INTRODUCTION to COMPUTATIONAL BIOPHYSICS

AIM

It is aimed to teach the students some widely-used computational techniques such as molecular modeling, molecular docking and molecular dynamics simulations along with the parameters used to optimize simulations.

CONTENT

This course contains; Introduction to Quantum Chemistry,An overview to the Quantum Chemical Methods,Introduction to Statistical Mechanics,Molecular Dynamics,Force Fields,Solvation Models,Electrostatics in Molecular dynamics,Free Energy Calculations,Enhanced Sampling Techniques,Hybrid Simulation Methods : QM/MM calculations,Coarse Grained Potentials ,Molecular Docking,Application of above-mentioned techniques to biological problems -I,Application of above-mentioned techniques to biological problems -II.

1. 1

   Different aspects between molecular mechanics and quantum mechanics are described on a comparative basis.

   Taught by: Discussion Method, Problem Solving Method, Case Study Method, Reverse Brainstorming Technique, Simulation Technique, Problem Baded Learning Model, Inquiry-Based Learning · Assessed by: Project Task

2. 2

   Different force-fields and water models can be analzyed on a comparative basis.

   Taught by: Discussion Method, Problem Solving Method, Case Study Method, Self Study Method, Simulation Technique, Problem Baded Learning Model, Inquiry-Based Learning

3. 3

   Simulations can be performed using parallel-computing systems.

   Taught by: Simulation Technique, Experiential Learning

4. 4

   Molecular dynamics simulations are performed and the results are analzyed.

   Taught by: Demonstration Method, Case Study Method, Simulation Technique

WEEKLY PLAN

1. WEEK 1

   Introduction to Quantum Chemistry

2. WEEK 2

   An overview to the Quantum Chemical Methods

3. WEEK 3

   Introduction to Statistical Mechanics

4. WEEK 4

   Molecular Dynamics

5. WEEK 5

   Force Fields

6. WEEK 6

   Solvation Models

7. WEEK 7

   Electrostatics in Molecular dynamics

8. WEEK 8

   Free Energy Calculations

9. WEEK 9

   Enhanced Sampling Techniques

10. WEEK 10

    Hybrid Simulation Methods : QM/MM calculations

11. WEEK 11

    Coarse Grained Potentials

12. WEEK 12

    Molecular Docking

13. WEEK 13

    Application of above-mentioned techniques to biological problems -I

14. WEEK 14

    Application of above-mentioned techniques to biological problems -II

ASSESSMENT

• Rate of Midterm Exam to Success30%
• Rate of Final Exam to Success70%

WORKLOAD

READING

• Frenkel and Smit, Understanding Molecular Simulation : From Algorithms to Applications, , Academic Press, Computational Science Series Sunum

TEACHING STAFF

• Assoc.Prof. Özge ŞENSOYCOORDINATOR
• Assoc.Prof. Özge ŞENSOY