Undergraduate Course Catalog

See also Carnegie Mellon Undergraduate Catalogue

BME Core Courses

42-101 Introduction to Biomedical Engineering | 12 units | Fall and Spring
(Required core course)
Sample Syllabus: 42-101 Tilton
This course will provide exposure to basic biology and engineering problems associated with living systems and health care delivery. Examples will be used to illustrate how basic concepts and tools of science & engineering can be brought to bear in understanding, mimicking and utilizing biological processes. The course will focus on four areas: biotechnology, biomechanics, biomaterials and tissue engineering and bioimaging and will introduce the basic life sciences and engineering concepts associated with these topics.
Pre-requisite or co-requisite: 03-121 Modern Biology.

42-201 Professional Issues in Biomedical Engineering | 3 units | Fall and Spring
(Required core course)
Sample Syllabus: 42-201 Zapanta / 42-201 Kovacevic
This course helps students learn to understand technical and professional challenges biomedical engineers face. First, it introduces students to applications of technology in medicine and biology. Second, it provides an overview of professional topics involving bioethics, regulatory issues, communication skills, team work, and contemporary issues. Outside speakers describe real world problems and professional issues in biotechnology and bioengineering, and progress toward their solution. Students have the opportunity to visit state-of-the-art laboratories in such areas as bioimaging, musculoskeletal biomechanics, rapid prototyping and manufacturing, and cardiac assist devices.
Pre-requisite: 42-101 Introduction to Biomedical Engineering or permission of instructor.

42-202 Physiology | 9 units | Fall and Spring
(Required core course)
Sample Syllabus: 42-202 Dahl
This course is an introduction to human physiology and includes units on all major organ systems. Particular emphasis is given to the musculoskeletal, cardiovascular, respiratory, digestive, excretory, and endocrine systems. Modules on molecular physiology, tissue engineering and physiological modeling are also included. Due to the close interrelationship between structure and function in biological systems, each functional topic will be introduced through a brief exploration of anatomical structure. Basic physical laws and principles will be explored as they relate to physiologic function.
Pre-requisite: 03-121 Modern Biology, or permission of instructor.

42-203/03-206 Biomedical Engineering Laboratory | 9 units | Fall and Spring
(Required core course)
Sample Syllabus: 42-203 Fall Zapanta / 42-203 Spring Zapanta
This laboratory course is designed to provide students with the ability to make measurements on and interpret data from living systems. The experimental modules reinforce concepts from 42-101 Introduction to Biomedical Engineering and expose students to four areas of biomedical engineering: bioimaging, biomaterials, biomechanics, and cellular and molecular biotechnology. Several cross-cutting modules are included as well. The course includes weekly lectures to complement the experimental component.
Students who have declared the Additional Major in Biomedical Engineering and who have registered with the Carnegie Mellon Health Professions Program should register for 03-206 instead of 42-203, which would count as fulfilling the requirement of both Biomedical Engineering additional major and medical school admission standard.
Pre-requisites: 42-101 Introduction to Biomedical Engineering and 03-121 Modern Biology. Pre-medical students should use the cross-listed course number 03-206 when registering for this course. Pre-med students in the classes of 2009-2011 who have already taken 03-124 Modern Biology Laboratory may use it as a substitute.

42-401 Foundations of Biomedical Engineering Design | 3 units | Fall, Mini-2 course
(Required core course and precursor to 42-402)
This course introduces Biomedical Engineering students to the design of useful biomedical products. Students will learn to identify product needs, how to specify problem definitions and to use project management tools. Methods to develop creativity in design will be introduced. Students will form project teams and select a project to be completed during the following semester in 42-402. This course culminates in the completion of a design brief.
Pre-requisite: Senior standing in BME.

42-402 Biomedical Engineering Design Project | 9 units | Spring
(Required core course)
This course focuses on integrated product development for biomedical products. Teams will consist of a variety of BME students. The course consists of modules including the development of a project plan, background research, hazard analysis, setting product specifications based on user requirements, detailed design and analysis, prototype development and final documentation and presentation. Additional relevant professional development topics are also covered, including technical public speaking, proposal preparation, personal time management, and other topics. All products developed will respond to the needs of appropriate market segments; resulting products will be deemed safe, effective, useful, usable and desirable by those segments. Students will produce a form model, functional prototype, marketing plan, and manufacturing plan of their product.
Pre-requisite: 42-401.

Required Biology Course
03-121 Modern Biology | 9 units | Fall and Spring
(Required core course)
This is an introductory course that provides the basis for further studies in biochemistry, cell biology, genetics and molecular biology. This course emphasizes the chemical principles underlying biological processes and cell structures as well as the analysis of genetics and heredity from a molecular perspective. This is the introductory biology course for all science and non-science majors, 3 hrs. lecture.
Pre-requisite: Fundamental knowledge of high school chemistry and biology.
Spring Pre-requisite: None.

