Course Descriptions

BM 500 Hospital Clinical Engineering and Management  (3+0+0) 3 ECTS 8
(Hastane Klinik Mühendisliği ve Yönetimi)
Principles of Clinical Engineering. Hospital organization. Procurement policies. Setting up a clinical engineering department. Maintenance program.

BM 501 Biology of Living Systems (3+0+0) 3 ECTS 8
(Canlı Sistemlerin Biyolojisi)
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 Human Physiology  (3+0+2) 4 ECTS 9
(İnsan Fizyolojisi)
Review of Cell Physiology. Physiology of Organ Systems: Nerve and Muscle; Physical Work; Autonomic Nervous System; Blood; Respiration; Acid-Base Homeostasis; Kidneys, Salt and Water Balance, Cardiovascular System, Thermal Balance and Thermoregulation, Nutrition and Digestion, Hormones, Central Nervous System, Special Senses. Electrocardiography, Blood Pressure, Heart Sounds.

BM 503 Basic Mathematics for Biomedical Science  (3+0+0) 3 ECTS 8
(Biyotıp Bilimleri için Temel Matematik)
Matrix Algebra, Matrix Calculus, Probability Theory, Multivariate Random Distributions, Probability Calculus, Expectation Maximization, Variational Bayes, Hidden Markov Models 

BM 504 Systems Theory for Biomedical Science  (3+0+2) 4 ECTS 9
(Biyotıp Bilimleri için Sistem Kuramı)
Introduction to Linear Systems, Laplace Transform, Continuous Time Fourier Transform, z-transform, Discrete Time Fourier Transform, Sampling and Interpolation, Digital Filters, Signal Modeling, Time Frequency Analysis and Wavelets.
Prerequisite: BM 503 or consent of the instructor.

BM 511 Lasers in Biomedicine  (3+0+0) 3 ECTS 8
(Biyotıpta Lazerler)
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 ECTS 8
(Laser-Doku Etkileşim Mekanizmaları)
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  (3+0+0) 3 ECTS 8
(Biyofotonik)
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 517 Novel Applications in Biomedical Optics  (3+0+0) 3 ECTS 8
(Biyomedikal Optikte Yeni Uygulamalar)
New research studies on bioimaging, confocal and multiphoton microscopy, optical coherent tomography, spectroscopic diagnostics, tissue engineering with light, laser tweezers and scissors, photodynamic therapy and biostimulation.

BM 518 Microprocessors in Medical Instrumentation  (3+0+0) 3 ECTS 8
(Tıbbi Cihazlarda Mikroişlemciler)
Introduction to digital electronics, Boolean algebra, basics of microprocessors; assembly programming, interfacing basics, programming examples in biomedical instrumentation.

BM 519 Biosensors (3+0+0) 3 ECTS 8
(Biyoalgılayıcılar)
Biological components involved in biosensors, immobilization of biological components to transducers; principal performance characteristics, fabrication and biomedical applications of electrochemical, optical, piezoelectric and thermistor based biosensors.

BM 520 Fundamental Mechanics for Biomedical Engineering  (3+0+0) 3 ECTS 8
(Biyomedikal Mühendisliği İçin Temel Mekanik)
Introduction to stress and strain. Axial, transverse and torsional loading. Bending of beams. Stress and strain transformations. Energy methods. Column buckling. Kinematics, kinetics and vibration analysis. Fundamentals of finite element method. Selected applicatios in biomechanics.

BM 522 Skeletal Muscle Mechanics  (3+0+0) 3 ECTS 8
(İskelet Kası Mekaniği)
Skeletal muscle architecture: morphology, uni- and multipennate muscles, mono- and multiarticular muscles. Mechanism of activation and sliding filament theory. Force production in the sarcomere level in isometric and isokinetic conditions. Force production in the muscle level and muscle architecture variations in relation to force production. Muscle mechanics: Hill’s muscle equation, Hill type muscle models, constancy of muscle volume, constitutive models, mechanisms of transmission of muscle force. Finite element modeling of muscle. Experimental techniques.

