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Description of Individual Course Units

Course Unit Code Course Unit Title Type Of Course D U L ECTS MBG 5038 INTRODUCTION TO MATHEMATICAL MODELING: APPLICATIONS IN STRUCTURAL BIOLOGY ELECTIVE 3 0 0 9

Offered By

Molecular Biology and Genetics

Level of Course Unit

Second Cycle Programmes (Master's Degree)

Course Coordinator

ASSISTANT PROFESSOR EZGI KARACA EREK

Offered to

Molecular Biology and Genetics Molecular Biology and Genetics

Course Objective

To have a basic understanding of how biomolecules can be modeled through computational techniques

Learning Outcomes of the Course Unit

1   1. Learning the basics of mathematical modeling 2   2. Learning the basics of protein and nucleic acid structural modeling 3   Learning

Mode of Delivery

Face -to- Face

Prerequisites and Co-requisites

None

Recomended Optional Programme Components

None

Course Contents

Week Subject Description 1 Introduction to Mathematical Modeling 2 Hands on practical 3 Linear Algebra and its Applications in Structural Modeling 4 Derivatives and Integrals and their use in Structural Modeling 5 Experimental Structure Determination Methods 6 Empirical Force Fields 7 Computational Structure Determination Techniques 8 Hands on practical 9 Potential energy surfaces, energy minimization methods 10 Hands on practical 11 Classical mechanics and molecular dynamics 12 Hands on practical 13 Basic statistical mechanics and monte carlo 14 Hands on practical 15 Project presentations 16 Final exam

Recomended or Required Reading

A.E. Leach, Molecular Modelling: Principles and Applications, 2nd edition C. Brandon & J. Tooze, Introduction to Protein Structure, 2nd edition

Planned Learning Activities and Teaching Methods

Theoretical PowerPoint lectures with literature review/discussion, applied computer practicals

Assessment Methods

SORTING NUMBER SHORT CODE LONG CODE FORMULA 1 ASG ASSIGNMENT 2 MTE MIDTERM EXAM 3 FIN FINAL EXAM 4 FCG FINAL COURSE GRADE ASG * 0.30 + MTE * 0.30 + FIN * 0.40 5 RST RESIT 6 FCGR FINAL COURSE GRADE (RESIT) ASG * 0.30 + MTE * 0.30 + RST * 0.40

Further Notes About Assessment Methods

None

Assessment Criteria

One minute paper should be delivered by the end of each lecture to the instructor. This paper should contain a couple of sentences summarizing what was taught during the lecture.

Language of Instruction

English

Course Policies and Rules

To be announced.

Contact Details for the Lecturer(s)

ezgi.karaca@deu.edu.tr

Office Hours

To be announced.

Work Placement(s)

None

Workload Calculation

Activities Number Time (hours) Total Work Load (hours) Lectures 15 3 45 Preparations before/after weekly lectures 14 2 28 Preparation for final exam 1 30 30 Preparing assignments 2 20 40 Project Preparation 1 45 45 Preparing assignments 2 15 30 Final 1 10 10 Midterm 1 5 5 TOTAL WORKLOAD (hours) 233

Contribution of Learning Outcomes to Programme Outcomes

PO/LO PO.1 PO.2 PO.3 PO.4 PO.5 PO.6 PO.7 PO.8 LO.1 4 4 4 LO.2 4 4 4 4 LO.3 4 4 4 4