Biomedical Engineering

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Biomedical Engineering, Master of Scienc
In the design of the master program, subject related and social competences gained in Bachelor of Science degree program are deepened and modified. The master’s program leads to the acquisition of advance analytical and methodological competences.
Upon completion of the MSc. in Biomedical Engineering, students will demonstrate the ability to:

Apply the rules of scientific research and ethics,
discuss complex biomedical engineering issues as well as own research results comprehensively and in the context of current international research and present these in writing and orally,
solve problems by systems analytical thinking both in subject specific and interdisciplinary concepts,
Combine specialised knowledge of various component disciplines,
Carry out independent scientific work and organise (capacity of teamwork), conduct and lead more complex projects,
To assess the social and environment-related effects of their actions.

Objectives of the MSc. Degree Programme
Biomedical engineering is an interdisciplinary field of study, which is a combination of fields such as engineering, medicine, material science, basic sciences and veterinary medicine. These interdisciplinary knowledges are applied to solve problems in medical diagnosis and therapy. Biomedical engineers work within the field of research & design, production, maintenance / repair and calibration activities of medical devices, and the life support systems. They also organize and manage health service units located in various institutions.
Producing innovative approaches to design high-tech medical devices, methods for measurements of physiological development medical data / signal, image processing and analysis, development of artificial organs are among the responsibilities of biomedical engineers.
The objective of the master program in Biomedical Engineering is to generate second cycle graduates who will be capable of understanding challenging biomedical engineering related research projects. The primary educational objective of the Master of Science program is to expose students to the latest developments in biomedicine and to provide them with the appropriate tools to understand and contribute further to these developments The master of Science degree program will provide the necessary education and immediately applicable skills that will enable to give people longer, healthier, and more productive lives.

  • Prof. Dr. Nesrin Hasırcı
  • Prof. Dr. Mahmut Ahsen Savaş
  • Prof. Dr. Rahib Abiyev
  • Assoc. Prof. Dr. Terin Adalı
  • Assoc. Prof. Dr. Fa’eq Radwan
  • Assoc. Prof. Dr. Hüseyin Kaya Süer
  • Assist. Prof. Dr. Boran Şekeroğlu
  • Assist. Prof. Dr. Dilber Uzun Özşahin
  • Assist. Prof. Dr. Murat Mustafa Uncu
  • Assist. Prof. Dr. Elbruz Imanov
BIOMEDICAL ENGINEERING EDUCATION PLAN MASTER PROGRAM (with THESIS)
Course Code Course Title T A C ECTS Compulsory/Elective
BME500 Thesis 0 0 0 40 Compulsory
BME543 Advance Tissue Engineering 3 0 3 10 Elective
BME507 Advance Biomedical Signal Processing 3 0 3 10 Elective
BME505 Advance Image Processing 3 0 3 10 Elective
BME503 Advance Bioformatics 3 0 3 10 Elective
BME510 Biomaterials for Medical Diagnosis and Therapy 3 0 3 10 Elective
BME512 Advance Artifical Organs 3 0 3 10 Elective
BME591 Advance Biomedical Instrumentation 3 0 3 10 Elective
BME502 Biomedical Seminars 0 0 0 10 Compulsory
BME504 Advance Biomechanics 3 0 3 10 Elective
BME580 Advance Artificial Neural Networks 3 0 3 10 Elective
BME590 Modelling of Complex Biological Systems 3 0 3 10 Elective
BME511 Magnetic Resonance Imaging 3 0 3 10 Elective
BME521 Clinical Engineering 3 0 3 10 Elective
BME520 Advance Biostatistics 3 0 3 10 Compulsory
BME570 Advance Electromagnetic & Medical Applications 3 0 3 10 Elective
BME518 Ultrasound Imaging and Doppler Techniques 3 0 3 10 Elective
BME555 Biomedical Micro and Nano Systems 3 0 3 10 Elective
BME535 Advance Microcontroller Systems 3 0 3 10 Elective
BME532 Pattern Recognition 3 0 3 10 Elective
BME560 Advance Biomechanical Cardiovascular Systems 3 0 3 10 Elective
BME562 Biomedical Reserach Methods 3 0 3 10 Compulsory
MAT501 Advanced and Applied Mathematics 3 0 3 10 Elective
BME536 Machine Vision 3 0 3 10 Elective
BME506 Information Theory & Coding 3 0 3 10 Elective
BME500 MASTER THESIS
At the final year all students must take a master thesis. The thesis lasts for two semesters. In the first semester students are expected to carry out literature survey and complete the theoretical, related experiment systems are set up, and first prototype of their thesis are also set by the students. The second semester of their thesis is allocated to improve their experimental works, prototype and modify their thesis.