BM 525 Tissue Biomechanics  (3+0+0) 3 ECTS 8
(Doku Biyomekaniği)
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  (3+0+0) 3 ECTS 8
(Hareket Biyomekaniği)
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 Fundamentals of Neuroscience (3+0+0) 3 ECTS 8
(Sinirbilimin Temelleri)
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 ECTS 8
(Sayısal Yöntemler 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 Advanced Molecular Neural Stem Cell and Neurugeneration (3+0+0) 3 ECTS 8
(İleri Nörobiyoloji: Moleküler Sinir Kök Hücre ve Nörojenerasyon)
Introduction to the neuron at the Cellular and Molecular Level; Development of the Nervous System - Embriyonic neurogenesis, axon growth and guidance; Molecular mechanisms of synaptic plasticity; Molecular mechanisms and gene expression in LTP and LTD; Adult neurogenic zones and adult neurogenesis; Neural stem cells-molecular identification, cell culture, and tissue engineering; Neurodegenerative disorders - Alzheimer's Disease pathology and genetics, Parkinson's Disease pathology and genetics, ALS pathology and genetics.

BM 533 Neural Networks (3+0+0) 3 ECTS 8
(Sinir Ağları)
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 534 Learning and Memory (3+0+0) 3 ECTS 8
(Öğrenme ve Bellek)
Structure and function of human memory networks, introduction to neurobiology, different types of memory and their neural substrates, interaction of memory networks, short term memory and sensory cortices, working memory and cortical network, episodic memory and medial temporal lobe, semantic memory and lateral temporal lobe, skill memory and basal ganglia-parietal lobe, observational learning and mirror neura system. emotional memory and amygdala.

BM 535 Computational Cell Biology  (3+0+0) 3 ECTS 8
(Hesaplamalı Hücre 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 536 Principles of Neuroimaging  (3+0+0) 3 ECTS 8
(Nörogörüntülemenin İlkeleri)
Overview of the Statistical Parameter Mapping, General Linear Model, Contrasts and Classical Inference, Thresholding, Hierarchical models, Classical and Bayesian Inference; expectation maximization, Restricted Maximum Likelihood Estimation, Expectation Maximization, Preprocessing and Segmentation of fMRI data,  EEG Source Imaging.  

BM 537 Neurochemistry (3+0+0) 3 ECTS 8
(Nörokimya)
Cellular neurochemistry and neural membranes. Evolution of neurochemical systems. Intracellular signaling; G Proteins, phosphoinositides, cyclic nucleotides in nervous system. Neurotransmitters and neuromodulators, Glutamate, GABA, glycine, Ach, adrenaline and noradrenaline, dopamine, serotonin and histamine, Neuroactive peptides, Related disorders.

BM 538 Computational Neuroscience   (3+0+0) 3 ECTS 8
(Hesaplamalı Nörobilim)
Neural spike trains and point processes. Spike rate and statistics. Neural encoding. Estimating firing rates. Reverse correlation methods. Static nonlinearities. Spatiotemporal receptive fields. Neural decoding. Discrimination. Spike-train decoding. Population decoding. Entropy and mutual information. Entropy maximization. Entropy and information in spike trains.

BM 541 Biomaterials (3+0+0) 3 ECTS 8
(Biyomalzemeler)
General properties of materials. Chemical, Physical and Mechanical Properties of Biomaterials. Biomaterial Degradation and Processing. Surface properties of Biomaterials. Metallic, ceramic, polymeric and composite materials for Biomedical Applications. Evaluation of standards used in Biomaterials.

BM 544 Failure Analysis of Implants  (3+0+0) 3 ECTS 8
(İmplantlarda 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 propagation. 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 545 Characterization of Biomedical Samples (3+0+0) 3 ECTS 8
(Biyomedikal Malzemelerin Karakterizasyonu)
Surface analysis of biomaterials using scanning electron microscopy (SEM), transmission electron microscopy (TEM), and atomic force microscopy (AFM). Chemical analysis of biomedical samples using X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR) and Raman spectroscopy. Mechanical characterization of biomaterials using stress and strain analyses, examination of types of deformation, strengthening mechanisms and modes of fracture, and application of Mohr’s circle and failure criteria.

