Director: Yekta Ulgen
Assistant Directors: Halil Ozcan Gulcur, Mehmed Ozkan
Professors: Ahmet Ademoglu, Mehmed Ozkan, Hale Saybasili, Hikmet Ucisik, Yekta Ulgen
Associate Professors: Halil Ozcan Gulcur, Albert Guvenis, Cengizhan Ozturk
Assistant Professors: Ata Akin, Burak Guclu, Murat Gulsoy, Can Yucesoy
Instructors: Dr. Mehmet Melek*, Dr. Aykut Sumer*, Mehmet Emin Yusuf*
DOCTOR OF PHILOSOPHY PROGRAM
The course load requirement for the Ph.D. program is minimum 24 credit hours. However, students with an M.S. degree in a field other than Biomedical Engineering shall also complete the prerequisite core courses suggested by their graduate advisor. All Ph.D. students shall complete a Doctoral dissertation.
Fields of Specialization:Biomedical Electronics
Biomechanics and Biocybernetics
Prosthetics and Artificial Organs
GRADUATE PROGRAMS IN BIOMEDICAL ENGINEERING
Science and Engineering Background
BM 501 Int. to Biological Sys.
BM 507 Biomedical Inst. Lab.
BM 563 Medical Imaging
BM -- Technical Elective
-- -- Technical Elective
BM 502 Int. to Physiology
BM 508 Biomed. Testing & Meas. Lab.
BM 564 Biomed. Inst. & Meas
BM -- Technical Elective
-- -- Technical Elective
Medical and Life Science Background
BM 503 Basic Math. for Biomed. Sci.
BM 507 Biomed. Inst. Lab.
BM 563 Medical Imaging
BM -- Technical Elective
-- -- Technical Elect.
BM 504 Sys. Theory for Biomed. Sci.
BM 508 Biomed. Testing & Meas.
BM 564 Biomed. Inst. & Meas.
BM -- Technical Elect.
-- -- Technical Elective
BM 500 Hospital Clinical Engineering and Management (3+0+0) 3
(Hastane Klinik Muhendisligi ve Yonetimi)
Principles of Clinical Engineering. Hospital organization. Procurement policies. Setting up a clinical engineering department. Maintenance program.
BM 501 Biology of Living Systems (Canli Sistemlerin Biyolojisi) (3+0+0) 3
Cell structure and organelles. Phospholipids, aminoacids and proteins, nucleotides and nucleic acids. Transport mechanisms: active and passive transports, osmosis. PH and buffers. Feedback control. Enzymes and coenzymes: glaycolysis and Krebs cycle, oxidative phosphorylation, chemical energy production. Genetic coding: replication, transcription (mRNA synthesis) and translation (protein synthesis), post-translational modification.
BM 502 Introduction to Medical Physiology (Tip Fizyolojisine Giris) (4+0+0) 4
Cardiovascular system; basic anatomy, and physiology of the heart and circulation, electrocardiogram. Respiratory system; anatomy, pulmonary ventilation and principles of gaseous exchange. Blood, body fluids and homeostasis, basic anatomy and physiology of kidneys. Overview of immunological, digestive, nervous and motor systems. Introduction to physiological changes in pathologies.
Prerequisite: BM 501 or consent of instructor.
BM 503 Basic Mathematics for Biomedical Science (3+0+0) 3
(Biyotip Bilimleri icin Temel Matematik)
Differential calculus. Mathematical models of linear system components. Dynamic system modeling. Signals and systems. Matrix algebra. Sequences and series. Complex analyis. Transforms.
(For students with medical background.)
BM 504 Systems Theory for Biomedical Science (3+0+0) 3
(Biyotip Bilimleri icin Sistem Kurami)
State models and numerical solutions. Response characteristics of linear. Convolution and deconvolution. Feedback systems. Operational amplifiers and applications. Frequency response. Sampling and filtering. Modulation and demodulation.
