Fall 2009 Special Topics Courses

ENG BE 500 A1 - Computational Biology: Genomes, Networks, Evolution (Galagan)

                               ***CANCELLED*** Replaced with ENG BE 562 A1

In this course we cover the algorithmic and machine learning foundations of computational biology, combining theory with practice.  We study principles of algorithm design and core methods in computational biology, we provide an introduction of important problems in
computational biology, and we provide hands on experience analyzing large-scale biological data sets.

Topics include:
* Genomes: sequence analysis, gene finding, RNA folding, genome alignment and assembly, database search;
* Networks: gene expression analysis, regulatory motifs prediction, regulatory network prediction and analysis, computational metabolic network modeling, and systems biology
* Evolution: comparative genomics, phylogenetics, genome evolution and rearrangement, molecular evolutionary theory.

These topics are grounded in fundamental algorithmic techniques including: dynamic programming, hashing, Gibbs sampling, Expectation Maximization, hidden Markov models, stochastic context-free grammars, graph analysis, flux balance analysis, and Bayesian networks.

4 credits TR 11-12:30

Note: This course satisfies the Biomedical, Engineering and/or Professional Elective requirement.

ENG BE 500 A2 - Human Physiology (Goldstein)

This course will provide an in-depth introduction to basic concepts and fundamental principles of human pathophysiology for advanced undergraduate and graduate students in engineering and other non-medical disciplines. Pathophysiology bridges basic science and clinical practice with an emphasis on integrated mechanistic understanding of the molecular, structural, and functional alterations in cells, tissues, and organ systems that underlie human disease. The course will follow the classical division between general pathology (molecular, cellualr, and tissue reactions) and systemic pathology (integrated tissue and organ system responses). An organizing didactic framework will emphasize integrative cause (etiology), mechanistic sequence (pathogenesis), structural and functional derangement (morphology), and clinical manifestation. The first half of the course will focus on fundamental concepts of cellular homeostasis; general cellular responses (adaptation, injury, cell death) induced by stress, injurious stimuli, and disease; and molecular disease. The second half of the course will follow an integrative systemic approach to illustrate the pathophysiology underpinnings of the 10 leading causes of death in the US. Cardiac, neoplastic, cerebrovascular, traumatic, neurodegenerative, diabetic, pulmonary, renal, and infectious diseases will be presented and explored in detail. Application of fundamental concepts from engineering, physics, chemistry, and molecular cell biology will be highlighted as the basis for rational therapeutic design.

4 credits TR 4-6

Note: This course satisfies the Professional elective requirement.

ENG BE 700 A1 - Single Molecule Approaches to Biophysics and Bioengineering - Fundamentals and Applications ( Meller)  ***CANCELLED***

                                                                    Replaced with ENG BE 705 A1

The emergence of single-molecule (SM) methods in biology and bioengineering in the past decade have revolutionized the way scientists approach the molecular biology of the cell. The ability to directly probe biomolecular process in real-time, in their native cellular environment, revealed the mechanism of fundamental processes in biology with unprecedented detail and accuracy. As SM methods are refined they are increasingly recruited by bioengineers to invent the future platforms for molecular diagnostics and analytical detection.

This course covers experimental methods for investigating the molecular machinery of a living cell in vitro and in live cells, and novel tools for sensing biomolecules and their application in biotechnology.
Fundamental principles underlying fluorescence of single molecules, force measurements of biomolecules, ion channel kinetics, and stochastic sensing, will be covered in the context of relevant biological and biotechnological examples. There will be an emphasis on fundamental physical concepts underlying these systems, coming from statistical mechanics of soft matter.

4 credits MW 4-6

ENG EC 500 A1 - Fundamentals of Nanomaterials and Nanotechnology (Altug/Swan)    ***CANCELLED*** Replaced with ENG EC 481 A1

Nanotechnology encompasses the understanding and manipulation of matter with at least one characteristic dimension measured in nanometers with novel size dependent physical properties as a result. This course will explore the electronic and optical properties of material at the nanoscale and applications of nano-scale devices. The parallels between light and electron confinement will be emphasized, e.g. in terms of normal modes, resonances and resonators, and the dispersion of light and electrons as affected by the periodicity of crystals and photonics crystals. Wave-mechanics and electromagnetics will be reviewed and used to understand confinement and energy quantization.  Nano-devices such as carbon nanotube transistors, nano-resonators, nanocavity lasers, nano-biosensor and their applications will be discussed.  Fabrication using top-down and bottom-up methods will be discussed, as well as characterization using scanning probe methods, electron microscopy, and spectroscopic techniques.

4 credits TR 12-2

NOTE: This course is an undergraduate level course and is not open to graduate level students. This course will fulfill the mandatory 400 level nanotechnology course for a concentration in nanotechnology.

ENG EC/MS 500 A2 - Electronic Optical and Magnetic Properties of Materials (Moustakas)    ***CANCELLED*** Replaced with ENG EC/MS 577 A1

This course in intended to develop an in depth knowledge of solid state concepts that are important for students in the areas of material science and  electrical engineering. Specifically,  this course  focuses on the study of different apsect of solid state physics necessary to study technologically relevant crytalline and amorphous systems.  Particular enphasis is placed on the study of the crystal structure, crystal diffraction and the related techniques used as diagnostic tools; the electronic, thermal, optical and magnetic properties of material systems important for electronics and photonics device applications. Furthermore the course will also  consider the theory of superconductivity, the chemistry aspcts of solid state materials and will provide an introduction to solid state biophysics. This course complements EC 574 (Physics of semiconductor material) and EC575 (semiconductor devices) with its focus on technologically relevant structural, optical, thermal and magnetic material properties. The course makes use of some of the formalism developed in EC574 which is therefore recommended as a prerequisite.

ENG EC 700 A1 - Design and Testing for Distributed Software-Intensive System (Brackett) *** CANCELLED*** Replaced with ENG EC 728 A1

Systems and software requirements definition, architectural software design, object-oriented software development and testing, with emphasis on distributed software-intensive systems (i.e., software for telecommunications, real-time control systems, etc.).   Individual project involving requirements definition and a team project involving object-oriented software architecture, design and testing.

4 credits MW 4-6

ENG ME 700 A1 - Advanced Topics in Mechanical Engineering: Biomed Ultrasound (Porter)  ***CANCELLED***

This course will cover scientific principles and concepts that lay the foundation for diagnostic and therapeutic applications of ultrasound in medicine. Fundamentals will include wave propagation and attenuation in biological materials, transducer design and operation, the design and characterization of ultrasound contrast agents, and the bioeffects of propagating acoustic waves and acoustic cavitation.
Applications of ultrasound technology to be discussed include harmonic imaging, targeted ultrasound contrast agents, and ultrasound-mediated drug and gene delivery.
4 credits MW 12-2