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ABET Course Descriptions: Bioengineering Undergraduate Program

This document contains the ABET-accredited course descriptions for Bioengineering courses. For the most up-to date course offerings, visit the Registrar’s listing of Bioengineering courses. Courses included in this list: BE099 Independent Study in Bioengineering BE100 Introduction to Bioengineering BE200 Introduction to Biomechanics and Biomaterials BE209 Bioengineering Lab I BE210 Bioengineering Lab II BE220 Structures and Properties of Biomaterials BE223 Chemical Basis of Bioengineering I BE225 Technology & Engineering in Medicine BE301 Bioengineering Signals and Systems BE303 Ethics and Professional Responsibilities for Engineers BE305 Engineering Principles of Human Physiology BE309 Bioengineering Lab III BE310 Bioengineering Lab IV BE324 Chemical Basis of Bioengineering BE330/MSE330 Soft Materials: Colloids, Polymers, Gels and Liquid Crystal BE350 Transport Processes in Living Systems BE400 Clinical Preceptorship in Bioengineering BE401 Probabilistic Analysis and Modeling in Bioengineering BE402 From Biomedical Science to the Marketplace BE421/BE521 Brain-Computer Interfaces BE441 Engineering Microbial Systems BE450/550 Hemodynamics BE455/MEAM455 Continuum Biomechanics BE459/BE559 Multiscale Modeling of Biological Systems BE470 Medical Devices BE480 Introduction to Biomedical Imaging BE483 Molecular Imaging BE490 Research in Bioengineering BE492 Research in Biomedical Science BE495/496 Senior Design Project BE497/8 Senior Thesis in Biomedical Science BE 502: From Biomedical Science to the Marketplace BE505 Quantitative Human Physiology BE510 Biomechanics and Biotransport BE511 Analysis and Design of Bioengineering Signals BE512 Bioengineering III: Biomaterials BE513 Cell Biology BE515 Case Studies in Bioengineering BE517 Optical Imaging BE520 Computational Neuroscience and Neuroengineering BE526 Neuromorphing: Building Brains in Silicon BE537/CIS537 Biomedical Image Analysis BE540 Biomolecular and Cellular Engineering BE546 Biomedical Image Analysis BE552 Cellular Bioengineering BE553 Introduction to Tissue Engineering BE554 Engineering Biotechnology BE557 From Cells to Tissue: Engineering Structure and Function BE559 Multiscale Modeling of Biological Systems BE562 Drug Discovery and Development BE567 Mathematical & Computational Methods for Modeling Biological Systems BE584 Mathematics of Medical Imaging and Measurement EAS280 Bioengineering in the World EAS545 Engineering Entrepreneurship I

http://www.upenn.edu/registrar/register/PDF/be.pdf�


BE099 Independent Study in Bioengineering Credit: 1 course unit Elective course Catalog Description:

An individualized research-based learning experience on a biomedical research problem. Requires preparation of a proposal, literature evaluation, and preparation of a research paper and presentation. Regular progress reports and meetings with a faculty advisor are required.

Prerequisites:

Freshman or Sophomore Standing in the Bioengineering Program (both BAS and BSE). Class/laboratory schedule: Arranged with project advisor Course Objectives:

This course provides an opportunity for students to create a customized lab-based research learning experience during their undergraduate education and touches upon all program objectives. It provides a comprehensive experience in the project process including technical aspects, communication and ethics.

Topics covered:

No set topics, but students completing this course should be able to 1. Define a clear motivation for the project chosen 2. Develop a working relationship with an advisor and/or team in a multidisciplinary environment 3. Learn and integrate technical material in new areas and review the essence of a new technical field

4. Be able to apply newly acquired engineering and scientific methods 5. Write a proposal for the project 6. Assess ethical issues related to responsible conduct of research 7. Assess progress and describe engineering and scientific accomplishments and failures of the project. 8. Prepare an effective poster to communicate the scientific findings to the public. 9. Translate the essence of the research project into a coherent oral presentation. 10. Write a professional final report with publication quality, which is written correctly for a defined format.

Contribution towards Professional Component:

Proportion of engineering science, engineering design, and basic science is dependent on particular project.

Contribution towards Program Outcomes:


Multidisciplinary Ability Med. Problem Solving Approach High Problem Solving Methods Med. Experimentation Med. Design Med. Professional Orientation Med. Person(s) Preparing Description and Date:

Gershon Buchsbaum July 2007


BE100 Introduction to Bioengineering Credit: 1 course unit Required course (freshman year) Catalog Description:

Covers, at an introductory level, a variety of topics such as cellular and molecular therapies, novel medical devices to diagnose and treat disease, engineering and computational models of the body, genomics, biomechanics, cell signaling, and tissue engineering. Students will do hands-on experiments in the Bioengineering Undergraduate Lab, learn about statistics and experimental design, government regulations, ethical and other professional considerations that affect bioengineering research and development. As an exercise, students will be asked to offer new bioengineering ideas and interventions, discuss and present them by applying the course and lab material.

Prerequisites: None Textbook(s) and/or other Required Material:

Materials on Blackboard site

Course Objectives:

This course introduces the students to basic concepts in bioengineering and important professional, societal, entrepreneurial and career related issues in the field. Students completing this course should be able to:

1. Understand the scope of Bioengineering Define a clear motivation for a new biomedical therapy project 2. Develop a working relationship with a team 3. Learn and integrate biomedical and engineering technical material in new areas 4. Be able to apply newly acquired engineering and scientific methods including elementary statistics 5. Design and conduct hypothesis-driven experiments 6. Understand ethical issues in engineering and biomedical research 7. Present design options and experimental data in a poster format 8. Write a professional final report, which is written correctly for a defined format

Topics Covered:

• Introduction, Term Projects • What do Bioengineers do? • Fields in Bioengineering • Engineering design process and scientific method • Statistics and error analysis • Experimental design • Product testing and ethics of human subjects research


BE200 Introduction to Biomechanics and Biomaterials Credit: 1 course unit Required course (sophomore year) Catalog Description:

Application of statics and dynamics to simple force analyses of the musculoskeletal system. Introduction to the fundamentals of strength of materials. Biomechanics of soft and hard tissues: microstructure and mechanical properties. This course is intended to provide a solid foundation in statics and mechanics of materials with particular focus on human joint biomechanics. The first portion of the course will present fundamental concepts of force and mechanics of rigid and deformable bodies. The remainder of the course will consist of an introduction to materials science and engineering, including the classification and bulk properties of implantable materials, and will also address specific topics including torsional loading and bending. By the end of the course, it is anticipated that students will be able to integrate the origin of tissue mechanical properties with structure/function analyses of load-bearing tissues in the human body

Prerequisites: Sophomore standing in SEAS including Math 140, 141, 240 (concurrent), Physics 150, Physics 151.

Textbook(s) and/or other required materials:

W. F. Riley, L. D. Sturges, D. H. Morris, Mechanics of Materials, Fifth Edition, John Wiley and Sons, New York, 1999. Additional reading materials and handouts will be selected from the recommended texts listed below. W. D. Callister, Materials Science and Engineering: An Introduction, Fifth Edition, John Wiley and Sons, New York, 2000. S. J. Hall, Basic Biomechanics, Fourth Edition, McGraw Hill, New York, 2003. N. Ozkaya, M. Nordin, Fundamentals of Biomechanics, Second Edition, Springer, New York, 1999.

Course Objectives: This course will provide a comprehensive introduction to principles of statics and mechanics of deformable bodies applied to biological systems. Specifically, the course will allow students to utilize fundamental knowledge of equilibrium mechanics and stress-strain analyses to perform structure/function assessments of load-bearing tissues and implantable materials in the human body. Students will be exposed to the multidisciplinary nature of biomechanics as the course will incorporate aspects of mechanical engineering, materials science and engineering, musculoskeletal anatomy, and clinical medicine .

Topics Covered

• Newton’s Laws, Forces and Vector Algebra • Moment and Torque • Statics and Equilibrium of Rigid Bodies • Musculoskeletal Anatomy • Musculoskeletal Statics • Mechanics of Deformable Bodies: Stress • Mechanics of Deformable Bodies: Strain • Material Properties: Bonding and Crystal Structure


• Material Properties: Stress-Strain Relationships • Composite Materials • Axial Loading • Pressure Vessels • Torsional Loading • Torsional Loading • Bending: Stresses in Beams • Bending: Deflections in Beams • Structure/Function Relationships of Musculoskeletal Tissues

Class/Laboratory Schedule:

Lecture: 3 hr/week Recitation

Contribution to Course to Meeting the Professional Component:

Engineering Topics: 100%


Multidisciplinary Ability Med Problem Solving Approach High Problem Solving Methods Low Experimentation Low Design Low Professional Orientation Low.

Person Preparing Description and Date:

Steven B. Nicoll January 2004


BE209 Bioengineering Lab I Credit: 1 course unit Required course (sophomore year) Description:

BE209 is the first laboratory course in the Bioengineering curriculum. It is required for both BSE and BAS majors. It is intended for the fall semester of the sophomore year.

Prerequisites:

All students taking BE 209 are required to be enrolled in BE 200, Introduction to Biomechanical and Biomaterials, and to have completed the physics and chemistry laboratories scheduled during the freshmen year.

Textbook(s) and/or other required material:

BE 209 Laboratory manual distributed to students. The contents of the print manual are also available on the BE 209 Blackboard (BB) site. The print version is restricted to material needed while working in the laboratory.

Course Objectives:

1. To provide real world experiences and applications of the engineering and scientific principles discussed in the course (BE 200) running co-currently with BE 209;

2. To introduce new scientific and engineering concepts not yet covered in other required courses of the BE curriculum. These include new areas of musculoskeletal mechanics, as well as new instrumentation measures;

3. To master laboratory techniques, as well as the ability to plan and implement a coherent series of measurements and analyze them quantitatively.

4. To learn the principles of basic statistical experimental testing and design. 5. To write coherent reports based on the laboratory work, consistent with formats and standards found in

engineering and scientific papers. 6. To help plan and carry out a series of assigned tasks as part of a working group, contributing to the

project goal both as an individual and group member, consistent with norms in the engineering profession.

Topics Covered:

Each group is assigned a specific experiment for completion each week. Over the semester, the students complete ten separate experiments. The areas covered by the experiments include bioinstrumentation, measurement, signal/data analysis, and biomechanics.

Laboratory Schedule:

Two independent sections per week, each 6 hr. Students in each section are organized in groups.


75% Engineering science 25% Engineering design



Multidisciplinary Ability High Problem Solving Approach High Problem Solving Methods Med Experimentation High Design Med Professional Orientation High.

Persons Preparing Description and Date:

David Meaney February 2004


BE210 Bioengineering Lab II Credit: 1 course unit Required course Catalog Description: Second term of a two-year sequence designed to integrate real world experiences into various Bioengineering and Bioengineering Science courses. Experiments and projects in mechanics, material and chemical applications to Biomedical Engineering Prerequisites:

Bioengineering Laboratory I, BE 209; Introduction to Biomechanics and Biomaterials; Math 240

Textbook(s) and/or other required course materials:

BE210 Lab Manual; Handouts on topics in Matlab use and exercises; Biostatistics: The Bare Essentials, Norman & Streiner, Second Edition, BC Decker, Inc.

Course Objectives:

To provide a rigorous introduction to laboratory experiences, experimental design and analysis and applications of engineering and scientific principles in the areas of biomechanics, biomaterials, biophysical chemistry, and physiology. This course incorporates a lecture series for presentation of relevant statistical applications and study designs as related to the experiments of the course; students will learn to implement basic t-test and ANOVA techniques, regressions and correlations to laboratory experiments. There is also a computer lab series of relevant mathematical approaches and techniques: students will have hands-on exercises to implement data analysis techniques in a computational software tool. They will also be exposed to power analysis and ANOVA techniques in the project period of the course. The course utilizes a team-approach to facilitate research and learning, instructing students to work in groups to plan experiments, carry them out, analyze data and present findings.

Topics Covered:

• Experimental methods and approaches in: • Cell Growth Kinetics • Fracture Energy of Bone • Materials Testing • Buffering Techniques & Titration • Imaging Techniques for Data Acquisition & Strain Estimation • Mathematical and computational techniques for:

- Modeling of physical systems - Analysis of data - Curve fitting and analysis





Multidisciplinary Ability High Problem Solving Approach High Problem Solving Methods Med. Experimentation High Design Med. Professional Orientation High.