Prerequisite: BM 503 or consent of the instructor.
BM 507 Biomedical Instrumentation Laboratory (1+0+2) 2
(Biyomedikal Cihazlar Laboratuvari)
Operational amplifiers, biopotential amplifiers, application. Biomedical data acquisition, signal averaging and filtering. Electrocardiography, electroencephalography and electromyography. Spirometry and respiratory function measurements. Heart sounds, cardiovascular system dynamics.
BM 508 Biomedical Testing and Measurement Laboratory (1+0+2) 2
(Biyomedikal Test ve Olcum Laboratuvari)
Electrical safety testing of medical equipment, electronic clinical thermometer, invasive blood pressure transducer and pressure monitoring, infusion pump testing, x-ray unit simulator, bioimpedance analysis and Cole-Cole plot.
BM 511 Lasers in Biomedicine (Biyo-Tipta Lazerler) (3+0+0) 3
Operation principles of different lasers. Nd-YAG and C02 Lasers. Laser surgery: the CO2 Laser in neuro-surgery, endoscopic high power Nd-YAG laser for control of acute gastrointestinal hemorrhage; ophthalmic uses of lasers. Laser safety.
BM 515 Laser-Tissue Interaction Mechanisms (3+0+0) 3
(Laser-Doku Etkilesim Mekanizmalari)
Physical principles of therapeutic uses of lasers in medicine. Optical properties of biological tissues and measurement techniques; photochemical, thermal, photoablative interaction mechanisms and their applications in photodynamic therapy; biostimulation, coagulation, vaporization, ablation, photodistruption, plasma formation, and shock wave generation; clinical applications of lasers.
BM 516 Biophotonics (Biyofotonik) (3+0+0) 3
Principles of optics and lasers in medicine, the interaction of light with biological tissues, and the applications of light in biomedicine. Electromagnetic waves and the nature of light, geometrical optics, optical instruments, physical optics, incoherent light sources, basic laser theory, optical fibers, interaction of light with biological materials; laser Doppler flowmetry, colorimetry, flame photometry, spectrophotometry, optical flow cytometry, ultraviolet and visible absorption spectroscopy, infrared spectroscopy, optical coherence tomography.
BM 518 Microprocessors in Medical Instrumentation (3+0+0) 3
(Tibbi Cihazlarda Mikroislemciler)
Introduction to digital electronics, Boolean algebra, basics of microprocessors; assembly programming, interfacing basics, programming examples in biomedical instrumentation.
BM 519 Biosensors (Biyoalgilayicilar) (3+0+0) 3
Biological components involved in biosensors, immobilization of biological components to transdurcers; principal performance characteristics, fabrication and biomedical applications of electrochemical, optical, piezoelectric and termistor based biosensors.
BM 521 Biosystems and Biomechanics (3+0+0) 3
(Biyo-Sistemler ve Biyo-Mekanik)
Mechanical properties and constitutive equation. Response of living tissues to prolonged load application. Dynamics of muscle and joints. Biorheology of physiological fluids. Spatial models of physiological systems.
BM 524 Applied Biomechanics (Uygulamali Biyomekanik) (3+0+0) 3
Applications of principles of mechanics to some specific problems in Biomechanics. Discussion of solutions offered for the biomechanical problems in clinical, orthopedic, rehabilitation, occupational and sports biomechanics: kinesiology, gait analysis, implant biomechanics, biomaterials.
BM 525 Tissue Biornechanics (Doku Biyornekanigi) (3+0+0) 3
Introduction to biomechanics and to the structures of the musculoskeletal system. Concepts of continuum mechanics, finite deformation analysis, viscoelasticity, anisotropy and inhomogeneity, used to describe the complex mechanical properties of biological tissues, with emphasis on the tissues comprising the musculoskeletal system.
