BENG501 Molecular Biology for Engineers

The molecular and cellular bases of life for bioengineering students. Analysis and engineering of biomolecular structure and dynamics, enzyme function, molecular interactions, metabolic pathways, signal transduction, and cellular mechanics.

BENG502 Emerging Topics in Biotechnology

This seminar-style, capstone course is an in-depth exploration of emerging technologies, innovations, and new products that are noteworthy to the biotechnology industry. The first half of the course focuses on examining and critiquing what new scientific discoveries will likely impact the industry and in what ways. In the second half of the course, students, working in teams, will give written and oral presentations on case studies that attempt to predict products derived from the new innovations and discoveries. The objective of the course is to give the student insight into the process of translating scientific discovery into innovative products.

BENG503 Advances in Bionanotechnology

This course covers nanotechnology applications in bioengineering. Students learn about cutting edge research that uses the tools of nanotechnology to tackle medical problems. Topics include bionanotechnology - related research for diagnosis, detection, and treatment of disease; cell targeting; drug design and delivery; gene therapy; nanotechnology approaches in the preparation of prostheses, implants and tissue regeneration.

BENG504 Advanced Molecular Biology

Advanced Molecular Biology is an advanced course on the molecular biology of pro- and eukaryotic organisms. Topics include chromosome structure and organization, RNA transcription, selected aspects of the molecular regulation of gene expression, protein synthesis and post-translational regulation, DNA synthesis, repair, and recombination.

BENG505 Current Topics in Molecular Biology

Current Topics in Molecular Biology is an advanced course on recent developments of molecular biology and its translational aspects.

BENG506 Introduction to Bioinformatics

The course covers computational techniques for mining large amount of information produced by recent advances in biology, including genome sequencing and microarrray technologies. Main topics of the course include DNA and protein sequence alignment, sequence motifs/patterns, phylogenetic trees, protein structures, microarray data analysis and biological networks.

BENG507 Human Molecular Genetics

Advanced molecular biology is an advanced course on the molecular biology of pro- and eukaryotic organisms. Topics include chromosome structure and organization, RNA transcription, selected aspects of the molecular regulation of gene expression, protein synthesis and post-translational regulation, DNA synthesis, repair and recombination.

BENG508 Advanced Cell Biology

Advanced Cell Biology course deals with the biology of cells of higher organisms: The structure, function, and biosynthesis of cellular membranes and organelles; cell growth and oncogenic transformation; transport, receptors, and cell signaling; the cytoskeleton, the extracellular matrix, and cell movements; chromatin structure and RNA synthesis.

BENG509 Introduction to Nanobiotechnology: Concepts and Applications

This course provides perspective for students and researchers who are interested in nanoscale physical and biological systems and their applications in medicine. It introduces concepts in nanomaterials and their use with biocomponents to synthesize and address larger systems. Applications include systems for visualization, labeling, drug delivery, and cancer research. Technological impact of nanoscale systems, synthesis, and characterizations of nanoscale materials are discussed.

BENG510 Applied Biochemistry

This course will review the chemistry of living systems, with an emphasis on topics of biotechnological and biomedical interest. The course will also survey the methods used in modern biochemistry, so that students will be able to understand the connection between empirical data and the established facts and concepts presented in the course. The first part of the course will focus on the relationship between structure and function of proteins, nucleic acids, carbohydrates, lipids, and membranes. Important chemical concepts relevant to these molecules and their components (amino acids, nucleotides, etc.), such as pH and weak chemical interactions, will be presented. After an introduction to enzyme kinetics, the course will concentrate on the principles and pathways of intermediary metabolism. The final topics will be concerned with informational biochemistry – DNA replication, recombination, repair, and transcription, as well as protein synthesis.

BENG511 Molecular Biology Laboratory for Engineers

Practical applications of biotechnology and molecular bioengineering including recombinant DNA techniques, molecular cloning, microbial cell growth and manipulation, and library screening. Emphasis is on experimental design and data analysis.

BENG512 Biotechnology and Biosafety

Modern Biotechnological approach. Historical development of biotechnology and biosafety. Transgenic applications. Biosafety of transgenic applications. Assessment methods to evaluate the effects of genetically changed organisms for food safety and environment. Biosafety systems. Biotechnological applications. Comparison of specific similarity and precaution principle approaches. Effect of biotechnological applications to human health and biological variation. Biosafety control systems. Risk assessment and risk management for biosafety systems. Internatiomal biosafety protocols and rules in different countries. Socioeconomical and ethical issues in Biotechnology.

