# Bioengineering (BE)

**BE 100 Introduction to Bioengineering**

Survey course introducing students to the breadth of bioengineering. Course consists of introductory lectures, guest speakers/panelists, and a series of small assignments that allow students to explore different facets of bioengineering and the Penn Bioengineering program.

Course usually offered in fall term

Corequisites: MATH 104, PHYS 140 or 150.

Activity: Lecture

0.5 Course Units

Notes: Freshmen Only.

**BE 101 Introduction to Bioengineering II**

Introduction to Bioengineering II. Continuation of the freshman introductory bioengineering course. This course introduces students to the design process and emphasizes its role in engineering.

Course usually offered in spring term

Prerequisite: BE 100

Activity: Lecture

0.5 Course Units

Notes: Freshmen Only

**BE 200 Introduction to Biomechanics**

This course investigates the application of statics and strength of materials to soft and hard biologic tissues. The course will cover simple force analyses of the musculoskeletal system and introduces the fundamentals of the mechanics of materials including axial loading, torsion and bending and their application to biomechanics. The lecture and recitation will be complemented with hands-on examples emphasizing connections between theoretical principles and practical applications.

Course usually offered in fall term

Prerequisites: MATH 114, PHYS 140, or PHYS 150

Corequisite: MATH 240

Activity: Lecture

1 Course Unit

**BE 220 Biomaterials**

This course investigates the application of materials science and engineering to biomedical applications, with a focus on polymers, ceramics, and metals. The course will cover concepts related to basic material fabrication and synthesis, structure and property characterization, as well as applications of biomaterials. The lecture and recitation will be complemented with laboratory examples of material assessment and characterization.

Course usually offered in spring term

Prerequisites: BE 200, CHEM 102

Activity: Lecture

1 Course Unit

**BE 225 Technology and Engineering in Medicine**

The course is appropriate for engineering and natural science majors including premeds. The prerequisites will not be waived. This course will provide an examination of technology with emphasis on engineering design and its impact on medicine and health. Planned topics change from year to year and include, for example, cochlear implants and visual sensory rehabilitative devices. The course includes homework and reading assignments. Every student presents a paper on a relevant biomedical technology and the underlying science and engineering design.

One-term course offered either term

Prerequisites: MATH 114, PHYS 140 and 141 or PHYS 150 and 151 or PHYS 170 and 171; sophomore and higher only.

Activity: Seminar

1 Course Unit

**BE 301 Bioengineering Signals and Systems**

Properties of signals and systems; Examples of biological and biomedical signal and systems; Signal operations, continuous and discrete signals; Linear, time invariant systems; Time domain analysis; Systems characterized by linear constant-coefficient differential equations; Fourier analysis with applications to biomedical signals and systems; Introduction to filtering; Sampling and the sampling theorem. Examples vary from year to year, but usually include signals such as the ECG and blood pressure wave, principles of signal coding in the auditory system and cochlear implants, and simple applications in biomedical imaging.

One-term course offered either term

Prerequisites: MATH 241, PHYS 141 OR 151, ENGR 105 can be taken as a prerequisite or corequisite.

Activity: Lecture

1 Course Unit

**BE 305 Engineering Principles of Human Physiology**

This course presents a quantitative, biophysical approach to physiology, focusing on the nervous, cardiovascular, and pulmonary systems. We will also emphasize computational modeling and analysis of physiological systems.

Course usually offered in spring term

Prerequisites: MATH 240 and ENGR 105 (or equivalent).

Activity: Lecture

1 Course Unit

**BE 306 Molecular Physiology and Cellular Engineering from Atoms to Disease**

This course explores physical biology of the cell across several length and timescales, while simultaneously emphasizing molecular specificity and clinical implications such as disease outcome or biomedical applications. The course emphasizes how the basic tools and insights of engineering, physics, chemistry, and mathematics combined with "Big Data" can illuminate the study of molecular and cell biology to make predictive biomedical models and subject them to clinical validation. Drawing on key examples and seminal experiments from the current clinical literature, the course demonstrates how quantitative models can help refine our understanding of existing biological data and also be used to make useful clinical predictions. The course blends traditional models in cell biology with the quantitative approach typical in engineering, in order to introduce the student to both the possibilities and boundaries of the emerging field of physical systems biology. While teaching physical model building in cell biology through a practical, case-study approach, the course explores how quantitative modeling based on engineering principles can be used to build a more profound, intuitive understanding of cell biology. Lab modules will be embedded in the lectures and all labs will be in silico (or computational) in nature.