BM 526 Motion Biomechanics (Hareket Biomekanigi) (3+0+0) 3
Analysis of movement of the musculoskeletal system: anthropometry, link-segment models, kinematics, kineties. Active and passive mechanical properties of skeletal muscle in relation to its structure. Mechanisms of transmission of muscle force. Effects of myofascial force transmission on muscle function. Motor control and coordination of muscular activity: types of muscle fibers, motor units, size principle, sensory information.
BM 530 Signal Transduction in CNS (3+0+0) 3
(Merkezi Sinir Sisteminde Sinyal Gecisi)
Functional parts and properties of a nerve cell. Signal integration in the central nervous system (CNS). Neurotransmitters and their action mechanisms. Receptors, structure and function of excitatory amino acid receptors. Plasticity in the nervous system. Mechanisms of learning and memory. Neuropathological diseases.
BM 531 Numerical Methods and C Programming (3+0+0) 3
(Sayisal Yontemler ve C Programlama)
An overview of C programming; variables, structures, type definitions, expressions, statements and functions. Data representations and machine precision. Using the C libraries for the solution of linear systems, approximation and interpolation, integration, optimization, solution of ordinary and partial differential equations. Fundamentals of Object Oriented Programming; inheritance, polymorphism and overloading. Class development for complex and matrix operations.
BM 532 Biological Time Series Analysis (3+0+0) 3
(Biyolojik Zaman Serileri Analizi)
Introduction to biological signals; EEG, EMG, ECG, EGG, Cellular Action Potentials. Discrete time random processes. Deterministic and stochastic linear signal modeling. Wiener and Kalman filtering. Spectrum estimation using parametric, nonparametric and eigenbased methods. Adaptive filtering using LMS. Applications to Biological Signals.
BM 533 Neural Networks (Sinir Aglari) (3+0+0) 3
Reverse engineering in the nervous system; anatomical, physiological and mathematical approaches. Computational action and interaction of brain networks; architecture, performance rules and learning rules. Dryware, wetware, connectivity. A biological neural network analysis of learning and memory. Computation modeling of neuronal network. Artificial implementations: VLSI, optical and holographic implementations, resistive networks for computer vision, silicon cortex. Static and dynamic networks. Pulse frequency modulation in the nervous system. Stability and periodic oscillations. Learning algorithms. Application examples.
BM 535 Computational Cell Biology (3+0+0) 3 ECTS: 6
(BM 535 Hesaplamali Hucre Biyolojisi)
Review on differential equations, numerical methods for differential equations. Voltage-gated ionic currents, transporters and pumps and calcium oscillations. Intra and inter cellular communication, biochemical kinetics, metabolic pathways, molecular motors; tumor modeling.
BM 541 Biological Materials (Biyolojik Malzemeler) (3+0+0) 3
Relationships between materials' science and medicine. Properties of crystalline and noncrystalline materials. Principles in strength of materials. Natural biological materials. Artificial biological materials. Applications of materials science to orthopedic surgery. Cardiology and materials science. Applications of materials science research methods to medicine.
BM 542 Prosthetics and Artificial Organs (3+0+0) 3
(Protezler ve Yapay Organlar)
Body segments kinetics. Lower, upper limb prostheses: functional requirements, design criteria, alignment. Control, body powered and externally powered prostheses. Implanted artificial joint: Joint pathologies, tissue reaction to implants, types and failures of implanted joints, body implants, heart valves, blood vessels, bones and joints, blood oxygenators and blood pumps, heart assisted devices, artificial heart, pancreas and kidney.
BM 543 Materials Engineering in Medicine (3+0+0) 3
(Tipta Malzeme Muhendisligi)
The Human body as engineering structure. Skeletal system; construction in macro level. C omponents of bone, muscle, cartilage, meniscus as composite materials. Tribological properties of joints and column vertebrae. Fatigue, creep and relaxation of soft and hard tissues. Nucleation, growth, degradation, remodelling and transformation mechanisms of the tissues from the point of view of materials engineering. Physics of damage, fracture-rupture and healing of skin, bone and soft tissues. Discussion of the benefits of materials science and engineering for medicine .
