Bioengineering Courses at a US University, Study notes of Quantum Mechanics

Download Bioengineering Courses at a US University and more Study notes Quantum Mechanics in PDF only on Docsity! Bioengineering (BE)           1 BIOENGINEERING (BE) BE 1000 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. Fall Corequisites: MATH 1400, PHYS 0140 0.5 Course Units BE 2000 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. Fall Prerequisite: (MATH 1410 OR PHYS 0140 OR PHYS 0150) AND MATH 2400 Corequisite: MATH 2400 1 Course Unit BE 2200 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. Spring Prerequisite: BE 2000 AND CHEM 1021 1 Course Unit BE 2250 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. Fall or Spring Prerequisite: MATH 1410 AND (PHYS 0140 OR PHYS 0150 OR PHYS 0170) AND (PHYS 0141 OR PHYS 0151 OR PHYS 0171) 1 Course Unit BE 2700 Bioengineering Laboratory Principles This course will cover a variety of bioengineering laboratory principles and techniques including data collection, analysis and reporting. Students will explore tools related to mechanics, materials and electronics with applications in the bioengineering field. Spring 1 Course Unit BE 3010 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. Fall or Spring Prerequisite: MATH 2410 AND (PHYS 0141 OR PHYS 0151) AND ENGR 1050 1 Course Unit BE 3050 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. Spring 1 Course Unit BE 3060 Cellular Engineering The biological cell is a complex machine and its function is at the root of all physiology and many pathologies. Recent advances in molecular and cell biology enable the redesign of cell function. This course aims to develop a quantitative understanding of cell function, and how we might go about changing cell function through intelligent redesign. The course covers topics ranging from receptor binding and endocytosis, cell adhesion and motility, cell function in the immune system, systems and synthetic biology, genetic knockdown and manipulation using CRISPR and gene therapy, and strategies for immunotherapy including chimeric antigen receptor therapy (carT). Fall Prerequisite: CHEM 1021 AND MATH 2410 AND (PHYS 0140 OR PHYS 0150 OR PHYS 0170) AND (PHYS 0141 OR PHYS 0151 OR PHYS 0171) AND BIOL 1121 1 Course Unit BE 3090 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. Fall Prerequisite: ENGR 1050 AND (PHYS 0141 OR PHYS 0151 OR PHYS 0171) AND MATH 2400 AND BE 2000 AND BE 2200 AND ENM 3750 1 Course Unit 2022-23 Catalog | Generated 12/01/22 2        Bioengineering (BE) BE 3100 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. Spring Prerequisite: ENGR 1050 AND (PHYS 0141 OR PHYS 0151 OR PHYS 0171) AND BE 2200 AND BIOL 1121 AND BIOL 1123 AND ENM 3750 AND MATH 2410 AND BE 3010 Corequisites: BE 3010, MATH 2410 1 Course Unit BE 3300 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. Fall Also Offered As: MSE 3300 Prerequisite: CHEM 1021 OR MSE 2200 OR BE 2200 1 Course Unit BE 3500 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. Spring Prerequisite: MATH 2400 AND (PHYS 0140 OR PHYS 0150 OR PHYS 0170) AND BE 2000 1 Course Unit BE 4000 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. Spring 1 Course Unit BE 4700 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. Prerequisite: Junior or Senior BE Majors only. Students who have taken ESE 3500 or a similar course may not enroll. Permission of instructor required if course prerequisites not met. Spring 1 Course Unit BE 4720 Medical Device Development Students will learn the process of developing medical devices that fulfill unmet patient needs. Students will be equipped with an understanding of what is required to lead a startup venture in medical devices including regulatory, legal, fundraising, team building and leadership. In lab, students will develop a proof-of-concept prototype device. Students will pitch their ideas to real med tech investors . The successful student will leave the class with the knowledge, skills and confidence to lead a startup venture in medical devices. If desired by the student, the proof-of- concept device can be used as the basis for their senior design project. Junior standing in Bioengineering or permission of the instructor if course prerequisite is not met. Spring 1 Course Unit BE 4800 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. Spring Prerequisite: BE 3010 OR ESE 3250 1 Course Unit BE 4830 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. Fall Prerequisite: MATH 2410 OR BIOL 2310 OR BE 3050 1 Course Unit BE 4900 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. Sophomore, Junior and Senior BE majors only. Fall or Spring 1 Course Unit BE 4920 Independent Project in Bioengineering Second semester of an independent project. Sophomore, Junior and Senior BE majors only. Fall or Spring 1 Course Unit 2022-23 Catalog | Generated 12/01/22 Bioengineering (BE)           5 BE 5300 Theoretical and Computational 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. A knowledge of multi-variable 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. Spring Also Offered As: NGG 5940, NRSC 5585, PHYS 5585, PSYC 5390 1 Course Unit BE 5370 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. Prerequisite: Mathematics through multivariate calculus (MATH 2410), programming experience, as well as some familiarity with linear algebra, basic physics, and statistics. Fall or Spring Also Offered As: CIS 5370, MPHY 6090 1 Course Unit BE 5400 Principles of Molecular and Cellular Bioengineering 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. 