Course usually offered in fall term

Prerequisites: CHEM 102, MATH 241, PHYS 140,141, BIOL 121

Activity: Lecture

1 Course Unit

**BE 309 Bioengineering Modeling, Analysis and Design Laboratory I**

BE 309 is a one course-unit laboratory course with a focus on combining experimental and mathematical approaches to understand biological systems and solve bioengineering problems. The course content integrates concepts from mathematics, physics, signal analysis, control engineering , mass transport, and heat transfer with applications in physiology and pharmacology. Areas of emphasis are model development and validation, statistical analysis, experimental design, error analysis and uncertainty, and scientific writing.

Course usually offered in fall term

Prerequisites: ENGR 105, PHYS 141 or PHYS 151, MATH 240, BE 200, BE 220, ENM 375 or equivalent.

Activity: Lecture

1 Course Unit

**BE 310 Bioengineeirng Modeling, Analysis and Design Laboratory II**

BE 310 is a one course-unit laboratory course on the design of technology to measure and control biological systems. The course is divided into four modules: (i) microfluidics for point of care diagnostics, (ii) synthetic biology for predicting cellular behavior, (iii) electronics and signal analysis of bioelectrical signals, and (iv) bioanalytical spectroscopy for low-cost diagnostics. Each module will have two components: (i) a series of structured learning exercises to teach key concepts and methods of the topic that we are studying, and (ii) a design challenge, in which the understanding gained in the first component is used to design a solution to an open ended bioengineering challenge.

Course usually offered in spring term

Prerequisites: ENGR 105, PHYS 141,151, BE 220, BIOL 121,123, MATH 240, ENM 375 (or equivalent)

Corequisites: MATH 241, BE 301

Activity: Laboratory

1 Course Unit

**BE 324 Chemical Basis of Bioengineering II**

Advanced topics in physical chemistry including solution and colloid chemistry, electrochemistry, surface phenomena, and macromolecules applied to biological systems.

Course usually offered in fall term

Prerequisites: PHYS 140, 141 or 150, 151, MATH 240, CHEM 101, 102

Activity: Lecture

1 Course Unit

**BE 330 Self Assembly of Soft Materials**

Soft matter is found in diverse applications including sports (helmets & cloths); food (chocolate, egg); consumer products (e.g., lotions and shampoo); and devices (displays, electronics). Whereas solids and liquids are typically hard and crystalline or soft and fluid, respectively, soft matter can exhibit both solid and liquid like behavior. In this class, we investigate the thermodynamic and dynamic principles common to soft matter as well as soft (weak) forces, self-assembly and phase behavior. Classes of matter include colloidal particles, polymers, liquid crystalline molecules, amphiphilic molecules, biomacromolecules/membranes, and food. About four active learning activities will be included.

One-term course offered either term

Also Offered As: MSE 330

Prerequisites: CHEM 102 or equivalent; MSE 220 or BE 220 or introductory physical chemistry course.

Activity: Lecture

1 Course Unit

**BE 350 Introduction to Biotransport Processes**

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

Course usually offered in spring term

Prerequisites: MATH 240, PHYS 140 or 150, BE 200

Activity: Lecture

1 Course Unit

**BE 400 Preceptorship in Clinical Bioengineering**

Introduction to the integration of biomedical engineering in clinical medicine through lectures and a preceptorship with clinical faculty. This course is for BE majors ONLY, with preference given to BSE students.

Course usually offered in spring term

Activity: Lecture

1 Course Unit

Notes: Junior and Senior BE majors only

**BE 455 Continuum Biomechanics**

Continuum mechanics with applications to biological systems. Fundamental engineering conservation laws are introduced and illustrated using biological and non-biological examples. Kinematics of deformation, stress, and conservation of mass, momentum, and energy. Constitutive equations for fluids, solids, and intermediate types of media are described and applied to selected biological examples. Class work is complemented by computational laboratory experiences.

Course usually offered in fall term

Prerequisite: MATH through 241; BE 200 or MEAM 210; BE 350 or MEAM 302

Activity: Lecture

1 Course Unit

**BE 470 Medical Devices**

Lab-based course where students learn the fundamentals of medical device design through hands-on projects using microcontrollers. Students first learn basic design building blocks regularly employed in microcontroller-based medical devices, and then carry out a small design project using those building blocks. Projects are informed by reverse-engineering of competing products, FDA regulations, and marketplace considerations.