BM 544 Failure Analysis of Implants (3+0+0) 3
(Implantlarda Hasar Analizi)
Clinical problems and their solution by use of implants. Implant-tissue interactions. Biocompatibility of implant materials. Expectations from implants. Types of failures in implants. Chemical and mechanical effects related to implants: corrosion and fatigue. Stress concentration. Mechanism of crack initiation and propogation. Modes of fracture. Ductile and brittle fracture; “ductile-brittle” transition. Analysis of failure via microscopical techniques; optical microscopy, scanning electron microscopy and atomic force microscopy. Life prediction. Case studies.
BM 554 Modelling of Biological Systems (3+0+0) 3
(Biyolojik Sistemlerin Modellenmesi)
Tools of modeling, Laplace Transform, parametric, non-parametric estimation techniques, physiological control systems, pharmacokinetic and pharmacodynamic models, compartment models, cellular dynamics, and complex dynamics in biology.
BM 555 Design and Evaluation of Clinical Trials (3+0+0) 3 ECTS:6
(BM 555 Klinik Arastirma Tasarimi ve Degerlendirilmesi)
Introduction to principles of medical research. New chemical entity cycle. Brief overview of ICH GCP (Good Clinical Practices). Analysis/Design of a protocol, CRF (Case Report Form) and a complete trial. Comparative review of laws, directives and conventions, ethical standards about clinical trials. SOPs (Standard Operating Procedure). Conducting, monitoring and auditing clinical trial processes. Data management. Reporting and documentation.
BM 561 Quality Assurance in Diagnostic Radiology (3+0+0) 3 ECTS:6
(BM 561 Tani Radyolojisinde Kalite Guvencesi)
Principle concepts in radiation safety and quality management procedures. Analysis of quality control testing for radiology and fluoroscopy systems including film processing, cassettes, view boxes and dark room; conventional tomography and mammography systems; dental ray and bone densitometry.
BM 563 Medical Imaging (Tibbi Goruntuleme) (3+0+0) 3
Radiation quantities and units, radioactivity, x-ray production and x-ray tube, interaction of radiation with matter, scattered radiation, x-ray film, fluoroscopy, digital imaging system, angiography, ultrasound imaging, gamma camera, x-ray CT and image reconstuction, emission tomography: PET and SPECT, MR imaging, LASER imaging, electrical impedance tomography, bone densitometer, patient exposure and protection, quality asurance in radiology.
BM 564 Biomedical Instrumentation and Measurement (3+0+0) 3
(Biyomedikal Cihazlar ve Olcumler)
Biomedical sensor, transducers and electrodes. Instrumentation amplifiers and their applications. Electrical safety in hospitals. Electrocardiography, electroencephalography; electromyography and electroretinography. Pulse oximetry, blood pressure and flow measurements, cardiac output measurements. Cardiac pacing, defibrillators and cardiovascular prostheses and assist devices. Physical therapy equipment. Electrosurgical unit, anesthesia equipment; ventilators and hemodialysis unit.
BM 571 Biomedical Signal Processing (Biyo-Medikal Isaret Isleme) (3+0+0) 3
Discrete-time signals and systems. Sampling, bandwidth and aliasing, convolution, recursive and nonrecursive difference equations, frequency response. The z-transform and its extensions. Discrete Fourier transform, circular convolution, expansion, Fast Fourier Transform (FFT) algorithms. Spectral analysis and detection. Digital and adaptive filter algorithms. Applications; processing of bioelectric signals; image and speech processing, estimation of echoes.
BM 573 Cardiovascular Imaging (Kardiyovaskuler Goruntuleme) (3+0+0) 3
Cardiovascular imaging from a biomedical engineering perspective. A short review of cardiovascular physiology. An overview of cardiac diseases which are the focus of advanced imaging systems. Detailed comparative analysis of specific imaging modalities like US, PET, MRI. Investigation of various applications through projects that stress special challenges of cardiovascular imaging with emphasis on cardiac MRI.