Description of Master Courses
BME543 – Advance Tissue Engineering
The course will cover the application of engineering principles, combined with molecular cell biology, to develop fundamental understanding of property function relationships in tissues. Exploitation of the understanding to manipulate cell and tissue properties rationally to alter, restore, maintain, or improve cell and tissue functions as well as to design bioartificial tissue substitutes.

BME507 – Advance Biomedical Signal-Image Processing
This course is designed for biomedical engineering master students. The purpose of the course is to provide biomedical signal and image processing background on technical aspects. Fundamentals of digital signal-image processing, signal-image conditioning, frequency analysis, digital filtering methods, feature extraction methods, classification methods and applications on EEG – ECG signals and CT-MRI images are introduced in detail. Students are provided with overviews of the major techniques that engineers have used to explore in biomedical engineering level.

BME505 – Advance Image Processing
Introduction to medical imaging and various medical, imaging systems. Nuclear magnetic moment, nuclear spin, resonance, connector constants, spin systems, MR spectroscopic data processing. Application of MR spectroscopy on brain, muscles, tissue and etc.

BME503 – Advance Bioinformatics
This course is graduate level bioinformatics course, which emphasizes as a basis for understanding bioinformatics and their applications. The course focuses on a general introduction to the uses of biological databases in the generating biological knowledge to better understand living systems, for purposes of aiding healing of diseases. Topics include Genomic Era, the anatomy of genome, probabilistic models of genome sequences, biological databases, sequence alignment, gene and promoter prediction, molecular phylogenetics, post-genomic epidemic, structural bioinformatics and proteomics. This course covers the fundamental concepts molecular biology, database management systems, and probabilistic models.

BME510 – Biomaterials for Medical Diagnosis and Therapy
This course highlights the capabilities of biomaterials and devices for patient diagnostics and therapy. It is broken down into four major areas: in vitro and in vivo diagnostics (optical, electrical, mechanical), nanotechnology-enhanced analytical tools and techniques for diagnostics, and the future for patient diagnostics.

BME512 – Advance Artificial Organs
Medical devices that replace the function of one of the major organs in the body must usually interface with flowing blood. Examples include total artificial hearts, left ventricular assist devices, membrane oxygenators, hemodialysis systems and encapsulated endocrine cells. The design of these devices relies on integration of knowledge from a variety of fields, in particular computational fluid dynamics and blood rheology. We will study the process by which a concept for a device eventually leads to a functioning, blood-contacting medical device. An introduction to computational fluid dynamics (the finite difference and finite volume methods) will be integrated with computer-aided design and testing of devices using the software package Fluent.

BME580 – Advance Artificial Neural Networks
This course explores the organization of synaptic connectivity as the basis of neural computation and learning. Perceptrons and dynamical theories of recurrent networks including amplifiers, attractors, and hybrid computation are covered. Additional topics include backpropagation and Hebbian learning, as well as models of perception, motor control, memory, and neural development.

BME590 – Modelling of Complex Biological Systems
This course introduces the current approaches for mathematical modelling and analysis of biological systems using both computer simulation and mathematical techniques. The course reviews the basic of modelling methodology, stochastic and deterministic models, numerical and analytical methods, and model validation. Examples throughout the course are drawn from population dynamics, biochemical networks, ecological models, neuronal modelling, and physiological systems.