Track Gateway and Capstone Courses

42-321 Cellular and Molecular Biotechnology | 9 units | Fall
(CMBT Gateway course)
Sample Syllabus: 42-321 Przybycien
This course provides the student with an introduction to biotechnology in an engineering context. The focus will be on using microorganisms to prepare therapeutically and technologically relevant biochemicals. Topics to be covered include cellular and microbial metabolism, recombinant DNA methodologies, bioreactor design, protein separation and purification, and systems approaches to biotechnology.
Pre-requisites: (42-202 Physiology or 03-121 Modern Biology or 03-232 Biochemistry) and (06-262 Mathematical Methods of Chemical Engineering or 21-260 Differential Equations) or permission of instructor.

42-341 Introduction to Biomechanics | 9 units | Fall
(BMEC Gateway course)
Sample Syllabus: 42-341 Antaki
This course provides a general survey of the application of solid mechanics and rigid body dynamics to the study of the human cardiovascular and musculoskeletal systems. The mechanical properties and behavior of heart, blood vessel, bone, muscle and connective tissues are discussed and methods for the analysis of human motion are developed. Both analytic and experimental results are presented through readings from reports in recent journals and the relevance of these results to the solution of unsolved problems is highlighted. The development of appropriate models for particular problems is also considered.
Pre-requisites: 21-260 Differential Equations and (24-262 Stress Analysis or 12-331 Solid Mechanics or equivalent). Useful, but not required: 24-141 Statics and Dynamics and 24-202 Mechanics of Deformable Solids.

42-419 Biomaterial/Host Interactions | 12 units | Fall
(BMTE Capstone course)
The goal of this course is to provide students with hands-on experience in investigating host responses to materials. Implant studies of tissue-engineering materials will be performed using animal models in a laboratory setting, and students will gain experience in the analysis of host responses. Material biocompatibility and tissue regeneration will be addressed. Characterization techniques will include histology, real-time polymerase chain reaction, and immunofluorescent staining. Laboratory work will be complemented with lectures.
Pre-requisite: Senior standing in BME, or consent of instructor.

03-231 Biochemistry I  (For BME/MSE students only) | 9 units | Fall
(BMTE Gateway course acceptable for BME/MSE students only)
This course provides an introduction to molecules and processes found in living systems. Amino acids, sugars, lipids and nucleotides and their corresponding higher structures, the proteins, polysaccharides, membranes and nucleic acids are studied. Kinetics and mechanisms of enzymes as well as elementary metabolic cycles and the energetics of biological systems are discussed.
Pre-requisite: 03121. Co-requisite: 09-217.

03-232 Biochemistry I  (For all BME students) | 9 units | Spring
(BMTE Gateway course acceptable for all BME students. BME/MSE students may take this but  are strongly discouraged from doing so, since MSE will not recognize credit for 03-232.)
This course provides an introduction to the application of biochemistry to biotechnology. The functional properties of amino acids, nucleotides, lipids, and sugars are presented. This is followed by a discussion of the structural and thermodynamic aspects of the organization of these molecules into higher-order structures, such as proteins, nucleic acids, and membranes. The kinetics and thermodynamics of protein-ligand interactions are discussed for non-cooperative, cooperative, and allosteric binding events. The use of mechanistic and kinetic information in enzyme characterization and drug discovery are discussed. Topics pertinent to biotechnology include: antibody production and use, energy production in biochemical systems, expression of recombinant proteins, and methods of protein purification and characterization.
Pre-requisite: 09-217.  Co-requisites: 09-106, 06-221.

18-290 Signals and Systems (BIMG Gateway Course) | 12 units | Fall and Spring
(BSIP Gateway course)
This course is a breadth course that also is a Pre-requisite for most courses in communications, signal processing and control systems. The objective of this course is to provide students with an integrated understanding of the relationships between mathematical tools and properties of real signals and systems. This is accomplished by motivating lectures and recitation problems using demonstrations and laboratory assignments which cover such topics as radio transmission and reception, audio synthesizers, CDs, image processing, and prosthetic devices. In the course of the semester, students are introduced to industry-standard computing and simulation tools that will be used in subsequent courses. Continuous and discrete-time signals and systems are treated in a unified manner through the concept of sampling. The course covers the basic concepts and tools needed to perform time and transform domain analyses of signals and linear time-invariant systems, including: unit impulse response and convolution; Fourier transforms and filtering; Laplace transforms, feedback and stability; and a brief introduction to z-transforms in the context of digital filtering of signals and LTI systems. Laplace transform and z-transform.
Pre-requisites: 18-220 and 18-202.