Person(s) Preparing Description and Date:

Beth Winkelstein July 2007


BE220 Structures and Properties of Biomaterials Credit: 1 course unit Required course (Sophomore year) Catalog description:

An examination of the structure of property, performance relationship for materials used in surgical implants and medical devices. Consideration is given to issues of biocompatibility, degradation of materials by biological systems, and biological response to artificial materials. Particular attention will be given to the materials of the total hip prosthesis and their relationship to the long-term outcomes for total hip arthoplasty.

Prerequisites:

BE209, Chem 101, Corequisites: BE210


Callister, Materials Science and Engineering, An Introduction 6th Ed. Supplementary Materials:

• Ratner, Hoffman, Schoen & Lemons, Biomaterials Science: An Introduction to Materials in Medicine 2nd Ed.

• Park & Lakes, Biomaterials: An Introduction 2nd Ed. • Finerman et al., Total Hip Arthroplasty Outcomes • Buckwalter et al, Orthopaedic Basic Science 2nd ed.

Course Objectives:

This course will provide a fundamental introduction to materials used for biomedical applications, focusing on both atomic structure and macroscopic bulk properties of the major classes of materials, as well as issues of biocompatibility and biological responses to implantable materials. As such, students are expected to gain a basic level understanding of the materials selection and design criteria required for engineering living tissue equivalents. The course will consist of an introduction to materials science and engineering, focusing on traditional classes of materials used for biomedical applications (i.e., metals, ceramics, polymers, and composites). Students will be exposed to the multidisciplinary nature of biomaterials as the course will incorporate aspects of materials science and engineering, the life sciences. The course will also allow students to develop an appreciation for important design criteria relevant to the biomedical implant industry.

Topics Covered:

• Atomic Bonding in Solids • Structure of Crystalline Solids • Imperfections in Solids • Dislocations & Strengthening • Mechanisms • Diffusion • Mechanical Properties • Corrosion & Degradation • Failure • Phase Diagrams • Phase Transformations • Thermal Processing of Metal Alloys • Metal Alloys


• Ceramics • Processing of Ceramics • Polymer Structures • Processing of Polymers • Composites

Class/Laboratory schedule:

Lecture – 3 hr/week Recitation – 1 hr/week

Contribution towards Program Outcomes: Multidisciplinary Ability High Problem Solving Approach High Problem Solving Methods Med. Experimentation Low Design Low Professional Orientation Low Contribution towards Professional Component:

100% Engineering science

Person preparing description and date:

William Graham June 2005


BE223 Chemical Basis of Bioengineering I Credit: 1 course unit Required course Catalog Description:

This course covers and expands on chemical principles including conservation of mass, reaction linetics, and the first and second law of thermodynamics. The primary goal of this course is to learn to apply these principles to solve engineering problems.

Prerequisites:

Chem. 1 or 101, Math 240, Biology 121 (or other introductory biology course) or consent of the instructor.

Textbook(s) and/or Other Required Materials:

Physical Chemistry for the Chemical and Biological Sciences (3rd edition) Xeroxed packets on kinetics and mass balances.

Course Objectives:

To provide fundamental understanding of mass balance in to biological systems to account for the transport and reaction of chemical species. Specific examples include artificial organs, pharmokinetics, and population dynamics. To provide understanding of rate laws and concentration vs. time data, using rate constants and half-life. To develop governing equations for enzyme kinetics, inhibitor effects, receptor-ligand interactions, and cellular trafficking. To introduce basic thermodynamic principles.

Topics Covered:

• Mass balances • Kinetics • Thermodynamics


Lecture: 3 hr/week Recitation: 1 hr/week



Contribution towards Program Outcomes: Multidisciplinary Ability High Problem Solving Approach Med. Problem Solving Methods Med. Experimentation Low Design


Low Professional Orientation Low Person(s) Preparing Description and Date:

Keith Gooch May 2003


BE225 Technology & Engineering in Medicine Bioengineering course for the Benjamin Franklin Scholars Program The course will be revised in Spring 2010 from the earlier posting at this location. Further course outline details will be posted later. Instructor: Gershon Buchsbaum, Bioengineering Spring 2010: This course will provide an examination of technology and its impact on medicine, with an emphasis on the intersection of engineering with medicine and health. Basic foundations of historical perspective, constraints on technological development, and the promise and peril of technological impact on medicine will be discussed. Modules will also focus on specific technological advances as a basis for the discussion. Planned topics include: implants with emphasis on cochlear devices and sensory rehabilitative devices. The course is geared to all students interested in aspects of medicine and engineering and applied science. Reading will integrate topics of the impact of technology on medicine, as well as examine societal issues related to effects technology in health care. The course will be discussion-based and structured around readings of primary sources, commentaries, and publications in the literature. Throughout the term, students will be expected to select a specific technology to follow in the medical, scientific and engineering, as well as popular and lay literature and discuss its applications and impact. Pre-requisite or co-requisite: First year college physics, chemistry, and biology or AP credits; Sophomore and higher classes only. Person(s) Preparing Description and Date: Gershon Buchsbaum November 2009


BE301 Bioengineering Signals and Systems Credit: 1 course unit Required course (Junior year) Catalog Description:

Properties of signals and systems and examples of biological and biomedical signals and systems; linear, time invariant systems; Fourier analysis of signals and systems with applications to biomedical signals such as ECG and EEG; frequency analysis of first and second order systems; frequency response of systems characterized by linear constant-coefficient differential equations; introduction to ditigal and analog filtering, sampling and sampling theorem and aliasing.

Prerequisites: BE 210, MATH 241 Textbook(s) and/or Other Required Materials:

Lathi, Signal Processing and Linear Systems (Oxford) Recommended: Matlab student edition

Course Objectives:

This course is a requirement for bioengineering majors. The goal of the course is to introduce students to the analysis of continuous and sampled signals using classical techniques including Laplace, Fourier and Z transforms, and the relevance of this theory to biomedical engineering. The course includes extensive computer assignments using Maple and Matlab for the analysis of linear systems and design of digital filters.

Topics Covered:

• Introduction to signals and systems • Introduction to Matlab and Maple • solution of ODEs • classical approach (complementary function* and particular integral solution*) • systems approach (zero state and zero input responses) • response of thermistor to temperature pulse in Swan-Ganz catheter (HW2) • Impulse response and convolution; graphical solution to convolution problems • Fourier series and frequency content of signals • Fourier transform and windows • Sampling; sampling theorem; reconstruction; DFT • Laplace transform, inverse Laplace transform, use of transform to solve differential equations • Analysis of CT systems; poles, zeros, frequency response; Bode plots • Analog Butterworth filter; frequency scaling, lowpass to highpass and bandpass transformation • Introduction to digital filtering • Bioengineering applications: • modeling dynamic properties of transducers • linearization of thermistor • step response of a thermistor • compartmental model • Fourier analysis of ECG signal • identification of aliasing artifacts • design of analog antialiasing filter • design of digital IIR and FIR filters for ECG



Lecture: 3 hrs/week Recitation (optional): 1 hr/week




Multidisciplinary Ability High Problem Solving Approach High Problem Solving Methods Med. Experimentation Low Design Low Professional Orientation Low


K. R. Foster July 2007


BE303 Ethics and Professional Responsibilities for Engineers Credit: 1 course unit Required course Catalog Description:

BE303/EAS 303 provides an overview of the ethical and professional responsibilities of engineers, as engineering professionals, as members of engineering organizations, and as participants in medical or scientific research. The course will make extensive use of student group presentations and role playing in the analysis of cases based on real-world problems with ethical dimensions. The case studies will vary from year to year, but will be chosen to reflect the full range of engineering fields and disciplines including areas of bioengineering and biomedical research.

Prerequisites: Junior Standing Textbook(s) and/or Other Required Materials:

Required: Harris, Pritchard, and Rabins, Engineering Ethics: Concepts and Cases, second edition (Wadsworth, 2000).

Course Objectives:

The goal of the course is to introduce students to the ethical and professional responsibilities of engineers, and ways to analyze these responsibilities in real-world situations. The course has a broader focus than a traditional “engineering ethics” course, but includes aspects of bioethics and research ethics to address needs of the many students at Penn who are headed for careers in medical research and practice.

Topics Covered:

• Methods for moral problem solving • Utilitarian and respect for persons approaches to analysis of ethical issues • Engineering codes of ethics: ACM, AIAA, AIChE, ASCE, ASME, IEEE, NSPE • Risk, safety, liability in engineering; expert and lay understanding of risk; acceptable risk • The engineer as employer and employee; whistleblowers • International dimensions of engineering ethics; diversity • Ethical issues in medical research relevant to engineers; IRB and human experimentation; informed

consent; Nuremberg Code and Belmont Report


Lecture (required) 1.5 hours/week Recitation (required) 1.5 hrs/week total


Understanding of professional and ethical responsibility of engineers 50% Understanding of the impact of engineering solutions in a global and societal context 50%


Multidisciplinary Ability Low Problem Solving Approach Low Problem Solving Methods Low


Experimentation Low Design Low Professional Orientation High




BE305 Engineering Principles of Human Physiology Credit: 1 course unit Required course (Junior year) Catalog Description:

Analysis of cellular and systems-level human physiology with an emphasis towards clinical applications. Particular emphasis on mechanisms of function in the neural and cardiovascular systems.

Prerequisites:

Junior standing; Math 240


Physiology 5th ed. by R. Berne, M. Levy, B. Koeppen, & B. Stanton. Mosby, St. Louis, 2004

Course Objectives:

This course is a junior-level course for bioengineering majors. The goal is to provide a rigorous introduction to the engineering principles underlying cellular and systems physiology.

Topics Covered:

• Diffusion in cellular systems • Ionic equilibria and membrane potentials • Generation of the action potential • Synaptic transmission • Receptors and Intracellular signaling pathways • Overview of the nervous system • Motor function • Vision, Hearing, Balance and Somatosensation • Autonomic nervous system • Skeletal muscle physiology • Electrical Activity of the Heart • Cardiac pump • Regulation of the Heartbeat • The arterial system • Structure and function of the respiratory system • Solute and water transport in the kidney • Control of body osmolarity • Acid-base balance • Hormones of the pancreatic islets


Lecture: 3 hr/week





Multidisciplinary Ability High Problem Solving Approach Med. Problem Solving Methods Low Experimentation Low Design Low. Professional Orientation Low


Leif Finkel July 2007


BE309 Bioengineering Lab III Credit: 1 course unit Required course (Junior year) Description:

BE309 is the first half of the third year of the bioengineering laboratory.

Prerequisites: BE 210 Textbook:

BE 309 Laboratory materials/manual distributed to available students on the Blackboard (BB) site. Other readings and references on library reserve.

Course Objectives:

The goal of the course is to integrate real world experiences into various Bioengineering and Bioengineering Science courses. The course is based on group work and includes an extensive, open-ended project with group oral presentation

Topics Covered:

Each group is assigned 4 laboratory projects for the term from technical areas of interest and importance in BE. For the academic year 2004/2005 the topics of the experiments are:

• Dialysis • Enzyme Kinetics • Compartment Analysis • Aspirin Hydrolysis • Surfactants


Laboratory: 6 hrs/week

Contribution of Course to Meeting the Professional Component:

Engineering science: 100%


Multidisciplinary Ability High Problem Solving Approach High Problem Solving Methods Med Experimentation High Design Med Professional Orientation High

Persons Preparing Description and Date:

Dan Hammer and Andrew Tsourkas September 2004


BE310 Bioengineering Lab IV Credit: 1.5 course units Required course (Junior year) Catalog Description:

Fourth semester of a two year sequence designed to integrate real world experiences into various Bioengineering and Bioengineering Science courses. Laboratory emphasizing biotransport and biomedical instrumentation.

Prerequisites:

Prerequisite(s): BE 301 Corequisite(s): BE 350


Laboratory handouts and assigned readings on Blackboard.

Course Objectives:

This course is a requirement for bioengineering majors. The goal of the course is to integrate real world experiences into various Bioengineering and Bioengineering Science courses.The course is based on group work and includes an extensive, open-ended project with group oral presentation.

Topics Covered:

• Signal analysis and data acquisition: use of FFT, digital and analog filters, sampling theorem and aliasing • Experiments: • Flow measurement by thermodilution; • ECG and pulse wave velocity • Determining vibrational spectra of cantilever beam • Design and construction of lowpass Butterworth filter • Compartmental analysis • Pressure-flow relations in a tube • Steady flow through a symmetric sacular aneurysm model • Measurement of taylor diffusion during slow laminar flow in a tube


Laboratory: 6 hrs/week




Multidisciplinary Ability High. Problem Solving Approach High. Problem Solving Methods Med. Experimentation High Design Med. Professional Orientation High


BE324 Chemical Basis of Bioengineering Credit: 1 course unit Required course (Junior year) Catalog Description:

This course aims to provide theoretical, and conceptual principles underlying biomolecular and biological systems. The course will start with basic and advanced concepts in physical chemistry and thermodynamics and introduce statistical mechanics as a tool to understand molecular interactions. The applications will be of relevance to bioengineering and biology disciplines. The course will not shy away from mathematical formulations and will stress the molecular perspective.

