Course Detail
Course Description
| Course | Code | Semester | T+P (Hour) | Credit | ECTS |
|---|---|---|---|---|---|
| THERMODYNAMICS of BIOMOLECULAR SYSTEMS | - | 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) | Assist.Prof. Mehmet Hikmet ÜÇIŞIK, Assoc.Prof. Özge ŞENSOY |
| Assistant(s) | |
| Aim | 1. To introduce basic concepts of thermodynamics. 2. To introduce the first law of thermodynamics together with the principle of conservation of energy and to teach the application of first law to closed and open systems. 3. To introduce the second and third laws of thermodynamics and concept of irreversibilty during energy transition in order to determine the performance of engineering systems. 4. To intoduce concepts of chemical equlibrium and phase equlibrium in thermodynamics. 5. To teach the definition of Boltzman distribution, driving force, free energy, chemical potential and solvation surface tension terms. 6. To introduce the basic concepts and principles of thermodynamics to be able to analyze biological systems. |
| Course Content | This course contains; Introduction to Thermo; 0th Law; Temperature; Work; Heat,State Functions, 1st Law, Paths (1st Law until Enthalpy),Joule and Joule-Thompson; Heat Capacity; Reversible and Irreversible Processes,Thermochemistry; 2nd Law; Entropy (Boltzmann and Clausius); ΔS for Reversible and Irreversible Processes,Fundamental Equations of Thermodynamics (Equilibrium; Maxwell Relations; Free Energy),Chemical Potential; Phase Equilibrium; Chemical Equilibrium; Equilibrium Constant,Standard States; Gibbs-Duhem ; ΔG0= -RTlnK; Example,Thermodynamic Driving Forces; Entropy and Statistical Probability; Boltzmann Distribution (First Half); Single Molecule Partition Function for Ideal Gases,Boltzmann Distribution (Second Half); Third Law of Thermodynamics ; Carnot Cycle ; Phase Diagrams of 1-Compound System; Clapeyron Equation; Claus-Clapeyron Equation,Regular Solutions; Mixing Energy; Mean Fields; Nonideal Solutions; Solvation; Colligative Properties; Osmotic Pressure and Phase Partitioning,Surface Tension; Equilibrium Between Liquids, Solids and Gases Polymer Solutions; Freely Jointed Chain; Chain Conformations; Rubber Elasticity (?),Special Topics w/ particular Focus on Self-Assembly and its Driving Forces ,Special Topics w/ Particular focus on Coarse Grain / Monte Carlo; M.D for obtaining state functions,Course Review & Evaluations ; Discussion Semester Project. |
| Dersin Öğrenme Kazanımları | Teaching Methods | Assessment Methods |
| Understand the concepts of thermodynamics and work, heat energy transformation. | 12, 13, 14, 16, 19, 2, 37, 5, 9 | A, E, F |
| Use the energy conversion on engineering applications and biological systems. | 12, 13, 14, 19, 2, 4, 9 | A, E, F |
| Use the relationship between the thermodynamics properties. | 12, 14, 16, 19, 9 | A, E, F |
| Understand and apply the Conservation of Energy Principle or First Law of Thermodynamics. | 12, 14, 16, 19, 9 | A, E, F |
| Solve the problems involving the open and closed systems, and to use the ideal gas equation. | 12, 14, 16, 9 | A, E |
| Understand and apply the second law of thermodynamics. | 12, 14, 16, 19, 9 | A, E |
| Understand the meaning of Entropy, Free energy, Driving force. | 12, 13, 14, 16, 19, 2, 37, 5, 9 | A, E, F |
| Understand the concept of equilibrium between solid, liquid and gas phases. | 12, 14, 16, 19, 5, 9 | A, E |
| Introduce solvation thermodynamic. | 12, 14, 16, 19, 5, 9 | A, E |
| Learn the science of thermodynamics in the field of materials science and biology. | 12, 13, 14, 16, 19, 2, 37, 5, 9 | A, E, F |
| Teaching Methods: | 12: Problem Solving Method, 13: Case Study Method, 14: Self Study Method, 16: Question - Answer Technique, 19: Brainstorming Technique, 2: Project Based Learning Model, 37: Computer-Internet Supported Instruction, 4: Inquiry-Based Learning, 5: Cooperative Learning, 9: Lecture Method |
| Assessment Methods: | A: Traditional Written Exam, E: Homework, F: Project Task |
Course Outline
| Order | Subjects | Preliminary Work |
|---|---|---|