Course usually offered in spring term

Prerequisites: Junior or Senior BE Majors only, ENGR 105, permission of the instructor

Activity: Laboratory

1 Course Unit

Notes: Students who have taken ESE 350 or a similar course may not enroll

**BE 480 Introduction to Biomedical Imaging**

Introduction to the mathematical, physical and engineering design principles underlying modern medical imaging systems including x-ray computed tomography, ultrasonic imaging, and magnetic resonance imaging. Mathematical tools including Fourier analysis and the sampling theorem. The Radon transform and related transforms. Filtered backprojection and other reconstruction algorithms. Bloch equations, free induction decay, spin echoes and gradient echoes. Applications include one-dimensional Fourier magnetic resonance imaging, three-dimensional magnetic resonance imaging and slice excitation.

Course usually offered in spring term

Prerequisite: BE 301 or ESE 325

Activity: Lecture

1 Course Unit

**BE 483 Molecular Imaging**

This course will provide a comprehensive survey of modern medical imaging modalities and the emerging field of molecular imaging. The basic principles of X-ray, ultrasound, nuclear imaging, and magnetic resonance imaging will be reviewed. The course will also cover concepts related to 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.

Course usually offered in fall term

Also Offered As: BE 583, MMP 507

Prerequisites: MATH 241, BIOL 215 or BE 305

Activity: Lecture

1 Course Unit

**BE 490 Independent Project in Bioengineering**

An intensive independent study experience on an engineering or biological 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 faculty advisor are required.

One-term course offered either term

Prerequisites: Sophomore, Junior and Senior BE majors only

Activity: Independent Study

1 Course Unit

**BE 492 Independent Project in Bioengineering**

Second semester of an independent project.

One-term course offered either term

Prerequisites: Sophomore, Junior and Senior BE majors only.

Activity: Independent Study

1 Course Unit

**BE 495 Senior Design Project**

Group design projects in various areas of bioengineering. Project ideas are proposed by the students in the Spring semester of the Junior year and refined during the Fall semester. The course guides the students through choosing and understanding an impactful biomedical problem, defining characteristics of a successful design solution to eliminate or mitigate a problem or fulfill a need, identifying and prioritizing constraints, creatively developing potential design solutions, iteratively refining design options, defining and implementing an optimal solution , and evaluating how well the solution fulfills the need. Final oral and written reports are required. Also emphasized are teamwork, project management, time management, regulations/standards, and effective communication.

Course usually offered in fall term

Prerequisite: Seniors in BE or Department Permission

Activity: Lecture

1 Course Unit

**BE 496 Senior Design Project**

Second semester of a two semester design project.

Course usually offered in spring term

Prerequisite: Seniors in BE or Department Permission

Activity: Lecture

1 Course Unit

**BE 497 Senior Thesis in Biomedical Science**

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.

Course usually offered in fall term

Prerequisites: Seniors in BAS or Department Permission.

Activity: Lecture

1 Course Unit

**BE 498 Senior Thesis in Biomedical Science**

Second semester of a year-long project.

Course usually offered in spring term

Prerequisite: Seniors in BAS or Department Permission

Activity: Lecture

1 Course Unit

**BE 502 From Biomedical Science to the Marketplace**

This course explores, through own work (this is, own discovery) the transition from 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, and the FDA process of proving safety and efficacy.

Course usually offered in fall term

Prerequisite: Graduate students or permission of the instructor

Activity: Lecture

1 Course Unit

**BE 504 Biological Data Science II: Data Mining Principles for Epigenomics**

This course will teach upper level undergraduates and graduate students how to answer biological questions by harnessing the wealth of genomic and epigenomic data sets generated by high-throughput sequencing technologies.

Course usually offered in spring term

Prerequisites: Graduate students or permission of the instructor.

Activity: Lecture

1 Course Unit

**BE 510 Biomechanics and Biotransport**

The course is intended as an introduction to continuum mechanics in both solid and fluid media, with special emphasis on the application 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.

Course usually offered in spring term

Prerequisites: MATH 241, BE 200, 350

Activity: Lecture

1 Course Unit

**BE 512 Bioengineering III: Biomaterials**

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 engineering tissue and organs.

Course usually offered in fall term

Prerequisites: General Chemistry, basic biomechanics

Activity: Lecture

1 Course Unit

**BE 514 Rehab Engineering and Design**

Students will learn about problems faced by disabled persons and medical rehabilitation specialists, and how engineering design can be used to solve and ameliorate those problems. The course combines lectures, multiple design projects and exercises, and field trips to clinical rehabilitation facilities. Students will have substantial interaction with clinical faculty, as well as with patients.