Prerequisites:

Physics 140 or 150, Phys 141 or 151, Math 240, Chemistry 101, 102.

Textbook(s) and/or other materials:

Required: Molecular Driving Forces by K. A. Dill and S. Bromberg Taylor and Francis publications ISBN: 0-8153-2051-5 Paperback edition Reference: (1) Raymond Chang, PHYSICAL CHEMISTRY for the chemical and biological sciences,University Science Books, 2000 (2) Biological Physics Energy, Information, Life by Philip Nelson ISBN: 0-7167-4372-8 (3) Quantum Theory (Paperback) David Bohm, ISBN: 0486659690 Dover Publications

Course Objectives and Relation to Program Objectives:

To provide a rigorous introduction to the topics listed below using math at the advanced calculus/differential eqn level, general physics- mechanics, electricity and magnetism, general chemistry- atomic structure, chemical bond, thermodynamics, kinetics, and to illustrate these topics with examples from physiology and bioengineering.

Topics Covered:

• Formulation of Thermodynamics in terms of energy, entropy, and free energy • Microscopic definition of heat, work, free energy, and laws of thermodynamics, Boltzmann

distribution • Formulation of Quantum Mechanics • Applications to ideal gas, crystals, complex biological molecules • Thermodynamics of liquids and liquid mixtures, surface tension • Intermolecular interactions and forces • Advanced topics and applications: Self assembly, hydrophobic effect, polymers, chemical

kinetics, drug design, binding and recognition

Class Schedule:

Lecture: 3 hrs/week Recitation: 1 hr/week





Multidisciplinary Ability High Problem Solving Approach High Problem Solving Methods High Experimentation Low Design Low Professional Orientation Low


Ravi Radhakrishnan July 2007


BE330/MSE330 Soft Materials: Colloids, Polymers, Gels and Liquid Crystal Credit: 1 course unit Elective course Catalog description:

Soft matter describes materials that are neither pure crystalline solids with long range atomic order or pure liquids characterized by one simple viscosity. Many times “soft materials” display both solid and liquid like behavior depending on the timescale of the applied stress. Colloids, polymers, amphiphiles, liquid crystals, and biomacromolecules are types of soft matter. The focus of this course is on the characteristics common to soft materials namely their length scale, fragile binding energies or proximity to phase transitions, dynamics and propensity to self-assemble.

Prerequisites:

Chemistry 102 ; MSE 220 (Intro. to Materials) or equivalent (Concurrent is okay). Textbook(s) and/or other required materials:

R. A. L. Jones. Soft Condensed Matter . New York : Oxford University Press. ISBN: 0198505892. I. W. Hamley. Introduction to Soft Matter: Polymers, Colloids, Amphiphiles and Liquid Crystals. John Wiley. ISBN: 0471899518.

Topics Covered:

• Forces, energies and time scales • Phase transitions • Colloidal dispersions • Polymers • Gelation Liquid Crystallinity Supramolecular self-assembly • Soft matter in nature


Lecture – 3 hr/week Person preparing description and date:

R. J. Composto July 2007


BE350 Transport Processes in Living Systems Credit: 1 course unit Catalog Description:

Introduction to basic principles of fluid mechanics and of energy and mass transport with emphasis on applications to living systems and biomedical devices.

Prerequisites:

Math 241 or equivalent, Physics 140 or 150.

Textbook(s):

Required: Welty,Wicks,Wilson, and Rorrer, Fundamentals of Momentum, Heat, and Mass Transfer, 4th Ed., 2001 Recommended: Hughs and Brighton, Schaum’s Outline on Fluid Dynamics, 2nd Ed. 1991.

Course Objectives: To provide a rigorous introduction to the basic concepts of fluid mechanics and transport with special applications to bioengineering and physiology. The approach used first builds up the basic equations and then applies them to specific examples of biological interest such as diffusion of gases in the lung airways, pulsatile blood flow in arteries and veins, and mass transfer of solutes in the renal tubules in the kidney. The development of problem solving skills using both analytical and computational approaches will be emphasized. Topics Covered:

• Basic definitions of the theoretical continuum, fluid velocity, pressure, temp, etc (1hr) • Fluid statics (2hrs) • Conservation of mass-integral form (4hrs) • Conservation of linear momentum-integral firm (4hrs) • Conservation of energy – integral form (4hrs) • Differential eqns of laminar incomp. flow – Navier Stokes eqns and applications (5hrs) • Heat conduction (6hrs) • Mass diffusion-1,2,&3 dimensional examples, Num. Methods (8hrs) • Potential and inviscid flow (3hrs) • Dimensional analysis (3hrs)

Class Schedule:

Lecture: 3 hrs/week Recitation: 1 hr/week



Contribution towards Program Outcomes

Multidisciplinary Ability High Problem Solving Approach High Problem Solving Methods Med. Experimentation Low


Design Low Professional Orientation Low


John Schotland July 2007


BE400 Clinical Preceptorship in Bioengineering Credit: 1 course unit Elective course Catalog Description:

Introduction to the integration of biomedical engineering in clinical medicine through lectures and a preceptorship with clinical faculty

Prerequisites:

None


Handouts and references to resource materials in the different areas of clinical medicine covered in the course.

Course Objectives and Relationship to Program Educational Objectives:

Students are introduced to real-life problems and opportunities in clinical medicine through lectures and an in-depth preceptorship in a clinical department. Lecturers and Preceptors are principally clinician scientists with backgrounds in the physical or engineering sciences who are involved in BE-related clinical practice and research. The use of bioengineering principles and practice is highlighted. An important aspect of engineering practice is the solution of quantitative technical problems, both for design and applications. Starting this semester there will be an option to complete homework problems related to the technical aspects of those lectures amenable to quantitative analysis with which students should be familiar. Although homework completion will be used strictly for extra credit, all students are encouraged to work on these problems.

Topics Covered: Lectures (80min) in:

• Anaesthesiology and Critical Care • Rehabilitation Medicine • Cardiac Electrophysiology • Epilepsy Neurology • Neurotrauma • Cardiac Surgery • Cancer Pharmacology Mass Spec. / Proteomics • Pulmonary Imaging • Neurosurgery • Orthopaedic Surgery • Medical Informatics • Cardiac Imaging


Lecture: 3 hr/week for 6 weeks Preceptorship : Begins week 4 for balance of semester. 10-15h/week



50% Engineering science 50% Clinical


Multidisciplinary Ability High Problem Solving Approach High Problem Solving Methods Low Experimentation Low Design Low Professional Orientation High


David M. Eckmann, Ph.D., M.D. Updated – July 20, 2007


BE401 Probabilistic Analysis and Modeling in Bioengineering Credit: 1 course unit Catalog Description: This course introduces Bioengineering students to fundamental concepts and methods in probability and random processes with applications in analysis and modeling of certain biological systems that are inherently probabilistic, such as neural activity and coding. Topics include probability concepts with emphasis on the Poisson and related distributions and applications in neural modeling, and basic concepts in discrete and continuous random processes with applications in bioengineering modeling and signal analysis. Prerequisites: BE301 or permission of the instructor Textbook(s) and/or Other Required Materials:

1. Probabilistic Methods of Signal and Systems Analysis, 3rd Edition, G. Cooper and C. D. McGillem, Oxford University Press, 1999.

2. Additional references and handouts Topics Covered:

1. Probability, probability of events, conditional probability, Bayes rule. 2. Random variables and probability distributions, discrete and continuous probability

distributions, joint probabilities, functions of a random variable 3. Examples of discrete and continuous probability distributions with emphasis of the Poisson,

Gaussian and related distributions 4. Applications of Poisson count and interval distributions to neuronal activity, histograms and

characterization of neuronal firing patterns 5. Random processes: definitions, discrete and continuous processes, Poisson process,

modulated and driven processes 6. Application of point processes in modeling neural code, saturation, dead time, thresholds,

modulated processes 7. Autocorrelation, spectral representation, noise as a random process, bandlimited processes,

principal component analysis 8. Applications in modeling visual and auditory signal coding and related image and sound

properties 9. Application in signal analysis [an ECG signal or an example from the BE lab] and effects of

noise. Class Schedule: Lecture: 3 hr/week Course Objectives and Relationship to Program Education Objectives: The purpose of this course is to introduce the students to bioengineering modeling and analysis applications and critical background and techniques in probability and random processes. Analysis of many biological systems and processes, especially in neural systems and biomedical signal applications, is based on probabilistic and random processes methods. The course fulfills the need to expand the analytical skills of Bioengineering students in these areas in the context of bioengineering applications.


Course Outcomes and Relationship to Program Outcomes: A student completing this course should be able to:

1. Understand basic probability concepts and properties of random variables and probability distributions. 2. Apply fundamental probability and random variable properties to characterize and model engineering

systems. 3. Understand the concepts of random processes and signals and their temporal and spectral properties. 4. Apply temporal and frequency domain techniques and properties of random processes to analysis and

modeling of signals and systems

All of above topics address program objectives of foundations, analysis, and depth. Contribution of Course to Meeting the Professional Component: 20% professional, 80% engineering topics Course Materials Made Available: Syllabus. Project assignments. Person(s) Preparing Description and Date:

Gershon Buchsbaum March 2004


BE402 From Biomedical Science to the Marketplace Credit: 1 course unit Elective course Catalog Description

This course explores the transition from discovery of fundamental knowledge to its ultimate application in a clinical device or drug. Emphasis is placed upon factors that influence this transition and upon the integrative requirements across many fields necessary to achieve commercial success. Special emphasis is placed upon entrepreneurial strategies, intellectual property, financing and the FDA process of proving safety and efficacy. Current public companies in the medical device and drug industry are studied in detail and critiqued against principles developed in class.

Prerequisites:

Senior standing in Bioengineering, or permission of the instructor


Material posted on the course Blackboard website.

Course objectives:

To understand biomedical product development, with emphasis on entrepreneurial strategies, intellectual property, financing and the FDA process of proving safety and efficacy.

Topics Covered:

• The process of discovery • Introduction to the Marketplace • Getting started • Protection of intellectual property • Financing the Venture and the Business Plan • The Regulatory (FDA) Process • Good Manufacturing Practices • Marketing Strategies for New Products •


Lecture: 3 hr/week


Multidisciplinary Ability High Problem Solving Approach Med. Problem Solving Methods Med. Experimentation Low Design Med. Professional Orientation High


Paul Ducheyne July 2007


BE421/BE521 Brain-Computer Interfaces Credit: 1 course unit Elective course Catalog Description:

This course will provide practical education in engineering technologies used to monitor and modulate the nervous system and their translation into clinical devices. Fundamental concepts in neurosignals, hardware and software will be reinforced by practical examples and in-depth study of three neurodevice platforms over the course of the semester: (1) localization of epileptic networks with intracranial electrodes, and modulation of these circuits with responsive brain stimulation (2) localization and stimulation of thalamic nuclei for treatment of movement disorders (e.g. Parkinson's disease), (3) systems for evoked-potential driven computer-guided communication for quadriplegic patients. Basic background in neurosignals will be provided, spanning scales from single neurons to large-scale field potentials, and across modalities from electrophysiology to optical and chemical recording. Algorithms for extracting, classifying, and modulating neurosignals will be covered, along with strategies for reducing them to practice on implantable computational platforms. Finally, some appreciation for hardware implemented in clinical systems will be given, along with their limitations and major design considerations. By the end of the course students will be able to design and implement a scaled-down brain-computer interface device in computer software simulations, and understand basic concepts involved in its implementation and approval. The course is geared to advanced undergraduates and graduate students interested in understanding the basics of implantable neuro-devices, their design, practical implementation, approval, and use. Reading will cover the basics of neuro signal recording, analysis, algorithms for controlling therapy and fundamental concepts governing clinical implementation, approval, and use. The focus of the course will be on lectures and homework assignments that build incrementally towards culmination in a complete Brain-Computer Interface (BCI) design. Guest lecturers and demonstrations will supplement regular lectures.