| 1 | Introduction to Thermo; 0th Law; Temperature; Work; Heat | |
| 2 | State Functions, 1st Law, Paths (1st Law until Enthalpy) | |
| 3 | Joule and Joule-Thompson; Heat Capacity; Reversible and Irreversible Processes | |
| 4 | Thermochemistry; 2nd Law; Entropy (Boltzmann and Clausius); ΔS for Reversible and Irreversible Processes | |
| 5 | Fundamental Equations of Thermodynamics (Equilibrium; Maxwell Relations; Free Energy) | |
| 6 | Chemical Potential; Phase Equilibrium; Chemical Equilibrium; Equilibrium Constant | |
| 7 | Standard States; Gibbs-Duhem ; ΔG0= -RTlnK; Example | |
| 8 | Thermodynamic Driving Forces; Entropy and Statistical Probability; Boltzmann Distribution (First Half); Single Molecule Partition Function for Ideal Gases | |
| 9 | Boltzmann Distribution (Second Half); Third Law of Thermodynamics ; Carnot Cycle ; Phase Diagrams of 1-Compound System; Clapeyron Equation; Claus-Clapeyron Equation | |
| 10 | Regular Solutions; Mixing Energy; Mean Fields; Nonideal Solutions; Solvation; Colligative Properties; Osmotic Pressure and Phase Partitioning | |
| 11 | Surface Tension; Equilibrium Between Liquids, Solids and Gases Polymer Solutions; Freely Jointed Chain; Chain Conformations; Rubber Elasticity (?) | |
| 12 | Special Topics w/ particular Focus on Self-Assembly and its Driving Forces | |
| 13 | Special Topics w/ Particular focus on Coarse Grain / Monte Carlo; M.D for obtaining state functions | |
| 14 | Course Review & Evaluations ; Discussion Semester Project |
| Resources |
| SAB : Silbey, R., R. Alberty, and M. Bawendi. Physical Chemistry. New York, NY: John Wiley & Sons, 2004. ISBN: 9780471215042 DB : Dill, Ken A., and Sarina Bromberg. Molecular Driving Forces: Statistical Thermodynamics in Chemistry and Biology. New York, Ny; Routhledge, 2002, ISBN: 9780815320517 |
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 | 8 | 2 | 16 | |||
| Resolution of Homework Problems and Submission as a Report | 2 | 20 | 40 | |||
| Term Project | 0 | 0 | 0 | |||
| Presentation of Project / Seminar | 1 | 20 | 20 | |||
| Quiz | 0 | 0 | 0 | |||
| Midterm Exam | 1 | 30 | 30 | |||
| General Exam | 1 | 40 | 40 | |||
| Performance Task, Maintenance Plan | 0 | 0 | 0 | |||
| Total Workload(Hour) | 188 | |||||
| Dersin AKTS Kredisi = Toplam İş Yükü (Saat)/30*=(188/30) | 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 |
|---|---|---|---|---|---|
| THERMODYNAMICS of BIOMOLECULAR SYSTEMS | - | 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) | Assist.Prof. Mehmet Hikmet ÜÇIŞIK, Assoc.Prof. Özge ŞENSOY |
| Assistant(s) | |
| Aim | 1. To introduce basic concepts of thermodynamics. 2. To introduce the first law of thermodynamics together with the principle of conservation of energy and to teach the application of first law to closed and open systems. 3. To introduce the second and third laws of thermodynamics and concept of irreversibilty during energy transition in order to determine the performance of engineering systems. 4. To intoduce concepts of chemical equlibrium and phase equlibrium in thermodynamics. 5. To teach the definition of Boltzman distribution, driving force, free energy, chemical potential and solvation surface tension terms. 6. To introduce the basic concepts and principles of thermodynamics to be able to analyze biological systems. |
| Course Content | This course contains; Introduction to Thermo; 0th Law; Temperature; Work; Heat,State Functions, 1st Law, Paths (1st Law until Enthalpy),Joule and Joule-Thompson; Heat Capacity; Reversible and Irreversible Processes,Thermochemistry; 2nd Law; Entropy (Boltzmann and Clausius); ΔS for Reversible and Irreversible Processes,Fundamental Equations of Thermodynamics (Equilibrium; Maxwell Relations; Free Energy),Chemical Potential; Phase Equilibrium; Chemical Equilibrium; Equilibrium Constant,Standard States; Gibbs-Duhem ; ΔG0= -RTlnK; Example,Thermodynamic Driving Forces; Entropy and Statistical Probability; Boltzmann Distribution (First Half); Single Molecule Partition Function for Ideal Gases,Boltzmann Distribution (Second Half); Third Law of Thermodynamics ; Carnot Cycle ; Phase Diagrams of 1-Compound System; Clapeyron Equation; Claus-Clapeyron Equation,Regular Solutions; Mixing Energy; Mean Fields; Nonideal Solutions; Solvation; Colligative Properties; Osmotic Pressure and Phase Partitioning,Surface Tension; Equilibrium Between Liquids, Solids and Gases Polymer Solutions; Freely Jointed Chain; Chain Conformations; Rubber Elasticity (?),Special Topics w/ particular Focus on Self-Assembly and its Driving Forces ,Special Topics w/ Particular focus on Coarse Grain / Monte Carlo; M.D for obtaining state functions,Course Review & Evaluations ; Discussion Semester Project. |