Course usually offered in fall term

Also Offered As: IPD 504

Prerequisite: Graduate students or permission of the instructor

Activity: Lecture

1 Course Unit

**BE 515 Bioengineering Case Studies**

This course has the unofficial title "What Makes Medical Technology Work?" We will examine biomedical devices and technologies with significant engineering components for use in breast cancern detection, for minimally invasive treatment of cancer and other disease, and applied neuroscience technologies for rehabilitation. Various factors that determine the success of particular medical systems will be discussed, including the "fit" of the technology with a medical need, testing for safety and efficacy, FDA premarket approval requirements, clinical studies used to assess the technology for evidence-based medicine. The class will examine successful and unsuccessful examples of these technologies. The course will require extensive reading of papers from the professional literature , group presentations and papers. BE seniors and graduate students are encouraged to enroll.

Course usually offered in fall term

Prerequisites: Graduate students or permission of the instructor.

Activity: Lecture

1 Course Unit

**BE 518 Optical Microscopy**

An introduction to the fundamental concepts of optics and microscopy. Geometrical optics: ray tracing, optical elements, imaging systems, optical aberrations. Physical optics: the electromagnetic spectrum, the wave equation, diffraction, interference and interferometers, optical resolution limits, optical coherence, lasers. Microscopy methods: phase contrast, differential interference contrast, fluorescence microscopy, confocal microscopy, multiphoton microscopy, optical coherence tomography, superresolution microscopy.

Course usually offered in fall term

Prerequisites: MATH 240 or equivalent. Graduate students or permission of the instructor.

Activity: Lecture

1 Course Unit

**BE 521 Brain-Computer Interfaces**

The course is geared to advanced undergraduate 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 signals, recording, analysis, classification, modulation, and fundamental principles of Brain-Machine Interfaces. The course will be based upon twice weekly lectures and "hands-on" weekly assignments that teach basic signal recording, feature extraction, classification and practical implementation in clinical systems. Assignments will build incrementally toward constructing a complete, functional BMI system. Fundamental concepts in neurosignals, hardware and software will be reinforced by practical examples and in-depth study. Guest lecturers and demonstrations will supplement regular lectures.

Course usually offered in spring term

Also Offered As: NGG 521

Prerequisites: BE 301 (Signals and Systems) or equivalent, computer programming experience, preferably MATLAB (e.g., as used the BE labs, BE 310). Some basic neuroscience background (e.g. BIOL 215, BE 305, INSC 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.

Activity: Lecture

1 Course Unit

**BE 530 Theoretical Neuroscience.**

This course will develop theoretical and computational approaches to structural and functional organization in the brain. The course will cover: (i) the basic biophysics of neural responses, (ii) neural coding and decoding with an emphasis on sensory systems, (iii) approaches to the study of networks of neurons, (iv) models of adaptation, learning and memory, (v) models of decision making, and (vi) ideas that address why the brain is organized the way that it is. The course will be appropriate for advanced undergraduates and beginning graduate students.

Course usually offered in spring term

Prerequisites: Knowledge of multivariable calculus, linear algebra and differential equations is required (except by permission of the instructor). Prior exposure to neuroscience and/or Matlab programming will be helpful.

Activity: Lecture

1 Course Unit

**BE 537 Biomedical Image Analysis**

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.

Course usually offered in fall term

Also Offered As: CIS 537

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

Activity: Lecture

1 Course Unit

**BE 540 Biomolecular and Cellular Engineering**

This course will introduce concepts and methods for the quantitative understanding of molecular and cellular phenomena. Topics include molecular recognition, receptor-ligand binding, viral infection, signal transduction, cell adhesion, motility, and cytoskeletal dynamics. The course requires mathematics at the level of differential equations, and some knowledge of Matlab programming. A basic knowledge of cell biology is suggested, although not required.

One-term course offered either term

Also Offered As: CBE 540

Prerequisites: Graduate students or permission of the instructor.

Activity: Lecture

1 Course Unit

**BE 541 Engineering and Biological Principles in Cancer**

This course provides an integrative framework and provides a quantitative foundation for understanding molecular and cellular mechanisms in cancer. The topics are divided into three classes: (1) the biological basis of cancer; (2) cancer systems biology; and (3) multiscale cancer modeling. Emphasis is placed on quantitative models and paradigms and on integrating bioengineering principles with cancer biology.

