CHM 579: Computational Chemistry
Instructor: Gaurav Chopra, DRUG 261, email@example.com, (765) 496-6108
Theoretical basis and practical applications of computational methods relevant to chemical and biochemical research problems. The objective of the course is learning, developing and using molecular modeling methodologies useful for research work in a variety of areas. The applications of the course range from computational modeling of biomolecules, drug discovery, to nanotechnology, depending on the system of interest. We will learn about theoretical concepts and techniques used in modern computational chemistry and biology that includes modeling of energetic interactions between atoms from polarizable to classical to statistical (knowledge-based) formulations that are applied to areas in drug design and discovery, nanotechnology, and other areas of molecular modeling and simulations taking into account the students background and interest.
Lectures: Monday and Wednesday, 9:30am-10:20am in BRWN 3102
Labs: Wednesday, 3:30pm-5:20pm in WTHR 214
Office hours: Monday and Friday from 4:00-5:00pm in DRUG 261 ; Online office hours: Follow the links separated by date on twitter. The handle for the class is @compchemclass.
Course notifications and discussion forum: Register at Piazza and add CHM 579 class
- Introduction to molecular modeling and applications
- Simulation methods: nanoscale to mesoscale simulations
- Force fields: knowledge-based, classical, polarizable potentials
- Environment: Vacuum, implicit, explicit and polarizable solvents
- Systems: Protein-ligand docking, interactome based drug discovery
- Free energy calculations in the context of simulation and potential functions
- Course readings: Publications
- Individual lab assignments: 41% (Assignment #0=1%, #1=5%, #2=10%, #3=15%, #4=10%)
- Quizzes: 14% (2% each, 7 best scores are included)
- Midterm exam: 15% (March 25, 2017 at 2:00pm-4:00pm in DRUG lobby conference room)
- Final project presentations: 15% (TBD: Last week of April or First week of May) - Topic to be mutually selected by student and instructor, maximum groups size of 3 permitted
- Final exam: 15% (TBD: April 26, 2017 at 3:30pm in WTHR 214 or Week of May 1-6, 2017)
- Late day policy: You can use 4 late days in total for all assignments (except final project) anyway you like including the day of submission. As an example, if an assignment is due on Wednesday at 3:29pm and you submitted it at a later time on Wednesday, one late day will be counted and only 2 late days will remain for other assignments.
- Late day penalty: Each additional late day costs 10% of the assignment grade.
The submission of all assignments and the final project for this course is in form of webpages. The assignments will be made available on the day we will discuss them in the lab sessions. Due dates and times of the assignments are shown as follows. Wednesday lab help sessions are mandatory. Assignments are written in the format of a research publication unless otherwise noted.
- Assignment Zero: Learning HTML, Due: 18 January 2017 at 3:29 pm
- Assignment 1: Molecular Structure and Monte Carlo, Due: Wednesday, 1 February 2017 at 3:29 pm
- Assignment 2: Molecular Simulation of Simple Homogenous Systems, Due: Wednesday, 15 February 2017 at 3:29 pm
- Assignment 3: Molecular Simulation and Sampling of Complex Systems, Due: Wednesday, 29 March 2017 at 3:29 pm
- Assignment 4: Ionic Interactions, Free Energy, Molecular Docking (a): Hydrated ions, (b): Hydration free energy of ions, (c): Molecular docking and design, Due: Wednesday, 26 April 2017 at 3:29 pm
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