Prerequisites: BE301 (signals and systems) or equivalent, computer programming experience, preferably in MATLAB (e.g., as used in the BE labs, BE209/210/310). Some basic neuroscience background [e.g., BIOL215, BE305, BE520, INS (neuroscience) core course], or independent study in neuroscience, is required. This requirement may be waived based upon practical experience on a case by case basis by the instructor. Grading:

50% Homework & Assignments 20% Midterm 30% Final Project (examples at the end of the syllabus)

Textbook(s) and/or other Required Material:

Bulk-pack of articles and book chapters including: 1. Chapters from: Pedley and Ebersole, Eds., Current Practice of Clinical Electroencephalography, Lippincott, Williams and Wilkins. 2. Chapter: Echauz J, Wong S, Smart O, Gardner A, Worrell G, and Litt B: Quantitative methods for tracking seizure generation in epileptic networks Computational Neuroscience in Epilepsy. Soltesz I and Staley K (eds.). Elsevier, 2008. 3. S Jensen, G Molnar, J Giftakis, W Santa, R Jensen, D Carlson, M Lent and T Denison. Information, Energy, and Entropy: Design Principles for Adaptive, Therapeutic Modulation of Neural Circuits. Plenary Talk Summary, European Solid-State Circuits Conference [ESSCIRC], Sept 2008.


4. Kossoff E, Ritzl E, Politsky J, Murro A, Smith J, Duckrow R, Spencer D, Bergey G. Effect of an External Responsive Neurostimulator on Seizures and Electrographic Discharges during Subdural Electrode Monitoring. Epilepsia. 2004 Dec; 45(12):1560-7. 5. Wong S, Danish S, Jagi J, and Baltuch G. Guiding Electrode Placement For Deep Brain Stimulation By Fuzzy Cluster Multi-Unit Activity. IEEE Transactions on Biomedical Engineering, in press. 6. Schalk G. Brain-computer Symbiosis. J. Neural Eng. 5 (2008) P1-P15. 7. Lewicki, M. S. A review of methods for spike sorting: the detection and classification of neural action potentials. Network 9, R53-78 (1998). 8. Buzsaki, G. Large-scale recording of neuronal ensembles. Nat Neurosci 7, 446-51 (2004). 9. Krusienski D, Sellers EW, Cabestaing F, Bayoudh S, McFarland D, Vaughan TM, and Wolpaw JR. A comparison of classification techniques for the P300 Speller. J. Neural Eng. 3 (2006) 299-305. 10. Viventi J, Maus D, Litt B. Evolution of Technology for Monitoring Brain Networks. Review Manuscript, in submission.

1.

Tools:

This course is designed around two core libraries: (1) a library of data collected from actual patients and devices, and (2) a library of algorithm routines that the students will use during the course to analyze the data archive. Homework will utilize these tools, and develop increasing proficiency gradually over the semester, culminating in their final projects.

Topics Covered:

Week 1: Introduction; Basics of Neurosignals: Signal Generators, dipoles, cells and circuits. Multi-scale recordings: EEG, evoked potentials, field potentials, units. Homework: Basic patterns in neurosignals. Week 2: Introduction to the feature library and human data archive. Basic algorithms: Computing basic features and classifying output using the library and archive. Guest Speaker: Javier Echauz, Ph.D., author of library tools. Homework: Downloading features from the library and simple processing assignment. Week 3: Event detection and basic classifiers: signal averaging, clustering, post- processing. Guest Speaker: Andrew Gardner, Ph.D., Momentics Corp. Homework: Separate two neural signals from a group of brief recording segments. Week 4: BCI Hardware I: types, systems, biocompatibility *Introduce final projects Guest Speaker: Tim Denison, Ph.D., Medtronic, Inc. Homework: Design specifications for BCI hardware given specific components. Week 5: Hardware II: design considerations: power, heat, processing Guest Speaker: Jonathan Viventi, MSEE, UPenn


Weeks 6 & 7: Communication in locked-in syndrome: A P-300 based communication syndrome. *Students choose final projects. Guest speaker: Gerwin Schalk: BCI-2000, Wadsworth Center, Albany Medical College Homework: P-300 averaging and processing for spelling words. Weeks 8 & 9: “Deep brain stimulation: localizing thalamic networks, and brain stimulation algorithms. Guest speaker: Stephen Wong, M.D. UPenn or Cameron Macyntire, Cleveland Clinic. Homework: Sorting and clustering multiunit recordings from implantation of deep brain stimulation electrodes. Weeks 10 & 11: Antiepileptic devices. Localizing epileptic networks and responsive devices for epilepsy. Homework: Detecting epileptic seizures. Week 12 & 13: Work on final projects. Guest speaker: TBA (J&J or Boston Scientific), getting a device from idea to market. The regulatory and approval process. Guest speaker: John Harris, CEO NeuroVista or Al Hershey, TCD Medical: Start-up companies and entrepreneurship in BCI. Hands on and help sessions. Week 14: Discussion of course. Last lecture on new developments in BCI since beginning of the course. *Hand in projects.

Projects:

These will build on the homework assignments. Students will choose one of three projects using unknown data sets from the archive. All projects will be graded 1/3 on design, 1/3 on implementation and code, and 1/3 on success at the required task. Students will be given a training set. They will upload code to be sure that it can run on the test set. Test set run will be performed after uploading final code so that final results are fixed and stored. The demands from the graduate students will be commensurate with their more advanced standing. For example, graduate students will need to localize two structures for the Parkinson's data set, or detect and stimulate two different seizure types, a considerably more difficult assignment (see examples below). 1. Designing a novel BCI device to decode evoked potential data to spell words. Students will first have to decode a training set, then turn algorithm in for decoding a message that is individualized to the student. 2. Localizing subthalamic nucleus coordinates based upon analyzing multi-unit activity. Students will have to give entry and exit coordinates for subthalamic nucleus (STN) based upon streams of real data. Students will be given a training data set for their algorithm. 3. Detecting and triggering stimulation to pre-empt clinical seizures. Students will have to detect a particular seizure pattern then choose a type of stimulation output to suppress seizures. Students will be given a training set. Test set will consist of seizures and artifacts. Successful suppression will require detecting below a specific latency and triggering the right form of stimulation.


Brian Litt September 2008


BE441 Engineering Microbial Systems Credit: 1 course unit Elective course Motivation:

The Bioengineering curricula at Penn and other BE/BME programs require extensive biology. BE students take 3 biology courses, BE121 (+lab), molecular biology, BIOL202, Cell Biology, and BIOL215 Vertebrate Physiology (or an equivalent physiology course). However, our students do not have an opportunity to be exposed to the basic engineering applications and design principles enabled by the biology. This course fills the gap.

Catalog Description:

This course is designed to expose students to the principles underlying engineering microbial systems. The fundamentals of DNA, RNA and proteins will be reviewed. An emphasis will be placed on recombinant DNA technologies, mutagenesis, cloning, gene knockouts, altered gene expression and analysis, with practical real world examples of their application. Throughout this course, we will also focus on case studies and critical literature evaluation.

Objectives:

Provide the scientific tools to design an application based on a microbial engineering platform. 1. Fundamental molecular biology of bacteria 2. Technology for microbial modification, with engineering approach 3. Analysis/evaluation of wild type and modified organisms 4. Identification and evaluation of existing technology/applications (academic, industrial, journal)

Prerequisites: Biol 121, Biol 202, BE209, BE210 or permission of instructor Grading:

45% Homework/quizzes 15% Midterm 25% Final Paper: Critically evaluate journal article 15% Final Presentation: Present critical review of journal article


Required: Molecular Genetics of Bacteria, L. Snyder and W. Champness, ASM Press 2007. Reference: Molecular Biotechnology, B. Glick and J. Pasternak, ASM Press 2007.

Tools:

This course is designed around two core libraries: (1) a library of data collected from actual patients and devices, and (2) a library of algorithm routines that the students will use during the course to analyze the data archive. Homework will utilize these tools, and develop increasing proficiency gradually over the semester, culminating in their final projects.

Topics Covered:

Week 1: Fundamentals of prokaryotes


Microbial Growth and Fermentation: O2, T, pH measurement, control, equations; Bacterial life cycle, stress response, small molecule (antibiotic) production Week 2: DNA – structure, function, replication (including errors), genome structure RNA – structure, function, production, regulation Week 3: Protein - structure, function, production, regulation Case study: Cell free protein synthesis Week 4: Recombinant DNA (rDNA) technology: Discovery, Enzymes involved, Fundamental principles, PCR rDNA for new products – examples: LS9 rDNA for affecting bacterial performance – examples: E. coli used in small molecule production, modified E. coli for laboratory use (removal of transposases etc.), E. coli minimal genome project Case study: Cohen and Boyer Week 5: Cloning and Plasmids – Fundamental Construction, Techniques, Overexpression, Gene expression regulation, Conjugation/transformation, Transduction, Phages, Temperature sensitive plasmids Guest Speaker: Jonathan Viventi, MSEE, UPenn Week 6: Gene knockouts: Fundamentals, Homologous recombination, Cosmid library examples: Antibiotic production competing pathway removal, Laboratory functionality studies Week 7: Mutagenesis: Natural mutations – rate/type, stress response, Site-directed mutagenesis, Error-prone PCR, UV/Chemical, Transposons Week 8: Mutagenesis Case Studies: Example: Maxygen genome shuffling Midterm Week 9: Analyses: Whole cells (microscopy) Separation (centrifugation, chromatography, electrophoresis) RNA, DNA, Protein, Arrays (Total NA, Protein), Snp arrays Specific component detection (Immunodetection…) Protein sequence/structure determination (edman degradation, mass spec, nmr, x-ray crystallography) DNA Sequencing Case Study: Pacific Biosciences Weeks 11 - 14: 50% Student presentations of literature 50% Technology application case studies Examples

Health: Artemisinin Project (Keasling) Tools: Pacific Biosciences – Enzyme modification and technology development for DNA

sequencing Energy: LS9

Person Preparing Description and Date: Elizabeth Widenbrant September 2008


BE450/550 Hemodynamics Credit: 1 course unit Elective course Catalog Description:

Development of concepts about the operation of the mammalian cardiovascular system as conceived in the years 198 (by Galenus, personal physician to Roman Emperor Marcus Aurelius), 1628, (by Willaim Harvey in his book "De motu cordis et sanguinis ), and 1998 (At Penn by Abraham Noordergraf).

Prerequisites:

BE 350 or equivalent, or permission of the instructor.


Noordergraaf: Circulatory System Dynamics, Academic Press, 1978. (This book has been sold out, but the SEAS Copy Center provides copies at cost.) Noordergraaf: Blood in Motion, to be published by Springer Verlag, NY (Preprints of most chapters will be made available as handouts.)

Course Objectives:

To train students in quantitative analysis of the cardiovascular system and its components, as currently conceived. Comprehend the difference between modeling and simulation. Understand the age old tension between theory and experiment.

Topics Covered:

Muscle structure and mechanical properties; the single band structure of the two ventricles; electrical stimulation; Frank’s mechanism; the mathematical description of the heart as a pump; ventricular load and venous supply; the impedance-defined flow principle; wave transmission in arteries; collapse of veins; the influence of respiration and ambulation; effect of gravity; the microcirculation as the site of communication with extra-vascular tissues; generalization of the Starling hypothesis; the closed system; control theory with specific applications in the circulatory system; transplanted and artificial hearts.


Lecture: 3hr/week




Multidisciplinary Ability High Problem Solving Approach Med. Problem Solving Methods Med. Experimentation Med. Design Low


Professional Orientation High Person(s) Preparing Description and Date:

Abraham Noordergraaf, Ph.D. July 2007


BE455/MEAM455 Continuum Biomechanics Credit: 1 course unit Elective course Catalog Description:

Biological and non-biological systems are both subject to several basic physical balance laws of broad engineering importance. Fundamental conservation laws are introduced and illustrated using examples from animate as well as inanimate systems. Topics include kinematics of deformation, the concept of stress, conservation of mass, momentum, and energy. Mechanical constitutive equations for fluids, solids, and intermediate types of media are described and complemented by hands-on experimental and computational laboratory experiences. Practical problem-solving using numerical methods will be introduced.

Prerequisites:

Statics, linear algebra, and differential equations Textbooks:

YC Fung, A First Course in Continuum Mechanics YC Fung, Biomechanics: Mechanical Properties of Living Tissues

Course Objectives:

The course is a senior-level elective for students interested in continuum mechanics theory and its application to living tissue modeling. (Juniors can enroll with instructor permission) Students will be exposed to applied mathematics ( theory and numerical methods) and will learn how to integrate analysis computation and mechanics.

