Course Catalog

| Bioinformatics | Chemical Engineering | Computer Science | Digital systems | Disaster Mangement | Electrical and Computer Engineering | Engineering |
Mechanical Engineering |

Bioinformatics (BioE)

BioE 439 Biostatistics
This course is designed for bioinformatics students. The industry standard in statistical software, which will be taught in this course, is R and S++. The application of basic algorithms and the theory behind the statistical analysis will be covered. Extensive examples and small projects will be used in order to learn how to use R and Java to accomplish bioinformatics tasks. Topics covered also include: sample analysis, interval-censored survival data analysis, longitudinal data analysis, multivariate analysis, theory of distributions in statistics, and experiment and design.

BioE 480 Intro to Bioinformatics
This is the general introductory course in bioinformatics. The main techniques covered in this course are related to sequence analysis and include: gene identification, genome sequencing, sequence comparison, database searching, and phylogenetic tree analysis. Molecular biology is also introduced including: the central dogma of molecular biology, DNA sequences, and protein sequences. Students will be introduced to all of the biology necessary to understand the applications of bioinformatics algorithms and software taught in this course.

BioE 483 Molecular Modeling in Bioinformatics
This course teaches the students how to elucidate the structure of a biopolymer using related modeling tools and algorithms in bioinformatics. The targeted areas are in protein structure modeling, structure based drug design, drug screening, cheminformatics, and binding prediction. Students will learn the principles and applications of each of the algorithms and programs used in structure modeling.

BioE 582 Computational Genomics
This course focuses on the study and implementation of methods for data mining and machine learning. Particular attention is given to those methods which are useful in the analysis of gene expression data from genome comparisons, microarray experiments, and protein function prediction. Students will gain practical skills in addition to theoretical knowledge, especially in the area of microarray data analysis. We will use the R and Bioconductor packages for the microarray data analysis and MATLAB for other implementation tasks. All three tools are widely used in industry and academia.

BioE 594 Biodatabase
Databases are used extensively in biological/medical data storage and analysis. Specific types of databases that are common and widely used include gene and protein sequence, protein structure, protein interaction, metabolic pathways, compounds and drugs, literature, medical records, and many others. Mastering the basic principles and design methods of databases is fundamental in bioinformatics training. In this course we are introduce how database design and application are used in the biomedical field. Students are not required to have prior database knowledge, but should be familiar with the basics of computer science. Fluency in at least one programming language (as well as cursory knowledge of at least one other), familiarity with common operating systems such as Windows XP and Unix/Linux, and experience using online biological and medical databases such as NCBI's PubMed and BLAST, PFAM, SWISS-PROT, etc. are basic requirements.

BioE 594 Biodatamining
Datamining of biological and medical data is an emerging area that is becoming increasingly popular in bioinformatics. Biological and medical phenomenons are being studied with high throughput methods that generate large amount of data. To understand the complicated and highly interactive nature of biology from this data, advanced datamining methods and algorithms are required. This course will focus on the basic knowledge of datamining and how it is applied and modified in order to adjust to special characteristics of biological and medical datamining.

BioE 594 Imaging Informatics
Imaging informatics is an emerging area from the intersection of biological science, medical practice, health care, computer algorithms, and information sciences. Naturally, it belongs to bioengineering, although it is developed and practiced in many other departments and hospitals, especially in the field of radiology.

BioE 594 Systems Biology and Omics Data
Description coming soon.

Chemical Engineering (ChE)

ChE 450 Air Pollution Engineering. (Also listed as ME 450).
4 Hours.
Same as Mechanical Engineering 450. Environmental aspects of combustion processes, pollutant formation. Control of pollutants and particulates. Air quality control. Fundamentals of combustion.

ChE 494 Computational Molecular Modeling (Also listed as ME 494).
4 Hours.
May be repeated for credit. Students may register for more than one section per term. Systematic study of selected topics in chemical engineering theory and practice.

ChE 512 Microhydrodynamics, Diffusion, and Membrane Transport.
4 Hours.
Theoretical and numerical fluid mechanics of microstructure: potential flow and virtual mass, quasistatic versus transient Stokes flow, integral theorems, multipole expansions, singularity solutions, fluctuations, and current applications.

ME 501 Advanced Thermodynamics.
4 hours.
Thermodynamic laws of closed and open systems; exergy destruction; property relations, single phase systems, Gibbs-Duhem relations, multiphase systems, equilibrium; engineering applications.

MEng 410 Transport Phenomena.
4 Hours.
Continuum theory of momentum, energy, and mass transfer. Viscous behavior of fluids, thermal conduction and convection, and diffusion. Multivariable transport problems and macroscopic balance analysis. Students will use vector and tensor mathematics and solutions methods for partial differential equations.