BM 574 Electrical Impedance Tomography (3+0+0) 3
(Elektrik Empedans Tomografisi)
Electrical impedance of tissues and detection of physiological events; electrodes; principles of electrical impedance tomography; EIT instrumentation; data collection methods and data collection errors; electrical safety; interfacing and computers; mathematical preliminaries; finite-element method; reconstruction algorithms; computational complexity; comparison of reconstruction techniques; biological tissue characterization; clinical applications.
BM 579 Graduate Seminar (Lisansustu Seminer) (0+1+0) 0 P/F
The widening of students' perspectives and awareness of topics of interest to biomedical engineers through seminars offered by faculty members, guest speakers and graduate students.
BM 582-589 Special Studies (Ozel Calismalar) (3+0+0) 3
Study of specific Biomedical Engineering subjects in biomechanics, biocybernetics, bioelectronics or prosthetics and artificial organs.
BM 590-599 Selected Topics (Secilmis Konular) (3+0+0) 3
In depth study of a selected topic in the field of Biomedical Engineering.
BM 601 Quality Assurance Principles for Biomedical Engineers (3+0+0) 3
(Biyo-Medikal Muhendisleri icin Kalite Guvence Kavramlari)
Introduction to quality assurance concepts; basic probability and statistics, quality indicators and measurement, statistical process control. Design of biomedical equipment, quality function deployment, failure analysis, Taguchi methods. Biomedical equipment standards, ISO-9000 and JCAHO standards.
BM 611 Nuclear Biomedical Instrumentation (3+0+0) 3
(Nukleer Biyo-Medikal Cihazlar)
Radioactivity, radioisotopes, radiation dosage, scanning with radionucleides, data presentation techniques, focusing, collimators, scintillation counters, rectilinear scanners, gamma camera, tomography and positron camera, computer processing of the image for uniformity, improved resolution, dynamic studies, radioactive tracers, compartment analysis for single pool, interchanging system and multiple pools, gamma and beta counters, radio-immuno assaying, clinical dosimetry, pocket dosimeters, thermoluminescent dosimetry, proportional counters, Geiger counters.
BM 614 Computerized Tomography (Bilgisayarli Tomografi) (3+0+0) 3
Three-dimensional imaging with X-Rays. Sources and detectors parallel and fan beam configurations. Image reconstruction by ART, effect of noise, instabilities. Movement, description of commercially available equipment. Three-dimensional imaging with positron emission, ultrasound and nuclear magnetic resonance techniques.
BM 616 Therapeutic Medical Devices (Tedavi Amacli Tibbi Cihazlar) (3+0+0) 3
Cardiac pacing; defibrillators, cardiovascular prostheses and assist devices, neural assist devices, sensory and communication aids, physical therapy equipment; electrosurgical equipment, anesthesia equipment, ventilators and respiratory therapy equipment. Artificial kidney.
BM 632 Sensory Systems (Duyu Sistemleri) (3+0+0) 3
Theories and principles of sensory vision, touch, hearing, taste and smell, sense of balance, sense of pain, sense of heat and cold, and other senses. Objective evaluation and measuring instruments for human sensory systems.
BM 633 Dynamics of Neoral Systems (Sinir Sistemlerinin Dinamigi) (3+0+0) 3
Introduction to neuroscience. Nonlinear dynamics and bifurcations. Computation by excitatory and inhibitory networks. Nonlinear oscillations. Dynamics of action potentials. Examples of chaotic regimes in neurons. Synaptic coupling and synchronicity in neural networks. Central pattern generation and traveling waves in locomotion. Lyapunov functions and dynamic temporal memories. Space-time model for dendritic computation.