Course usually offered in spring term

Also Offered As: CBE 541

Prerequisite: Seniors in BE or permission of the instructor

Activity: Lecture

1 Course Unit

**BE 546 Fundamental Techniques of Imaging I**

This course covers the fundamentals of modern techniques in biological and in vivo biomedical imaging. This practical course consists of a series of hands-on lab exercises, covering major imaging modalities, but also extends to non-radiology modalities of interest in biological, pathological or animal imaging (e.g., optical imaging). Topics include x-ray, mammography, CT, proton therapy, radiation safety and brachytherapy. The emphasis will be on hands-on aspects of all areas of imaging and imaging analysis. Small groups of students will be led by a faculty member with technical assistance as appropriate.

Course usually offered in spring term

Prerequisites: Graduate students or permission of the instructor.

Activity: Lecture

1 Course Unit

**BE 547 Fundamental Techniques of Imaging 2 (BE 483/583 or MMP 507 preferred).**

This laboratory course covers the fundamentals of modern medical imaging techniques. Students will participate in a series of hands-on exercises, covering the principals of X-ray imaging, CT imaging, photoacoustic imaging, diffusion tensor imaging, localized magnetic resonance (MR) spectroscopy, MR contrast agents, diffuse optical spectroscopy, and bioluminescence imaging. Each lab is designed to reinforce and expand upon material taught in BE483/583 Molecular Imaging and MMP507 Physics of Medical Imaging

Course usually offered in spring term

Prerequisites: Graduate students or permission of the instructor.

Activity: Lecture

1 Course Unit

**BE 550 Continuum Tissue Mechanics**

This course introduces tensor calculus and continuum mechanics, with a focus on finite-deformation behavior of biological tissues including skin, tendon/ligament, cartilage, bone, blood vessels, nerves.

Course usually offered in spring term

Prerequisite: Senior/Graduate Student in Bioengineering or permission of the instructor

Activity: Lecture

1 Course Unit

**BE 551 Biomicrofluidics**

The focus of this course is on microfluidics for biomedical applications. Topics to be covered in the first half of this course include microscale phenomena, small-scale fabrication techniques, and sensing technologies that are often leveraged in the development of microfluidic systems for the study of biomolecules, cells, tissues, and organs in living biological systems. In the second half of this course, strong emphasis will be placed on the application of microfluidics in cell biology, bioanalytical chemistry, molecular biology, tissue engineering, and drug discovery.

Course usually offered in fall term

Prerequisites: Experience with an undergraduate level fluid mechanics course is preferred. Examples of relevant SEAS courses include BE 350 (Biotransport), CBE 350 (Fluid Mechanics), and MEAM 302 (Fluid Mechanics).

Activity: Lecture

1 Course Unit

**BE 553 Principles, Methods, and Applications of Tissue Engineering**

Tissue engineering demonstrates enormous potential for improving human health. This course explores principles of tissue engineering, drawing upon diverse fields such as developmental biology, cell biology, physiology, transport phenomena, material science, and polymer chemistry. Current and developing methods of tissue engineering, as well as specific applications will be discussed in the context of these principles. A significant component of the course will involve review of current literature within this developing field.

Course usually offered in spring term

Prerequisite: Graduate Standing or instructor's permission

Activity: Lecture

1 Course Unit

**BE 554 Engineering Biotechnology.**

Advanced study of re DNA techniques; bioreactor design for bacteria, mammalian and insect culture; separation methods; chromatography; drug and cell delivery systems; gene therapy; and diagnostics.

Course usually offered in fall term

Also Offered As: CBE 554

Prerequisites: Graduate standing, Senior standing, Admitted Junior submatriculants

Activity: Lecture

1 Course Unit

**BE 555 Nanoscale Systems Biology**

Nano-science and engineering approaches to systems in biology are of growing importance. They extend from novel methods, especially microscopies that invite innovation to mathematical and/or computational modeling which incorporates the physics and chemistry of small scale biology. Proteins and DNA, for example, are highly specialized polymers that interact, catalyze, stretch and bend, move, and/or store information. Membranes are also used extensively by cells to isolate, adhere, deform, and regulate reactions. In this course, students will become familiar with cell & molecular biology and nano-biotechnology through an emphasis on nano-methods, membranes, molecular machines, and 'polymers' - from the quantitative perspectives of thermodynamics, statistical physics, and mechanics. We specifically elaborate ideas of energetics, fluctuations and noise, force, kinetics, diffusion, etc. on the nano- thru micro- scale, drawing from very recent examples in the literature. Laboratory experiments will provide hands-on exposure to microscopies in a biological context (eg. fluorescence down to nano-scale, AFM), physical methods (eg. micromanipulation, tracking virus-scale particles or quantum dots), and numerical problems in applied biophysics, chemistry, and engineering. A key goal of the course is to familiarize students with the concepts and technology (plus their limitations) as being employed in current research problems in nanoscale systems biology, extending to nanobiotechnology.