Track Electives from the BME Department

Either 42-660 Surgery for Engineers (9 Units) or a BME research project completed for at least 9 units of academic credit (42-200/300/400 Sophomore/Junior/Senior Biomedical Engineering Research project or 39-500 CIT Honors Thesis supervised or co-supervised by a BME faculty member) may be counted as fulfilling one track elective for the Additional Major in BME. Students may not count both Surgery for Engineers and a BME research project as track electives.

42-200 Sophomore BME Research Project | 3-12 units | Fall and Spring
(Must take at least 9 units to count as a track elective course)
(Track Elective Course)
Research projects under the direction of a regular or courtesy BME faculty member. Arrangements may also be made via the Associate Head of BME for off-campus projects at local hospitals provided that a regular or courtesy BME faculty member agrees to serve as a co-advisor. The nature of the project, the number of units and the criteria for grading are to be determined between the student and the research advisor. The agreement should be summarized in a one-page project description with sign-off by the research advisor and a copy submitted for review and filing to the student’s academic advisor. A final written report or oral presentation of the results is required. Units may vary from 3 to 12 according to the expected time commitment.

42-300 Junior BME Research Project | 3-12 units | Fall and Spring
(Must take 9 units to count as a track elective course)
(Elective Course)
Research projects under the direction of a regular or courtesy BME faculty member. Arrangements may also be made via the Associate Head of BME for off-campus projects at local hospitals provided that a regular or courtesy BME faculty member agrees to serve as a co-advisor. The nature of the project, the number of units and the criteria for grading are to be determined between the student and the research advisor. The agreement should be summarized in a one-page project description with sign-off by the research advisor and a copy submitted for review and filing to the student’s academic advisor. A final written report or oral presentation of the results is required. Units may vary from 3 to 12 according to the expected time commitment.

42-400 Senior BME Research Project | 3-12 units | Fall and Spring
(Must take 9 units to count as a track elective course)
(Elective Course)
Research projects under the direction of a regular or courtesy BME faculty member. Arrangements may also be made via the Associate Head of BME for off-campus projects at local hospitals provided that a regular or courtesy BME faculty member agrees to serve as a co-advisor. The nature of the project, the number of units and the criteria for grading are to be determined between the student and the research advisor. The agreement should be summarized in a one-page project description with sign-off by the research advisor and a copy submitted for review and filing to the student’s academic advisor. A final written report or oral presentation of the results is required. Units may vary from 3 to 12 according to the expected time commitment.

42-311/27-311 Polymeric Biomaterials | 9 units | Spring
(BMTE Track Elective)
This introductory course will address basic and applied concepts of polymers as biomaterials. The students will be exposed to both fundamental synthetic mechanisms of polymers and their physical and chemical properties. Specific emphasis will be placed on biodegradation mechanism, mechanical properties and surface chemistry of polymeric materials. Cellular interactions with various surfaces and immunological responses will be covered. Applications of biomaterials to be discussed include tissue engineering and artificial organs.
Pre-requisite: None, but 09-105 Introduction to Modern Chemistry and 42-101 Introduction to Biomedical Engineering will be useful.

42-312/27-312 Metallic and Ceramic Biomaterials | 9 units | intermittent
(BMTE Track Elective)
The course addresses basic and applied concepts of metals and ceramics as biomaterials. The students will be exposed to the principles, properties and applications of amorphous and crystalline inorganic and metallic systems for biological applications. Specific emphasis will be placed on processing biochemical activity, biodegradation mechanisms, and various properties relevant for biological response. Cellular interactions with various surfaces and immunological responses will also be covered. Applications of biomaterials to be discussed include tissue engineering, artificial implants and devices..
Pre-requisite: None, but 09-105 Introduction to Modern Chemistry and 42-101 Introduction to Biomedical Engineering will be useful.

42-334/03-310 Introduction to Computational Molecular Biology | 12 units | Spring
(BSIP Track Elective)
A general introduction to computational tools for biology, divided into two modules.  The computational molecular biology/genomics module examines sources and archival of biological data. Specific topics to be covered include sequence data, searching and alignment, structural data, genome sequencing, genome analysis, genetic variation, gene and protein expression, and biological networks and pathways.  The computational cell biology module includes biological modeling and image analysis.  Topics include computer models of population dynamics, biochemical kinetics, cell pathways, neuron behavior, mutation, morphological image analysis, image classification and image-based models.  This course is intended primarily for biological sciences or biomedical engineering majors at the undergraduate or graduate level who have not had extensive prior experience with computer science or programming.  Students may not take both 03-310/42-334 and either 03-311 or 03-312 for credit.
Pre-requisites: 03-121 Modern Biology or instructor permission.