BME511 – Magnetic Resonance Imaging
This course is designed for biomedical engineering master students. The purpose of the course is to provide detailed information on technical aspects of magnetic resonance imaging. Biomedical diagnostic magnetic resonance imaging systems and the physical principles of nuclear magnetic resonance imaging are introduced in detail. Students are provided with overviews of the major physical techniques that engineers have used to explore in biomedical engineering level.

BME570 – Advanced Electromagnetic and Medical Applications
Coulomb’s Law, Electric Field Intensity, Electric Potential, The Field Outside an Electrically Charged Body, Gauss Law, Poisson’s Equation, Laplace’s Equation, Conductors, Calculation of the Electric Field Produced by A Simple Cahrge Distribution, Electric Dipole, The Linear Electric Quadrupole, Electric Field Outside An Arbitrary Charge Distribution, Ptential Energy of A Charge Distribution, Energy Density in an Electric Field, Forces on Conductors, Dielectric Materials, Electric Polarization, Electric Field at an Exterior Point, The Bound Charge Densities, Electric Field at an Interior Point, The Electric Susceptibility, Divergence of E and the Dielectric Displacement D, Relative Permittivity, Calculation of Electric Fields Involving Dielectrics, Frequency Dependence, Anisotropy and Nonhomogeneity, Potential Energy of a Charge Distribution in the Presence of Dielectrics, General Methods for Solving Laplace’s and Poisson’s Equations, Continuity of V, D,E, at the Interface Between Two Dielectric Media, Normal Component of the Electric Displacement, Tangential Component of the Electric Field Intensity, Bending of Lines of Force, The Uniqueness Theorem, Images, Point Charge Near an Infinite Grounded Conducting Plane, Solution of Laplace’s Equation in Rectangular Coordinates, Solution of Laplace’s Equation in Spherical Coordinates, Solution of Poisson’s Equation for E, Magnetic Forces, The Magnetic Induction B, The Biot Savart Law, The Force on a Point Charge Moving in a Magnetic Field, The Divergence of the Magnetic Induction B, The Vector Potential A, The Line Integral of the A over a Closed Curve, The Curl of B, Ampere’s Circuital Law, Magnetic Dipole, Faraday Induction Law, Faraday Induction Law in Differential Form, Induced Electric Field Intensity in Terms of the Vector Potential A, Energy Stored in a Magnetic Field, Magnetic Energy in terms of B, Magnetic Energy in terms of J and A, Magnetic Energy in terms of I and ?, Magnetic Field Intenisty H, Ampere’s Circuit Law, The Equivalent Current Density and J, Boundary Conditions, Maxwell Equations, Maxwell Equations in Integral Form, Nonhomogeneous Wave Equations for E and B, Plane Electromagnetic Waves in Free Space, Poynting Vector, The E, H Vectors in Homogeneous, Isotropic, Linear and Stationary Media, Propagation of Plane Electromagnetic Waves in Nonconductors, Propagation of Plane Electromagnetic Waves in Conducting Media, Propagation of Plane Electromagnetic Waves in Good Conductor Media, Reflection and Refraction, The Laws of Reflection and Snell’s Law of Refraction, Fresnel’s Equations, Refelction and Refraction at the Interface Between Two Nonmagnetic Nonconductors, Guided Waves, Radiation of the Electromagnetic Waves, The Vector Potential A and H, The Electric Field Intensity E, Radiation From a Half-Wave Antenna

BME518 – Ultrasound Imaging and Doppler Techniques
The course is designed for biomedical engineering master students. The purpose of the course is to provide detailed information on technical aspects of ultrasound imaging. Biomedical diagnostic ultrasound imaging systems and the physical principles of Ultrasound and Doppler techniques are introduced in detail. Students are provided with overviews of the major physical techniques that engineers have used to explore in biomedical engineering level.

