General electives can be selected from all the courses offered at Koç University.

CHBI 506 / BIOINFORMATICS
Sınıf: Credit: 3Precondition:

The principles and computational methods to study the biological data generated by genome sequencing, gene expressions, protein profiles, and metabolic fluxes. Application of arithmetic, algebraic, graph, pattern matching, sorting and searching algorithms and statistical tools to genome analysis. Applications of Bioinformatics to metabolic engineering, drug design, and biotechnology.

CHBI 510 / INDUSTRIAL MICROBIOLOGY
Sınıf: Credit: 3Precondition:

Key aspects of microbial physiology; exploring the versatility of microorganisms and their diverse metabolic activities and products; industrial microorganisms and the technology required for large-scale cultivation.

CHBI 516 / BIOTECHNOLOGY
Sınıf: Credit: 3Precondition:

Recombinant DNA, enzymes and other biomolecules. Molecular genetics. Commercial use of microorganisms. Cellular reactors; bioseparation techniques. Transgenic systems. Gene therapy. Biotechnology applications in environmental, agricultural and pharmaceutical problems.

CHBI 530 / SYSTEM BIOLOGY
Sınıf: Credit: 3Precondition:

Reconstruction of metabolic network from genome information and its structural and functional analysis, computational models of biochemical reaction networks; system biology in drug discovery and proteomics, flux balance analysis; modeling of gene expression; system biology in artificial intelligence. These concepts will be supported with statistic, thermodynamic, structural biology and learning machine

CHBI 550 / SELECTED TOPICS IN CHEMICAL AND BIOLOGICAL ENGINEERING
Sınıf: Credit: 3Precondition:

Topics will be announced when offered.

CHBI 584 / TISSUE ENGINEERING
Sınıf: Credit: 3Precondition:

The fundamentals of tissue engineering at the molecular and cellular level; techniques in tissue engineering; problems and solution in tissue engineering; transplantation of tissues in biomedicine using sophisticated equipments and materials; investigation of methods for the preparation of component of cell, effect of growth factors on tissues.

CHBI 585 / MOLECULAR MODELING AND SIMULATIONS
Sınıf: Credit: 3Precondition: CHBI. 204 or consent of the instructor

Principles of molecular modeling in chemical engineering applications; fundamentals for molecular simulation of adsorption and diffusion processes in nanoporous materials; molecular dynamics methods for gas transport in nanopores; Monte Carlo methods for equilibrium based gas separations; molecular modeling of zeolites and metal organic frameworks for gas storage.

CMSE 501 / INTRODUCTION TO DATA SCIENCE WITH PYTHON
Sınıf: Credit: 3Precondition:

An introduction to interactive Python and Jupyter Notebooks, Python built-in data structures, conditional statements, loops, functions, strings and basic input/output, basics of data manipulation and visualization with relevant Python libraries, different types of plots, vector/matrix representations, linear algebra operations, probability/statistics operations, data analysis applications

CMSE 520 / BIOMOLECULAR STRUCTURE, FUNCTION AND DYNAMICS
Sınıf: Credit: 3Precondition: CMSE. 501 or consent of the instructor

Relationship between structure, function and dynamics in biomolecules. Overview of the biomolecular databases and application of computational methods to understand molecular interactions; networks. Principles of computational modeling and molecular dynamics of biological systems.

COMP 513 / INFORMATION THEORY
Sınıf: Credit: 3Precondition:

Entropy, Relative Entropy and Mutual Information; Asymptotic Equipartition Theory; Entropy Rates of a Stochastic Process; Data Compression; Kolmogorov Complexity; Channel Capacity; Differential Entropy; The Gaussian Channel; Maximum Entropy and Spectral Estimation; Rate Distortion Theory, Network Information Theory.

COMP 529 / PARALLEL PROGRAMMING
Sınıf: Credit: 3Precondition:

Fundamental concepts of concurrency, non-determinism, atomicity, race-conditions, synchronization, mutual exclusion. Overview of parallel architectures, multicores, distributed memory. Parallel programming models and languages, multithreaded, message passing, data driven, and data parallel programming. Design of parallel programs, decomposition, granularity, locality, communication, load balancing. Patterns for parallel programming, structural, computational, algorithm strategy, concurrent execution patterns. Performance modeling of parallel programs, sources of parallel overheads.

COMP 570 / BIOINFORMATICS AND ALGORITHMS IN COMPUTATIONAL BIOLOGY
Sınıf: Credit: 3Precondition:

Algorithms, models, representations, and databases for collecting and analyzing biological data to draw inferences. Overview of available molecular biological databases. Sequence analysis, alignment, database similarity searches. Phylogenetic trees. Discovering patterns in protein sequences and structures. Protein 3D structure prediction: homology modeling, protein folding, representation for macromolecules, simulation methods. Protein-protein interaction networks, regulatory networks, models and databases for signaling networks, data mining for signaling networks.

ELEC 510 / INFORMATION THEORY
Sınıf: Credit: 3Precondition:

Entropy, Relative Entropy and Mutual Information; Asymptotic Equipartition Theory; Entropy Rates of a Stochastic Process; Data Compression; Kolmogorov Complexity; Channel Capacity; Differential Entropy; The Gaussian Channel; Maximum Entropy and Spectral Estimation; Rate Distortion Theory, Network Information Theory.