42-413 Biomaterial Interfaces | 12 units | intermittent
(BMTE Track Elective)
This course introduces fundamentals and applications of surfactants and macromolecules at interfaces. The interfacial physical chemistry of surfactants, synthetic polymers and biopolymers including proteins and DNA will be discussed. Applications will be drawn from materials technology, pharmaceutical processing, and biotechnology.

42-426 Biosensors and BioMEMS | 9 units | Spring, every other year
(CMBT Track Elective)
Sample Syllabus: 42-426 Zappe
This course emphasizes the principles of biomolecule-based sensing, including molecular recognition, biomolecular binding kinetics and equilibrium; methods of detection and signal transduction, including optical, colorimetric, fluorescence, potentiometric, and gravimetric techniques; statistical principles of high throughput screening; microfluidic and microarray device design principles and fabrication technologies; molecular motors.
Pre-requisite: 03-231 Biochemistry or 03-232 Biochemistry.

42-431/18-496 Introduction to Biomedical Imaging and Image Analysis | 12 units | Fall
(BSIP Track Elective)
Course Website: 42-431 Rohde
This course gives an overview of tools and tasks in various biological and biomedical imaging modalities, such as microscopy, magnetic resonance imaging, x-ray computed tomography, ultrasound and others. Students will be exposed to the major underlying principles in modern imaging systems as well as state of the art methods for processing biomedical images such as deconvolution, registration, segmentation, pattern recognition, etc. The discussion of these topics will draw on approaches from many fields, including physics, statistics, signal processing, and machine learning. As part of the course, students will be expected to complete an independent project. Students will have the opportunity to visit laboratory to see real biomedical imaging devices in action.
Pre-requisites: 18-396 Signals and Systems (or 18-290) or permission of the instructor, working knowledge of Matlab, and some image processing experience.

42-441 Cardiovascular Biomechanics | 9 units | Spring, every other year
(BMEC Track Elective)
This course covers the solid and fluid mechanics of the heart and vascular system as well as the mechanics of medical devices used to assist or replace cardiovascular function.
Pre-requisite: 42-341 Introduction to Biomechanics.

42-444 Medical Devices | 9 units | Fall
(BMEC Track Elective)
This course is an introduction to the engineering, clinical, legal and regulatory aspects of medical device performance and failure. Topics covered include a broad survey of the thousands of successful medical devices in clinical use, as well as historical case studies of devices that were withdrawn from the market. In-depth study of specific medical devices will include: cardiovascular medicine (pacemakers, heart valves, vascular grafts, heart-assist pumps..), orthopedics (fixation devices, prostheses…), and general medicine (defibrillators, blood pressure cuffs, stethoscopes…) We will study the principles of operation (with hands-on examples), design evolution, and modes of failure. Additional lectures will provide basic information concerning biomaterials used for implantable medical devices (metals, polymers, ceramics) and their biocompatibility, mechanisms of failure (wear, corrosion, fatigue, fretting, etc.). Guest lectures will be provided by practicing engineers from regional medical device companies to provide real-world perspective of the development process.
In addition to a mid-term and final exam covering topics presented in class, students will prepare a written report that critically investigates a particular medical device that has been recalled by the FDA, of the student’s choosing. The report will include the design history, engineering analysis, and recommendations for future improvements (re-design). [Students enrolled in 42-744 will also be required to produce a lo-fi prototype, which they will present in class at the end of the semester.]
The ultimate objectives of this course are to (1) provide students with a broad understanding of the medical device industry, (2) stimulate critical analysis of medical device design, and (3) convey practical knowledge and skills that are valuable for a future career in the medical device industry.
Pre-requisite: Junior or senior status.

42-445/24-415 Microfluidics | 9 units | intermittent
(CMBT, BMTE or BMEC Track Elective)
This course offers an introduction to the emerging field of microfluidics with an emphasis on chemical and life sciences applications. During this course students will examine the fluid dynamical phenomena underlying key components of “lab on a chip” devices. Students will have the opportunity to learn practical aspects of microfluidic device operation through hands-on laboratory experience, computer simulations of microscale flows, and reviews of recent literature in the field. Throughout the course, students will consider ways of optimizing device performance based on knowledge of the fundamental fluid mechanics. Students will explore selected topics in more detail through a semester project. Major course topics include pressure-driven and electrokinetically-driven flows in microchannels, surface effects, micro-fabrication methods, micro/nanoparticles for biotechnology, biochemical reactions and assays, mixing and separation, two-phase flows, and integration and design of microfluidic chips.  3 hours lecture.
Pre-requisite: 24-231 or 06-261 or 12-255.

42-447 Rehabilitation Engineering | 9 units | Fall
(BMEC Track Elective)
Sample Syllabus: 42-347 Friedman(link to 42-347.pdf, separate window)
Rehabilitation engineering involves the application of engineering sciences to design, develop, adapt, and apply assistive technologies to problems confronted by individuals with disabilities in functional area, such as mobility, communication, hearing, vision, and cognition, and in activities associated with employment, independent living, education, and integration into the community. It differs from classical biomedical engineering by its focus on improving the quality of people’s lives, rather than improving their medical treatment. This course will require participation in simulations of disabilities and projects to develop new technologies.
Pre-requisite: 42-202 Physiology.