Course usually offered in fall term

Also Offered As: CBE 555

Prerequisites: Background in Biology, Physics, Chemistry or Engineering with coursework in Thermodynamics or permission of the instructor.

Activity: Lecture

1 Course Unit

**BE 558 Principles of Biological Fabrication**

BE 558 introduces methodological approaches that are currently used for the de novo construction of biological molecules - primarily, nucleic acids and proteins - and how to use these molecules to engineer the properties of cells and intact tissue. By the end of the semester, students should (i) possess a molecular-scale understanding of key biological synthesis (ii) and assembly processes, (ii) gain an intuition for how to create novel (iii) methodologies based on these existing processes, and (iii) appreciate (iv) the drivers of technology adoption (e.g. cost, time, ease, and (v) reproducibility). Throughout the course, we will place the material in context of applications in bioengineering and human health, including: protein engineering, drug discovery, synthetic biology & optogenetics, bio-inspired materials, and bio-electronic devices.

Course offered fall; odd-numbered years

Prerequisites: Graduate standing or permission of the instructor. Undergraduate level biology, physics and chemistry.

Activity: Lecture

1 Course Unit

**BE 559 Multiscale Modeling of Chemical Systems**

This course provides theoretical, conceptual, and hands-on modeling experience on three different length and time scales - (1) electronic structure (A, ps); (2) molecular mechanics (100A, ns); and (3) deterministic and stochastic approaches for microscale systems (um, sec). Students will gain hands-on experience, i.e., running codes on real applications together with the following theoretical formalisms: molecular dynamics, Monte Carlo, free energy methods, deterministic and stochastic modeling.

Course not offered every year

Also Offered As: CBE 559

Prerequisites: Undergraduate courses in numeral analysis and statistical mechanics.

Activity: Lecture

1 Course Unit

**BE 561 Musculoskeletal Biology and Bioengineering**

The goal of this course is to educate students in core principles and expose them to cutting-edge research in musculoskeletal biology and bioengineering through (1) lectures covering the basic engineering principles, biological fundamentals, and clinical practices involved in the function, repair, and regeneration of the musculoskeletal tissues; (2) critical review and presentation by student groups of recent and seminal publications in the field related to the basic science, translation, and clinical practice of musculoskeletal biology and bioengineering, with discussion input by faculty members with relevant expertise. This course will place an emphasis on delivering multidisciplinary knowledge of cell and molecular biology, mechanics, material science, imaging, and clinical medicine as it relates to the field of musculoskeletal bioengineering and science.

Course offered fall; odd-numbered years

Prerequisites: Graduate student standing in Engineering and/or CAMB. Undergraduate students with permission of the instructor.

Activity: Lecture

1 Course Unit

**BE 562 Drug Discovery and Development**

Intro to Drug Discovery; Overview of Pharmaceutical Industry and Drug Development Costs, Timelines; High Throughput Screening (HTS): Assay Design and Sensitivity Solid Phase Synthesis and Combinatorial Chemistry; Enzyme Kinetics; Fluorescence, Linearity, Inner-filter effect, quenching; Time dynamics of a Michaelis-Menton Reaction; Competitive Inhibitor; FLINT, FRET, TRF, FP, SPA, alpha-screen; Enzyme HTS (protease); Cell based screening; Fura-2 ratio, loading signaling; Gfpcalmodulin-gfp integrated calcium response; Estrogen/ERE-Luc HTS; Problems with cell based screening (toxicity, permeability, nonspecificity); Instrumentation, Robotics/Automation; Z-factor; SAR, Positioning Scanning; Microarray HTS; IC50, % Conversion in HTS and IC50, Assay Optimization.

Course usually offered in spring term

Also Offered As: CBE 562

Prerequisite: Graduate standing or permission of the instructor

Activity: Lecture

1 Course Unit

**BE 566 Network Neuroscience**

The human brain produces complex functions using a range of system components over varying temporal and spatial scales. These components are couples together by heterogeneous interactions, forming an intricate information-processing network. In this course, we will cover the use of network science in understanding such large-scale and neuronal-level brain circuitry.