BENG513 Ethics in Biotechnology

History of bioengineering, definition of bioengineering, research, publishing principles and human and animal rights in terms of technology, place of environmental consciousness on the application of bioengineering subjects and important ethical terms, legal and social laws.

BENG514 Cancer Biology  and Treatment

Provides an integrated lecture series summarizing current knowledge in cancer biology and integrating current literature with basic concepts. Topics include molecular mechanisms of cancer initiation, progression and metastasis, signal transduction, types of cancer, pathology, sources of carcinogens, genetic and epigenetic mechanisms and consequences, therapeutic resistance, cancer markers and therapeutic targets, statistics of incidence/survival, Students will learn to use online databases to develop independent strategies for analyzing datasets. There will be several writing assignments and in class oral presentations of research articles.

BENG515 Introduction to Tissue Engineering

Description of tissue engineering. Fundamentals; importance of cell-scaffold-biosignal molecule integration. Scaffold characteristics, general design criteria will be covered. Selection of cell sources and stem cells, in vitro culture conditions, and tissue engineered products and problems in their clinical utilization will be discussed. Organ tissue engineering.

BENG516 Tissue Engineering andRegenerative Medicine

Basics concepts of tissue engineering andregenerative medicine field will be covered in the first part of the course. The repair and regeneration of varying tissues for therapeutic purposes will be discussed.  Mechanism of cell differentiation into specific tissues in response to biological signal molecules will be explored. Cellular mechanism involved in animal clonning. Molecular basis of cellular tissue remodelling and regeneration fort he discovery of new drugs.

BENG517 Polymeric Biomaterials

Basics of polymer structure. Classification of polymers by source, chemistry, shape, end-use, etc.  Natural and synthetic polymers. Criteria of polymer type selection. Types of natural polymers, structures, isolation-purification, applications (chitosan, alginate, cellulose, collagen, starch, gelatin); types of synthetic polymers, synthesis-purification, applications (biodegradable polymers, silicones, PET, PTFE, PU, polyamides, acrylate-based polymers). Applications of biomedical polymers; dental, orthopedical applications, adhesives, sutures, vascular grafts, wound dressings, controlled release materials, carriers for drug/gene delivery.

BENG518 Biomaterials

Description and history of biomaterials. Criteria for the success of a biomaterial. Biocompatibility definition. Classification and general application types will be discussed. Biomaterials surface characteristics, investigation techniques: FTIR-ATR, SEM, surface tension, ESCA, etc. Mechanical properties and measurement, optical and diffusion properties. Material types, advantages and disadvantages: metals, ceramics, composites, polymers. Material fabrication techniques. Material- tissue interaction; coagulation, immune response, foreign body reaction. Discussion of a biomaterial journey: from lab to body.

BENG519 Physiology

Biological control systems: homeostatic mechanisms and cellular transport (membrane transport, transportation mechanisms), neutral control mechanisms (membrane potentials, diffusion); central nervous system; hormonal control mechanisms; skeletal muscle system; coordinal body functions: blood circulation system, respiration, kidneys, digestive system, growth and procreation, defense mechanisms of the body.

BENG520 Artificial Organs

Introduction to artificial organs. Mass transfer and basic principles of fluid mechanics.  Chemical reactions in biological systems. Information on biomaterials. Basic principles of artificial organ design (biomimetics). Effects of artificial organs on the development of society health. Mass transfer. Basic principles of fluid mechanics. Chemical reactions in biological systems. Chemical reactions in biological systems. Basic components of biological systems. Working principles of biological systems. Production of biomaterials used in artificial organs. Basic principles of artificial organ design (biomimetics). Artificial organ (heart, lung, kidney, etc) design Effects of artificial organs on the development of society health.

BENG521 Biomedical Electronics

Introduction of biomedical system. Principle and design of various biomedical devices such as pacemaker, EEG, ECG, EMG, ve ICU equipment, diagnostic imaging devices, blood bank monitor, CT, MRI, mammography,  ultrasound, endoscope, confocal microscope, multiphoton flourescent microscope.