Topics covered:

• Mathematics and continuum mechanics: Tensor analysis, Deformation and Strain, Conservation Laws, Invariance;Constitutive Laws (Elastic Solids, Newtonian Fluids), bending and buckling, fluid-solid interaction

• Biomechanics: Arterial wall mechanics, heart valves, blood rheology, biopolymer mechanics, cytoskeleton regeneration, tissue engineering

•


Lecture: 3 hr/week




Multidisciplinary Ability High Problem Solving Approach High Problem Solving Methods Med. Experimentation Low Design Low


Professional Orientation Low Person Preparing Description and Date:

George Biros July 2007


BE459/BE559 Multiscale Modeling of Biological Systems Credit: 1 course unit Elective course Catalog Description:

This course aims to provide theoretical, conceptual, and hands-on modeling experience on three different length and time scales that are crucial to biochemical phenomena in cells and to nanotechnology applications. Special Emphasis will be on cellular signal transduction. 60% lectures, 40% computational laboratory. No programming skills required.

Prerequisites: None* *Undergraduates who have taken BE324 or equivalent courses in Quantum Mechanics and/or Statistical Physics need no permission. Others, email instructor [email protected] for permission.


Course notes, online manuals, journal articles, review articles Reference Textbooks


BE470 Medical Devices Credit: 1 course unit Elective course Catalog Description:

This course discusses the design, development, and evaluation of medical devices. Emphasis is placed on the process of matching technological opportunities to medical needs. Medical devices are analyzed from three viewpoints: technology driven applications, competing technologies, and disease-related technology clusters.

Prerequisites:

Junior or Senior standing in Bioengineering, or permission of the instructor


Ulrich, Karl and Eppinger, Steven. (2000). Product Design and Development, 2nd Edition. McGraw-Hill.

Course Objectives and Relationship to Program Education Objectives:

The goal of this course is to develop the thinking and research tools that will enable students to understand medical devices as products: commercially available technological solutions to medical needs. This total understanding is based upon the coordinated separate understandings of: (1) underlying medical science and clinical practice; (2) underlying technologies and the potential choices between available technologies; (3) engineering design; and (4) technological and business directions of companies.

Topics Covered:

• Concepts of medical device, medical technology, and medical product • Classifications of medical devices • Reverse engineering methods • Product portfolios and architectures • Specifications • Constraints • Functional decomposition • Function-Structure relationships • Selection, evaluation, and comparison methods • Safety, reliability measures • Clinical evaluation methods


Lecture: 3 hr/week




Multidisciplinary Ability Med.


Problem Solving Approach Med Problem Solving Methods Med Experimentation Med Design High Professional Orientation High


Daniel Bogen June, 2003


BE480 Introduction to Biomedical Imaging Credit: 1 course unit Elective course Catalog Description

Physical principles of different imaging modalities, instrumentation,and image reconstruction and fundamentals. X-ray computed tomography, emission tomography (SPECT, PET), ultrasound imaging, optical imaging methods and magnetic resonance imaging.

Prerequisites: BE 301 or EE 224 or permission of the instructor Textbooks:

A.C.Kak, M.Slaney, "Principles of Computerized Tomographic Imaging," IEEE Press, 1999, New York. Online at http://www.slaney.org/pct/ William R. Hendee, E. Russel Ritenour, "Medical Imaging Physics"


Lecture: 3 hr/week Course Objectives:

To provide an overview of fundamentals of imaging modalities with an emphasis on basic algorithmic and mathematical techniques for image reconstruction.

Topics Covered

• Overview of imaging modalities • X-ray computed tomography

a) Physical principles and instrumentation b) Radon transform and radon transform inversion c) Filtered backprojection formula

• Nuclear imaging and emission tomography a) Principles and instrumentation for Single-photon emission computed tomography (SPECT) b) Principles and instrumentation for positron emission tomography (PET) c) Image reconstruction in emission tomography

• Ultrasound a) Physical principles of ultrasound imaging b) Ultrasound transducers c) Propagation of ultrasound waves d) Presentation modes of ultrasound images e) Diffraction tomography

• Optical imaging methods a) Propagation of near-IR light in tissues

b) Contrast mechanisms c) Image reconstruction in diffuse optical tomography d) Spectroscopic methods

• Magnetic resonance imaging a) Magnetic resonance as a probe of the body

http://www.slaney.org/pct/�


b) Contrast agents c) Spectroscopic applications d) Instrumentation for MRI e) Image reconstruction in MRI


100% Engineering Science Contribution towards Program Outcomes:

Multidisciplinary Ability High Problem Solving Approach Med Problem Solving Methods Med. Experimentation Low Design Med Professional Orientation Low


Vadim Markel October 2005


BE483 Molecular Imaging Credit: 1 course unit Elective course (Junior or senior year) Catalog Description:

This course will provide a comprehensive survey of modern medical imaging modalities with an emphasis on the emerging field of molecular imaging. The basic principles of X-ray, computed tomography, nuclear imaging, magnetic resonance imaging, and optical tomography will be reviewed. The emphasis of this course, however, will focus on the concept of contrast media and targeted molecular imaging. Topics to be covered include the chemistry and mechanisms of various contrast agents, approaches to identifying molecular markers of disease, ligand screening strategies, and the basic principles of toxicology and pharmacology relevant to imaging agents.

Prerequisites:

BIOL 215 Vertebrate Physiology, or BE 305 Engineering Principles of Human Physiology, or permission of instructor.

Textbook(s) and/or other materials:

Course notes, handouts, journal articles Reference Books: 1. Textbook of Contrast Media, P. Dawson, D. Cosgrove, D. Allison, R.G. Grainger, T&F STM, 1999 2. Introduction to Biomedical Imaging (IEEE Press Series on Biomedical Engineering), A. G. Webb,

Wiley-IEEE Press, 2002


BE490/BE492 Research in Bioengineering Credit: 1 course unit Elective course Catalog Description:

An intensive independent study experience on an engineering or biomedical science problem related to bioengineering. Requires preparation of a proposal, literature evaluation, and preparation of a paper and presentation. Regular progress reports and meetings with a faculty advisor are required.

Prerequisites:

Junior or senior standing in Applied Science Biomedical Science (BAS) or the BSE Program.

Course Objectives:

This course is the ultimate opportunity for students to apply what they have learned during their undergraduate education and touches upon all program objectives. It provides a comprehensive experience in the project process including technical aspects, communication and ethics. Projects can span two consecutive semesters, enabling more comprehensive and extensive projects with one report at the end of the second semester. The second semester of the same project is BE492 and a grade is given for each semester.

Topics covered:

No set topics, but students completing this course should be able to • Define a clear motivation for the project chosen • Develop a working relationship with an advisor and/or team in a multidisciplinary environment • Learn and integrate technical material in new areas and review the essence of a new technical field • Be able to apply newly acquired engineering and scientific methods • Write a proposal for the project • Assess ethical issues related to responsible conduct of research • Assess progress and describe engineering and scientific accomplishments and failures of the project. • Prepare an effective poster to communicate the scientific findings to the public. • Translate the essence of the research project into a coherent oral presentation. • Write a professional final report with publication quality, which is written correctly for a defined format

Class/laboratory schedule: Arranged with project advisor Contribution towards Professional Component:

Proportion of engineering science, engineering design, and basic science is dependent on particular project.


Multidisciplinary Ability Med. Problem Solving Approach High Problem Solving Methods Med. Experimentation Med. Design Med. Professional Orientation Med.



Gershon Buchsbaum July 2007


BE492 Research in Biomedical Science Credit: 1 course unit Catalog Description: An intensive research experience on a biomedical science problem related to bioengineering. Requires preparation of a research proposal, literature evaluation, and preparation of a research paper and presentation. Regular progress reports and meetings with a faculty advisor are required. Prerequisites: Junior or Senior Standing in Applied Science Biomedical Science (BAS) or the BSE Program. Course Objectives and Relationship to Program Educational Objectives: This course is the ultimate opportunity for students to apply what they have learned during their undergraduate education and touches upon all program objectives. It provides a comprehensive experience in the project process including technical aspects, communication and ethics (1, 2, 3). Course Outcomes and Relationship to Program Outcomes: Students completing this course should be able to 1. Define a clear motivation for the project chosen (professional skills) 2. Develop a working relationship with an advisor and/or team in a multidisciplinary environment (professional

skills) 3. Learn and integrate technical material in new areas and review the essence of a new technical field

(breadth, depth, professional skills) 4. Be able to apply newly acquired engineering and scientific methods (breadth, depth, professional skills) 5. Write a proposal for the project (professional skills) 6. Assess ethical issues related to responsible conduct of research (professional skills) 7. Assess progress and describe engineering and scientific accomplishments and failures of the project.

(design, professional skills) 8. Prepare an effective poster to communicate the scientific findings to the public. (professional skills) 9. Translate the essence of the research project into a coherent oral presentation. (professional skills) 10. Write a professional final report with publication quality, which is written correctly for a defined format.

(professional skills)


BE495/496 Senior Design Project Credit: 1 course unit in each of the Fall and Spring semesters of the senior year Required course (Senior year) Catalog Description:

Design projects in various multidisciplinary areas of bioengineering. Students work in teams as Bioengineering Design Consultants, providing engineering design services -- emphasizing project definition, feasibility analysis, evaluation of alternative designs, and design computations. For each project, the scope of work is developed and negotiated between client and student consultants. The scope of work may also include fabrication, device testing, and field-testing. Projects are arranged by the students with approval of the instructor in the Spring semester of the Junior year. Continually updated project briefs, planning documents, interim reports, a final report, a final poster, and presentations are required. In addition to technical design, students develop skills in communication, planning, project management, and project risk management.

Prerequisites:

Bioengineering senior standing or permission of the instructor.

Textbook(s) and/or other required Materials:

Planning documents and procedures posted on website.

Course Objectives:

This course is the ultimate opportunity for students to apply what they have learned during their undergraduate education and touches upon all program objectives. It provides a comprehensive experience in the project process including technical aspects, communication, and ethics.

Topics Covered:

The design and project processes, identification of need, problem definition, constraints, specifications, project definition, project planning, decision-making, resource assessment, planning documents, team work, scheduling, risk assessment, testing, records and documentation, communications, ethics.


Lecture: Wednesday & Friday, 8:00 – 9:00, for approximately the first month of the Fall semester. Thereafter, occasional class meetings throughout the year.


100% Engineering design


Multidisciplinary Ability High Problem Solving Approach High Problem Solving Methods High Experimentation High Design High Professional Orientation High



D. Bogen September 2005


BE497/8 Senior Thesis in Biomedical Science Credit: 1 course unit Catalog Description: An intensive independent project experience incorporating both technical and non-technical aspects of the student's chosen career path. Chosen topic should incorporate elements from the student's career path electives, and may involve advisors for both technical and non-technical elements. Topics may range from biomedical research to societal, technological and business aspects of Bioengineering. A proposal, regular progress reports and meetings with a faculty advisor, a written thesis, and a presentation are required. Prerequisites: Senior Standing in the Applied Science Biomedical Science Program. (BAS students only). Course Objectives and Relationship to Program Educational Objectives: This course is the ultimate opportunity for students to apply what they have learned during their undergraduate education and touches upon all program objectives. It provides a comprehensive experience in the project process including technical aspects, communication and ethics (1, 2, 3). Course Outcomes and Relationship to Program Outcomes: Students completing this course should be able to 1. Define a clear motivation for the project chosen (design, professional skills) 2. Develop a working relationship with an advisor and/or team in a multidisciplinary environment (professional

skills) 3. Learn and integrate technical material in new areas and review the essence of a new technical field

(breadth, depth, professional skills) 4. Be able to apply newly acquired engineering and scientific methods (breadth, depth, professional skills) 5. Write a proposal for the project (professional skills) 6. Assess ethical issues related to responsible conduct of research (professional skills) 7. Assess progress and describe engineering and scientific accomplishments and failures of the project.

(design, professional skills) 8. Prepare an effective poster to communicate the scientific findings to the public. (design, professional skills) 9. Translate the essence of the research project into a coherent oral presentation. (professional skills) 10. Write a professional final report with publication quality, which is written correctly for a defined format.

(professional skills)


BE 502: From Biomedical Science to the Marketplace Credit: 1 course unit Elective course Catalog Description

This course explores the transition from discovery of fundamental knowledge to its ultimate application in a clinical device or drug. Emphasis is placed upon factors that influence this transition and upon the integrative requirements across many fields necessary to achieve commercial success. Special emphasis is placed upon entrepreneurial strategies, intellectual property, financing and the FDA process of proving safety and efficacy. Current public companies in the medical device and drug industry are studied in detail and critiqued against principles developed in class.

Prerequisites:

First year graduate level, or Senior standing in Bioengineering with GPA exceeding 3.4 , or permission of the instructor


There is no text, material is posted on the course Blackboard WEB site.