Course usually offered in spring term

Also Offered As: ESE 566

Prerequisites: Graduate standing or permission of the instructor. Experience with Linear Algebra and MATLAB.

Activity: Lecture

1 Course Unit

**BE 567 Mathematical Computation Methods for Modeling Biological Systems**

This course will cover topics in systems biology at the molecular/cellular scale. The emphasis will be on quantitative aspects of molecular biology, with possible subjects including probabilistic aspects of DNA replication, transcription, translation, as well as gene regulatory networks and signaling. The class will involve analyzing and simulating models of biological behavior using MATLAB.

One-term course offered either term

Also Offered As: GCB 567

Prerequisites: Graduate standing or permission of the instructor.

Activity: Lecture

1 Course Unit

**BE 568 Causality for Medicine and Biology**

The goal of this course is to introduce students to the analysis of data which aims at understanding causal relations. Within biomedical research there are randomized experiments that effortlessly get at certain kinds of causality but generally only allow low-dimensional probing. There are also observational studies that generally do not meaningfully get at causality. The field of econometrics has worked out a great deal of approaches that meaningfully allow the estimation of causality without randomized experiments. This set of techniques is largely unknown in much of biology and medicine. We will thus review the econometric approaches with an eye towards applications to biology and medical problems. We will also review ways of infusing these techniques with machine learning approaches to obtain more meaningful estimates.

One-term course offered either term

Activity: Lecture

1 Course Unit

**BE 570 Biomechatronics**

Mechatronics is the combination of mechanical, electrical and computer engineering principles in the design of electromechanical systems. Biomechatronics is the application of these principles to human biology and includes orthopaedic, hearing, respiratory, vision and cardiovascular applications. In this hands-on, project-based course, these biomechatronic systems will be explored. Students will learn the basic mechanical and electrical elements needed to complete a biomechatronic design challenge including basic circuits, design considerations, material fabrication, microcontrollers and mechanisms (e.g. converting rotational motion into linear motion). Students will carry out a final design project utilizing these building blocks.

Course usually offered in fall term

Prerequisites: A first course in programming (Matlab and/or C++ preferred) , Senior standing in BE or permission of the instructor

Activity: Lecture

1 Course Unit

**BE 581 Techniques of Magnetic Resonance Imaging**

Detailed introduction to physics and engineering of magnetic resonance imaging as applied to medical diagnosis. Covered are: Bloch equations, spatial encoding principles, Fourier analysis, spin relaxation, imaging pulse sequences and pulse design, contrast mechanisms,imaging, induced magnetism, flow encoding, diffusion and perfusion, high-field MRI and a discussion of the most relevant clinical applications.

Course offered spring; odd-numbered years

Also Offered As: BMB 581

Prerequisites: Graduate standing or permission of the instructor.

Activity: Lecture

1 Course Unit

**BE 583 Molecular Imaging**

This course will provide a comprehensive survey of modern medical imaging modalities and the emerging field of molecular imaging. The basic principles of X-ray, ultrasound, nuclear imaging, and magnetic resonance imaging will be reviewed. The course will also cover concepts related to 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.

Course usually offered in fall term

Also Offered As: BE 483, MMP 507

Prerequisites: MATH 241, BIOL 215 or BE 305

Activity: Lecture

1 Course Unit

**BE 584 Mathematics of Medical Imaging and Measurements**

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 which is accesible is typically some collection of 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.

Course not offered every year

Prerequisites: MATH 314, MATH 508 and 509 or permission of the instructor.

Activity: Lecture

1 Course Unit

**BE 597 Master's Thesis Research**

For students working on an advanced research program leading to the completion of master's thesis.

One-term course offered either term

Activity: Masters Thesis

1 Course Unit

**BE 599 Master's Independent Study**

The purpose of BE 599 is to allow a student to create a customized curriculum to study material beyond or outside the scope of our standard BE course offerings. Independent study is NOT a research or design project, it is a one-on-one or small-group course with a professor. The course should require an effort comparable to that of a regular course, about 10-12 hours per week. A paper or presentation is required

One-term course offered either term

Activity: Independent Study

1 Course Unit

**BE 608 Translational Therapeutics**

To provide an in-depth view of the process by which scientific discoveries are commercialized. This course covers discovery in the laboratory , technology transfer, regulatory, financial, and managerial issues involved in moving a technology from the lab into the market place. The course contents fall into three broad categories: (1) examples of scientific discoveries that are candidates for commercialization, (2) fundamental elements of technology transfer, such as intellectual property protection and licensing, and (3) aspects of commercialization, such as regulatory approval, financing, and startup formation. In using this structure, the course provides parallel coverage of both the science and the commercialization process, in such a way that the elements of one contribute to the student's experience in learning the other.

