Doctor of Philosophy (Ph.D.) in Chemical and Biological Engineering - Sarıyer - İstanbul - Koç Üniversitesi - I464

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Doctor of Philosophy (Ph.D.) in Chemical and Biological Engineering
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Doctor of Philosophy (Ph.D.) in Chemical and Biological Engineering - Sarıyer - İstanbul

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Doctor of Philosophy (Ph.D.) in Chemical and Biological Engineering - Sarıyer - İstanbul Doctor of Philosophy (Ph.D.) in Chemical and Biological Engineering - Sarıyer - İstanbul
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Program Description

Chemical & Biological Engineering is a discipline that integrates chemistry and biology at the molecular level and uses this broad foundation along with engineering fundamentals to study the synthesis of new processes and products. Our graduate program in Chemical and Biological Engineering is an interdisciplinary program that combines chemical engineering fundamentals and systems biology to meet the research challenges of the future.

Research Areas

The research areas of interest are:
  •   Drug Discovery
  •   Tissue Engineering                
  •   Plant Biotechnology
  •   Protein-Protein Interactions
  •   Protein Folding
  •   Process Dynamics, Control and Optimization
  •   Systems Engineering
  •   Catalysis 
  •   Supercritical Fluids
  •   Synthesis of Nanostructured Materials 
  •   Fuel Cells and Sustainable Development
  •   Computational Fluid Dynamics
  •   Polymer Science and Engineering
  •   Microfluidics
  •   Biological Clock
  •   Interaction Networks and Pathways


Students can apply to the Ph.D. programs with a B.S. or M.S. degree. The Ph.D. degree requires successful completion of 14 courses beyond the B.S. degree or 7 courses beyond the M.S. degree. All courses have 3 credits unless specified.

Required Courses

The following courses are required for Ph.D. students:

MATH 503 Applied Math
ChBi 501 Transport Phenomena
ChBi 502 Reaction Engineering
ChBi 503 Thermodynamics

Elective Courses

In addition the required courses students choose electives from the list below in accordance with their specialty area. Advisors help the students to prepare their plan of study and course selection.

ChBi 504  Advanced Thermodynamics
ChBi 505  Polymer Engineering
ChBi 506  Bioinformatics
ChBi 507  Advanced Mass transfer
ChBi 509  Fundamentals of Environmental Technologies
ChBi 510  Industrial Microbiology
ChBi 511  Sustainable Energy
ChBi 516  Biotechnology
ChBi 521/MECH 521 Advanced Fluid Dynamics
ChBi 522/MECH 522 Computational Fluid Dynamics
ChBi 530  Systems Biology
ChBi 584  Tissue Engineering
CMSE 520  Biomolecular Structure, Function and Dynamics
CMSE 580  Selected Topics in Computational Sciences and Engineering
ENGR 500  Applied Optimal Control
INDR 501  Optimization Models and Algorithms
MASE 501  Structure of Materials (1,5 credits)
MASE 502  Electrical & Optical Properties of Materials (1,5 credits)
MASE 504  Thermal Properties of Materials (1,5 credits)
MASE 505  Mechanical Properties of Materials (1,5 credits)
MASE 506  Synthesis, Characterization & Processing of Materials
MASE 538  Intermolecular and Surface Forces
MASE 540  Surface & Interface Properties of Materials
MASE 542  Biomaterials
MASE 570  Micro and Nanofabrication

Courses can be also selected from other graduate courses which are not listed here. In addition, each student has to take a seminar course, ChBi 590 Seminar and register for ChBi 695 Ph.D. Thesis. 

Students who have TA assignments must take TEAC 500: Teaching Experience during the semesters of their assignments. Students must also take ENGL 500: Graduate Writing course.

Students from other disciplines

Students who do not have a formal degree in Chemical and Biological Engineering are encouraged to apply. Once they are admitted, their course program is designed to make up for any lack of background. These students will attend our undergraduate courses in fluid mechanics, heat and mass transfer, and reaction engineering, if they have not taken such courses earlier. With this additional course work they will be able to take the graduate required courses and obtain a strong educational background. For these students the course schedule will be tailored but a typical coarse load during transition includes:

Fall Semester
ChBi 301 Fluid Mechanics
MATH 503 Applied Math
ChBi 503 Thermodynamics

Spring Semester
ChBi 302 Heat and Mass Transfer
ChBi 308 Reaction Engineering
Graduate Electives

Fall Semester
ChBi 501 Transport Phenomena
Graduate Electives

Spring Semester
ChBi 502 Reaction Engineering
Graduate Electives

Course Descriptions
MATH 503
Applied Mathematics
Review of Linear Algebra and Vector Fields: Vector Spaces, Eigenvalue Problems, Quadratic Forms, Divergence Theorem and Stokes' Theorem. Sturm-Liouville Theory and Orthogonal Polynomials, Methods of Solution of Boundary Value Problems for the Laplace Equation, Diffusion Equation and the Wave Equation. Elements of Variational Calculus.

ChBi 501
Transport Phenomena
Fluids classification; transport coefficients; momentum transfer and velocity profiles; energy and mass transfer for isothermal and multicomponent systems; mass transfer with chemical reaction; applications for chemical and biological systems.

ChBi 502
Reaction Engineering

Design and operation of chemical reactors. Homogeneous, heterogeneous and biochemical reactions. Ideal and non-ideal reactors. Kinetics of enzyme-catalyzed reactions. Kinetics of substrate utilization and biomass production.