42-509 Special Topics: Stem Cell Engineering | 9 units | Spring, every other year
(BMTE or CMBT Track Elective)
This course will give an overview over milestones of stem cell research and will expose students to current topics at the frontier of this field. It will introduce students to the different types of stem cells as well as environmental factors and signals that are implicated in regulating stem cell fate. The course will highlight techniques for engineering of stem cells and their micro-environment. It will evaluate the use of stem cells for tissue engineering and therapies. Emphasis will be placed on discussions of current research areas and papers in this rapidly evolving field. Students will pick a class-related topic of interest, perform a thorough literature search, and present their findings as a written report as well as a paper review and a lecture. Lectures and discussions will be complemented by practical lab sessions, including: stem cell harvesting and culture, neural stem cell transfection, differentiation assays, and immunostaining, polymeric microcapsules as advanced culture systems, and stem cell integration in mouse brain tissue. The class is designed for graduate students and upper undergraduates with a strong interest in stem cell biology, and the desire to actively contribute to discussions in the class.
Pre-requisite: Instructor Permission.

42-511 Introduction to Biomaterials | 9 units | Spring, intermittent
(BMTE Track Elective)
This introductory course will address basic and applied concepts of both inorganic and organic/polymeric biomaterials. The students will be exposed to fundamental properties, characterization, applications, interactions with host tissues, and degradation.
Pre-requisite: None.

42-590 Neural Signal Processing | 12 units | Spring
(BSIP Track Elective)
The brain is among the most complex systems ever studied. Underlying the brain's ability to process sensory information and drive motor actions is a network of 10^11 neurons, each making 10^3 connections with other neurons.  Modern statistical and machine learning tools are needed to interpret the plethora of neural data being collected, both for (1) furthering our understanding of how the brain works, and (2) designing biomedical devices that interface with the brain.
This course will cover a range of statistical methods and their application to neural data analysis.  The statistical topics include latent variable models, dynamical systems, point processes, dimensionality reduction, Bayesian inference, and spectral analysis. The neuroscience applications include neural decoding, firing rate estimation, neural system characterization, sensorimotor control, spike sorting, and field potential analysis.
Pre-requisites: 18-290 for ECE students; 36-217, or equivalent introductory probability theory and random variables course; an introductory linear algebra course; senior or graduate standing.  No prior knowledge of neuroscience is needed.

42-620 Engineerng Molecular Cell Biology | 12 units | Fall
(BMTE or CMBT Track Elective)
Cells are not only basic units of living organisms but also fascinating engineering systems that exhibit amazing functionality, adaptability, and complexity. Applying engineering perspectives and approaches to study molecular mechanisms of cellular processes plays a critical role in the development of contemporary biology. At the same time, understanding the principles that govern biological systems provides critical insights into the development of engineering systems, especially in the micro- and nano-technology. The goal of this course is to provide basic molecular cell biology for engineering students with little or no background in cell biology, with particular emphasis on the application of quantitative and system perspectives to basic cellular processes. Course topics include the fundamentals of molecular biology, the structural and functional organization of the cell, the cytoskeleton and cell motility, the mechanics of cell division, and cell-cell interactions. 
Pre-requisites: 21-260 Differential Equations, or 06-262 Mathematical Methods of Chemical Engineering, or 18-202 Mathematical Foundations of Electrical Engineering. Advanced undergraduate or graduate student standing is required. Prior completion of 03-121Modern Biology is suggested but not required.

42-622/06-622 Bioprocess Design | 9 units | Spring, intermittent
(CMBT Track Elective)
This course is designed to link concepts of cell culture, bioseparations, formulation and delivery together for the commercial production and use of biologically-based pharmaceuticals; products considered include proteins, nucleic acids, and fermentation-derived fine chemicals. Associated regulatory issues and biotech industry case studies are also included. The format of the course is a mixture of equal parts lecture, open discussion and participant presentation. Course work consists of team-oriented problem sets of an open ended nature and individual-oriented industry case studies. The goals of the course are to build an integrated, technical knowledge base of the manufacture of biologically based pharmaceuticals and the US biotechnology industry. Working knowledge of basic cell and modern biology, biochemistry, and differential equations/partial differential equations is assumed.
Pre-requisite: 42-321 Cellular and Molecular Biotechnology or both 03-232 Biochemistry and 06-422 Chemical Reaction Engineering, or instructor permission.