Course usually offered in spring term

Also Offered As: MTR 620

Prerequisite: Engineering students only or permission of the instructor

Activity: Lecture

1 Course Unit

**BE 640 The Extracellular Matrix**

This course is geared towards first and second year graduate students in BGS/CAMB and SEAS/BE with an interest in the interface of extracellular matrix (ECM) cell biology and biomechanics. Students will learn about the ECM and adhesion receptors and their impact on the cytoskeleton and signaling, as well as fundamental concepts in biomechanics and engineered materials. We will discuss how these topics can inform the study of cell biology, physiology and disease . An additional objective of the course is to give students experience in leading critical discussions and writing manuscript reviews. Invited outside speakers will complement the strengths of the Penn faculty.

Course offered spring; even-numbered years

Prerequisites: BIOM 600. Graduate students only.

Activity: Lecture

1 Course Unit

**BE 650 Advanced Biomedical Imaging Applications**

The course will cover a broad range of biomedical imaging technologies including X-ray, MRI, US, molecular and optical imaging. The curriculum will focus on the design of biomedical imaging based research studies spanning from basic technology development through clinical trials. This discussion oriented course is expected prepare students for integrating imaging technology and biomedical concepts to answer biological and medical questions.

Course usually offered in fall term

Activity: Lecture

1 Course Unit

**BE 662 Advanced Molecular Thermodynamics**

This course begins with a brief review of classical thermodynamics, including the development of Maxwell relationships and stability analysis. The remainder of the course develops the fundamental framework of statistical mechanics, then reviews various related topics including ideal and interacting gases, Einstein and Debye models of crystals, lattice models of liquids, and the basics of distribution function theory.

Course usually offered in spring term

Also Offered As: CBE 618

Prerequisites: Graduate Standing or permission of the instructor.

Activity: Lecture

1 Course Unit

**BE 699 Bioengineering Seminar**

This is a required course for BE PhD candidates and involves attendance at seminars related to bioengineering topics, which can be either within the departmental seminar series or through other relevant seminar series on campus. The goal is to expose students to a breadth of bioengineering topics beyond their specific dissertation work. Students are required to submit summaries of the attended seminars to receive course credit.

One-term course offered either term

Activity: Seminar

0.5 Course Units

**BE 711 Integrative Plant and Animal Mechanobiology**

This course aims to provide students with an understanding of biomechanics that spans the plant and animal kingdoms, with the goal of emphasizing principles common to both. Modules include 1) Plant and Animal Cell Biology; 2) Solid, Fluid, and Transport Mechanics; and 3) Integrating Biology and Mechanics - Big Questions. Most lectures will be given by Penn faculty, although selected topics (particularly in plant biology and mechanics) will be covered by faculty at other sites through lectures broadcase remotely. The Penn director will be present at all sessions of the class.

Course usually offered in fall term

Corequisite: Undergraduates require special permission

Activity: Lecture

1 Course Unit

**BE 899 PhD Independent Study**

The purpose of BE 899 is to allow a student to create a customized curriculum to study material beyond or outside the scope of our standard BE course offerings. Rather than a research or design project, BE 899 is a one-on-one or small-group course with a professor. Students must submit a proposal outlining the study area along with the professor's approval. A paper or presentation is required.

One-term course offered either term

Activity: Independent Study

1 Course Unit

Notes: Graduate Students Only

**BE 990 Masters Thesis**

For Master's students who have completed the course requirements for the Master's degree and are strictly working to complete the Master's Thesis leading to the completion of a Master's degree. Permission Required.

One-term course offered either term

Activity: Masters Thesis

1 Course Unit

**BE 995 Doctoral Dissertation Status**

Ph.D. Students register for Doctoral Dissertation Status after they have advanced to Ph.D. candidacy by completing the Candidacy Exam which consists of the Dissertation Proposal Defense.. Permission required

One-term course offered either term

Prerequisites: For Ph.D. Candidates only

Activity: Dissertation

1 Course Unit

**BE 999 Thesis/Dissertation Research**

For students working on an advanced research program leading to the completion of master's thesis or Ph.D. dissertation requirements.

One-term course offered either term

Activity: Independent Study

1 Course Unit