BM 546 Tissue-Biomaterials Interactions (3+0+0) 3 ECTS 8
(Doku-Malzeme Etkileşimleri)
Biomaterials, Proteins, Protein-Surface Interactions, Blood-Biomaterials Interactions and Coagulation, Inflammation and Infection, Immune System and Infection, Wound Healing, Surfaces of Biomaterials and Physiological Environment, Biocompatibility, Example Case Investigations. 

BM 547 Biomedikal Nanostructures (3+0+0) 3 ECTS 8
(Biyomedikal Nanoyapılar)
Nanotechnology and Nanobiotechnology terms and their definitions, Synthesis and Characterization of Nanostructures, Nanoproduction, Nanostructures-Protein, Cell and Tissue Interactions, Biomedical and Clinical applications of Nanostructures.

BM 554 Modeling of Biological Systems  (3+0+0) 3 ECTS 8
(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 8
(Klinik Araştırma Tasarımı ve Değerlendirilmesi)
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 560 Introduction to Medical Device and Implant Design (3+0+0) 3 ECTS 8
(Medikal Cihaz ve İmplant Tasarımına Giriş)
 Review on Selection of biocompatible materials, surface properties of biomaterials, host response, medical manufacturing technologies, design control, pre-clinical device testing for safety and efficiency and include the risk/benefit ratio assessment evaluation of clinical performance and design of clinical trials.

BM 561 Quality Assurance in Diagnostic Radiology  (3+0+0) 3 ECTS 8
(Tanı Radyolojisinde Kalite Güvencesi)
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  (3+0+0) 3 ECTS 8
(Tıbbi Görüntüleme)
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 reconstruction, emission tomography: PET and SPECT, MR imaging, LASER imaging, electrical impedance tomography, bone densitometer, patient exposure and protection, quality assurance in radiology.

BM 564 Biomedical Instrumentation and Measurement  (3+0+2) 4 ECTS 9
(Biyomedikal Cihazlar ve Ölçümler)
Basic Electrical Circuits, Amplifiers, Sensors and Transducers, Biopoential Signals and Amplifiers, Electrodes, Measurement of Blood Pressure and Sound,  Measurement of Blood Flow and Volume, Respiratory System Measurements, Chemical Sensors, Audiometry, Electrical Safety.

BM 570 Magnetic Resonance Spectroscopic Imaging (3+0+0) 3 ECTS 8
(Manyetik Rezonans Spektroscopic Görüntüleme)
Magnetic Resonance Spectroscopic Imaging (MRSI), spin-spin interactions, nuclear magnetic resonance chemical structure identification, molecular spectroscopy, metabolism, MRSI data acquisition protocols, MRSI data processing and analysis, clinical applications including cancer, neurological disorders, and pediatric diseas.

BM 571 Biomedical Signal Processing  (3+0+0) 3 ECTS 8
(Biyomedikal İşaret İşleme)
IOverview of Probability and Random Processes. Statistical Signal Modeling: AR, ARMA, Prony Methods. Optimal filtering; Wiener and Kalman Approach. Bayesian Signal Processing. Power Spectrum Estimation.  Adaptive Filters. Application to Bioelectric Signals; ECG, EMG, EEG, HRV, fMRI-BOLD and others.

BM 573 Cardiovascular Imaging (3+0+0) 3 ECTS 8
(Kardiyovasküler Görüntüleme)
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 578 Graduate Seminar (0+1+0) 0 P/F ECTS 2
(Lisansüstü Seminer)
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  579 Graduate Seminar (0+1+0) 0 P/F ECTS 2
(Lisansüstü Seminer)
Seminars offered by faculty, guest speakers and/or graduate students designed to widen students' perspectives on specific topics of interest and to expand their range of scientific research techniques and publication ethics.

BM 580-589 Special Studies (3+0+0) 3 ECTS 8
(Özel Çalışmalar)  
Study of specific Biomedical Engineering subjects in biomechanics, biocybernetics, bioelectronics or prosthetics and artificial organs.

BM 590-599 Selected Topics (3+0+0) 3 ECTS 8
(Seçilmiş Konular)  
In depth study of a selected topic in the field of Biomedical Engineering.

