COURSE DESCRIPTION AND APPLICATION INFORMATION
| Course Name | Code | Semester | T+A+L (hour/week) | Type (C / O) | Local Credit | ECTS |
|---|---|---|---|---|---|---|
| Quantum Biology | MBG 438 | Fall-Spring | 03+00+00 | Elective | 3 | 5 |
| Academic Unit: | Department of Molecular Biology & Genetics |
| Mode of Delivery: | Face to face |
| Prerequisites: | None |
| Language of Instruction: | English |
| Level of Course Unit: | Undergraduate |
| Course Coordinator: | - - |
| Course Objectives: | Quantum biology, an emerging discipline, holds great potential for transformative advancements in science and engineering. Nevertheless, it poses a substantial challenge for prospective researchers due to its demand for proficiency across diverse domains, encompassing molecular biology and quantum physics. The traditional biophysics and biochemistry courses often overlook foundational mathematical and quantum information theoretical tools crucial to this burgeoning field. Similarly, quantum physics courses typically do not include vital quantum chemistry and molecular biology concepts. This course serves as a bridge to rectify these knowledge gaps and strives to foster a shared conceptual framework among students. Its overarching objective is to cultivate a new cohort of interdisciplinary scholars proficient in the concepts of molecular biology and quantum physics. This course is designed for undergraduate and postgraduate students who want to understand and analyze the role of quantum physical processes in bonding, molecular structure, and complex biological processes such as enzyme catalysis, olfaction, magnetoreception, and vision but lack the tools of quantum physics and information theory. On completing this course, the students can critically evaluate research papers in this field and formulate sensible research questions they may wish to pursue. This course does not aim to offer a comprehensive or opinionated review of the research field. Instead, it selects six illustrative examples of quantum effects in biosystems with increasing complexity in the final six weeks. It embarks the students to analyze these systems using the tools learned in the first eight weeks. The rationale for the selected examples is that they offer an ideal training ground to illustrate how quantum information tools help analyze biosystems. An incremental approach, starting with simple examples, ensures that students are given opportunities to consolidate their knowledge and skills before tackling more complex systems. |
| Course Contents: | 1. Chemical Bonding and Molecular Structure: The initial section of the course aims to acquaint students with the quantum superposition principle and its pivotal role in the quantum mechanical explanation of chemical bonding phenomena. It covers the concepts of molecular orbitals, hybridization, and resonance. Additionally, this section explores the intricate interplay between the dynamic structure and biological functions of water, proteins, enzymes, and DNA molecules. 2. Quantum Information Tools: The subsequent section predominantly concentrates on the concept of quantum superpositions shared within composite systems, namely quantum correlations such as entanglement and quantum discord. These correlations serve as valuable resources in the realm of quantum technologies. After presenting a comprehensive framework for quantifying quantum correlations via density matrix formalism, we move on to the theory of open quantum systems to illustrate how these correlations can survive in their environments. To achieve this, we employ quantum master equations as instrumental tools. The section concludes with an emphasis on non-equilibrium quantum thermodynamics as a practical approach to characterizing biological systems. This is particularly pertinent as living systems constantly expend energy to maintain a significant departure from thermal equilibrium with their surroundings. To this end, we introduce tools such as majorization-based extensions of equilibrium concepts, including entropy and free energy. 3. Quantum Biosystems: This section encapsulates the culmination of the course, effectively applying the knowledge and skills acquired in the preceding sections. Various mathematical tools, such as correlation measures, master equations, and thermo-majorization, are judiciously employed to analyze six specific biosystems of ascending complexity. These six biosystems include enzyme catalysis, olfaction, magnetoreception, vision, photosynthesis, and cognition. |
| Learning Outcomes of the Course Unit (LO): |
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| Planned Learning Activities and Teaching Methods: | Assignments: The assignments given bi-weekly throughout the first eight weeks of the course aim to elevate students to a level where they can read and comprehend a research paper in the field of quantum biology. Presentations: Each student, individually or in a group, will select a different research paper in the field of quantum biology. Over the last six weeks, a different student or group will present the assigned material, while the instructor will provide additional insights and commentary. Active Participation: Not attendance but in-class discussions, especially after the presentations of other students. Final Reports: In light of the knowledge acquired during the first eight weeks of the course, students must write a critical evaluation of the research paper they presented as a report. Well-prepared reports are envisioned to evolve into independent research projects after the conclusion of the course. |