Course objectives:

To understand biomedical product development, with emphasis on entrepreneurial strategies, intellectual property, financing and the FDA process of proving safety and efficacy.

Topics Covered:

• The process of discovery • Introduction to the Marketplace • Getting started • Protection of intellectual property • Financing the Venture and the Business Plan • The Regulatory (FDA) Process • Good Manufacturing Practices • Marketing Strategies for New Products


Lecture: 3 hr/week

Contribution towards Program Outcomes: Multidisciplinary Ability High Problem Solving Approach Med. Problem Solving Methods Med. Experimentation Low Design Med.


Professional Orientation High Person(s) Preparing Description and Date:

Paul Ducheyne February 2004


BE505 Quantitative Human Physiology Credit: 1 course unit Elective course Catalog Description:

Introduction to human physiology using the quantitative methods of engineering and physical science. Emphasis is on the operation of the major organ systems at both the macroscopic and cellular level.

Prerequisites:

Engineering Principles of Human Physiology, BE 305


J Keener & J Sneyd. Mathematical Physiology, Springer. AC Guyton & JE Hall. Textbook of Medical Physiology, 10th Edition, WB Saunders.

Course Objectives:

To provide a rigorous integration of mathematical analysis and applications of engineering and scientific principles in human physiology, on both the cellular and organ system levels. The course utilizes a combination of physiology presentations and mathematical proofs, derivations and problem sets to encourage students to apply quantitative approaches to studying human physiologic phenomena.

Topics Covered:

Quantitative approaches and mathematical applications in: • Cellular Membrane Diffusion, Transport • Hodgkin-Huxley Models & Action Potential Concepts • Quantal Models of Synaptic Transmission • Muscoloskeletal System • Cardiovascular Physiology • Immunology & Leukocyte Trafficking • Respiratory Physiology • Nervous Systems Physiology – Central & Peripheral

Class Schedule:

Lecture: 3hr/week




Multidisciplinary Ability Med. Problem Solving Approach Med. Problem Solving Methods Low Experimentation Low Design Low Professional Orientation Low



Beth Winkelstein October, 2003


BE510 Biomechanics and Biotransport Credit: 1 course unit Elective course Catalog description:

The course is intended as an introduction to continuum mechanics in both solid and fluid media, with special emphasis on the applications to biomedical engineering. Once basic principles are established, the course will cover more advanced concepts in biosolid mechanics that include computational mechanics and bio-constitutive theory. Applications of these advanced concepts to current research problems will be emphasized.

Prerequisites:

Math through 241; BE350, BE324 as pre- or corequisites


Fung, Y.C., A first course in continuum mechanics, Prentice Hall, 3rd edition

Course Objectives:

This course will cover at an intermediate to advanced level mechanics methods and biomechanics applications and fundamentals of finite element analysis. The course will focus stress strain and deformation analysis, the governing mathematical model and equations for solids fluids and viscoelasticity and applications hard and soft tissues and Biofluid mechanics. This course is intended to support the prime objective of integrating classical mechanical engineering with biomechanics application within a physiological context.

Topics Covered:

• Cartesian Tensors • Analysis of Stress • Deformation Analysis • Antiplane strain and torsion • Plane strain and plane stress • Constitutive equations for solids and fluids • Energy Theorems and Finite element analysis (fundamentals) • Viscoelasticity (3 weeks)

- Time dependent behavior: - Creep, relaxation, recovery – classical models - Creep compliance, modulus - Boltzmann superposition principle - Hereditary integrals - Applications to hard and soft tissues – Quasi-linear viscoelasticity - Viscoelastic stress analysis – application to boundary value problems

• Applications to Biosolid mechanics


Lecture – 3 hrs/week





Multidisciplinary Ability Med. Problem Solving Approach High Problem Solving Methods Low Experimentation Low Design Low Professional Orientation Low




BE511 Analysis and Design of Bioengineering Signals Credit: 1 course unit Elective course Catalog Description:

This is a practically-oriented course in the analysis of biomedical signals focusing on medically significant applications. The specific applications will vary from year to year, but will lectures include the nature of major signals of biomedical importance, digital signal processing including convolution, digital filtering, wavelet analysis. The course will include student experiments using Matlab and independent projects.

Prerequisites:

BE 301 or graduate status. Not intended for students with previous courses in digital signal processing.


Required: Digital Signal Processing: A Practical Approach, 2nd Ed. Ifeachor and Jervis, Addison-Wesley Recommended: Matlab student edition

Course Objectives:

This course is an elective for upper-level bioengineering majors and bioengineering graduate students other than those with backgrounds in digital signal processing. The goal of the course is to introduce students to the use of computer methods to acquire and process biomedical signals, focusing on practical applications of medical significance. The course extends the theoretical background in a previous required course (BE 301) to enable students to develop practical applications of biomedical significance, including design of digital processing systems to meet specific medical requirements. The course includes extensive computer assignments using Matlab and a semester project.

Topics Covered:

• Nature of biomedical signals; overview of signal analysis. • Sampling Theorem and A/D Conversion; aliasing artifacts in biomedical signals • Discrete transforms • Windows • z - Transform • Correlation and Convolution • Design of IIR and FIR filters • Adaptive filters • Wavelet analysis • Specific biomedical applications: ECG analysis (including QRS detector using digital filters),

fetal ECG monitor using adaptive filter, heart rate variability monitor, impedance cardiography


Lecture: 3 hrs/week



BE512 Bioengineering III: Biomaterials Credit: 1 course unit Elective course Catalog Description:

This course provides a comprehensive background in biomaterials. It covers surface properties, mechanical behavior and tissue response of ceramics, polymers and metals used in the body. It also builds on this knowledge to address aspects of tissue engineering, particularly the substrate component of engineered tissue and organs.


Readings materials and handouts will be selected from journal articles and the recommended texts listed below. Biomaterials Science: An Introduction to Materials in Medicine, B. D. Ratner, A. S. Hoffman, F. J. Schoen, and J. E. Lemons (eds.), Academic Press, San Diego, 1996. Callister, W. D., Materials Science and Engineering: An Introduction, 5th ed., John Wiley and Sons, New York, 2000. Black, J., Biological Performance of Materials: Fundamentals of Biocompatibility, 3rd ed., Marcel Dekker, New York, 1999. Principles of Tissue Engineering, R. P. Lanza, R. Langer, W. L. Chick (eds.), Academic Press, San Diego, 1997.

Course Objectives:

This course will provide a comprehensive introduction to materials used for biomedical applications, focusing on both atomic structure and macroscopic bulk properties of the major classes of materials, as well as issues of biocompatibility and biological responses to implantable materials. As such, students are expected to gain an understanding of the materials selection and design criteria required for engineering living tissue equivalents. The first portion of the course will consist of an introduction to materials science and engineering, focusing on traditional classes of materials used for biomedical applications (i.e., metals, ceramics, polymers, and composites). Students will be exposed to the multidisciplinary nature of biomaterials as the course will incorporate aspects of materials science and engineering, the life sciences and clinical medicine. The remaining sections will deal with issues of biocompatibility and biological responses to materials, followed by selected topics on emerging technologies such as gene delivery and nanofabrication/bioMEMs. The course will also allow students to develop an appreciation for important design criteria relevant to the biomedical implant industry.

Course Topics:

Introduction, Bonding, Bulk Properties, Metals, Structure, Metals: Properties; Fabrication, Ceramics: Structure, Ceramics: Properties; Fabrication, Polymers: Structure, Polymers: Properties; Fabrication, Biodegradable Polymers, Composites, Natural Materials, Surface Properties; Adsorption, Cell Adhesion Cell-ECM/Substrate Interactions, Biocompatibility; Inflammation, Immunological Responses, Hypersensitivity; Hemocompatibility, Implant-Associated Infection; Sterilization, Degradation, Corrosion; Wear, Surface Characterization, Surface Modification, Nanofabrication; BioMEMs, Drug Delivery; Gene Insertion/Therapy; Review



Lecture: 3 hr/week




Multidisciplinary Ability Med. Problem Solving Approach Med. Problem Solving Methods Low Experimentation Med. Design Low Professional Orientation Low


Jason Burdick July 2007


BE513 Cell Biology Credit: 1 course unit Elective course Catalog Description

Introduction to cell and molecular biology with emphasis on quantitative concepts and applications to multicellular systems

Prerequisites: Graduate standing or permission of instructor Textbook(s) and/or Other Required Materials:

Required: Molecular Biology of the Cell. Alberts et al., 4th Edition Garland Press Recommended: Biological Physics. Philip Nelson, WH Freeman and Co. Mechanics of the Cell. David Boal, Cambridge Univ. Press

Course Objectives:

The objective of this course is to integrate structure with function at the molecular level. With emphasis on cellular structures, students are introduced to the major tissue types found in the human body and the kinds of specialized cells which comprise them. Specialized functions and proteins associated with each of these tissues are examined in detail at the molecular level. The cellular mechanisms associated with ion transport, cell adhesion, cell division, DNA, RNA and protein synthesis are explored in detail as well as relevant control mechanisms involving signal transduction and intracellular signaling. The role of the immune system is investigated as well as its molecular regulation. The function of growth factors in altering cell behavior is examined with emphasis on the cellular response to these types of signals.

Topics Covered:

Basic concepts; Techniques and Terminology in Cell Biology Cellular Biochemistry; Cell Structures and Organelle Function; Protein Structure and Function; DNA Synthesis; RNA Transcription; Membrane Structures and Receptors; Protein Translation; Gene Regulation; Cytoskeleton; Connective Tissue; Immunology; Nervous System; Molecular Motors and Cell Motility; Cell Adhesion and Signaling; Mechanical Stimulation of cells in vitro; Functional Genomics; Tissue Engineering; Gene Therapy; Cardiovascular System


Lecture: 3 hr/week




Multidisciplinary Ability High Problem Solving Approach Med.


Problem Solving Methods Low. Experimentation Med. Design Low Professional Orientation Low.


Paul Janmey July 2007


BE515 Case Studies in Bioengineering Credit: 1 course unit Elective course Catalog Description:

This course introduces students to bioengineering research and development as related to meeting clinical needs. The course is broadly organized about the question of "what makes medical technology work". It introduces students to the assessment of medical technology including studies to evaluate safety and effectiveness of new devices. Introduction to regulatory, ethical, legal, and economic issues as they relate to the success of new medical technologies. The course will be taught through examination of case studies, which may vary from year to year. Recent case studies have included mammography, heart assist devices and the artificial heart, hyperthermia, safety of radiofrequency energy. The course is taught partly as a seminar, with lectures by departmental and invited outside experts and student presentations in addition to lectures by the instructor.

Prerequisites:

Graduate standing. Undergraduates can enroll with approval of advisor and instructor. BE seniors are encouraged to take the course.


Journal articles and handouts from instructor

Course Objectives:

This course is presently a graduate course, is being renumbered as BE 515 to encourage more undergraduates to take it. The goal of the course is to introduce students to the wider cluster of issues related to “what makes medical technology work” focusing on the interplay of medical, technical engineering, and social (regulatory,legal,ethical,economic) constraints.

Topics Covered:

• Introduction: what makes medical technology work? Constraints on medical technology (regulatory, economic, medical, technical)

• Regulatory constraints: FDA premarket approval requirements for medical devices; 510(k) and PMA, postmarket surveillance

• Medical constraints: defining the medical need for a new technology • Economic constraints: Third party reimbursement as it impacts the success of new medical

technologies • Introduction to clinical trials: Phase 1,2,3; elements of study design; sample size and power

considerations • Sample case studies: Mammography; The artificial heart and assist devices; RF fields

Class Schedule:

Lecture: 3 hrs/week





Multidisciplinary Ability Med. Problem Solving Approach High Problem Solving Methods Low Experimentation Low Design Low Professional Orientation High




BE517 Optical Imaging Credit: 1 course unit Elective course Catalog Description:

A modern introduction to the physical principles of optical imaging with biomedical applications. Propagation and interference of electromagnetic waves. Geometrical optics and the eikonal. Plane-wave expansions, diffraction and the Rayleigh criterion. Scattering theory and the Born approximation. Introduction to inverse problems. Multiple scattering and radiative transport. Diffusion approximation and physical optics of diffusing waves. Imaging in turbid media. Introduction to coherence theory and coherence imaging. Applications will be chosen from the recent literature in biomedical optics.

Prerequisites: EE 310 and EE 325 or equivalent Textbook(s) and/or Other Required Materials:

Class notes, handouts and papers.