| Dersin Öğrenme Kazanımları | Teaching Methods | Assessment Methods |
| Understand the concepts of thermodynamics and work, heat energy transformation. | 12, 13, 14, 16, 19, 2, 37, 5, 9 | A, E, F |
| Use the energy conversion on engineering applications and biological systems. | 12, 13, 14, 19, 2, 4, 9 | A, E, F |
| Use the relationship between the thermodynamics properties. | 12, 14, 16, 19, 9 | A, E, F |
| Understand and apply the Conservation of Energy Principle or First Law of Thermodynamics. | 12, 14, 16, 19, 9 | A, E, F |
| Solve the problems involving the open and closed systems, and to use the ideal gas equation. | 12, 14, 16, 9 | A, E |
| Understand and apply the second law of thermodynamics. | 12, 14, 16, 19, 9 | A, E |
| Understand the meaning of Entropy, Free energy, Driving force. | 12, 13, 14, 16, 19, 2, 37, 5, 9 | A, E, F |
| Understand the concept of equilibrium between solid, liquid and gas phases. | 12, 14, 16, 19, 5, 9 | A, E |
| Introduce solvation thermodynamic. | 12, 14, 16, 19, 5, 9 | A, E |
| Learn the science of thermodynamics in the field of materials science and biology. | 12, 13, 14, 16, 19, 2, 37, 5, 9 | A, E, F |
| Teaching Methods: | 12: Problem Solving Method, 13: Case Study Method, 14: Self Study Method, 16: Question - Answer Technique, 19: Brainstorming Technique, 2: Project Based Learning Model, 37: Computer-Internet Supported Instruction, 4: Inquiry-Based Learning, 5: Cooperative Learning, 9: Lecture Method |
| Assessment Methods: | A: Traditional Written Exam, E: Homework, F: Project Task |
Course Outline
| Order | Subjects | Preliminary Work |
|---|---|---|
| 1 | Introduction to Thermo; 0th Law; Temperature; Work; Heat | |
| 2 | State Functions, 1st Law, Paths (1st Law until Enthalpy) | |
| 3 | Joule and Joule-Thompson; Heat Capacity; Reversible and Irreversible Processes | |
| 4 | Thermochemistry; 2nd Law; Entropy (Boltzmann and Clausius); ΔS for Reversible and Irreversible Processes | |
| 5 | Fundamental Equations of Thermodynamics (Equilibrium; Maxwell Relations; Free Energy) | |
| 6 | Chemical Potential; Phase Equilibrium; Chemical Equilibrium; Equilibrium Constant | |
| 7 | Standard States; Gibbs-Duhem ; ΔG0= -RTlnK; Example | |
| 8 | Thermodynamic Driving Forces; Entropy and Statistical Probability; Boltzmann Distribution (First Half); Single Molecule Partition Function for Ideal Gases | |
| 9 | Boltzmann Distribution (Second Half); Third Law of Thermodynamics ; Carnot Cycle ; Phase Diagrams of 1-Compound System; Clapeyron Equation; Claus-Clapeyron Equation | |
| 10 | Regular Solutions; Mixing Energy; Mean Fields; Nonideal Solutions; Solvation; Colligative Properties; Osmotic Pressure and Phase Partitioning | |
| 11 | Surface Tension; Equilibrium Between Liquids, Solids and Gases Polymer Solutions; Freely Jointed Chain; Chain Conformations; Rubber Elasticity (?) | |
| 12 | Special Topics w/ particular Focus on Self-Assembly and its Driving Forces | |
| 13 | Special Topics w/ Particular focus on Coarse Grain / Monte Carlo; M.D for obtaining state functions | |
| 14 | Course Review & Evaluations ; Discussion Semester Project |
| Resources |
| SAB : Silbey, R., R. Alberty, and M. Bawendi. Physical Chemistry. New York, NY: John Wiley & Sons, 2004. ISBN: 9780471215042 DB : Dill, Ken A., and Sarina Bromberg. Molecular Driving Forces: Statistical Thermodynamics in Chemistry and Biology. New York, Ny; Routhledge, 2002, ISBN: 9780815320517 |
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 | |