MEng 411 Non-Newtonian Fluid Mechanics.
4 Hours.
Fluid mechanics and transport processes involving non-Newtonian fluids. Purely viscous and viscoelastic behavior. Viscometric functions and rheometry. Heat and mass transfer in non-Newtonian fluids.

Computer Science (CS)

Note: Courses under this rubric were previously listed under Electrical Engineering and Computer Science (EECS).

CS 475 Object-Oriented Programming.
4 Hours.
No credit given if the student has credit in CS 340 or CS 474. OO Paradigm: classes, messages, methods, variables, inheritance, polymorphism; the C++ and Java languages. Extensive computer use required.

CS 493 Advanced Computer Architecture.
Previously listed as EECS 466. Credit is not given for CS 493 if the student has credit in CS 466. Heterogeneous, adaptable multicore systems can be considered the established trend in modern computing architectures. Silicon resources are increasingly abundant, runtime reconfigurable elements can be combined together with heterogeneous processing elements and many cores on a chip by processor designers. Such architectures provide important improvements in system performance, but also pose new research questions to be answered. The Advanced Computer Architecture class will guide you through this scenario. The first part will be used to poses the bases to understand modern computer architecture while in the second part of the class modern multicore architectures and reconfigurable (e.g. FPGA-based architectures) computing systems will be presented. Finally, the last part of the class will be used to present hot-topics in the research area of advanced computer architecture. These topics will include: self-aware adaptive systems, heterogeneous multicore architecture and OS for multicore computing systems.

CS 493 Introduction to Database Management and Databases
4 Hours.
There are two “targets” of this course: – breadth, the intention of which is to help you familiarize yourselves with as many topics of relevance for the field of the database management; – depth, the intention of which is to enable you to develop capabilities that are expected (at least as an ”entry-level”) from a database person when admitted for a position at any enterprize. Towards this, after a brief introduction to the field, we will firstly present many of the abstractions and concepts that are relevant for a database designer to know and understand. The goal of this part course is for you to understand some essential aspects of the data modeling, representation and querying. Subsequently, we will cover topics that are relevant for the Database Management systems-knowledge, in a manner that will enable you to understand what are the main aspects of the databases as software products.

Disaster Management

MEng 405 Foundations of Emergency Management and Continuity Programs
4 Hours.
Foundations of Emergency Management introduces the scope, objectives, and principles of emergency management. It is intended to be an introductory course with topics including the history of emergency management in the United States; the profession of emergency management; the roles of federal, state and local emergency management agencies; national response concepts; and preparedness, response, recovery and mitigation strategies. A project is required.

MEng 406 Critical Infrastructure & Resource Protection Planning
4 hours.
This course is designed to enable students to formulate protection policies regarding the leading critical infrastructure sectors in the U.S. (e.g., energy, water, telecommunications, Internet, etc.), by understanding the regulatory and technical architecture issues behind them. The course introduces students to the tools used to identify critical strategies for the protection of private and public sector infrastructure. Students learn how to evaluate the vulnerability and risks regarding each, and how to formulate protection strategies. A project is required.

MEng 505 Environmental Risk Assessment and Management
4 Hours.
This course familiarizes students with methods of assessing health and business risks related to man-made or natural events. Emphasis is given on decision tree methodologies for facilitating the analysis and identification of optimum remedial risk management alternatives. Characterization of hazard sources, exposure pathways, and vulnerability analysis would be presented. A project is required.

MEng 506 Disaster Response and Recovery Operations
4 Hours.
This course discusses the basic framework of emergency management known as “concept of operations” (CONOPS), provides a structure for creating CONOPS and discusses examples of the appropriate use of CONOPS. Students learn to create CONOPS for selected man made of natural events, provide guidance on the roles and responsibilities of fictional participants and define program organization and management approaches. This course is taught in collaboration with subject matter specialists from the Argonne National Laboratory and business continuity executives. A project is required.

MEng 594 Advanced Special Topics
4 Hours.
Subject matter may vary from term to term and section to section, depending on the interests and background of the class.

Electrical and Computer Engineering (ECE)

Note: Courses under this rubric were previously listed under Electrical Engineering and Computer Science (EECS).

ECE 401 Quasi-Static Electric and Magnetic Fields
4 Hours.
Previously listed as EECS 401. Static electric and magnetic fields. Material description, boundary value problems. Field energy, its conversion and scaling laws. Quasi-static fields, field diffusion, eddy currents, energy loses.