This course is taught at the graduate level and may be taken as a senior-level elective for bioengineering majors. The goal is to provide a rigorous introduction to the mathematical and physical principles of biomedical optical imaging.

Topics Covered:

• Review of Maxwell's equations, boundary conditions, conservation laws • Vector and scalar wave equations, integral theorems, Huygen's principle • Geometrical optics and the eikonal, interference, refraction • Plane-wave expansions, diffraction, Rayleigh criterion • Scattering, optical theorem, Born approximation • Introduction to inverse problems, Radon transform, inverse scattering and imaging in

transparent media, applications to computational microscopy • Multiple scattering and the radiative transport equation • Diffusion approximation, boundary conditions • Physical optics of diffusing waves, applications to photodynamic therapy • Imaging in turbid media, applications to diffusion tomography • Introduction to coherence theory • Coherence imaging, applications to optical coherence tomography •


Lecture: 3 hr/week




Multidisciplinary Ability Med. Problem Solving Approach High Problem Solving Methods Low


Experimentation Low Design Low Professional Orientation Low




BE520 Computational Neuroscience and Neuroengineering Credit: 1 course unit Elective course Catalog Description:

Computational modeling and simulation of the structure and function of brain circuits. A short survey of the major ideas and techniques in the neural network literature. Particular emphasis on models of hippocampus, basal ganglia and visual cortex. A series of lab exercises introduces techniques of neural simulation.

Prerequisites:

Permission of the instructor Textbook(s) and/or Other Required Materials:

Papers from the literature provided online.

Suggested additional references: Anders Krogh, Richard Palmer and John Hertz (1997) Introduction to the Theory of Neural Computation.

Santa Fe Institute Studies in the Science of Complexity. Lecture Notes, vol 1. (1991). Christof Koch (1999) The Biophysics of Computation: Information Processing in Single Neurons. Oxford

University Press. Bertil Hille (1992) Ionic Channels of Excitable Membranes, 2nd edition, Sinauer Associates. W.W. Lytton (2002) From Computer to Brain: Foundations of Computational Neuroscience,

Springer-Verlag. Peter Dayan and Larry Abbott (2001) Theoretical Neuroscience: Computational and Mathematical Modeling

of Neural Systems. MIT Press E.R. Kandel, J.H. Schwarz and T.M. Jessel (2000) Principles of Neural Science, 4th ed., McGraw Hill.

Course Objectives and Relationship to Program Education Objectives:

The goal of this course is introduce students to techniques used in simulating neural systems both at the network and the biophysical/cellular level. Students are introduced to the NEURON (Hines and Carnevale, 1997) simulation environment. Emphasis is placed on contrasting different modeling approaches to understanding function in the same brain region. Objective is to give students a view of the use of computational simulation in understanding biological function, as well as to develop an ability to read the neuroscience literature from a critical standpoint.

Topics Covered:

• Neural networks: Perceptrons, Backpropagation • Attractor Dynamics (Hopfield) • Support vector machines • Hippocampus and Memory (Lisman, Hasselmo) • Cognitive Maps (Sejnowski, Tsodyks, Rao & Sejnowski, Sakmann) • Neuromodulation (Berns & Sejnowski, Durstewitz & Sejnowski, Dayan) • Models of Basal Ganglia (procedural memory, reinforcement learning, categorization, salience) • Texture (Malik & Perona) • Salience (Adelson & Weiss, Gilbert, Geisler, Elder) • Hyperacuity (Miller & Zucker) • Spike-based computation (Hopfield & Brody, Van Rullen & Thorpe) • Synchronization and attention (Niebur)


• Cortical mechanisms of recognition (Poggio, Ullman, Hopfield) • Predictive Coding (Rao & Ballard) • Neural Decision Theory (Gold) • Similarity and Generalization (Tenenbaum) • Integration and Inference (Weiss)


Lecture: 3 hr/week Lab sessions




Multidisciplinary Ability High Problem Solving Approach Med. Problem Solving Methods Med. Experimentation Med. Design Med. Professional Orientation Med.


Leif H. Finkel July 2007


BE526 Neuromorphing: Building Brains in Silicon Credit: 1 course unit Elective course Catalog Description:

We model the structure and function of neural systems in silicon using very large scale integration (VLSI) complementary metal-oxide-semiconductor (CMOS) technology. To build these neuromorphic systems, we proceed from the device level, through the circuit level, to the system level. At the device level, we mimic electrodiffusion of ions through membrane channels with electrodiffusion of electrons through transistor channels. At the circuit level, we derive minimal implementations of synaptic interaction, dendritic integration, and active membrane behavior. At the system level, we synthesize the spatiotemporal dynamics of the cochlea, the retina, and early stages of cortical processing.

Prerequisites:

Students with advanced knowledge in neurobiology but rudimentary knowledge in electrical engineering or vice versa are welcome: Biology students should have BIOL251 Cellular Neurobiology and BIOL451 Systems Neuroscience. Engineering students should have ESE218 Physics and Models of Semiconductor Devices and ESE319 Fundamentals of Solid-State Circuits.


C Mead, Analog VLSI and Neural Systems, Addison-Wesley, 1989 J G Nicholls et al., From Neuron to Brain, Sinauer Associates, 2001


(1) To introduce neurobiologists to the physical constraints on neural computation—like noise, wiring, and energy. (2) To introduce engineers to the unrivaled performance of biological systems—achieved despite physical constraints. (3) To develop physical models of neural computation by emulating the structure as well as the function of the nervous system. These objectives are achieved through analytical (deriving mathematical solutions), computational (simulating device and circuit behavior), and experimental (testing fabricated chips) exercises conducted in groups of two. This course, which is available to advanced undergraduates, develops students’ ability to translate knowledge from one discipline to another and to work in multidisciplinary teams.

Topics Covered:

• Electrodiffusion in liquids and solids: Ion-channels and PN-junctions • Controlling electrodiffusion: MOS transistors • Excitation, inhibition and conduction: Transistor as synapse • Global inhibition: The winner-take-all circuit • Temporal integration: Diode-capacitor dynamics • Spike generation: Sodium channels analogs • Spike-rate adaptation: Potassium channels analogs • Improving spike-timing precision • The cochlea: Morphing mechanical forces and fluid dynamics • The retina: Morphing cell syncytia and neural microcircuits • Analyzing spatiotemporal filtering and adaptation • Silicon neuron arrays: Address-event transceivers • Characterizing variability in silicon neurons • Synchrony: Inhibitory recurrent networks • Multistability: Excitatory recurrent networks


• Self-organization: Layered feedforward networks


Lecture: 3 hr/week Laboratory: 3hr/week

Contribution towards Outcomes (including professional):



Kwabena Boahen May 2004


BE537/CIS537 Biomedical Image Analysis Credit: 1 course unit Elective course Catalog Description

This course covers the fundamentals of advanced quantitative image analysis that apply to all of the major and emerging modalities in biological/biomaterials imaging and in vivo biomedical imaging. While traditional image processing techniques will be discussed to provide context, the emphasis will be on cutting edge aspects of all areas of image analysis (including registration, segmentation, and high-dimensional statistical analysis). Significant coverage of state-of-the-art biomedical research and clinical applications will be incorporated to reinforce the theoretical basis of the analysis methods.

Prerequisites:

Mathematics through multivariate calculus (Math 241), programming experience, as well as some familiarity with linear algebra, basic physics, and statistics.


Course notes, handouts, journal articles Reference Books: Insight into Images: Principles and Practice for Segmentation, Registration, and Image Analysis, T.S. Yoo, A.K. Peters, 2004 Introduction to Applied Mathematics, G. Strang, Wellesley-Cambridge Press, 1986 Human Brain Function, Second Edition: C. J. Price, S. Zeki, J.T.Ashburner, W. D. Penny, K. J. Friston, C. D. Frith, R. J. Dolan, Academic Press, 2003 (available online)

Course objectives:

The goal of this course is to introduce the basic principles of contemporary biomedical image analysis, including the relevant mathematics, statistics, or signal processing as needed for background, and to highlight clinical and basic science applications that draw on these techniques.

Topics Covered:

• Basic image processing and linear operators Pattern theory Segmentation

Basics: edge detection, Bayesian framework, active snakes Geodesic active contours and level sets Active shape and appearance models EM algorithms and Markov random field models

Registration Rigid and Affine methods Deformable registration Non-parametric approaches

Human Brain Mapping Structural morphometry Functional analysis, statistical parametric mapping

Developing image analysis applications with the Insight Toolkit Class/Laboratory Schedule:


Lecture: 3 hr/week

Contribution towards Professional Component 100% Engineering Science Contribution towards Program Outcomes: Multidisciplinary Ability High Problem Solving Approach High Problem Solving Methods High Experimentation Low Design Low Professional Orientation Med Person(s) Preparing Description and Date:

James Gee July 2007


BE540 Biomolecular and Cellular Engineering Credit: 1 course unit Elective course Catalog description:

This course provides an introduction to the quantitative methods used in characterizing and engineering biomolecular properties and cellular behavior, focusing primarily on receptor-mediated phenomena. The thermodynamics and kinetics of protein/ligand binding are covered, with an emphasis on experimental techniques for measuring molecular parameters such as equilibrium affinities, kinetic rate constants, and diffusion coefficients. Approaches for probing and altering these molecular properties of proteins are also described, including site-directed mutagenesis, directed evolution, rational design, and covalent modification. Equilibrium, kinetic, and transport models are used to elucidate the relationships between the aforementioned molecular parameters and cellular processes such as ligand/receptor binding and trafficking, cell adhesion and motility, signal transduction, and gene regulation.

Prerequisites:

Senior BSE standing in BE or CBE – including MATH 241, [BE 324 & BE 350 (as co-requisite) or CBE 350] – or permission of instructor.


None required. All necessary materials will be provided in class. Recommended textbook (in addition to those from the prerequisite courses): D.A. Lauffenburger and J.J. Linderman. Receptors: Models for Binding, Trafficking, and Signaling. New

York: Oxford University Press, 1996. ISBN: 0195106636. Course Objectives:

This course introduces the approaches that are currently used for engineering biomolecular properties and how these properties can, in turn, affect cellular phenomena. The focus is on quantitative experimental methods and mathematical modeling of molecular and cellular processes. By the end of the course, students should be able to: identify crucial molecular parameters involved in cellular events; understand how such parameters can be experimentally measured or manipulated; and, formulate mathematical models that incorporate these molecular parameters and appropriately capture the salient features of the cellular phenomena being analyzed.

Topics Covered:

• Protein biochemistry o Energetics of protein-protein interactions o Equilibrium and kinetic binding models o Deviations from simple monovalent binding models o Experimental methods for measuring constants and coefficients

• Protein engineering o Alanine-scanning mutagenesis to isolate energetic “hot spots” o Covalent modification to alter diffusivity or association/dissociation rates o Electrostatic steering to increase association rates o Directed evolution to alter equilibrium affinity or dissociation rates

• Ligand/receptor binding and trafficking o Effect of diffusion on receptor binding


o Models of endocytosis, recycling, and degradation • Cell adhesion and motility

o Adhesion strength per ligand/receptor bond (Bell model) o Migration models based on adhesion strength o Leukocyte rolling

• Signal transduction o Michaelis-Menten enzyme kinetics o Signal initiation at cell membranes; Signal propagation and amplification o Oscillations o Adaptation models

• Gene regulation o Introduction to non-linear dynamics, stability, and bifurcations o Genetic switches and cell cycle progression


Lecture – 3 hr/week Contribution towards Professional Component:



Multidisciplinary Ability High Problem Solving Approach Med. Problem Solving Methods High Experimentation High Design Low Professional Orientation Med.


