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.
Course 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.
Dersin Öğrenme Kazanımları
Teaching Methods
Assessment Methods
Different aspects between molecular mechanics and quantum mechanics are described on a comparative basis.
10, 12, 13, 20, 21, 3, 4
F
Different force-fields and water models can be analzyed on a comparative basis.
10, 12, 13, 14, 21, 3, 4
Simulations can be performed using parallel-computing systems.
21, 6
Molecular dynamics simulations are performed and the results are analzyed.
11, 13, 21
Teaching Methods:
10: Discussion Method, 11: Demonstration Method, 12: Problem Solving Method, 13: Case Study Method, 14: Self Study Method, 20: Reverse Brainstorming Technique, 21: Simulation Technique, 3: Problem Baded Learning Model, 4: Inquiry-Based Learning, 6: Experiential Learning
Assessment Methods:
F: Project Task
Course Outline
Order
Subjects
Preliminary Work
1
Introduction to Quantum Chemistry
2
An overview to the Quantum Chemical Methods
3
Introduction to Statistical Mechanics
4
Molecular Dynamics
5
Force Fields
6
Solvation Models
7
Electrostatics in Molecular dynamics
8
Free Energy Calculations
9
Enhanced Sampling Techniques
10
Hybrid Simulation Methods : QM/MM calculations
11
Coarse Grained Potentials
12
Molecular Docking
13
Application of above-mentioned techniques to biological problems -I
14
Application of above-mentioned techniques to biological problems -II
Resources
Frenkel and Smit, Understanding Molecular Simulation : From Algorithms to Applications, , Academic Press, Computational Science Series Sunum
Course Contribution to Program Qualifications
Course Contribution to Program Qualifications
No
Program Qualification
Contribution Level
1
2
3
4
5
1
An ability to apply knowledge of mathematics, science, and engineering
X
2
An ability to identify, formulate, and solve engineering problems
X
3
An ability to design a system, component, or process to meet desired needs within realistic constraints such as economic, environmental, social, political, ethical, health and safety, manufacturability, and sustainability
X
4
An ability to use the techniques, skills, and modern engineering tools necessary for engineering practice
X
5
An ability to use the techniques, skills, and modern engineering tools necessary for engineering practice
X
6
An ability to function on multidisciplinary teams
X
7
An ability to communicate effectively
X
8
A recognition of the need for, and an ability to engage in life-long learning
X
9
An understanding of professional and ethical responsibility
X
10
A knowledge of contemporary issues
X
11
The broad education necessary to understand the impact of engineering solutions in a global, economic, environmental, and societal context
X
12
Capability to apply and decide on engineering principals while understanding and rehabilitating the human body
X
Assessment Methods
Contribution Level
Absolute Evaluation
Rate of Midterm Exam to Success
30
Rate of Final Exam to Success
70
Total
100
ECTS / Workload Table
Activities
Number of
Duration(Hour)
Total Workload(Hour)
Course Hours
14
3
42
Guided Problem Solving
6
3
18
Resolution of Homework Problems and Submission as a Report
5
4
20
Term Project
0
0
0
Presentation of Project / Seminar
1
40
40
Quiz
0
0
0
Midterm Exam
1
20
20
General Exam
1
40
40
Performance Task, Maintenance Plan
0
0
0
Total Workload(Hour)
180
Dersin AKTS Kredisi = Toplam İş Yükü (Saat)/30*=(180/30)
6
ECTS of the course: 30 hours of work is counted as 1 ECTS credit.
Detail Informations of the Course
Course Description
Course
Code
Semester
T+P (Hour)
Credit
ECTS
INTRODUCTION to COMPUTATIONAL BIOPHYSICS
-
Spring Semester
3+0
3
6
Course Program
Prerequisites Courses
Recommended Elective Courses
Language of Course
English
Course Level
First Cycle (Bachelor's Degree)
Course Type
Elective
Course Coordinator
Assoc.Prof. Özge ŞENSOY
Name of Lecturer(s)
Assoc.Prof. Özge ŞENSOY
Assistant(s)
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.
Course 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.
Dersin Öğrenme Kazanımları
Teaching Methods
Assessment Methods
Different aspects between molecular mechanics and quantum mechanics are described on a comparative basis.
10, 12, 13, 20, 21, 3, 4
F
Different force-fields and water models can be analzyed on a comparative basis.
10, 12, 13, 14, 21, 3, 4
Simulations can be performed using parallel-computing systems.
21, 6
Molecular dynamics simulations are performed and the results are analzyed.
11, 13, 21
Teaching Methods:
10: Discussion Method, 11: Demonstration Method, 12: Problem Solving Method, 13: Case Study Method, 14: Self Study Method, 20: Reverse Brainstorming Technique, 21: Simulation Technique, 3: Problem Baded Learning Model, 4: Inquiry-Based Learning, 6: Experiential Learning
Assessment Methods:
F: Project Task
Course Outline
Order
Subjects
Preliminary Work
1
Introduction to Quantum Chemistry
2
An overview to the Quantum Chemical Methods
3
Introduction to Statistical Mechanics
4
Molecular Dynamics
5
Force Fields
6
Solvation Models
7
Electrostatics in Molecular dynamics
8
Free Energy Calculations
9
Enhanced Sampling Techniques
10
Hybrid Simulation Methods : QM/MM calculations
11
Coarse Grained Potentials
12
Molecular Docking
13
Application of above-mentioned techniques to biological problems -I
14
Application of above-mentioned techniques to biological problems -II
Resources
Frenkel and Smit, Understanding Molecular Simulation : From Algorithms to Applications, , Academic Press, Computational Science Series Sunum
Course Contribution to Program Qualifications
Course Contribution to Program Qualifications
No
Program Qualification
Contribution Level
1
2
3
4
5
1
An ability to apply knowledge of mathematics, science, and engineering
X
2
An ability to identify, formulate, and solve engineering problems
X
3
An ability to design a system, component, or process to meet desired needs within realistic constraints such as economic, environmental, social, political, ethical, health and safety, manufacturability, and sustainability
X
4
An ability to use the techniques, skills, and modern engineering tools necessary for engineering practice
X
5
An ability to use the techniques, skills, and modern engineering tools necessary for engineering practice
X
6
An ability to function on multidisciplinary teams
X
7
An ability to communicate effectively
X
8
A recognition of the need for, and an ability to engage in life-long learning
X
9
An understanding of professional and ethical responsibility
X
10
A knowledge of contemporary issues
X
11
The broad education necessary to understand the impact of engineering solutions in a global, economic, environmental, and societal context
X
12
Capability to apply and decide on engineering principals while understanding and rehabilitating the human body
