutorial: http://www.ks.uiuc.edu/Training/Tutorials/namd-index.html#namdtut. Describes how to use NAMD to set up basic molecular dynamics simulations, and how to understand typical NAMD input and output files, with an emphasis on such files for protein energy minimization and equilibration in water, as well as Steered Molecular Dynamics Simulations. Tutorial versions available for Windows, or Mac and Unix/Linux platforms.

• Membrane Proteins Tutorial: http://www.ks.uiuc.edu/Training/Tutorials/spectop-index.html#memtut. Step by step tutorial for setting up and running molecular dynamics simulations of membrane proteins. Requires VMD, NAMD, and Solvate. Tutorial works on Unix/Linux platform.

• Electrostatic Maps and Ion Conduction: http://bionano.physics.illinois.edu/Tutorials/. This tutorial guides through all necessary steps to compute the ionic current and electrostatic potential map of a membrane channel or a synthetic nanopore. Requires VMD, NAMD, and Solvate. Tutorial works on Unix/Linux platform.

• Water case study: http://www.ks.uiuc.edu/Training/CaseStudies/.