General Elective

MATH 503 / APPLIED MATHEMATICS I**Sınıf:** **Credit:** 3**Precondition:**

Linear algebra: Vector and inner product spaces, linear operators, eigenvalue problems; Vector calculus: Review of differential and integral calculus, divergence and Stokes' theorems. Ordinary differential equations: Linear equations, Sturm-Liouville theory and orthogonal functions, system of linear equations; Methods of mathematics for science and engineering students.

MATH 504 / NUMERICAL METHODS I**Sınıf:** **Credit:** 3**Precondition:**

A graduate level introduction to matrix-based computing. Stable and efficient algorithms for linear equations, least squares and eigenvalue problems. Both direct and iterative methods are considered and MATLAB is used as a computing environment.

MATH 506 / NUMERICAL METHODS II**Sınıf:** **Credit:** 3**Precondition:**

Development and analysis of numerical methods for ODEs, an introduction to numerical optimization methods, and an introduction to random numbers and Monte Carlo simulations. The course starts with a short survey of numerical methods for ODEs. The related topics include stability, consistency, convergence and the issue of stiffness. Then it moves to computational techniques for optimization problems arising in science and engineering. Finally, it discusses random numbers and Monte Carlo simulations. The course combines the theory and applications (such as programming in MATLAB) with the emphasis on algorithms and their mathematical analysis.

PHYS 509 / CONDENSED MATTER PHYSICS I**Sınıf:** **Credit:** 3**Precondition:** PHYS. 203 or consent of the instructor

Free electron theory of metals. Crystal lattices. Reciprocal lattice. Classification of Bravais lattices. X-ray diffraction and the determination of crystal structures. Electrons in a periodic potential. Tight binding method. Band structures. Semi-classical theory of conduction in metals. Fermi surface. Surface effects.

PHYS 510 / CONDENSED MATTER PHYSICS II**Sınıf:** **Credit:** 3**Precondition:**

Classification of solids. Theory of harmonic crystals. Phonons and phonon dispersion relations. Anharmonic effects in crystals. Phonons in metals. Dielectric properties of insulators. Semiconductors. Diamagnetism and paramagnetism. Electron interactions and magnetic structure. Magnetic ordering. Superconductivity.

CHBI 503 / ADVANCED THERMODYNAMICS**Sınıf:** **Credit:** 3**Precondition:**

Classical thermodynamics: enthalpy, entropy, free energies, equilibria; introduction to statistical thermodynamics to describe the properties of materials; kinetic processes; diffusion of mass, heat, energy; fundamentals of rate processes in materials, kinetics of transformations.

CHBI 505 / POLYMER ENGINEERING**Sınıf:** **Credit:** 3**Precondition:**

Differences between small molecules and polymers; thermosets; thermoplastics. Relationships between molecular structure and properties. Major types of polymers. Supramolecular architectures, composites, copolymers.

CHBI 506 / BIOINFORMATICS**Sınıf:** **Credit:** 3**Precondition:**

The principles and computational methods to study the biological data generated by genome sequencing, gene expressions, protein profiles, and metabolic fluxes. Application of arithmetic, algebraic, graph, pattern matching, sorting and searching algorithms and statistical tools to genome analysis. Applications of Bioinformatics to metabolic engineering, drug design, and biotechnology.

CHBI 507 / ADVANCED MASS TRANSFER**Sınıf:** **Credit:** 3**Precondition:**

Fundamentals of diffusion; primary mechanisms for mass transfer; mass transfer coupled with chemical reactions; membrane processes and controlled release phenomena.

CHBI 516 / BIOTECHNOLOGY**Sınıf:** **Credit:** 3**Precondition:**

Recombinant DNA, enzymes and other biomolecules. Molecular genetics. Commercial use of microorganisms. Cellular reactors; bioseparation techniques. Transgenic systems. Gene therapy. Biotechnology applications in environmental, agricultural and pharmaceutical problems.

CHEM 420 / COMPUTATIONAL CHEMISTRY**Sınıf:** **Credit:** 3**Precondition:** CHEM. 303 or consent of the instructor

Quantum mechanical description of the molecular structure; exact solution of simple systems, approximate solutions to molecular problems; variational solutions, molecular orbital theory, Hückel approximation, self-consistent-field theory, semiempirical and ab-initio methods, and electron correlation. Properties such as interaction potential functions, electrostatic potential maps and population analysis will be analyzed using MOPAC, GAUSSIAN 94 and MOLCAD.

