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. In this way, students are expected to run a molecular dynamics simulation by their own.

CONTENT

This course contains; Introduction to Quantum Chemistry,An overview to the Quantum Chemical Methods,Introduction to Statistical Mechanics,Comperative Study of Classical and Enhanced Molecular Dynamics Simulations,Analysis of force fields used in molecular dynamics simulations and investigation of the Transferability of the force fields,Comperative Study of classical and polarizable water models used in molecular dynamics simulations,Derivation of potentials used to calculate long-range electrostatic interactions,Calculation of free energies using metadynamics, thermodynamics integration and umbrella sampling and comperative interpretation of the results.,Investigation of the impact of enhanced sampling techniques on the conformational energy landscapes of proteins,Investigation of the impact of hybrid potentials, which are formed by quantum and classical mechanics, on the structure and dynamics of proteins. ,Investigation of coarse grained models that are used to achieve long time scales in biological systems.,Investigation of free and constrained molecular docking calculations and impact of water therein.,Discussion on the widely and currently used computational biophysical techniques -I,Discussion on the widely and currently used computational biophysical techniques-II.

1. 1

   Different aspects between molecular mechanics and quantum mechanics are understood and the student can decide which method is appropriate for solving a given biological problem.

   Taught by: Discussion Method, Problem Solving Method, Case Study Method, Self Study Method, Question - Answer Technique, Project Based Learning Model, Simulation Technique, Inquiry-Based Learning, Experiential Learning · Assessed by: Traditional Written Exam, Project Task

2. 2

   The force-fields as well as water models which are needed to perform a molecular dynamics simulation can be determined.

   Taught by: Discussion Method, Problem Solving Method, Case Study Method, Question - Answer Technique, Project Based Learning Model, Reverse Brainstorming Technique, Simulation Technique, Problem Baded Learning Model, Inquiry-Based Learning · Assessed by: Traditional Written Exam

3. 3

   Knowledge can be gathered related to the basic commands used in Linux.

   Taught by: Problem Solving Method, Case Study Method, Brainstorming Technique, Problem Baded Learning Model, Experiential Learning · Assessed by: Project Task

4. 4

   A molecular dynamics simulation can be started on the clusters.

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

5. 5

   Molecular dynamics simulations can be performed

   Taught by: Discussion Method, Problem Solving Method, Case Study Method, Reverse Brainstorming Technique, Simulation Technique, Experiential Learning · Assessed by: Project Task

6. 6

   Select the optimum technique can be proposed to solve a problem related to computational biophysics.

   Taught by: Discussion Method, Problem Solving Method, Case Study Method, Question - Answer Technique, Project Based Learning Model, Simulation Technique, Inquiry-Based Learning, Experiential Learning · Assessed by: Project Task

7. 7

   Analyzes molecular dynamics simulation results.

   Taught by: Discussion Method, Problem Solving Method, Case Study Method, Project Based Learning Model, Reverse Brainstorming Technique, Simulation Technique, Experiential Learning

8. 8

   Biological systems can be modelled by computational biophysics methods and the results can be interpreted.

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

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

   Comperative Study of Classical and Enhanced Molecular Dynamics Simulations

5. WEEK 5

   Analysis of force fields used in molecular dynamics simulations and investigation of the Transferability of the force fields

6. WEEK 6

   Comperative Study of classical and polarizable water models used in molecular dynamics simulations

7. WEEK 7

   Derivation of potentials used to calculate long-range electrostatic interactions

8. WEEK 8

   Calculation of free energies using metadynamics, thermodynamics integration and umbrella sampling and comperative interpretation of the results.

9. WEEK 9

   Investigation of the impact of enhanced sampling techniques on the conformational energy landscapes of proteins

10. WEEK 10

    Investigation of the impact of hybrid potentials, which are formed by quantum and classical mechanics, on the structure and dynamics of proteins.

11. WEEK 11

    Investigation of coarse grained models that are used to achieve long time scales in biological systems.

12. WEEK 12

    Investigation of free and constrained molecular docking calculations and impact of water therein.

13. WEEK 13

    Discussion on the widely and currently used computational biophysical techniques -I

14. WEEK 14

    Discussion on the widely and currently used computational biophysical techniques-II

ASSESSMENT

• Rate of Midterm Exam to Success50%
• Rate of Final Exam to Success50%

WORKLOAD

READING

• Frenkel and Smit, Understanding Molecular Simulation : From Algorithms to Applications, , Academic Press, Computational Science Series Sunum
• 1) Frenkel and Smit, Understanding Molecular Simulation : From Algorithms to Applications, , Academic Press, Computational Science Series 2)Allen and Tildesley, Computer Simulation of Liquids, Clarendon Press 3)Zhou, Molecular Modeling at the Atomic Scale, CRC Press, Taylor & Francis.

TEACHING STAFF

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