WEEKLY SUBJECTS AND RELATED PREPARATIONS
| Week | Subjects | Related Preperation |
|---|---|---|
| 1 | Chemical bonding as a quantum superposition phenomenon: hybridized atomic orbitals vs molecular orbitals, resonance vs configuration interaction | Reading the related chapters from textbook 1 and review 1 |
| 2 | Role of quantum superposition in the structure and function of biomolecules: covalent vs hydrogen bonds in water, proteins, enzymes, and DNA | Reading the related chapters from textbook 1 and review 2 |
| 3 | Contextuality of quantum probabilities provided by quantum superposition: effect of measurements on state vectors vs density matrices | Reading the related chapters from textbook 2 and review 3 |
| 4 | Quantification of quantum superpositions shared between different systems: quantum entanglement, quantum discord, classical correlations | Reading the related chapters from textbook 2 and review 4 |
| 5 | Fragility of quantum superpositions in open quantum systems: decoherence vs thermalization by intra- vs inter-molecular interactions | Reading the related chapters from textbooks 2 & 3 and review 5 |
| 6 | Open quantum system dynamics described by quantum collision models: memory of the environment in Markovian vs non-Markovian molecular processes | Reading the related chapters from textbooks 2 & 3 and review 6 |
| 7 | Open quantum system dynamics described by quantum master equations: information vs energy exchange with molecular baths | Reading the related chapters from textbooks 2 & 3 and review 7 |
| 8 | Non-equilibrium quantum thermodynamics of single systems: majorization-based generalization of entropy and free energy | Reading the related chapters from textbooks 2 & 3 and review 8 |
| 9 | Quantum effects in enzyme catalysis and DNA replication | Reading the related chapters from textbook 4 and chosen research articles |
| 10 | Quantum effects in molecular recognition and olfaction | Reading the related chapters from textbook 4 and chosen research articles |
| 11 | Quantum effects in light-sensitive radical pair mechanism and magnetoreception | Reading the related chapters from textbook 4 and chosen research articles |
| 12 | Quantum effects in photoisomerization and vision | Reading the related chapters from textbook 4 and chosen research articles k |
| 13 | Quantum effects in biological energy transport and photosynthesis | Reading the related chapters from textbook 4 and chosen research articles k |
| 14 | Quantum effects in cognition and decision making processes | Reading the related chapters from textbook 4 and chosen research articles |
At Kadir Has University, a Semester is 14 weeks; The weeks 15 and 16 are reserved for final exams.
REQUIRED AND RECOMMENDED READING
| 1. The Nature of the Chemical Bond, Edition: 2 (ISBN: 9783527252176) Author: Pauling, L. Publisher: Cornell University Press (Year: 1960) Material Status: Recommended 2. Quantum Computation and Quantum Information, Edition: 10 (ISBN: 978-1107002173) Author: Nielsen, M., & Chuang, I. Publisher: Cambridge University Press (Year: 2010) Material Status: Recommended Additional Notes: (Chapters 2.1 – 2.4 & 8) 3. The Theory of Open Quantum Systems, Edition: 1 (ISBN: 978-0198520634) Author: Breuer, H., & Petruccione, F. Publisher: Oxford University Press (Year: 2002) Material Status: Recommended Additional Notes: (Chapters 3 & 4) 4. Quantum Effects in Biology, Edition: 1 (ISBN: 978-1-107-01080-2) Author: Mohseni, M., et al. Publisher: Cambridge University Press (Year: 2014) Material Status: Recommended |
OTHER COURSE RESOURCES
| 1. F.A. Weinhold. (1999). Chemical Bonding as a Superposition Phenomenon. J. Chem. Edu. 76, 1141. (doi: 10.1021/ed076p1141) 2. F. Weinhold and R.A. Klein. (2014). What is a hydrogen bond? Resonance covalency in the supramolecular domain. Chem. Educ. Res. Pract.15, 276. (doi: 10.1039/c4rp00030g) 3. M.P. Mueller. (2021). Probabilistic theories and reconstructions of quantum theory. SciPost Phys. Lect. Notes 28. (doi: 10.21468/SciPostPhysLectNotes.28) 4. G. Adesso et al. (2016). Measures and applications of quantum correlations, J. Phys. A: Math. Theor. 49(47), 473001. (doi: 10.1088/1751-8113/49/47/473001) |
ASSESSMENT METHODS AND CRITERIA
| Semester Requirements | Number | Percentage of Grade (%) |
|---|---|---|
| Attendance / Participation | 14 | 10 |
| Project | 1 | 25 |
| Homework Assignments | 4 | 40 |
| Presentation / Jury | 1 | 25 |
| Total: | 20 | 100 |
WORKLOAD
| Events | Count | Duration (Hours) | Total Workload (hour) |
|---|---|---|---|
| Course Hours | 14 | 3 | 42 |
| Project | 1 | 15 | 15 |
| Homework Assigments | 4 | 12 | 48 |
| Preparation for Presentation / Jury | 1 | 20 | 20 |
| Total Workload (hour): | 125 | ||
1 ECTS = 25 Hours Workload
THE RELATIONSHIP BETWEEN COURSE LEARNING OUTCOMES (LO) AND PROGRAM QUALIFICATIONS (PQ)
| # | PQ1 | PQ2 | PQ3 | PQ4 | PQ5 | PQ6 | PQ7 | PQ8 | PQ9 | PQ10 |
| LO1 | ||||||||||
| LO2 | ||||||||||
| LO3 | ||||||||||
| LO4 | ||||||||||
| LO5 | ||||||||||
| LO6 | ||||||||||
| LO7 |
Contribution: 1 Low, 2 Average, 3 High