Casim Sarkar July 2007


BE546 Biomedical Image Analysis Credit: 1 course unit Elective course Catalog Description: This course covers the fundamentals of advanced quantitative image analysis that apply to all of the major and emerging modalities in biological/biomaterials imaging and in vivo biomedical imaging. While traditional image processing techniques will be discussed to provide context, the emphasis will be on cutting edge aspects of all areas of image analysis (including registration, segmentation, and high-dimensional statistical analysis). Significant coverage of state-of-the-art biomedical research and clinical applications will be incorporated to reinforce the theoretical basis of the analysis methods. Prerequisites: Mathematics through multivariate calculus (Math 241), programming experience, as well as some familiarity with linear algebra, basic physics, and statistics. Textbook(s) and/or other Related Material: Course notes, handouts, journal articles Reference Books: * Insight into Images: Principles and Practice for Segmentation, Registration, and Image Analysis, T.S. Yoo, A.K. Peters, 2004 * Introduction to Applied Mathematics, G. Strang, Wellesley-Cambridge Press, 1986 * Human Brain Function, Second Edition: C. J. Price, S. Zeki, J. T. Ashburner, W. D. Penny, K. J. Friston, C. D. Frith, R. J. Dolan, Academic Press, 2003 (available online) Topics Covered: * Basic image processing and linear operators * Pattern theory * Segmentation o Basics: edge detection, Bayesian framework, active snakes o Geodesic active contours and level sets o Active shape and appearance models o EM algorithms and Markov random field models * Registration o Rigid and Affine methods o Deformable registration o Non-parametric approaches * Human Brain Mapping o Structural morphometry o Functional analysis, statistical parametric mapping


* Developing image analysis applications with the Insight Toolkit Class/Laboratory Schedule: Lecture: 3 hr/week Course Objectives: The goal of this course is to introduce the basic principles of contemporary biomedical image analysis, including the relevant mathematics, statistics, or signal processing as needed for background, and to highlight clinical and basic science applications that draw on these techniques. Contributions towards Professional Component: 100% Engineering Science Contribution towards Program Outcomes: Multidisciplinary Ability: High Problem Solving Approach: Low Problem Solving Methods: Low Experimentation: High Design: Med Professional Orientation: Low Person(s) Preparing Description and Date: James Gee

November 2005


BE552 Cellular Bioengineering Credit: 1 course unit Elective course Catalog description:

The goal of this course is to introduce students to quantitative concepts in understanding and manipulating the behavior of biological cells. We will try to understand the interplay between molecules in cells and cell function. A particular focus is on receptors – cell surface molecules that mediate cell responses. We will also try to understand processes such as adhesion, motility, cytoskeleton, signal transduction, differentiation, and gene regulation.

Prerequisites:

Math through 241; BE350, BE324 as pre- or corequisites; Molecular & cellular biology


Required: Lauffenberger and Linderman’s Receptors ( Oxford, 1993). ISBN 0-19-506466-6. Suggested references: Alberts et al. Molecular Biology of the Cell. 4th Edition. ISBN 0-8153-3218-1. Howard, J. Mechanics and Motor Proteins and the Cytoskeleton. Sinauer Associates, Inc. (2001). ISBN 0-87893-334-4. Magrab, et al. An engineer's guide to Matlab. Prentice Hall (2000). ISBN: 0-13-011335-2.

Course Objectives:

The goal of this course is to introduce engineering concepts in understanding and manipulating the behavior of biological cells, focusing on understanding the interplay between molecules in cells and cell function. In particular, we will explore the use of quantitative approaches to describe cellular processes, as well as modern experimental approaches to characterize and manipulate cells. In this context, we will focus on several topics, including receptor biology, signal transduction, adhesion, cytoskeleton, and genomics.

Topics Covered:

• Receptors • Receptor binding in solution • Receptor binding on a cell surface • Trafficking • Adhesion • Signaling • Motility and Cytoskeletal • Growth and the cell cycle • Differentiation • Gene regulation and genomics • Immune system and therapies • Viruses


Lecture – 3 hr/week





Multidisciplinary Ability High Problem Solving Approach Med. Problem Solving Methods High Experimentation High Design Low Professional Orientation Med.


Dan Hammer July 2007


BE553 Introduction to Tissue Engineering Credit: 1 course unit Elective course Catalog Description:

Principles, Methods, and Applications of Tissue Engineering. Tissue engineering demonstrates enormous potential for improving human health. While there is an extensive body of literature discussing the state of the art of tissue engineering, the majority of this literature is descriptive and does little to address the principles that govern the success or failure of an engineered tissue. This course explores principles of tissue engineering, drawing upon diverse fields such as developmental biology, immunology, cell biology, physiology, transport phenomena, material science, and polymer chemistry. Current and developing methods of tissue engineering as well as specific applications are discussed in the context of these principles.

Prerequisites:

Graduate Standing or instructor’s permission.


Primarily research and reviews articles from scientific journals. Additional materials will be compiled from other texts.

Course Objectives:

This course is an elective for bioengineering and is also offered to Masters and Ph.D. students. The objective of the course is to provide the student with basic tools and skills necessary to model biological systems. The course aims to teach basic skills, and apply them to a range of areas within bioengineering, giving the student a broad overview of the applications of modeling in biology. Subject areas covered in the course will include model selection and validation, statistics, and fundamentals of Matlab.

Topics Covered:

• Natural examples of Tissue Engineering:Embryogenesis and Development; Embryonic and Adult Stem Cells; Cellular differentiation; Remodeling and Wound Healing; Tissue Regeneration

• Factors controlling cell and tissue growth and differentiation: Cell Shape; Growth Factors; ECM; Cell-cell interactions; Mechanical forces; Transport; Gene expression

• Applications of Tissue Engineering. Example applications:Bone, Cartilage,, Small-diameter vascular grafts, Heart tissue, Liver, Islets, Peripheral nerve regeneration


Lecture: 3 hrs/week




Multidisciplinary Ability High Problem Solving Approach Low


Problem Solving Methods Low Experimentation Med. Design Low Professional Orientation Low


Keith Gooch November 2003


BE554 Engineering Biotechnology Cross-listed course with Chemical and Biomolecular Engineering 554 (CBE554). http://www.upenn.edu/registrar/register/PDF/cbe.pdf

http://www.upenn.edu/registrar/register/PDF/cbe.pdf�


BE557 From Cells to Tissue: Engineering Structure and Function Credit: 1 course unit Elective course Catalog description:

The goal of this course is to introduce students to quantitative concepts in understanding and manipulating the behavior of biological cells. We will try to understand the interplay between molecules in cells and cell function. A particular focus is on receptors – cell surface molecules that mediate cell responses. We will also try to understand processes such as adhesion, motility, cytoskeleton, signal transduction, differentiation, and gene regulation.

Prerequisites:

Math through 241; BE350, BE324 as pre- or corequisites; Molecular & cellular biology


Lauffenberger and Linderman’s Receptors (Oxford, 1993). ISBN 0-19-506466-6. Primary literature, which will be provided in class. Suggested references: Alberts et al. Molecular Biology of the Cell, (ISBN: 0815332181) or Pollard’s Cell Biology (ISBN: 0721639976).

Course Objectives:

The goal of this course is to introduce engineering concepts in understanding and manipulating the behavior of biological cells, focusing on understanding the interplay between molecules in cells and cell function. In particular, we will explore the use of quantitative approaches to describe cellular processes, as well as modern experimental approaches to characterize and manipulate cells. In this context, we will focus on several topics, including receptor biology, signal transduction, adhesion, cytoskeleton, and genomics.

Topics Covered:

• Receptors • Receptor binding in solution • Receptor binding on the cell surface • Trafficking • Adhesion • Signaling • Cytoskeletal dynamics • Cytoskeletal mechanics • Cell motility • Cell mechanics and mechanotransduction • Cell phenotypes • Genomics and systems biology


Lecture – 3 hr/week


Chris Chen


July 2007


BE559 Multiscale Modeling of Biological Systems Credit: 1 course unit Elective course Catalog Description:

This course aims to provide theoretical, conceptual, and hands-on modeling experience on three different length and time scales that are crucial to biochemical phenomena in cells and to nanotechnology applications. Special Emphasis will be on cellular signal transduction. 60% lectures, 40% computational laboratory. No programming skills required.

Prerequisites: None* *Undergraduates who have taken BE324 or equivalent courses in Quantum Mechanics and/or Statistical Physics need no permission. Others, email instructor [email protected] for permission.


Course notes, online manuals, journal articles, review articles Reference Textbooks:


BE562 Drug Discovery and Development Cross-listed course with Chemical and Biomolecular Engineering 562 (CBE562). http://www.upenn.edu/registrar/register/PDF/cbe.pdf

http://www.upenn.edu/registrar/register/PDF/cbe.pdf�


BE567 Mathematical & Computational Methods for Modeling Biological Systems Credit: 1 course unit Elective course Catalog Description:

This is an introductory course in mathematical biology. The emphasis will be on the use of mathematical and computational tools for modeling physical phenomena which arise in the study of biological systems. Possible topics include random walk models of polymers, membrane elasticity, electrodiffusion and excitale systems, single-molecule kinetics, and stochastic models of biochemical networks.

Prerequisites:

BE 324 and BE 350


Lecture notes will be provided.

Course Objectives:

This course is an elective for advanced undergraduates and is also offered to masters and Ph.D. students. The objective of the course is to provide the student with basic mathematical and computational tools which are useful for modeling biological systems. The course aims to cover a variety of areas, giving the student a broad overview of the applications of modeling in biology.

Topics Covered:

• Random walk models of polymers • Membrane elasticity • Electrodiffusion and excitable systems. • Single-molecule kinetics • Stochastic models of biological networks


Lecture: 3 hrs/week




Multidisciplinary Ability Problem Solving Approach Problem Solving Methods


John C. Schotland September 2008


BE584 Mathematics of Medical Imaging and Measurement Credit: 1 course unit Elective course Catalog Description:

In the last 25 years there has been a revolution in image reconstruction techniques in fields from astrophysics to electron microscopy and most notably in medical imaging. In each of these fields one would like to have a precise picture of a 2 or 3 dimensional object, which cannot be obtained directly. The data that is accessible is typically some collection of weighted averages. The problem of image reconstruction is to build an object out of the averaged data and then estimate how close the reconstruction is to the actual object. In this course we introduce the mathematical techniques used to model measurements and reconstruct images. As a simple representative case we study transmission X-ray tomography (CT).In this context we cover the basic principles of mathematical analysis, the Fourier transform, interpolation and approximation of functions, sampling theory, digital filtering and noise analysis.

Prerequisites:

Mathematics through multivariate calculus (Math 241), as well as some familiarity with linear algebra and basic physics.


Introduction to the Mathematics of Medical Imaging, by Charles L. Epstein, Prentice Hall, 2003.

Topics Covered:

• Mathematical models and measurement. • Linear equations and an introduction to function spaces. • Integral transforms: the Fourier transform, the Radon transform, the Abel transform, convolution. • Sampling and digitization, interpolation and approximation. • Nyquist's theorem and basic concepts of signal processing. • Implementing shift invariant filters. • Imaging hardware and the basic algorithms of image reconstruction. • Analysis of systematic artifacts. • Introduction to probability and statistics • Analysis of noise in tomography.


Lecture: 3 hr/week

Course Objectives:

The goal of this course is to introduce the mathematical techniques underlying most signal and image processing in a manner that will allow the students to see the big picture. While the course is constructed around the analysis of X-Ray computed tomography, the intention is to provide tools that can be applied to essentially any imaging modality.





Multidisciplinary Ability High Problem Solving Approach High Problem Solving Methods High Experimentation Low Design Low Professional Orientation Low


Charles L. Epstein August 2007


EAS280 Bioengineering in the World Credit: 1 course unit Elective course Catalog Description:

This course will provide Penn undergraduate students with the opportunity to learn fundamental engineering concepts behind a wide-range of bioengineering applications in the world. Students will reinforce their learning of these concepts by teaching them to high school students. For the Fall 2005 semester, this will take place at the Science, Engineering, and Math Academy at University City High School (UCHS). Students will spend a portion of their time teaching at the high school. At UCHS the Penn students will teach the bioengineering topics, relate them to familiar elements of students’ lives, and lead UCHS students in hands-on inquiry based activities. The activities are intended to compliment the curriculum of an elective class recently begun at UCHS. In addition, the Penn students will develop activities for use in future semesters, and will present their new activities to each other in class. The course will be capped by a poster project performed by teams of UPenn and UCHS students.

Prerequisites: None Textbook(s) and/or other required material: Coursepack Course Objectives:

1. Learn and develop effective methods for teaching technical concepts 2. Learn fundamental concepts behind bioengineering applications 3. Discuss ethical questions related to each topic 4. Reinforce their own learning by teaching concepts to high school students

Topics covered

• Principles of teaching science • DNA and Genetics • Gene Therapy • Stem Cells and Neuroengineering • Tissue Engineering • Biomechanical Engineering • Imaging • Medical Devices


Lecture: 3 hr/week


50% Basic science 50% General education / ethics


Multidisciplinary Ability High Problem Solving Approach Low Problem Solving Methods Low


Experimentation Low Design Low Professional Orientation High


Dawn M. Elliott July 2007


EAS545 Engineering Entrepreneurship I See syllabus on Engineering Entrepreneurship site. http://www.seas.upenn.edu/entrepreneurship/eas445-545.php

http://www.seas.upenn.edu/entrepreneurship/eas445-545.php�

abet course descriptions: bioen gineering undergraduate ... · biostatistics: the bare essentials,...

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