BME555 – Biomedical Micro and Nano Systems
The course defines the understanding of biomedical micro and nano systems manufacturing techniques. Design, fabrication and operation issues in applications of micro-total analysis systems, drug delivery systems, devices and instrumentation for diagnosis and treatment of human disease will be presented.

BME532 – Pattern Recognition
This course is designed for biomedical engineering master students. Purpose of this course is to provide pattern recognition and classification techniques. Different event detection, feature extraction and classification methods are introduced in detail. Students are provided with overviews of the major techniques that engineers have used to explore in biomedical engineering level.

BME560 – Advance Biomechanical Cardiovascular Systems
Introduction and basic concepts of biomechanics, Dynamics of mechanics, Materials properties of Hard and soft tissues, and mechanical properties, Biomechanical behaviors, Materials for prosthesis and mechanical properties, Applications and behaviors of human body, Biomechanical systems and examples.

BME562 – Biomedical Research Methods
The course defines the understanding of science and engineering and describes the links between the interrelated technical subjects. Further, it considers the methods of scientific research and focuses on the five methods mostly widely used for natural sciences and engineering, giving much emphasis on experimental and field studies research methods. It also stresses the importance of integrated research methods. It stresses the important aspects of writing research proposal, presenting and report (thesis) writing. Finally, it provides some information on research ethics and on resolving controversies in research.

MAT501- Advanced and Applied Mathematics
This course aims to review of vector analysis, complex numbers, review of ordinary differential equations, variation of parameters and Cauchy-Euler differential equations, system of linear differential equations. Laplace Transforms and fourier series, beta gamma functions, bessel2s functions and partial differential equations.

BME506 – Information Theory and Coding
This course covers intermediate to advanced information theory and channel coding topics. Topics covered include fundamentals of channel coding as well as powerful error-correcting codes such as low-density parity-check codes and turbo codes.

Course Code Course Title T A C Compulsory / Elective
BME600 Thesis 0 0 0 Compulsory
BME601 Tissue and Cell Engineering 3 0 3 Elective
BME603 Advance Biomedical Signal Processing 3 0 3 Elective
BME605 Advance Image Processing 3 0 3 Elective
BME607 Advance Bioinformatics 3 0 3 Elective
BME609 Biomaterials for Medical Diagnosis and Therapy 3 0 3 Elective
BME611 Advance Artificial Organs 3 0 3 Elective
BME613 Advance Biomedical Instrumentation Techniques 3 0 3 Elective
BME602 Seminar 0 2 0 Compulsory
BME604 Advance Biomechanics 3 0 3 Elective
BME606 Applications of Artificial Neural Networks in Biomedical Engineering 3 0 3 Elective
BME608 Modelling of Complex Biological Systems 3 0 3 Elective
BME610 Magnetic Resonance Imaging 3 0 3 Elective
BME612 Clinical Engineering 3 0 3 Elective
BME614 Advance Biostatistics 3 0 3 Compulsory
BME616 Quality Assurance of Biomedical Devices 3 0 3 Elective
BME618 Ultrasoud Imaging and doppler Techniques 3 0 3 Elective
Course Descriptions
BME600 THESIS (0, 0, 0)
The aim of this copurse is to make a study for problem solving on a specific field of Biomedical Engineering by considering the ethics in obtaining, analysing and comprehension of knowledge.

BME601 TISSUE AND CELL ENGINEERING (3, 0, 3)
Tissue development, tissue modelling, cell and tissue in the mass transfer properties, tissue restoration, angiogenesis, spread of drag, protection of immunity, inflammation, tissue engineering approaches, induction of tissues (nerve, blood vessel, tendon, ligament, skin, nerve), cell transplantation, biybrid systems, extracellular matrix analog and extracellular matrix, cell function and regulation, stem-cells and cell-adhesion.

BME603 ADVANCE BIOMEDICAL SIGNAL PROCESSING (3, 0, 3)
Introduction to biomedical signals, simultaneous, coublage and related process, filtering of artefact, determining activity, methods of noise elimination on biomedical signals, modelling of biomedical signals, pattern recognition and diagnostic decides,complexing wave form and wave pattern, characterization frequency domain.

