CHBI 406 / BIOINFORMATICS
Kredi: 3Önkoşul: Prerequisites: MATH. 107 or consent of the instructor

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 statictical tools to genome analysis. Applications of Bioinformatics to metabolic engineering, drug design, and biotechnology.

CHBI 501 / TRANSPORT PHENOMENA
Kredi: 3Önkoşul:

Fluids classification; transport coefficients; momentum transfer and velocity profiles; energy and mass transfer for isothermal and multicomponent systems; mass transfer with chemical reaction; applications for chemical and biological systems.

CHBI 502 / ADVANCED REACTION ENGINEERING
Kredi: 3Önkoşul:

Kinetics of homogeneous and heterogeneous chemical reactions; catalysts; design of chemical reactors; applications for chemical and biological systems.

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 504 / ADVANCED THERMODYNAMICS
Kredi: 3Önkoşul:

Principles of phase and chemical equilibria; computational methods for phase and chemical equilibria calculations; applications for chemical and biological systems.

CHBI 505 / POLYMER ENGINEERING
Kredi: 3Önkoşul:

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
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 507 / ADVANCED MASS TRANSFER
Kredi: 3Önkoşul:

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

CHBI 509 / FUNDAMENTALS OF ENVIRONMENTAL TECHNOLOGIES
Kredi: 3Önkoşul:

Fundamentals of physicochemical and biological processes used for waste minimization, air pollution control, water pollution control, hazardous waste control; environmentally conscious design of chemical processes.

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 511 / SUSTAINABLE ENERGY
Kredi: 3Önkoşul:

Examine the technologies, environmental impacts and economics of main energy sources of today and tomorrow including fossil fuels, nuclear power, biomass, geothermal energy, hydropower, wind energy, and solar energy. Comparison of different energy systems within the context of sustainability. Hydrogen economy and fuel cells.

CHBI 512 / CATALYSIS AT SURFACES
Kredi: 3Önkoşul:

Adsorption on surfaces, structural and dynamic considerations in adsorption, thermodynamics of adsorption, methods for catalyst characterization, pore structure and surface area, surface chemistry of catalysis, metals, highly dispersed catalysts, industrial examples with emphasis on energy production

CHBI 515 / REFINING TECHNOLOGIES
Kredi: 3Önkoşul:

Crude oil and biomass refining technologies. Fractionation, catalytic- and thermo- cracking, gasoline and diesel upgrading and other side processes in crude oil refining; gasification, pyrolysis, transesterification and condensation processes in biomass refining; economical and environmental factors in refining.

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 517 / DRUG DESIGN
Kredi: 3Önkoşul:

Drug design consists of identifying a target (DNA, RNA, proteins) that is known to cause a certain disease and selectively inhibiting or modifying its activity by binding a drug molecule to a specified location on that target. In this course, computational techniques for designing such a drug molecule will be taught. The topics to be covered are: Identification of the active part. Forces involved in drug-receptor interactions. Screening of drug libraries. Use of different software to determine binding energies. Identifying a lead molecule. Methods of refining a lead molecule for better suitability. Case studies: A survey of known drugs, success and failure stories.

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 531 / MODELING AND SIMULATION OF CHEMICAL AND BIOLOGICAL PROCESSES
Kredi: 3Önkoşul:

Modeling concepts and tools for chemical and biological systems. Steady state and transient modeling and simulation. MATLAB based case studies. Selected topics from the curriculum such as reaction stoichiometry, kinetics modeling, reactors, equation of state, phase equilibria, staged operations, fluxes, diffusion and convection, parameter estimation.

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.

CHBI 590 / SEMINAR
Kredi: 0Önkoşul:

CHBI 595 / MASTER THESIS
Kredi: 0Önkoşul:

Independent research towards M.S. degree with thesis option.

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.

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.