BİYOMÜHENDİSLİK DOKTORA PROGRAMI
Fermantation processing and characteristics, function and ecology of responsible microorganisms. Fermentative activities, growth responses and culture interactions related to metabolism, physiology and genetics of lactic acid bacteria and selected yeasts and molds. Current developments in starter culture technology and genetics; application to food and industrial fermentations.
Current advanced biochemical concepts focusing on research topics, Emphasis in protein chemistry on membrane topology and structural analysis of oxidases. Other topics will include the role of complement in the functions of the immune system, tumor suppressor proteins and cancer, and RNA protein interactions.
Study and discussion of experimental and computational approaches for contemporary problems in functional genomics. Topics include DNA chip design, experimental data normalization, expression data representation standards, proteomics, gene clustering, selforganizing maps, Boolean networks, statistical graph models, Bayesian network models, continuous dynamic models, statistical metrics for model validation, model elaboration, experiment planning, and the computational complexity of functional genomics.
Mathematical modeling techniques to address key questions in modern biology. Overview of modeling techniques in molecular biology and genetics, cell biology and developmental biology. Description of key experiments that validate mathematical models. Topics include molecular systems biology — constructing and modeling of genetic networks, control theory and genetic networks, lambda phage as a genetic switch, synthetic genetic switches, bacterial chemotaxis, genetic oscillators, and circadian rhythms; cellular systems biology — reaction diffusion equations, local activation and global inhibition models, gradient sensing systems, and center-finding networks; developmental systems biology — general pattern formation models, modeling cell-cell communication.
The Environmental Bioengineering lecture is designed to introduce the fundamental principles and current trends in the microbiology and effective treatment solutions for wastewater engineering. Some selected topics in microbiology of activated sludge, biological nitrogen and phosphorus removal and anaerobic digestion systems will be covered. Discussions of concepts of biotechnology as applied to biodegration of solid and toxic wastes, and degradation of recalcitrant organic matters will be conferred. This will be accomplished by providing basic information in the form of lectures and demonstrations. Recent advances in biological wastewater treatment and in application of new bioreactor configurations will also be discussed.
BIOCHEMICAL ENGINEERING AND NEW BIOPROCESS CHALLENGES
Bioprocess Synthesis and Mapping
Bioengineering design and regulations
Biotransport processes and biomaterials
Bioprocessing of new medicines and vaccines
DRUG DELIVERY SYSTEMS I
Drug delivery systems; definition, an overview; function and preparation of drug delivery system, Colloidal drug delivery systems (ointment, microemulsion, liposomes), Site-spesific drug delivery, Micro and nanoparticular systems; use of nanotechnology in drug delivery,
DRUG DELIVERY SYSTEMS II
Bioadhesif systems, Transdermal systems, Implants, Other dosage forms applied to different areas (ocular, nasal, pulmonary etc.), Biotechnology drug development (protein delivery systems)
2DE ELECTROPHORESIS AND MASS SPECTROMETRY
Characterisation and identification of macromolecules by using mass spectrometry. Course is supported by a series of experiments in the department’s laboratories. Course cover a variety of research projects. The initial plan of work is prepared by the instructer and the student starts the mini project. Reports of progress are written each mounth and, at the end of the first semester the student gives a short oral presentation to the department.
STATISTICAL BIOINFORMATICS Statistical analysis of genomic data. Includes probability and statistics application to DNA sequence analysis, phylogenetic inference, statistical population genetics and genetic mapping, statistical molecular evolution, and macromolecular structure prediction. Algorithms for microarray analysis and DNA pattern identification. Emphasis on large datasets.
BIOCHEMISTRY OF TISSUES
Connective, Muscle, Nerve, Fat and Epithelial tissues
NANOMATERIALS AND APPLICATIONS
Introduction. Properties of nanomaterials: electrical and optical, superconducting, magnetic, mechanical properties. Characterization of nanomaterials. Nanoparticles production method, Applications of nanomaterials. Special nanomaterials.
COMPUTATIONAL MOLECULAR BIOLOGY
Algorithms for alignment of biological sequences and structures, computing with strings, phylogenetic tree construction, hidden Markov models, computing with networks of genes, basic structural computations on proteins, protein structure prediction, protein threading techniques, homology modeling, molecular dynamics and energy minimization, statistical analysis of 3D biological data, integration of data sources, knowledge representation and controlled terminologies for molecular biology, graphical display of biological data, machine learning (clustering and classification), and natural language text processing.
Consideration of practical and theoretical aspects of modifying metabolic pathways to produce products of interest. After reviewing basic principles of metabolism and the scope of the metabolic engineering field, case studies of metabolic engineering will be examined, including detailed consideration at a genetic level. Thereafter, techniques and applications of metabolic modeling will be considered, including structured modeling and metabolic control theory. Example applications include the production of central metabolites, amino acids, pharmaceutical proteins, and isoprenoids.
Various methods of optimization and their uses in modern bioengineering. Students will learn to formulate and analyze optimization problems and apply optimization techniques in addition to learning the basic mathematical principles on which these techniques are based. Topic coverage includes linear programming, nonlinear programming, dynamic programming, combinatorial optimization and Monte Carlo methods.