ECE 423 Electromagnetic Compatibility
4 Hours.
Previously listed as EECS 423. EMC requirements for electronic systems. Nonideal behavior of components. Radiated and conducted emissions. Susceptibility. Coupling and shielding. Electrostatic discharge. System design for EMS.

ECE 432 Digital Communications
4 Hours.
Previously listed as EECS 432. Source coding, quantization, signal representation, channel noise, optimum signal reception, digital modulation: ASK, PSK, FSK, MSK, M-ary modulation. Probability of error. Inter-symbol interference.

ECE 434 Multimedia Sysyems
4 Hours.
Extensive computer use required. Multimedia systems; compression standards; asynchronous transfer mode; Internet; wireless networks; television; videoconferencing; telephony; applications.

ECE 435 Wireless Communication Networks
4 hours.
Radio technology fundamentals; channel and propagation models; multiple access technologies (CDMA, OFDM); wireless mobile communication fundamentals; modulation and detection; source and channel coding; antennas, MIMO and smart antenna systems

ECE 465 Digital Systems Design
4 Hours.
Topics include: Digital Design process, Boolean Algebra, Gate and basic function design, Elementary sequential blocks, Latches and Flip-Flops, RT-level combinational and sequential Memory Devices, Manual synthesis of combinational blocks, Manual synthesis of sequential blocks, RT level synthesis, VHDL syntax and semantics, Design with VHDL, VHDL simulation and synthesis, Datapath-Controller partitioning, Complete RT-level simulation and synthesis. [Certificate Program]

ECE 491 Analog Circuits and Networks
4 Hours.
Matrix methods. Elements of graph theory. Topological network analysis.
Multiport network analysis. Sensitivity analysis. Analysis and design be
S-parameters. Feedback. Models of active devices.

ECE 491 Computer Networks
4 Hours.
Computer networking fundamentals through the review of the Internet architecture; Link layer protocols and technologies: Medium Access protocols, switching, Ethernet and VLANs; IP protocol and routing algorithms, UDP/IP and TCP/IP; wireless networks and mobility management; Latest trends in networking (e.g., cloud networks, software defined networks (SDN) and Internet of Things (IoT)).

ECE 491 Image Processing and Computer Vision for Medical Applications
4 Hours.
This course aims at teaching methods for the processing and analysis of digital images, with focus on applications to medical images. An important aspect of the course is that students will be introduced to the field of scientific research and will be provided with the essential skills necessary to understand and present research papers pertaining to the subject matter being studied.

Topics include image enhancement in spatial and frequency domains; image restoration and reconstruction; color image processing; wavelet analysis; image compression, segmentation, and description; object recognition. Programming will be done in MATLAB and project documentation will be written in LaTex.

ECE 491 Introduction to Radio Frequency Circuits
4 Hours.
 This course teaches the design and analysis of radio circuits that operate at frequencies up to 300 MHz (lumped-element, not transmission line analysis). Topics include: narrowband transistor amplifiers, impedance matching networks, oscillators, mixers, amplitude and frequency modulation/demodulation, phase-lock loop circuits, amplifier noise and stability analysis. [Course Syllabus]

ECE 491 Transmission Lines for Communication and Power
4 Hours.
Time and frequency domain analyses of transmission lines. Smith chart.
Impedance matching. Wideband systems. Waveguiding systems. Line
parameters. Artificial lines. Circuit theory for guiding systems.
Scattering matrix. Three-phase systems.

ECE 491 Wave Propagation and Communication Links
4 Hours.
Previously listed as EECS 422. Antennas and propagation; wave propagation over ground, through ionosphere and troposphere; diversity principles; propagation effects in microwave systems, satellite, space, and radar links.

ECE 520 Electromagnetic Field Theory
4 hours.
Previously listed as EECS 520. Maxwells equations. Potentials. Constitutive relations. Special relativity. Boundary conditions. Green's functions. Polarization. Radiation from antennas and charged particles. Waveguides and resonators. Exterior boundary-value problems.

ECE 526 Electromagnetic Scattering
4 hours.
Previously listed as EECS 526. Exact solutions of exterior boundary-value problems. Low-frequency expansions. High-frequency methods, including geometrical and physical theories of diffraction. Hybrid techniques. Radar cross-sections.

ECE 527 Optical Electronics
4 hours.
Optical resonators. Radiation and atomic systems. Laser oscillation. Laser systems. Parametric amplification and oscillation. Phase conjugate optics. Modulation, detection and noise. Prerequisite(s): ECE 520

ECE 535 Advanced Wireless Communication Networks
4 hours
(This course is being updated and will be offered in Fall 2015.)