ChBi 503
Classical thermodynamics: enthalpy, entropy, free energies, equilibria; introduction to statistical thermodynamics to describe the properties of materials; kinetic processes; diffusion of mass, heat, energy; fundamentals of rate processes in materials, kinetics of transformations.

ChBi 504      
Advanced Thermodynamics
Principles of phase and chemical equilibria; computational methods for phase and chemical equilibria calculations; applications for chemical and biological systems.

ChBi 505
Polymer Engineering
Polymers, their synthesis and properties. Relationships between molecular structure and properties. Rheology in polymer processing. Fabrication methods and applications.

ChBi 506
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 507
Advanced Mass Transfer
Fundamentals of diffusion; primary mechanisms for mass transfer; mass transfer coupled with chemical reactions; membrane processes and controlled release phenomena.

ChBi 509
Fundamentals of Environmental Technologies
Fundamentals of physicochemical and biological processes used for waste minimization, air pollution control, water pollution control, hazardous waste control; environmentally conscious design of chemical processes.

ChBi 510
Industrial Microbiology
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 511
Sustainable Energy
Examination of the technologies, environmental impacts and economics of main energy sources of today and tomorrow including fossil fuels, nuclear power, biomass, geothermal energy, hydropower, wind energy, and solar energy. Comparison of different energy systems within the context of sustainability.

ChBi 516
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
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 580             
Selected Topics in Chemical and Biological Engineering

Topics will be announced when offered. 

CHBI 584             
Tissue Engineering
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.

CMSE 520
Biomolecular Structure, Function and Dynamics
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.

ENGR 500
Applied Optimal Control
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.

INDR 501  
Optimization Models and Algorithms
Convex analysis, optimality conditions, linear programming model formulation, simplex method, duality, dual simplex method, sensitivity analysis; assignment, transportation, and transshipment problems.

MASE 501 (1,5 credits)
Structure of Materials
Structure of materials; atomic structure and bonding, crystalline solids, symmetry, lattice and unit cell, determination of crystal structures; imperfections, defects in metals, vacancies, substitutional and interstitial impurities, dislocation defects in ionic solids.

MASE 502 (1,5 credits)
Electrical & Optical Properties of Materials
Electrical properties of materials, band theory of solids, electrical conductivity, metals, semiconductors, and dielectrics; magnetic phenomena, ferromagnetism and diamagnetism, superconductors; optical properties of materials, refractive index, dispersion, absorption and emission of light, nonlinear optical properties, second- and third-order susceptibilities, Raman effect.

MASE 504 (1,5 credits)
Thermal Properties of Materials
Thermal properties of metals, polymers, ceramics and composites in relation to their structure & morphology; change in microstructural mechanisms and macroscopic behaviour with temperature; crystallization, melting & glass transition.

MASE 505 (1,5 credits)
Mechanical Properties of Materials
Mechanical properties of metals, polymers, ceramics and composites in relation to their structure & morphology; stress-strain behaviour; elastic deformation, yielding, plastic flow; viscoelasticity; strengthening mechanisms, fracture, fatigue, creep.

MASE 506
Synthesis, Characterization & Processing of Materials
Experimental projects in the laboratory including topics from polymer synthesis & processing, composite materials, inorganic material/ceramic processing, metal processing, optical properties, electrical & magnetic properties, interfacial properties.

MASE 538
Intermolecular and Surface Forces
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 “hands-on” experience with nanostructures.

MASE 540
Surface & Interface Properties of Materials
Fundamental physico-chemical concepts of surface and interface science; interaction forces in interfacial systems; surface thermodynamics, structure and composition, physisorption and chemisorption; fluid interfaces; colloids; amphiphilic systems; interfaces in polymeric systems & polymer composites; liquid coating processes.

MASE 542
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. Prerequisite: At least one semester of organic chemistry or consent of the instructor.

MASE 570
Micro and Nanofabrication
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.

ChBi 521
Advanced Fluid Dynamics
Foundations of fluid mechanics introduced at an advanced level. Aspects of kinetic theory as it applies to formulation of continuum fluid dynamics. Introduction to tensor analysis and derivation of Navier Stokes equations and energy equation for compressible fluids. Boundary conditions and surface phenomena. Viscous flows, boundary layer theory, potential flows and vorticity dynamics. Introduction to turbulence and turbulent flows. Prerequisite: MATH 204,and MECH 301 or consent of the instructor

ChBi 522
Computational Fluid Dynamics

Numerical methods for elliptic, parabolic, hyperbolic and mixed type partial differential equations arising in fluid flow and heat transfer problems. Finite-difference, finite-volume and some finite-element methods. Accuracy, convergence, and stability; treatment of boundary conditions and grid generation. Review of current methods. Assignments require programming a digital computer.

ChBi 590
A series of lectures given by faculty or outside speakers. Participating students must also make presentations during the semester.

ChBi 695 
Ph.D. Thesis Independent research towards Ph.D. degree.

TEAC 500
Teaching Experience
Provides hands-on teaching experience to graduate students in undergraduate courses. Reinforces students' understanding of basic concepts and allows them to communicate and apply their knowledge of the subject matter.

ENGL 500
Graduate Writing
This is a writing course specifically designed to improve academic writing skills as well as critical reading and thinking. The course objectives will be met through extensive reading, writing and discussion both in and out of class. Student performance will be assessed and graded by Satisfactory/Unsatisfactory.  

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