42-624 Biological Transport | 9 units | Spring, intermittent
(CMBT, BMEC or BMTE Track Elective)
Sample Syllabus: 42-424 Przybycien
Analysis of transport phenomena in life processes on the molecular, cellular, organ and organism levels. Material covered: Fick's Laws; electrolyte diffusion; coupled diffusion and chemical reaction; membrane transport mechanisms; osmosis; Donnan equilibrium; receptor-mediated binding; ultrafiltration and nephron function; blood flow; pharmacokinetic modeling.
Pre-requisites: 06-262 Mathematical Methods of Chemical Engineering or 21-260 Differential Equations.

42-640/24-658 Computational Bio-Modeling and Visualization | 12 units | Spring
(BSIP or BMEC Track Elective)
Biomedical modeling and visualization play an important role in mathematical modeling and computer simulation of real/artificial life for improved medical diagnosis and treatment. This course integrates mechanical engineering, biomedical engineering, computer science, and mathematics together. Topics to be studied include medical imaging, image processing, geometric modeling, visualization, computational mechanics, and biomedical applications. The techniques introduced are applied to examples of multi-scale biomodeling and simulations at the molecular, cellular, tissue, and organ level scales.
Pre-requisite: none

42-645/24-655 Cellular Biomechanics | 9 units | Spring, every other year
(CMBT or BMEC Track Elective)
Sample Syllabus: 42-645 LeDuc
This course discusses how mechanical quantities and processes such as force, motion, and deformation influence cell behavior and function, with a focus on the connection between mechanics and biochemistry. Specific topics include: (1) the role of stresses in the cytoskeleton dynamics as related to cell growth, spreading, motility, and adhesion; (2) the generation of force and motion by moot molecules; (3) stretch-activated ion channels; (4) protein and DNA deformation; (5) mechanochemical coupling in signal transduction. If time permits, we will also cover protein trafficking and secretion and the effects of mechanical forces on gene expression. Emphasis is placed on the biomechanics issues at the cellular and molecular levels; their clinical and engineering implications are elucidated. 3 hours lecture.
Pre-requisite: Instructor Permission.

42-646/06-646/24-657 Molecular Biomechanics | 9 units | Spring, every other year
(CMBT or BMEC Track Elective)
This class is designed to present concepts of molecular biology, cellular biology and biophysics at the molecular level together with applications. Emphasis will be placed both on the biology of the system and on the fundamental physics, chemistry and mechanics which describe the molecular level phenomena within context. In addition to studying the structure, mechanics and energetics of biological systems at the nano-scale, we will also study and conceptually design biomimetic molecules and structures. Fundamentals of DNA, globular and structured proteins, lipids and assemblies thereof will be covered.
Pre-requisite: Thermodynamics (06-221 or 24-221) or instructor permission.

42-660 Surgery for Engineers | 9 units | Fall and Spring
(Track Elective for All Tracks)
Sample Syllabus: 42-660 Burgess
This course explores the impact of engineering on surgery. Students will interact with clinical practitioners and investigate the technological challenges that face these practitioners. In addition to weekly seminars, all students must sign up for one of the three accompanying practicums: Clinical Neuroscience, Clinical Cardiovascular, or Clinical Orthopedic. Students will complete a final report on the practicum that will describe an important clinical problem that can be solved with a new technology or a significant optimization of an existing technology.
1. Clinical Neuroscience Practicum involves on-site experiences with a variety of neuroscience faculty: neurosurgeons, neurologists, neuro-interventionalists, neuro-radiologists, clinical neuro-physiologists, neuro-otologists and neuro-ophthalmologists. Direct contact will be at least 3 hours a week.
2. Clinical Cardiovascular Practicum involves on-site experiences with cardiology and cardiovascular surgery faculty: cardiac surgeons, thoracic surgeons, cardiologists, interventional cardiologists, cardiac perfusionists, and cardiac radiologists. Direct contact will be at least 3 hours a week.
3. Clinical Orthopedic Practicum This practicum involves on-site experiences with orthopedic faculty: shoulder surgeons, hip surgeons, knee surgeons, hand surgeons, sports medicine surgeons, and physiatrists. Direct contact will be at least 3 hours a week.
The final report of the practicums will involve the most interesting, innovative, important problem uncovered which in the view of the team can be solved with a technology or a significant optimization of a technology. The report form will be the NIH R21. Opportunities to collaborate with engineering students from an outside institution will be sought.
The Primary Instructor is Jim Burgess, MD, Department of Neruosurgery, Allegheny General Hospital. This course meets once a week for 3 hours in addition to the practicum held at the Allegheny General Hospital, transport provided.
Pre-requisite: Physiology 42-202.