ECE 594 Advanced Digital Systems Design - Instructor video introduction
4 hours.
Topics include: Advanced VHDL Topics, System Design at the Register Transfer Level, FPGA-based Design, Top-down RTL design, Control-data Partitioning, RTL Timing, Control-Data Synchronization, Handshaking Methods, Busses and Bus Level Communications, Design of Configurable Cores, RTL Design of Processors, Developing Testbenches, Component Testing, Built-In Self-Test, Memory BIST, Board Testing. [Certificate Program]

ECE 594 Artificial Neural Networks
4 hours. Introduction to artificial neural networks. Linear models for regression and classification. Single layer neural networks. Multilayer neural networks. Radial basis function networks. Self-organizing maps. Advanced topics including support vector machines, Hopfield networks and Boltzmann machines.

ECE 594 Embedded Processors & Architectures
4 hours.
Topics include: RTL design with Verilog, Embedded Design, Altera ModelSim and Quartus II, Computer Arithmetic, Floating Point Arithmetic, Floating Point Processors, Instruction Set Architecture, Processor Architectures, Single Cycle, Multi-cycle, Pipelining, Memory Interfacing, Processor Interfaces, Interrupts, DMA, Embedded Processors, Altera Nios II and Avalon Switch Fabric, SOPC Embedded Hardware Configuration Tool, IDE Embedded Software Design Tool. [Course Information - PDF] [Course Syllabus] [Certificate Program]

ECE 594 Methodologies for System Level Designs & Modeling
4 hours.
Topics include: System Level Design, Abstract RTL, Object Oriented C++ Logic Modeling and Simulation, RT level modeling with C++, RT Level Description with SystemC, SystemC Language Structure, Abstract Communications, SystemC Channels, System Level Interfaces (TLM-2.0), Transport interfaces and use of TLM 2.0 sockets, Direct Memory Interface, System Level Architectures, Message Passing, Pipelining, Interconnects, Hardware / software interface. [Certificate Program]

Engineering (Engr)

Engr 494 Engineering Management and Commercialization of Intellectual Property.
4 Hours.
This course will present the major dimensions of intellectual property management, focusing on the following issues: establishing a competitive position of intellectual property related products; the valuation of intellectual property; the development and implementation of intellectual property protection strategies; the management of key corporate resources needed to implement intellectual property management strategies; and international and regulatory issues associated with the implementation of intellectual property asset management.

Engineering (MEng)

MEng 400 Engineering Law.
4 Hours.
Overview of the legal system. Legal principles affecting the engineering profession. Professional ethics in engineering. Intellectual property law. Basic contract and tort principles. Environmental law.

MEng 401 Engineering Management.
4 hours.
Theory, strategy, and tactics of the use of project management including project planning, matrix management concept, and team meetings

MEng 402 Intellectual Property Law.
4 hours.
Patent, copyright, trade secret, mask work, and cyber-squatting legal and procedural principles; protection for novel software, biotech inventions, and business methods; and trademark protection for domain names.

MEng 403 Reliability Engineering.
4 hours.
Probability overview; statistics overview; system reliability modeling and prediction-static methods; system reliability modeling and prediction-dynamic methods; maintainability and availability; reliability optimization; and risk analysis.

MEng 436 Wireless Data.
4 hours. Review of communication fundamentals; 802.11 family of standards
(a/g/n/ac): PHY layer, MAC layer, interoperability and coexistence, transmit beamforming, MU-MIMO; cognitive radio; UWB communications; wireless ad hoc sensor networks; RFIDs; ZigBee

Mechanical Engineering (ME)

ME 450 Air Pollution Engineering. (Also listed as ChE 450)
4 Hours.
Environmental aspects of combustion processes, pollutant formation. Control of pollutants and particulates. Air quality control. Fundamentals of combustion.

ME 494 Computational Molecular Modeling (Also listed as ChE 494)
4 Hours.
May be repeated for credit. Students may register for more than one section per term. Systematic study of selected topics in chemical engineering theory and practice.

ME 501 Advanced Thermodynamics.
4 hours.
Thermodynamic laws of closed and open systems; exergy destruction; property relations, single phase systems, Gibbs-Duhem relations, multiphase systems, equilibrium; engineering applications.

ME 533 Plasma Engineering
4 hours.
Plasma-assisted applications. Kinetic theory of non-equilibrium processes. Plasma dynamics. Elementary processes-collisions. Diffusion and transport. Chemical reactions and surface treatment. Particle and energy balance in plasmas. Prerequisite(s): ME 433 or consent of the instructor.

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