BMSE 590 / SEMINAR
Kredi: 0Önkoşul:

BMSE 595 / THESIS
Kredi: 0Önkoşul:

BMSE 695 / PhD THESIS
Kredi: 0Önkoşul:

CHBI 503 / ADVANCED THERMODYNAMICS
Kredi: 3Önkoşul:

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 506 / BIOINFORMATICS
Kredi: 3Önkoşul:

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 510 / INDUSTRIAL MICROBIOLOGY
Kredi: 3Önkoşul:

Key aspects of microbial physiology; exploring the versatility of microorganisms and their diverse metabolic activities and products; industrial microorganisms and the technology required for large-scale cultivation.

CHBI 516 / BIOTECHNOLOGY
Kredi: 3Önkoşul:

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.

CHBI 530 / SYSTEM BIOLOGY
Kredi: 3Önkoşul:

Reconstruction of metabolic network from genome information and its structural and functional analysis, computational models of biochemical reaction networks; system biology in drug discovery and proteomics, flux balance analysis; modeling of gene expression; system biology in artificial intelligence. These concepts will be supported with statistic, thermodynamic, structural biology and learning machine

CHBI 550 / SELECTED TOPICS IN CHEMICAL AND BIOLOGICAL ENGINEERING
Kredi: 3Önkoşul:

Topics will be announced when offered.

CHBI 584 / TISSUE ENGINEERING
Kredi: 3Önkoşul:

The fundamentals of tissue engineering at the molecular and cellular level; techniques in tissue engineering; problems and solution in tissue engineering; transplantation of tissues in biomedicine using sophisticated equipments and materials; investigation of methods for the preparation of component of cell, effect of growth factors on tissues.

CHBI 585 / MOLECULAR MODELING AND SIMULATIONS
Kredi: 3Önkoşul: Prerequisite: CHBI. 204 or consent of the instructor

Principles of molecular modeling in chemical engineering applications; fundamentals for molecular simulation of adsorption and diffusion processes in nanoporous materials; molecular dynamics methods for gas transport in nanopores; Monte Carlo methods for equilibrium based gas separations; molecular modeling of zeolites and metal organic frameworks for gas storage.

CMSE 501 / INTRODUCTION TO COMPUTATIONAL SCIENCE
Kredi: 3Önkoşul:

An introduction to methods and software tools used in scientific computing. Software development, data abstraction and the concept of object oriented programming. Hands-on exploration of some of the principal modern software tools of computational science including computing environments, symbolic computing, numerical libraries and software repositories. An introduction to high performance computing and parallel programming.

CMSE 520 / BIOMOLECULAR STRUCTURE, FUNCTION AND DYNAMICS
Kredi: 3Önkoşul: Prerequisite: 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.

COMP 513 / INFORMATION THEORY
Kredi: 3Önkoşul:

Entropy, Relative Entropy and Mutual Information; Asymptotic Equipartition Theory; Entropy Rates of a Stochastic Process; Data Compression; Kolmogorov Complexity; Channel Capacity; Differential Entropy; The Gaussian Channel; Maximum Entropy and Spectral Estimation; Rate Distortion Theory, Network Information Theory.

COMP 529 / PARALLEL PROGRAMMING
Kredi: 3Önkoşul:

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 570 / BIOINFORMATICS AND ALGORITHMS IN COMPUTATIONAL BIOLOGY
Kredi: 3Önkoşul:

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 510 / INFORMATION THEORY
Kredi: 3Önkoşul:

Entropy, Relative Entropy and Mutual Information; Asymptotic Equipartition Theory; Entropy Rates of a Stochastic Process; Data Compression; Kolmogorov Complexity; Channel Capacity; Differential Entropy; The Gaussian Channel; Maximum Entropy and Spectral Estimation; Rate Distortion Theory, Network Information Theory.

ELEC 522 / INTRODUCTION TO MEMS AND MOEMS
Kredi: 3Önkoşul:

Introduction to Microsystems, MEMS and its integration with optics; Microfabrication and process integration; MEMS Modeling and design; Actuator and sensor design; Mechanical structure design; Optical system design basics; Packaging; Optical MEMS application case studies; Scanning systems (Retinal Scanning Displays, Barcode scanners); Projection display systems (DMD and GLV); Infrared imaging cameras; Optical switching for telecommunications.

ELEC 523 / OPTICAL INFORMATION PROCESSING
Kredi: 3Önkoşul: Prerequisite: (ELEC. 201 and ELEC. 429) or consent of the instructor

Review of 2-D linear system theory and 2-D Fourier transforms. Integral transforms used in optical signal processing; Fundamentals of physical optics and diffraction theory; Fourier and imaging properties of optical systems; Coherent and Incoherent optical image processing; Fundamental architectures for correlation and spectrum analysis; Interferometry; Discrete analog optical processors; Holography; Review of 3D Display technologies.

ELEC 562 / MICRO AND NANOFABRICATION
Kredi: 3Önkoşul:

Fabrication and characterization techniques for micro and nano electro mechanical systems, MEMS & NEMS (including: microlithography; wet & dry etching techniques; physical & chemical vapor deposition processes; electroplating; bonding; focused ion beams; top-down approaches - electron-beam lithography, SPM, soft lithography - ; bottom-up techniques based on self-assembly). Semiconductor nanotechnology. Nanotubes & nanowires. Biological systems. Molecular electronics.

ENGL 500 / ACADEMIC WRITING
Kredi: 0Önkoşul:

The following objectives will be met through extensive reading, writing and discussion both in and out of class.Build a solid background in academic discourse, both written and spoken. Improve intensive and extensive critical reading skills. Foster critical and creative thinking. Build fundamental academic writing skills including summary, paraphrase, analysis, synthesis. Master cohesiveness as well as proper academic citation when incorporating the work of others.

ENGR 500 / APPLIED OPTIMAL CONTROL
Kredi: 3Önkoşul:

Optimization problems for dynamical systems. Pontryagin?s Maximum Principle. Optimality conditions for nonlinear dynamical systems. Linear Quadratic Optimal Control of continuous and discrete linear systems using finite and infinite time horizons. Stability and performance analysis of the properties of the optimal feedback solutions. Moving horizon optimal control of constrained systems using Model Predictive Control formulation. Applications from different disciplines and case studies.

MASE 538 / INTERMOLECULAR AND SURFACE FORCES
Kredi: 3Önkoşul: Prerequisite: CHEM. 301 or consent of the instructor

Intermolecular forces which govern self-organization of biological and synthetic nanostructures. Thermodynamic aspects of strong (covalent and coulomb interactions) and weak forces (dipolar, hydrogen bonding). Self-assembling systems: micelles, bilayers, and biological membranes. Computer simulations for ôhands-onö experience with nanostructures.

MASE 542 / BIOMATERIALS
Kredi: 3Önkoşul:

Materials for biomedical applications; synthetic polymers, metals and composite materials as biomaterials; biopolymers, dendrimers, hydrogels, polyelectrolytes, drug delivery systems, implants, tissue grafts, dental materials, ophthalmic materials, surgical materials, imaging materials.