ENG BE 700 A1 - Brain Machine Interfacing (Ritt)

Brain Machine Interfacing will be a graduate level course emphasizing major approaches and central challenges in BMI applications. Topics range from interfacing with neural tissue, including electrode designs, types of neural signals, and issues of biocompatibility and signal degradation; decoding approaches, including motor control applications, signal to noise requirements, and effects of training and plasticity; and neural stimulation, including choice of peripheral vs. central targets, consequences of topographic organization, types of perceptual responses, and limits to control of distributed systems. To follow rapid changes in the field, course materials will be drawn primarily from research literature. In addition to readings, discussions and computational exercises, students will complete a final project.

4 credits TR 2-4

ENG BE 700 A1 - The Cell as a Machine (Zaman)

The goals of this course are to provide a working understanding of the basic cell functions and the physical and chemical principles underlying them. In practical terms, we will attempt to solve a number of important problems relevant to replication, transcription, translation, translocation, motility, and other important functions using a quantitative engineering approach. For each section in the course, we will merge fundamental physical and mechanical framework with relevant biological information with a particular physiological processes at those length-scales.

Permission of Instructor required
4 credits TR 5-7 pm

ENG BE 500 A1 - Systems Biology of Human Disease (Kasif)

This course will train students to apply or develop new computational network and machine learning concepts to probe into the systems biology of disease.

The course will cover computational frameworks such as biological networks (including metabolic, regulatory and signal transduction networks), microarray analysis, proteomic analysis, next. generation sequencing, imaging, machine learning, genetics, pathway analysis and other technologies to medical diseases initially focusing on clinical problems such as cancer, diabetes, inflammation and aging.

The course is aimed at seniors and graduate students in biomedical engineering or bioinformatics. However, students from other disciplines ranging from medicine and biology to physics or computer science can attend the class with some prerequisites.

4 credits MW 2-4 pm

NOTE: This course satisfies the Professional elective requirement only

ENG BE 500 A3 - Structure and Function of the Extracellular Matrix (Suki)

This is an introductory course dealing with the detailed structure of the basic units of the extracellular matrix including collagen, elastin, microfibrils and proteoglycans as well as the functional properties of these molecules. The focus is mostly on how the structure of these components determine the functional properties such as elasticity at different scales from molecule to fibrils to organ level behavior. The biological role of these components and their interaction with cells is also covered. Interaction of enzymes and the matrix in the presence of mechanical forces is discussed. Mathematical modeling is applied at various length scales of the extracellular matrix that provides quantitative understanding of the structure and function relationship. Special topics include how diseases affect extracellular matrix in the lung, cartilage and vasculature. The relevance of the properties of native extracellular matrix for tissue engineering is also discussed.

4 credits MW 2-4 pm

NOTE: This course satisfies the Professional/Engineering/Biomedical Elective requirements.

ENG EC 500 A1 - Introduction to Computational Computer Vision (Tannenbaum)

We will introduce the students to the area of computer vision with an emphasis on computations and problem solving. Applications will be given to autonomous vehicles, tracking, robotics, and image-guided surgery. The Project is an essential part of the course. The students will be required to choose a topic in computer vision, and work out a computer implementation of their idea. This may involve the implementation of a smoothing filter, segmentation method, and edge detector. This will allow students to have hands-on experience in understanding and implementing a given computer vision algorithm.

Requirements: Basic course in signal processing.
Knowledge of some programming language (Matlab or C/C++ or FORTRAN).

4 credits TR 10 am -12 pm

ENG ME 500 A1 - Principles of Biological Physics (Schneider)

Did Albert Einstein contribute to the understanding of life?

Applying physical concepts and technologies to "living matter" is still at is beginning. However, many exciting discoveries have been made. From Single Molecules Mechanics, Biomembranes to the Swimming of individual Bacteria or the design of NMR-PET tubes to image the entire human body and our brain in action.

In this course I raise the question: Where do we stand in understanding the laws of the living using the laws of physics? Each part of the course will not only consist of the facts to the particular topic, but also on a critical discussion on the major flaws of the common textbook explanations of life.