BENG522 Biomechanics

Introduction to biomechanics and muscle-skeletal system. Introduction to Biomechanics in biological systems and transport process. Dynamics of mechanical systems. Dynamics of muscle and arthrosis. Response of living tissues under the strain. Application methods of mechanical engineering on human muscle- skeletal system. Mechanical properties of tissues. Investigation of orthopedic materials and mechanical properties. Tension and deformations on materials. Analysis of fracture-crack, fracture-crack fictions, frictional, polish and overwear, process of implants. Headlines on heart dynamics and heart beating, blood circulation, microcirculation and muscle mechanics. Modern developments on biomechanics at advanced mathematical level. Main research areas and problems related with biomechanics.

BENG523 Multifunctional Polymeric Nanocarriers

Multifunctional nanocarriers and main characteristics. A typical nanocarrier. Pathways and problems in drug delivery. Types of nanocarriers: liposomes, inorganics, polymeric nanoparticles, micelles, etc. Polymeric nanoparticle preparation methods (emulsion, phase separation, coaservation). Micelle formation; controlled polymerization for uniform polymer chains (RAFT, ATRP). Cross-linked micelles. Stimuli-responsive systems. Drug-conjugated systems. Surface modification, PEGylation. Targeting ligands and targeting approaches.

BENG539 Nanocarriers and Drug Delivery

Definiton of drug delivery. Criteria for a nanocarrier design. Physiochemical characteristics. Types of nanocarriers: lipid-based, inorganic-based, polymer-based nanoparticles, biological nanoparticles (viruses). Quantum dots for nuclear and cytoplasmic visualization. Targeting and biodistribution of nanoparticles, EPR effect, renal clearance, etc.  Toxicological issues. Examples of FDA approved nanodrugs in addition to nano formulations at the pre-clinical and clinical stages.

BENG524 Materials Design and Fabrication for Tissue Engineering

Description of a tissue engineering scaffold; characteristics of an ideal scaffold. Cells, scaffold, biosignal molecules relationship. Design criteria of a scaffold; material selection. Methods for scaffold fabrication: salt leaching, ice-particle leaching, gas-foaming, particle aggregation, freeze drying, thermally induced phase separation, centrifugation, supercritical carbon dioxide, fiber production, electrospinning, solid freeform fabrication, 3D printing. Bioplotter. nanopatterning, microcontact printing.

BENG525 Instrumental Analysis

Students will develop an understanding of the analytical capabilities of a number of instrumental methods and be able to suggest suitable instrumental methods for particular analytical problems. The main objective of instrumental analysis is to learn the theory of operation for several types of instruments used for chemical measurements in the analytical sciences. Lecture topics cover spectrophotometric and chromatographic methods. In the laboratory, students gain hands-on experience both by performing selected basic chemical determinations and by undertaking special projects.

BENG526 Basic Patent Principles in Science and Engineering

This course will provide an introduction to the basic principles of the national and international patent systems. It covers the function of the patent system; the nature of patents as property and as legal instruments; comparisons with other forms of intellectual property; subject matter eligible for patenting; the conditions for patentability of an invention; and the disclosure requirements for a patent application. This course mainly focuses on the preparation technics of a patent application. The students will each be assigned an case study, and will write a patent application draft. Students will be instructed as to best practices drafting the application, and then will be critiqued regarding written patent applications. The patent applications will be written in stages, including invention disclosure considerations, drawings, claims, and specification, with critique on each step in the process.

BENG527 Biosensors

Underlying engineering principles used to detect small molecules, DNA, proteins, and cells in the context of applications in diagnostic testing, pharmaceutical research, and environmental monitoring. Biosensor approaches including electrochemistry, fluorescence, acoustics, and optics; aspects of selective surface chemistry including methods for biomolecule attachment to transducer surfaces; characterization of biosensor performance; blood glucose detection; fluorescent DNA microarrays; label-free biochips; bead-based assay methods. Case studies and analysis of commercial biosensors.

BENG528 Polymer Science

Polymer terminology, nomenclature. Stereochemistry in polymers, conformation, configuration, isomerization, optical activity. Morphology of polymers, crystaline, amorphous and semi-crystalline polymers, glass-transition temperature, melting temperature. Methods for the molecular weight determination of polymers, colligative properties and molecular weight, size-exclusion chromatography, light-scattering, etc. Mechanical properties and other properties of polymers. Polymerization reactions, radical polymerization, addition polymerization, condensation polymerization, etc. Polymerization processes, bulk, solution, suspension, emulsion polymerizations. Processing of polymers.