BME605 ADVANCE IMAGE PROCESSING (3, 0, 3)
Digital image analysis, image enhancement and restoration. Image segmentation and classification. Medical image processing and noise reduction, medical picture archival and communication systems.

BME611 ADVANCE ARTIFICIAL ORGANS (3, 0, 3)
Basic principles of artificial organ design, Tissue-material interaction, Biomimetic materials, extracorperial devices, implants, Hemodialysis, artificial blood, bio-artificial liver, artifical heart valves, artificial lung, oxygenetors, dental implants, artificial eye, cohlea implant.

BME609 BIOMATERIALS FOR MEDICAL DIAGNOSIS AND THERAPY (3, 0, 3)
This course highlights tha capabilities of biomaterials and devices for patient diagnostic and therapy. It is broken down four major areas: in vitro and in vivo diagnostics (optical, electrical, magnetic and mechanical), nanotechnology-enhanced analytical tools and techniques for diagnostics, and future for patient diagnostics.

BME604 ADVANCE BIOMECHANICS (3, 0, 3)
Advance biomechanics is the course to answer “How physical forces interact with living systems?” Cellular biomechanics, hemodynamics, the circulatory system, the interstitium, ocular biomechanics, the respiratory system, muscles and movement, skeletal biomechanics, terrestrial locomotion.

BME606 APPLICATIONS OF ARTIFICIAL NEURAL NETWORKS IN BIOMEDICAL ENGINEERING (3, 0, 3)
Fundamental concepts of biological neurons. The structure of artificial neouron models. Basic of artificial neural networks: feed forward network, feedback network, back propagation of errors. Single layer and multi-layer neural networks. Neural network learning rules. Calculation of network weights and selection of activat,on function. Dynamics and discreate time neural networks. Neural network applications: Pattern recognition, image processing. Controller design and system parameter estimation using neural networks.

BME612 CLINICAL ENGINEERING (3, 0, 3)
The departments of clinical engineering, Hospital management, Computer systems in clinic engineering’s departments, Establishment of intensive care units, Standarization and Total quality management, Sterilization, Hospital wastes, Medical gas systems, Safety in clinic departments, Electrical safety in hospital, Ethics and Morality, Future directions in clinical engineering.

BME608 MODELLING OF COMPLEX BIOLOGICAL SYSTEMS (3, 0, 3)
Generalized system properties, Linear Models of Physiological Systems, Linear Systems and Superposition Principle; Laplace Transforms and Transfer Functions, Statis Analysis of Physiological Systems; Open loop, Closed loop, Regulation of glucose, Time domain Analysis of linear control systems, Linearized Respiratory mechnics, Open loop and close loop transient responsee; Descriptors of impulse and step responses, Frequency Domain Analysis of Linear Contro Systems, Application of Physiological control systems using SIMULINK.

BME607 ADVANCE BIOINFORMATICS (3, 0, 3)
The nature of information, the transmission of information, sets and combinatorics, probability and likelihood, randomness and complexicty systems, networks and circuits, algorithms, the organization of knowledge. Interactions of regulatory networks.

BME613 ADVANCE BIOMEDICAL INSTRUMENTATION TECHNIQUES (3, 0, 3)
Human instrumention systems, Sampling methods, History of medical devices, Bioelectrodes, Variations, Transducers and specialities active and passive transducers, Biological signals and specialities (buffer amplifiers, differentional, inverting, noninverting), Instrumentation amplifiers specialities and usage samples, Signal processing circuits, ECG, Photocardiogram and other cardiac systems, Photopletismography, intensive and coroner care units, Hemodialysis systems, Medical ultrasound systems.

BME610 MAGNETIC RESONANCE IMAGING (3, 0, 3)
This course comprises fundamentals of Magnetic Resonance Imaging. MR equipment, MRI physics, MR image parameters and optimization.