42-735/16-725 Medical Image Analysis | 12 units | Intermittent
(BSIP Track Elective)
The fundamentals of computational medical image analysis will be explored, leading to current research in applying geometry and statistics to segmentation, registration, visualization, and image understanding. Student will develop practical experience through projects using the National Library of Medicine Insight Toolkit (ITK), a new software library developed by a consortium of institutions including CMU. In addition to image analysis, the course will describe the major medical imaging modalities and include interactions with practicing radiologists at UPMC. See Class Web Site.
Pre-requisites: Knowledge of C++, vector calculus and basic probability.

Track Electives from Other Departments

Students should verify the information listed below with the departments offering the courses.

03-240 Cell Biology | 9 units | Spring
(CMBT or BMTE Track Elective)
This course provides descriptive information and mechanistic detail concerning key cellular processes in six areas: membrane function, protein targeting, signaling, cytoskeleton, cell division, and cell interaction. An attempt is made to introduce the methodology that was used to obtain this information and to discuss how our understanding of these processes relates to the treatment of human disease.
Pre-requisites: 03-121 and (03-231 or 03-232).

03-534 Biological Imaging and Fluorescence Spectroscopy | 9 units | Spring
(BSIP Track Elective)
This course covers principles and applications of optical methods in the study of structure and function in biological systems. Topics to be covered include: absorption and fluorescence spectroscopy; interaction of light with biological molecules, cells, and systems; design of fluorescent probes and optical biosensor molecules; genetically expressible optical probes; photochemistry; optics and image formation; transmitted-light and fluorescence microscope systems; laser-based systems; scanning microscopes; electronic detectors and cameras: image processing; multi-mode imaging systems; microscopy of living cells; and the optical detection of membrane potential, molecular assembly, transcription, enzyme activity, and the action of molecular motors. This course is particularly aimed at students in science and engineering interested in gaining in-depth knowledge of modern light microscopy.
Pre-requisites: (03-231 or 03-232) and 03-240 and 09-218 and (09-144 or 09-214)

09-217 Organic Chemistry I | 9 units | Fall
(BMTE Track Elective)
This course presents an overview of structure and bonding as it pertains to organic molecules. Selected topics include: introduction to functional group chemistry, stereochemistry, conformational analysis, reaction mechanisms and use of retrosynthetic analysis in the development of multistep syntheses. Methods for structure determination of organic compounds by modern spectroscopic techniques are introduced.
Pre-requisite: 09-105 or 09-107.

09-218 Organic Chemistry II | 9 units | Spring
(BMTE Track Elective)
This course further develops many of the concepts introduced in Organic Chemistry I, 09-217. Emphasis is placed on the utilization of reaction mechanisms for understanding the outcome of chemical transformations, and the employment of a wide variety of functional groups and reaction types in the synthesis of organic molecules. Also included in the course will be special topics selected from the following: polymers and advanced materials, biomolecules such as carbohydrates, proteins and nucleic acids, and drug design.
Pre-requiste: 09-217.

18-491 Digital Signal Processing | 12 units | Fall or Spring
(BSIP Track Elective)
This course addresses the mathematics, implementation, design and application of the digital signal processing algorithms widely used in areas such as multimedia telecommunications and speech and image processing. Topics include discrete-time signals and systems, discrete-time Fourier transforms and Z-transforms, discrete Fourier transforms and fast Fourier transforms, digital filter design and implementation, and multi-rate signal processing. The course will include introductory discussions of 2-dimensional signal processing, linear prediction, adaptive filtering, and selected application areas. Classroom lectures are supplemented with implementation exercises using MATLAB. 4 hours lecture and 1 hour recitation.
Pre-requisite: 18-290 or 18-396.

18-792 Advanced Digital Signal Processing | 12 units | Fall
(BSIP Track Elective)
This course will examine a number of advanced topics and applications in one-dimensional digital signal processing, with emphasis on optimal signal processing techniques. Topics will include modern spectral estimation, linear prediction, short-time Fourier analysis, adaptive filtering, plus selected topics in array processing and homomorphic signal processing, with applications in speech and music processing. 4 hours lecture.
Pre-requisites: 18-491 or 18-791 and 36-217, and senior or graduate standing.

18-798 Image, Video, and Multimedia | 12 units | intermittent
(BSIP Track Elective)
The course studies image processing, image understanding, and video sequence analysis. Image processing deals with deterministic and stochastic image digitization, enhancement, restoration, and reconstruction. This includes image representation, image sampling, image quantization, image transforms (e.g., DFT, DCT, Karhunen-Loeve), stochastic image models (Gauss fields, Markov random fields, AR, ARMA) and histogram modeling. Image understanding covers image multiresoltuion, edge detection, shape analysis, texture analysis and recognition. This includes the motion estimation methods, e.g., optical flow and block-based methods, and motion segmentation. The course emphasizes experimenting with the application of algorithms to real images and video. Students are encouraged to apply the algorithms presented to problems in a variety of application areas, e.g., synthetic aperture radar images, medical images, entertainment video image, and video compression. 3 hous lecture.
Pre-requisite: 18-491.