Major topics will be: The physics of nerves, life in a shell (membrane biophysics), cell mechanics, cell adhesion, life under flow, microfluidics, blood clotting etc. A thorough introduction to polymer physics and classical thermodynamics including the role of A. Einstein in biological physics will be given.

4 credits MW 2 pm - 4 pm

ENG EC 700 C3 - Sensor Networks and Cooperative Control (Cassandras)

This is a course for graduate students interested in the state of the art in the theory and applications of sensor networks and cooperative control, emphasizing the interconnection between the two. The purpose is to learn about advanced methodologies used in these areas and about open research problems and to critically review and present papers from the very recent literature. Students will develop the ability to conceptualize cutting-edge research issues in the sensor network and cooperative control domain, and to formulate problems for potential research projects.

Prerequisites: EK 500 or equivalent, SE 501 or equivalent, SE 524 or equivalent
Students undertake a course project and deliver a final report.
4 credits MW 12 pm -2 pm
Meets with ENG SE 700 C3

ENG SE 700 C3 - Sensor Networks and Cooperative Control (Cassandras)

This is a course for graduate students interested in the state of the art in the theory and applications of sensor networks and cooperative control, emphasizing the interconnection between the two. The purpose is to learn about advanced methodologies used in these areas and about open research problems and to critically review and present papers from the very recent literature. Students will develop the ability to conceptualize cutting-edge research issues in the sensor network and cooperative control domain, and to formulate problems for potential research projects.
Prerequisites: EK 500 or equivalent, SE 501 or equivalent, SE 524 or equivalent
VAR (2 or 4) credits: 2 credits normally awarded. 4 credits awarded to students interested in undertaking a course project and delivering a final report. First-year SE students may enroll in this course under the Division’s Research Rotation system. The course will count as one rotation.

VAR credits MW 12 pm -2 pm

ENG BE 500 A1 - Epigenomics: Off the Information Highway (C. Smith)

The Human Genome Project provided robust genetic approaches for finding the cause(s) of rare single gene diseases, but not complex common diseases or even normal phenotypes in eukaryotes. Complex characteristics have strong genetic and environmental components that interact. This course focuses on epigenomics and complexity - the interactions between the genome and the environment, and the methods used to study these interactions at the DNA, RNA, and protein level. The course will cover types, biochemical basis, biological consequences, and approaches to discovery, measurements and understanding, and integrating environmental and gene interactions.

4 credits TR 10am-12pm

ENG BE 500 A3 - Mechanics and Thermodynamics of Cell Structure and Chemical Interactions (Evans)

An engineering foundation course in chemical thermodynamics applied to molecular structures and processes important in the biology, physiology, and mechanics of living organisms.

Meets with ENG ME/MS 505

4 credits MW 12-2 pm

ENG BE 500 A4 - Next Generation Sequencing (Kasif/Meller)

Sequencing and comparative analyses of human genome sequences, as well as other genomes form the basis to address questions such as: what makes us human? what specific genomic markers make cancer cells resistant to specific drugs? what are the causes of anti-biotic resistance in microbes? what portion of the genome is transcribed in a disease population vs normal populations? Next Generation Sequencing (NGS) is driving personalized medicine and other applications in biomedical science and engineering. In this course we will review the foundations of the field, current and emerging single molecule DNA sequencing techniques, through an introduction to the analytical tools to analyze NGS Data, and finally discussing clinical applications focusing on cancer.The course will involve bi-weekly homework assignments that include theoretical analysis and modeling, working with multiple analysis tools for NGS data including assembly, re-sequencing, alignments, RNA-seq, ChIP-seq, DNA methylation, mutation analysis and detection, copy number variation detection, and their applications to cancer.

4 credits TR 4-6 pm

NOTE: This course satisfies the Professional/Engineering/Biomedical elective requirements

ENG BE 700 A1 - The Cell as a Machine (Zaman)

The goals of this course are to provide a working understanding of the basic cell functions and the physical and chemical principles underlying them. In practical terms, we will attempt to solve a number of important problems relevant to replication, transcription, translation, translocation, motility, and other important functions using a quantitative engineering approach. For each section in the course, we will merge fundamental physical and mechanical framework with relevant biological information with a particular physiological processes at those length-scales.

