Description of Individual Course Units
Course Unit CodeCourse Unit TitleType of Course UnitYear of StudySemesterNumber of ECTS Credits
9101036412011Biocatalysis-Multiscale Quantum Models Elective117
Level of Course Unit
Third Cycle
Language of Instruction
Turkish
Objectives of the Course
Biyokataliz tanımı ve kavramının öğretilmesi. Çok ölçekli kuantum modellerinin biyokatalizde kullanımının anlatılması.
Name of Lecturer(s)
Assoc. Prof. Dr. Cenk Selçuki
Learning Outcomes
1To be able to use the required softwares for efficient use of the methods
2To understand the fundamental principles of biocatalysis
3To be skilled to choose the method that will be used in biocatalysis.
4To be able to interpret the computed data
5To gain ability to compare and interpret the advantages and disadvantages of the applied methods
6To understand the fundamental principles of computational methods in biocatalysis
7To learn the terminology used in computational science and technology
Mode of Delivery
Face to Face
Prerequisites and co-requisities
None
Recommended Optional Programme Components
None
Course Contents
Biyokataliz: tanım ve kavramlar. Biyokatalizde ihtiyaçlar ve sorunlar. Kuantum metodları. Klasik metodlar. Hibrit metodların özellikleri: avantajları ve dezavantajları. QM/MM, MD/QM, ONIOM ve ilgili metodlar. Biyokatalize uyarlamalar. Protonlanma dengesinin modellenmesi. Ribozim katalizinde çok ölçekli simulasyonlar.
Weekly Detailed Course Contents
WeekTheoreticalPracticeLaboratory
1Biocatalysis: definitions and concepts
2Requirements and Problems in Biocatalysis
3Molecular Modelling and Biocatalysis
4Classic Mechanic Methods
5Classic Mechanic Methods
6Quantum Mechanical Methods
7Quantum Mechanical Methods
8Mid-term Exam
9Properties of hybrid methods: advantages and disadvantages
10QM/MM
11MD/QM
12ONIOM and related methods
13Applications to biocatalysis. Modeling protonation equilibria
14Multiscale simulations on ribozyme catalysis
15Project presentation
16Final Exam
Recommended or Required Reading
York, D. M., Lee, T.-S., Eds. 2009. “Multiscale Quantum Models for Biocatalysis-Modern Techniques and Applications”, Challenges and Advances in Computational Chemistry and Physics Volume 7, Series Ed. J. Leszczynski, Springer, Dordrecht.¬¬ Canuto, S., Ed. 2008. “Solvation Effects on Molecules and Biomolecules-Computational Methods and Applications”, Challenges and Advances in Computational Chemistry and Physics Volume 6, Series Ed. J. Leszczynski, Springer, Dordrecht.¬¬ Warshel, A., 1991. “Computer Modeling of Chemical Reactions in Enzymes and Solutions”, John Wiley & Sons, Inc. Fessner, W.-D., Anthonsen T., Eds. 2009. “Modern Biocatalysis”, Wiley-VCH Verlag GmbH & Co. KGaA
Planned Learning Activities and Teaching Methods
Activities are given in detail in the sections of "Assessment Methods and Criteria" and "Workload Calculation".
Assessment Methods and Criteria
Term (or Year) Learning ActivitiesQuantityWeight
Midterm Examination1100
SUM100
End Of Term (or Year) Learning ActivitiesQuantityWeight
Final Sınavı1100
SUM100
Term (or Year) Learning Activities40
End Of Term (or Year) Learning Activities60
SUM100
Work Placement(s)
None
Workload Calculation
ActivitiesNumberTime (hours)Total Work Load (hours)
Midterm Examination122
Final Examination122
Attending Lectures14342
Practice14342
Report Preparation11010
Project Preparation13030
Project Presentation122
Self Study14228
Individual Study for Mid term Examination12020
Individual Study for Final Examination13030
TOTAL WORKLOAD (hours)208
Contribution of Learning Outcomes to Programme Outcomes
PO
1
PO
2
PO
3
PO
4
PO
5
PO
6
PO
7
PO
8
PO
9
PO
10
PO
11
PO
12
LO1543 44      
LO2      5 5  5
LO34454 444344 
LO4444 44 5 445
LO5444455444435
LO6 5 4544 45 4
LO74345 4434 54
* Contribution Level : 1 Very low 2 Low 3 Medium 4 High 5 Very High
 
Ege University, Bornova - İzmir / TURKEY • Phone: +90 232 311 10 10 • e-mail: intrec@mail.ege.edu.tr