Course Detail
Course Description
Course | Code | Semester | T+P (Hour) | Credit | ECTS |
---|
INTRODUCTION to COMPUTATIONAL BIOPHYSICS | BME3249570 | Spring Semester | 3+0 | 3 | 6 |
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 | | 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 | BME3249570 | Spring Semester | 3+0 | 3 | 6 |
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 | | X | | | |
Assessment Methods
Contribution Level | Absolute Evaluation |
Rate of Midterm Exam to Success | | 30 |
Rate of Final Exam to Success | | 70 |
Total | | 100 |
Numerical Data
Ekleme Tarihi: 09/10/2023 - 10:40Son Güncelleme Tarihi: 09/10/2023 - 10:41
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