Permission of Instructor required
4 credits TR 5-7 pm

ENG EC 500 A1 - Cybersecurity (Starobinski)

Fundamentals of security related to computers and computer networks. Social engineering, including ethics, identity and authentication, privacy, biometrics, and attacks based on psychology. Hardware and operating system security related to access control, exploits and disk forensics. Wireless and wire network security at the physical, network and application layers. Theoretical lessons are augmented with case studies and demonstrative experimental labs.

4 cr MW 10am - 12pm

ENG BE 500 A1 - Systems Biology of Human Disease (Kasif)

This course will train students to apply or develop new computational network and machine learning concepts to probe into the systems biology of disease.

The course will cover computational frameworks such as biological networks (including metabolic, regulatory and signal transduction networks), microarray analysis, proteomic analysis, next. generation sequencing, imaging, machine learning, genetics, pathway analysis and other technologies to medical diseases initially focusing on clinical problems such as cancer, diabetes, inflammation and aging.

The course is aimed at seniors and graduate students in biomedical engineering or bioinformatics. However, students from other disciplines ranging from medicine and biology to physics or computer science can attend the class with some prerequisites.

4 credits M 1-5 pm

NOTE: This course satisfies the Professional elective requirement only

ENG BE 500 A2 - Epigenomics: Off the Information Highway (C. Smith)

****CANCELLED****

The Human Genome Project provided robust genetic approaches for finding the cause(s) of rare single gene diseases, but not complex common diseases or even normal phenotypes in eukaryotes. Complex characteristics have strong genetic and environmental components that interact. This course focuses on epigenomics and complexity - the interactions between the genome and the environment, and the methods used to study these interactions at the DNA, RNA, and protein level. The course will cover types, biochemical basis, biological consequences, and approaches to discovery, measurements and understanding, and integrating environmental and gene interactions.

4 credits ARR

ENG BE 700 A1 - Nanomedicine: Principles and Applications (Cabodi)

Nanomedicine is a rapidly growing field that exploits the novel properties at the nanoscale to advance the study of human biology and the practice of medicine. This course develops understanding of fundamental nanoscience and the synthesis and characterization of nanomaterials, coupled with applications for detection and treatment of pathogenic, cancerous, and cardiovascular diseases. Students analyze and develop research ideas, hypotheses and experimental designs through proposal writing and literature review. Lectures are led by rotating faculty with expertise in core subject areas: nanoparticle drug delivery and imaging; microfluidic diagnostics; label-free sensing and mass spectrometry for biomarker discovery; and nanofabricated substrates and porous media for cellular studies.

2 credits R 4-6 pm

ENG ME 500 A1 - Principles of Biological Physics (Schneider)

Did Albert Einstein contribute to the understanding of life?

Applying physical concepts and technologies to „living matter“ is still at is beginning. However, many exciting discoveries have been made. From Single Molecules Mechanics, Biomembranes to the Swimming of individual Bacteria or the design of NMR-PET tubes to image the entire human body and our brain in action.    

In this course I raise the question: Where do we stand in understanding the laws of the living using the laws of physics? Each part of the course will not only consist of the facts to the particular topic, but also on a critical discussion on the major flaws of the common textbook explanations of life.

Major topics will be: The physics of nerves, life in a shell (membrane biophysics), cell mechanics, cell adhesion, life under flow, microfluidics, blood clotting etc. A thorough introduction to polymer physics and classical thermodynamics including the role of A. Einstein in biological physics will be given.

4 credits MW 10 am - 12 pm

ENG ME 500 A2 - Viscous Flow (Grace)

This course begins with a review of the fundamental conservation and constitutive equations governing fluid mechanics.  Solutions methods including exact solutions of the viscous Navier-Stokes equations, similarity solutions, and thin shear layer approximations will be covered. Topics that will be explored include boundary layer theory, creeping flows, jets and wakes, hydrodynamic instability and transition to turbulence, microfluidics and the Reynolds-averaged Navier-Stokes equations and turbulence modeling.

4 credits TR 12-2 pm