BENG529 Nanofabrication for Biological Applications

Importance of surface characteristics for biological applications (i.e., biomaterials, biosensors). Lithography, optical and e-beam lithography; X-ray lithography, focused-ion lithography, soft lithography, imprinting lithography, Thin film deposition, physical vapor deposition, chemical vapor deposition; Etching: wet and dry; Self-assembling; Microelectromechanical systems.

BENG531 Biosignal and Image Analysis

Fundamentals of signal processing (linear time invariant systems, Fourier transforms for continuous and discrete  signals, sampling, filter design; Imaging system: Point spread function, resolution (pixel, voxel, spatial, temporal); Image quality and uncertainties in image formation (digitization, quantum efficiency, calibration, CNR, SNR); Image registration, filtering and noise removal; Basic clustering methods; Time –frequency analysis; Compressed sensing; Applications for biomedical signal and images.

BENG532 Medical Imaging

General characteristics of imaging systems; X-ray and CT: general principles, interaction of X-rays with tissues, contrast agents, imaging techniques, image reconstruction, radiation dose; Nuclear Medicine: general principles, radionuclide, radioactive decay, gamma camera, imaging techniques, SPECT, PET; Ultrasound imaging: general principles, interaction of acoustic waves with tissue, acoustic impedance, instrumentation, scanning modes, artifacts, blood velocity measurements, contrast agents; MR imaging: general principles, nuclear magnetism, magnetic resonance, instrumentation, imaging sequences, contrast agents, imaging techniques, functional MRI.

BENG536 Introduction to UNIX/Linux

This course aims to make student familiar with UNIX-like computational environment.  No background is required. The course may be combined with workshop (or students are required to bring their notebook to the class). Upon completion of this course, students will : 1) understand UNIX systems; 2) be able to handle data files on UNIX; 3) be able to submit a job to the high-performance computing clusters. Topics include: UNIX file systems, basic/useful UNIX commands, vim editor, shell scripting, filters (sed, awk), etc.

BENG537 Molecular & Statistical Mechanics

This course covers statistical mechanics theory and its applications to molecular systems, and computer simulation methods to study the dynamics/energetics of macromolecules.  No background is required. Upon completion of this course, students should be able to: 1) explain the concepts of statistical mechanics; 2) use computational methods. Topics include: Maxwell-Boltzmann distributions, ensembles, partition functions, energy optimization, Monte Carlo methods, and molecular dynamics simulations.

BENG533 Biophysics

Jarzynski’s equality, FRET, low-barrier H-bond, amphiphatic polymers, and computational methods (Monte Carlo, MD, replica exchange, multi-canonical, etc.)

BENG538 Biological Sciences for Bioengineers

This compulsory course intends to provide students with engineering background with basic biological knowledge. In this course, the students will acquire the knowledge in the following topics: Cell structure and function, Central Dogma, Macromolecules, Membrane Proteins and Signalling Cascades, Blood System, Immune System and research approach and techniques to these subjects. In addition to that, the students will learn how to search the literature to find the recent advances in research and be involved in scientific discussions 

BENG534 Research Techniques in Bioengineering

This is a core course that provides practical experience in a variety of techniques currently employed in biological research, providing an understanding of their application and result interpretation. Students will learn how to work in a laboratory (safety and regulations).  Also, students will learn to become familiar with some major techniques used in Biology. This course presents the principles of micro- and molecular techniques. This course will prepare students to design and execute experiments and how to record and interpret the data out of these experiments. In addition to that, student will learn how to search the literature and write scientific papers.

BENG537 Stem Cells

It will introduce important biological concepts like stem cell biology, pluripotency, adult and embryonic and cancer stem cell and the barriers to regenerative medicine, including scientific, ethical, regulatory and proprietary issues. We will also consider the potential consequences and limitations of stem cell therapy, particularly the connection between stem cells and cancer. Students will have a comprehensive overview of this exciting new field of research and its clinical relevance.

BENG530 Basic Principles of Engineering

This course aims to provide students with non-engineering background with general engineering fundamental. It consists of four parts. Part I, an introduction; engineering calculations and data analysis. Part II, material and energy balances. Part III, process engineering; fluid mechanics, heat transfer, mass transfer, unit operations. Part IV, reactions and reactors, homogeneous reactions, heterogeneous reactions, reactors.