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 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 bioengineering 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. Worksheets will be integral to this course. Recitation will comprise of biweekly illustrations of problems and concepts from the worksheets and biweekly quizzes Fall or Spring Also Offered As: CBE 5400 1 Course Unit BE 5410 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. Prerequisite: Seniors in BE or permission of the instructor. Spring Also Offered As: CBE 5410 1 Course Unit BE 5460 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. Graduate students or permission of the instructor. Spring 1 Course Unit 2022-23 Catalog | Generated 12/01/22 6        Bioengineering (BE) BE 5470 Fundamental Techniques of Imaging 2 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 BE 4830/BE 5830 Molecular Imaging and MMP 5070 Physics of Medical Imaging Graduate students or permission of the instructor. Spring 1 Course Unit BE 5500 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. Senior/Graduate Student in Bioengineering or permission of the instructor. Spring 1 Course Unit BE 5510 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. Prereqisite: Experience with an undergraduate level fluid mechanics course is preferred. Examples of relevant SEAS courses include BE 3500 (Biotransport), CBE 3500 (Fuild Mechanics), and MEAM 3020 Fluid Mechanics). Fall 1 Course Unit BE 5530 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. Graduate Standing or instructor's permission. Spring 1 Course Unit BE 5540 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. Spring Also Offered As: CBE 5540 1 Course Unit BE 5550 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. Prerequisite: Background in Biology, Physics, Chemistry or Engineering with coursework in Thermodynamics or permission of the instructor. Fall Also Offered As: CBE 5550, MEAM 5550 1 Course Unit BE 5580 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. Graduate standing or permission of the instructor. Undergraduate level biology, physics and chemistry. Fall, odd numbered years only 1 Course Unit BE 5590 Multiscale Modeling of Chemical and Biological 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, multiscale modeling. Prerequisite: Undergraduate courses in numerical analysis and physical chemistry. Not Offered Every Year Also Offered As: CBE 5590, SCMP 5590 1 Course Unit 2022-23 Catalog | Generated 12/01/22 Bioengineering (BE)           7 BE 5610 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. Graduate student standing in Engineering and/or CAMB. Undergraduate students with permission of the instructor. Fall, odd numbered years only 1 Course Unit BE 5620 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. Fall Also Offered As: CBE 5620 1 Course Unit BE 5650 Developmental Engineering of Tissues This course discusses systems biology approaches to understanding tissue development, homeostasis, and organogenesis. Emphasis is placed on modern technologies, models, and approaches to understanding collective cell behaviors that sculpt tissue form and function, placing developmental principles within an engineering framework. We will consider morphogenetic, mechanobiology, and micro- engineering/sensing analyses. Senior Standing in Bioengineering or permission of the instructor. In keeping with modern graduate-level engineering classes, this course will assume some basic knowledge of coding and/or willingness to learn coding practices. The course will not attempt to serve as a comprehensive introduction to developmental biology (CAMB 5110: Principles of Development is a recommended potential companion course). However, your success in the course will not require familiarity with developmental biology. Fall 1 Course Unit BE 5660 Networked 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. Prerequisite: Graduate standing or permission of the instructor. Experience with Linear Algebra and MATLAB. Spring Also Offered As: ESE 5660 1 Course Unit BE 5670 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. Prereqisite: Graduate standing or permission of the instructor. Fall or Spring Also Offered As: AMCS 5670, GCB 5670 1 Course Unit BE 5680 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. Fall or Spring 1 Course Unit BE 5690 Systems Biology of Cell Signaling Behavior This course discusses the principles of cell signaling and cell decisions. We start from a molecular description of cell signaling components. The course builds towards understanding how their interactions govern cell and tissue behavior and how these processes can breakdown in disease. We conclude with a survey of modern approaches to analyze and manipulate signaling networks to study and control biological systems. Graduate, Junior or Senior standing in Bioengineering or permission of the instructor. Spring 1 Course Unit 2022-23 Catalog | Generated 12/01/22