18-799A Special Topics in Signal Processing: Bioimage Registration | 12 units | intermittent
(BSIP Track Elective)
This course will cover the fundamentals of image matching (registration) methods with applications to biomedical engineering. As the fundamental step in image data fusion, registration methods have found wide ranging applications in biomedical engineering, as well as other engineering areas, and have become a major topic in image processing research. Specific topics to be covered include manual and automatic landmark-based, intensity-based, rigid, and nonrigid registration methods. Applications to be covered include multi-modal image data fusion, artifact (motion and distortion) correction and estimation, atlas-based segmentation, and computational anatomy. Course work will include Matlab programming exercises, reading of scientific papers, and independent projects. Upon successful completion, the student will be able to develop his/ her own solution to an image processing problem that involves registration.
Pre-requisites: 18-290 or 18-396 or permission of the instructor, working knowledge of Matlab, and some image processing experience.

24-779A Special Topics in Controls and Robotics: Bio-Inspired Robotics | 12 units | Fall
(BMEC Track Elective)
This course will explore design of biologically inspired robot locomotion systems. Locomotion principles of many agile animals such as lizards, snakes, insects, fishes, and birds will be studied with corresponding bio-inspired robotic platforms. Required bio-inspired robotic mechanisms, materials, actuators, sensors, and power sources to enable similar locomotion principles will be discussed. Besides the basic background knowledge, it will include the current trends in literature, detailed case studies and discussions, and guest lecturer talks. Some movies related to bio-inspiration will be shown in the class, and a field trip will be held to Schenley Park. Course projects will involve analyzing biological locomotion systems, materials, mechanisms, sensors, and actuators and proposing and prototyping bio-inspired robot locomotion systems.
Pre-requisite: Instructor Permission.

33-441/03-439 Introduction to BioPhysics | 10 units | Fall
(BMEC Track Elective)
This intermediate level course is primarily offered to Physics and Biology undergrads (junior/senior) and provides a modern view of molecular and cellular biology as seen from the perspective of physics, and quantified through the analytical tools of physics. This course will not review experimental biophysical techniques (which are covered, e.g., in 03-871). Rather, physicists will learn what sets “bio” apart from the remainder of the Physics world and how the apparent dilemma that the existence of life represents to classical thermodynamics is reconciled. They also will learn the nomenclature used in molecular biology. In turn, biologists will obtain (a glimpse of) what quantitative tools can achieve beyond the mere collecting and archiving of facts in a universe of observations: By devising models, non-obvious quantitative predictions are derived which can be experimentally tested and may lead to threads that connect vastly different, apparently unrelated phenomena. One major goal is then to merge the two areas, physics and biology, in a unified perspective.
Pre-requisite: No formal requirements. However, a good working knowledge of undergrad- level calculus, as well as basic (Physics I level) thermodynamics will definitely help.

Other Elective Courses

42-512 Special Topics: Basic Statistics for Biomedical Research | 9 units | Fall
This is a lecture/seminar course designed to cover medical experimental design, types of statistical error and the mechanics of commonly used statistical methods. Emphasis will be placed on use of appropriate statistical tools as opposed to the mathematical underpinnings of the statistical tests themselves. Students will be expected to solve statistical problems derived from clinical practice as well as the medical literature. Web-based resources as well as a statistical software package will be provided.
There is no textbook for the course. The biostatistics software package to be used for the course is Medcalc which is available as a free download for 25 uses (PC platform only) at www.medcalc.be. Students will also be directed to public-domain web sites which run Java applets capable of performing most of the problems presented in class.
The instructor is Matthew R Quigley, MD., Associate Professor of Neurosurgery, Drexel University and staff neurosurgeon at Allegheny General Hospital. Dr Quigley has taught the Graduate Medical Education Biostatistics course at Allegheny General Hospital for the last 5 years and obtained extensive hands-on experience with experimental design and data analysis as the Chair of the Institutional Review Board, the oversight committee for all human research performed at the hospital.

Additional Introductory Engineering Courses for Non-CIT Students Taking BME Minor (require one)

Students should verify the information listed below with the departments offering the courses

06-100 Introduction to Chemical Engineering | 12 units | Fall and Spring

12-100 Introduction to Civil & Environmental Engineering | 12 units | Fall and Spring

18-100 Introduction to Electrical & Computer Engineering | 12 units | Fall and Spring

19-101 Introduction to Engineering & Public Policy | 12 units | Spring

24–101 Fundamentals of Mechanical Engineering | 12 units | Fall and Spring

27-100 Engineering the Materials of the Future | 12 units | Fall and Spring

(Updated 10/03/09)