Introduction and definitions, demand and applications of biomaterials, general classification, recent advances and applications of metallic biomaterials, recent advances and applications of ceramic biomaterials, recent advances and applications of polymeric biomaterials, recent advances and applications of composite biomaterials, novel coating applications in biomaterials, advanced biosencors, advanced absorbant biomaterials, novel artificial organs, novel drug delivery systems, future prospects and perspectives of biomaterials
Basic concepts of statistical models and use of samples; variation, statistical measures, distributions, tests of significance, analysis of variance and elementary experimental design, regression and correlation, chi-square. Covariance, multiple regression, curvilinear regression, concepts of experimental design, factorial experiments, confounded factorials, individual degrees of freedom and split-plot experiments. Computing laboratory addressing computational issues and use of statistical software.
BIOLOGİCAL NETWORKS THEORY
Components of biological systems, their biochemical properties and function. The technology used for obtaining component lists. Relationship within and integration of component lists. Structured vocabularies and component ontologies. Algorithms for comparative approaches in deciphering and mining component lists. The process of reconstructing complex biological reaction networks. Reconstruction of metabolic networks, regulatory networks and signaling networks. Bottom-up and top-down approaches. The use of collections of historical data. The principles underlying high-throughput experimental technologies and examples given on how this data is used for network reconstruction, consistency checking and validation. Statistical mechanics of network topology.
MODERN CONTROL THEORY
Emphasis on digital control, state-space analysis and design, and optimal control of dynamic systems. Topics include review of classical control theory; discrete-time system theory; discrete modeling of continuous-time systems; transform methods for digital control design; the state-space approach to control system design; optimal control; and effects of quantization and sampling rate on performance of digital control systems.
MUTAGENESIS AND GENE THERAPY
Mutation types, DNA repair, gene therapy and vectors, recombinant DNA methods used in gene therapy, gene transfer methods, various genetic disease mutations and their gene therapy protocols.
METHODS IN BIOTECHNOLOGY
A laboratory-based course designed to provide hands-on experience with modern biotechnological research, high throughput screening, and production tools. The course provides familiarity with processes commonly used in the biotechnology.
PHYSIOLOGY FOR BIOENGINEERS
This course is an introduction to physiological principles and concepts necessary for understanding basic regulatory phenomena and the pathophysiology of disease in living organisms. An analytical approach will be emphasized and terminology essential for understanding and describing these processes will be developed. The course will include some aspects of cellular biology, excitable tissue phenomena, cardiopulmonary and renal physiology, and neuroendocrine regulation of some of these processes.
REGULATION OF GENE EXPRESSION
Genetic code, protein targeting, mutations, Complementation, mRNA, translational control, gene regulation in prokaryotes, gene regulation in Eukaryotes,
DNA structure, DNA replication, Reapair, Transcription, Translation, Cloning, Recombination, Mutagenesis, Viruses, Transposable elements
V arious G-protein pathways, kinase signaling, nuclear receptor signaling, and other common intracellular signaling pathways
PROTEINS: STRUCTURE AND FUNCTION
The 3 dimesional structure of proteins will be investigated in relation to their functions. What causes protiens to have the structures they have and how does this correlate with the functions they have? Is the amino acid sequence important for determining the structure and the function?
APPRISAL AND APPLICATION OF LIFE SCIENCES
Microbial metabolism and engineering
Structural biology and protein engineering
Cellulare fonction: genome to metabolome
COMPUTATIONAL STRUCTURAL BIOLOGY
The architechture of macromolecules, in particular of proteins, will be investigated using molecular dynamic tools. This will include generation of protein complex structures using molecular dynamic simulatons and calculation of binding free energies for protein-ligand binding.
Introduction to the application of basic genetic principles to the study of human health and disease, Mendelian genetics, cytogenetics, population genetics, molecular cytogenetics, oncocytogenetics and clinical applications of principles. The importance and implication of genetic disease at the levels of the population and individual families.
Mechanisms and evaluation of biodegradability of polymers, methods used in biodegradation, biodegradation behaviour of polymers in liquid environments, biodegradation behaviour of polymers in the soil, ecotoxicological aspects in the biodegradation process of polymers, general characteristics, processability, ındustrial applications and market evolution of biodegradable polymers, polyhydroxyalkanoates, starch-based technology, poly(lactic acid) and copolyesters, aliphatic-aromatic polyesters, material formed from proteins, enzyme catalysis in the synthesis of biodegradable polymers, environmental life cycle comparisons of biodegradable plastics.
Advanced techniques in the isolation, purification and manipulation of nucleic acids and proteins.
BIOPROCESS DESIGN AND IMPLEMENTATION
Design, planning, conduct and analysis of full pilot scale bioprocess
Research Project business appraisal
Bioprocess validation and quality control
MANAGEMENT OF BIOPROCESS VENTURES
Management: discovery to manufacture
PLANNING AND MANAGEMENT OF RESEARCH
Design and evolution of biotechnology strategies, biotechnology infrastructure, biotechnology sourcing, biotechnology transfer, R&D management, process development and planning, Team-based projects on the design of processes for producing advanced materials
ADVANCEDTOPICS IN BIOENGINEERING I
Courses not listed in the catalogue. Advanced topics vary from year to year according to interest of students and faculty.
ADVANCED TOPICS IN BIOENGINEERING II
Courses not listed in the catalogue. Advanced topics vary from year to year according to interest of students and faculty.
Program of research leading to Ph.D. degree arranged between the student and a faculty member. Students register to this course in all semesters after passing the qualifier exam.