ELEC 522 / INTRODUCTION TO MEMS AND MOEMS
Sınıf: Credit: 3Precondition:

Introduction to Microsystems, MEMS and its integration with optics; Microfabrication and process integration; MEMS Modeling and design; Actuator and sensor design; Mechanical structure design; Optical system design basics; Packaging; Optical MEMS application case studies; Scanning systems (Retinal Scanning Displays, Barcode scanners); Projection display systems (DMD and GLV); Infrared imaging cameras; Optical switching for telecommunications.

ELEC 523 / OPTICAL INFORMATION PROCESSING
Sınıf: Credit: 3Precondition: (ELEC. 201 and ELEC. 429) or consent of the instructor

Review of 2-D linear system theory and 2-D Fourier transforms. Integral transforms used in optical signal processing; Fundamentals of physical optics and diffraction theory; Fourier and imaging properties of optical systems; Coherent and Incoherent optical image processing; Fundamental architectures for correlation and spectrum analysis; Interferometry; Discrete analog optical processors; Holography; Review of 3D Display technologies.

ELEC 562 / MICRO AND NANOFABRICATION
Sınıf: Credit: 3Precondition:

Fabrication and characterization techniques for micro and nano electro mechanical systems, MEMS & NEMS (including: microlithography; wet & dry etching techniques; physical & chemical vapor deposition processes; electroplating; bonding; focused ion beams; top-down approaches - electron-beam lithography, SPM, soft lithography - ; bottom-up techniques based on self-assembly). Semiconductor nanotechnology. Nanotubes & nanowires. Biological systems. Molecular electronics.

ENGL 500 / ACADEMIC WRITING
Sınıf: Credit: 0Precondition:

The following objectives will be met through extensive reading, writing and discussion both in and out of class.Build a solid background in academic discourse, both written and spoken. Improve intensive and extensive critical reading skills. Foster critical and creative thinking. Build fundamental academic writing skills including summary, paraphrase, analysis, synthesis. Master cohesiveness as well as proper academic citation when incorporating the work of others.

ENGR 500 / APPLIED OPTIMAL CONTROL
Sınıf: Credit: 3Precondition:

Optimization problems for dynamical systems. Pontryagin?s Maximum Principle. Optimality conditions for nonlinear dynamical systems. Linear Quadratic Optimal Control of continuous and discrete linear systems using finite and infinite time horizons. Stability and performance analysis of the properties of the optimal feedback solutions. Moving horizon optimal control of constrained systems using Model Predictive Control formulation. Applications from different disciplines and case studies.

MASE 538 / INTERMOLECULAR AND SURFACE FORCES
Sınıf: Credit: 3Precondition: CHEM. 301 or consent of the instructor

Intermolecular forces which govern self-organization of biological and synthetic nanostructures. Thermodynamic aspects of strong (covalent and coulomb interactions) and weak forces (dipolar, hydrogen bonding). Self-assembling systems: micelles, bilayers, and biological membranes. Computer simulations for ôhands-onö experience with nanostructures.

MASE 542 / BIOMATERIALS
Sınıf: Credit: 3Precondition:

Materials for biomedical applications; synthetic polymers, metals and composite materials as biomaterials; biopolymers, dendrimers, hydrogels, polyelectrolytes, drug delivery systems, implants, tissue grafts, dental materials, ophthalmic materials, surgical materials, imaging materials.

MASE 568 / MECHANICS AND MATERIALS IN MEDICINE
Sınıf: Credit: 3Precondition:

Bioengineering, engineering materials, medicine, polymers, metals, smart materials, surgical implants, surgical instruments, cell and tissue mechanics, microsurgery, self-expanding stents, physical therapy, phase transformations, shape memory alloys.

MATH 504 / NUMERICAL METHODS I
Sınıf: Credit: 3Precondition:

A graduate level introduction to matrix-based computing. Stable and efficient algorithms for linear equations, least squares and eigenvalue problems. Both direct and iterative methods are considered and MATLAB is used as a computing environment.

MATH 506 / NUMERICAL METHODS II
Sınıf: Credit: 3Precondition:

Development and analysis of numerical methods for ODEs, an introduction to numerical optimization methods, and an introduction to random numbers and Monte Carlo simulations. The course starts with a short survey of numerical methods for ODEs. The related topics include stability, consistency, convergence and the issue of stiffness. Then it moves to computational techniques for optimization problems arising in science and engineering. Finally, it discusses random numbers and Monte Carlo simulations. The course combines the theory and applications (such as programming in MATLAB) with the emphasis on algorithms and their mathematical analysis.

MBGE 501 / ADVANCED MOLECULAR AND CELL BIOLOGY
Sınıf: Credit: 3Precondition: MBGE. 204 or consent of the instructor

The advanced methodology used for modern biological science research. Topics include the interpretation of data gained from both hypothesis-driven and high-throughput experiments from research articles focusing on DNA repair, DNA replication, transcription, cell cycle, organelle biogenesis, proteomics and genetics.