BM 641 Magnetic Resonance Imaging Principles (3+0+0) 3
(Manyetik Rezonans Goruntuleme Prensipleri)
Fundamental principles of magnetic resonance imaging (MRI). MRI methods and techniques; flow and flow-related MRI, diffusion and perfusion imaging. MRI angiography; chemical shift and spectroscopic MRI. Instrumentation, quality assurance and safety issues. Term project.
BM 642 Medical Image Processing (Tibbi Goruntu Isleme) (3+0+0) 3
Image processing applications in medicine. Digital images. Image quality. ROC analysis for evaluating diagnostic capability. Image enhancement and restoration. Image segmentation and classification. Tomographic reconstruction algorithms. 3-D display of organs. Picture archival and communication systems.
BM 645 Formation and Deformation of Tissues (3+0+0) 3
(Canli Dokularin Olusumu ve Deformasyonu)
Crystalline, amorphous and liquid components of living tissues. Nucleation and growth kinetics, solubility of components, segregation of new phases on the tissues, blood and blood biomechanics. Studies of kidney stone and cataract formation from material science point of view. Crack initiation and growth in the bone and soft tissues. Body responses to trauma; rate and time dependencies.
BM 652 Biological Control Systems (Biyolojik Kontrol Sistemleri) (3+0+0) 3
Dynamic systems and control. Mathematical modeling of biological control systems. Biological receptors, their characteristics and transfer function models. Examples of biological feedback systems: Pupil control system, visual fixation, thermoregulation, skeletal-muscle servo mechanism, blood pressure control, cardiac output and other biological regulatory systems. Biological performance criteria and adaptive control mechanisms.
BM 658 Medical Instrumentation Design (Tibbi Cihazlar Tasarimi) (3+0+0) 3
Physiological specifications for designers; design principles of various transducers for use in Biomedicine; basics of designing for low noise, high gain and stability.
BM 660 Nerve System Analysis (Sinir Sistemi Analizi) (3+0+0) 3
Excitable cells, origin of membrane potentials, Hodgkin-Huxley model of action potentials. Cholinergic mechanisms and other neurotransmitters. Mechanisms of nervous control.
BM 671 Introduction to Medical Informatics (Tibbi Bilisime Giris) (3+0+0) 3
An overview of medical informatics. Stages in system analysis and design, principles of database systems, medical language, coding and classification systems, computer based patient records, hospital information systems, physiological signal processing, bio-statistical methods, medical imaging applications, PACS and teleradiology. Standards for medical informatics.
BM 672 Picture Archiving and Communication Systems in Biomedical Imaging (Biyo-Medikal Alanda Goruntu Depolama ve Iletisim Sistemleri (PACS)) (3+0+0) 3
Introduction to PACS; principles of digital radiologic imaging, projection radiography, digital radiography, other imaging modalities, microscopic imaging, image compression, image processing and computer assisted diagnosis. PACS industry standards, computer networks, PACS components, Hospital Information Systems (HIS) and Radiology Information Systems (RIS) interface, display workstation, image acquisition, PACS data management, telemedicine and teleradiology.
BM 681-689 Special Studies (Ozel Calismalar) (3+0+0) 3
Studies of advanced topics in the specialization areas of Biomedical Engineering.
BM 690 Master's Thesis in Biomedical Engineering
(Biyo-Medikal Muhendisligi Yuksek Lisans Tezi)
Investigation in depth of a special topic related with the student's major area of study and research in Biomedical Engineering, with the aim of original contribution to the subject. Preparation and defense of an M.S. thesis.
BM 691-698 Special Topics (Ozel Konular) (3+0+0) 3
In depth study of a special topic in the field of Biomedical Engineering.
BM 699 Guided Research (Yonlendirilmis Arastirmalar) (2+4+0) 4
Research in the field of Biomedical Engineering, by arrangement with members of the faculty; guidance of doctoral students towards the preparation and presentation of a research proposal.