CMSE 501 / INTRODUCTION TO DATA SCIENCE WITH PYTHON**Sınıf:** **Credit:** 3**Precondition:**

An introduction to interactive Python and Jupyter Notebooks, Python built-in data structures, conditional statements, loops, functions, strings and basic input/output, basics of data manipulation and visualization with relevant Python libraries, different types of plots, vector/matrix representations, linear algebra operations, probability/statistics operations, data analysis applications

CMSE 520 / BIOMOLECULAR STRUCTURE, FUNCTION AND DYNAMICS**Sınıf:** **Credit:** 3**Precondition:** CMSE. 501 or consent of the instructor

Relationship between structure, function and dynamics in biomolecules. Overview of the biomolecular databases and application of computational methods to understand molecular interactions; networks. Principles of computational modeling and molecular dynamics of biological systems.

CMSE 590 / SEMINAR**Sınıf:** **Credit:** 0**Precondition:**

CMSE 595 / MS THESIS**Sınıf:** **Credit:** 0**Precondition:**

COMP 510 / COMPUTER GRAPHICS**Sınıf:** **Credit:** 3**Precondition:** COMP. 202 or consent of the instructor

Theory and practice of 3D computer graphics. Topics covered include graphics systems and models; geometric representations and transformations; graphics programming; input and interaction; viewing and projections; compositing and blending; illumination and color models; shading; texture mapping; animation; rendering and implementation; hierarchical and object-oriented modeling; scene graphs; 3D reconstruction and modeling.

COMP 515 / DISTRIBUTED COMPUTING SYSTEMS**Sınıf:** **Credit:** 3**Precondition:** COMP. 304 or consent of the instructor

Introduction to distributed computing, overview of operating systems, process synchronization and deadlocks, threads and thread synchronization, communication protocols, synchronization in distributed systems, management of time, causality, logical clocks, consistent global states, distributed mutual exclusion, distributed deadlock detection, election algorithms, agreement protocols, consensus, multicast communication, distributed transactions, replication, shared memory model, scheduling, distributed file systems, fault tolerance in distributed systems, distributed real-time systems.

COMP 529 / PARALLEL PROGRAMMING**Sınıf:** **Credit:** 3**Precondition:**

Fundamental concepts of concurrency, non-determinism, atomicity, race-conditions, synchronization, mutual exclusion. Overview of parallel architectures, multicores, distributed memory. Parallel programming models and languages, multithreaded, message passing, data driven, and data parallel programming. Design of parallel programs, decomposition, granularity, locality, communication, load balancing. Patterns for parallel programming, structural, computational, algorithm strategy, concurrent execution patterns. Performance modeling of parallel programs, sources of parallel overheads.

COMP 554 / SELECTED TOPICS IN COMPUTER ENGINEERING**Sınıf:** **Credit:** 3**Precondition:**

COMP 556 / SELECTED TOPICS IN COMPUTER ENGINEERING**Sınıf:** **Credit:** 3**Precondition:**

COMP 570 / BIOINFORMATICS AND ALGORITHMS IN COMPUTATIONAL BIOLOGY**Sınıf:** **Credit:** 3**Precondition:**

Algorithms, models, representations, and databases for collecting and analyzing biological data to draw inferences. Overview of available molecular biological databases. Sequence analysis, alignment, database similarity searches. Phylogenetic trees. Discovering patterns in protein sequences and structures. Protein 3D structure prediction: homology modeling, protein folding, representation for macromolecules, simulation methods. Protein-protein interaction networks, regulatory networks, models and databases for signaling networks, data mining for signaling networks.

ELEC 501 / RANDOM PROCESSES**Sınıf:** **Credit:** 3**Precondition:** ENGR. 200 or consent of the instructor

Discrete and continuous random variables and processes, functions of random variables, independence of random variables. Central Limit Theorem. Discrete-time random processes, continuous-time random processes, stationary random processes, ergodicity, auto and cross correlation functions, power spectral density; spectral estimation, white noise processes, Markov chains.

ELEC 505 / LINEAR SYSTEM THEORY**Sınıf:** **Credit:** 3**Precondition:**

Linear Algebra Review, Normal Matrices, Quadratic Forms and Semidefinite Matrices, Inner Product and Norm Spaces, State Space Descriptions for Continuous and Discrete Time Systems, Controllability, Observability, Stability, Realization Theory.

ELEC 508 / COMPUTER VISION AND PATTERN RECOGNITION**Sınıf:** **Credit:** 3**Precondition:**

Study of computational models of visual perception and their implementation in computer systems. Topics include: image formation; edge, corner and boundary extraction, segmentation, matching, pattern recognition and classification techniques; 3-D Vision: projection geometry, camera calibration, shape from stereo/silhouette/shading, model-based 3D object recognition; color texture, radiometry and BDRF; motion analysis.