BM 597 Human Cognition and Behavior (3+0+0) 3 ECTS 8
(İnsan Bilişi ve Davranışı)
Human brain development, Human nervous system, Brain imaging techniques, Brain and physiology, Biology of behavior, Sensory areas, Emotions; stress, fear, pain, Attention, Consciousnes, Alertness, Brain rhythms and sleep, Memory and learning, Decision making, Addiction, Cognitive impairment

BM 598 Multimodal Brain Imaging (3+0+0) 3 ECTS 8
(Çok Modlu Beyin Görüntüleme)
The basics of MRI and functional MRI (fMRI), Neurobiological principles of fMRI, Experiment design, data acquisition, and preprocessing, Physiological signals, Spatiotemporal brain patterns, Simultaneous EEG-fMRI, EEG artifacts, EEG data preprocessing, EEG data analysis, Multimodal brain imaging in clinics, Hands-on analyses with AFNI and EEGLAB

BM 601 Quality Assurance Principles for Biomedical Engineers  (3+0+0) 3 ECTS 8
(Biyomedikal Mühendisleri için Kalite Güvence Kavramları)
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 ECTS 8
(Nükleer Biyomedikal 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, radioimmuno assaying, clinical dosimetry, pocket dosimeters, thermoluminescent dosimetry, proportional counters, Geiger counters.

BM 616 Therapeutic Medical Devices   (3+0+0) 3 ECTS 8
(Tedavi Amaçlı Tıbbî Cihazlar)
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 System  (3+0+0) 3 ECTS 8
(Duyu Sistemleri)
Basic psychophysics, anatomy and physiology of sense organs, neural pathways andinformation processing, skin and peripheral afferent fibery, somatosensory cortex, cortical maps, tactile psychophysics, cochlea and auditory nerve fibers, central auditory nuclei, auditory cortex, auditory psychophysics, retina, ganglion cells and LGN, primary visual cortex, spatiotemporal receptive fields, higher visual areas, visual psychophysics, laboratory techniques in sensory research.

BM 633 Dynamics of Neural Systems  (3+0+0) 3 ECTS 8
(Sinir Sistemlerinin Dinamiği)
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 ECTS 8
(Manyetik Rezonans Görüntüleme 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 671 Introduction to Medical Informatics  (3+0+0) 3 ECTS 8
(Tıbbî Bilişime Giriş)
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 (3+0+0) 3 ECTS 8
(Biyomedikal Alanda Görüntü Depolama ve İletişim Sistemleri (PACS))   
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 679 Graduate Seminar (0+1+0) 0 P/F ECTS 2 
(Lisansüstü Seminer)
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 681-689 Special Studies  (3+0+0) 3 ECTS 8
(Özel Çalışmalar)
Studies of advanced topics in the specialization areas of Biomedical Engineering.

BM 690 Master's Thesis in Biomedical Engineering   ECTS 60
(Biyomedikal Mühendisliği Yüksek 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   (3+0+0) 3 ECTS 8
(Özel Konular)
In depth study of a special topic in the field of Biomedical Engineering.

BM 699 Guided Research (2+0+4) 4 ECTS 30
(Yönlendirilmiş Araştırmalar)
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.

BM 700 Graduate Seminar (0+1+0) 0 ECTS 2
(Lisansüstü Seminer)
Seminars offered by faculty, guest speakers and graduate students designed to widen students' perspectives on specific topics of interest and to expand their range of scientific research techniques and publication ethics.

BM 790 Doctoral Dissertation in Biomedical Engineering ECTS 120
(Biyomedikal Mühendisliği Doktora Tezi)
Original research on the theoretical and/or application aspects of a special topic related with the student's major area of specialization in Biomedical Engineering. Preparation and defense of a Ph.D. dissertation.

UNDERGRADUATE COURSES OFFERED BY THE INSTITUTE

BM 402 Engineering in Medicine (3+0+0) 3 ECTS 5
(Tıpta Mühendislik)
The human body as a machine; physiological principles, modeling, neural networks; diagnostic techniques and related instrumentation; high technology in patient care and therapy. Computers in medicine; signal and image processing, picture archiving, telemedicine; biomaterials and prostheses; principles of clinical engineering and safety considerations; technology management in hospitals.
Prerequisite: Technical elective for engineering and science undergraduate students only.