CHEMICAL AND BIOMOLECULAR ENGINEERING

540.203 (E)

ENGINEERING THERMODYNAMICS (3) Frechette   Limit 145 60 per section Prereq: 540.202, 110.202; Coreq: 030.102, 171.101 Formulation and solution of material, energy, and entropy balances with an emphasis on open systems. A systematic problem-solving approach is developed for chemical and biomolecular process-related systems. Extensive use is made of classical thermodynamic relationships and constitutive equations for one and two component systems. Applications include the analysis and design of engines, refrigerators, heat pumps, compressors, and turbines.
Sec. 02 added 10/26/07

Lec.

Sec. 01

02

MWF 9-9:50

T 9:30

T 10:30

540.301 (E)

KINETIC PROCESSES (4) Hanes Limit 100   Prereqs: 540.203, 540.303      Review of numerical methods applied to kinetic phenomena and reactor design in chemical and biological processes. Homogeneous kinetics and interpretation of reaction rate data. Batch, plug flow, and stirred tank reactor analyses, including reactors in parallel and in series. Selectivity and optimization considerations in multiple reaction systems. Non isothermal reactors. Elements of heterogeneous kinetics, including adsorption isotherms and heterogeneous catalysis. Coupled transport and chemical/biological reaction rates.

Sec. 01

MWF 11-11:50

540.303 (E,N)

TRANSPORT PHENOMENA I (4) Konstantopoulos   Limit 145  Coreq: Differential Equations Introduction to the field of transport phenomena. Molecular mechanisms of momentum transport (viscous flow), energy transport (heat conduction), and mass transport (diffusion). Isothermal equations of change (continuity, motion, and energy). The development of the Navier Stokes equation. The development of non isothermal and multi component equations of change for heat and mass transfer. Exact solutions to steady state, isothermal unidirectional flow problems, to steady state heat and mass transfer problems. The analogies between heat, mass, and momentum transfer are emphasized throughout the course.

Sec. 01

MTThF 3-3:50

540.306 (E)

CHEMICAL AND BIOLOGICAL SEPARATIONS (4) Betenbaugh      Limit 100   Prereq: 540.303, 540.202   This course covers staged and continuous-contacting separations processes critical to the chemical and biochemical industries. Processes considered include distillation, liquid-liquid extraction, gas absorption, leaching chromatography, crystallization, precipitation, filtration, and drying. Particular emphasis is placed on the biochemical uses of these processes
and consequently on how the treatment of these processes differs from the more traditional approach.

Sec. 01

TTh 3-4:45

540.314 (E)

CHEMICAL ENGINEERING PROCESS DESIGN (4) Katz/Dahuron  Limit 25 per section  Prereq: 540.311 or 540.313, 540.301 and 540.306  This course guides the student through the contrasting aspects of product design and of process design. Product design concerns the recognition of customer needs, the creation of suitable specifications, and the selection of best products to fulfill the needs. Process design concerns the quantitative description of processes, which serve to produce many commodity chemicals, the estimation of process profitability, and the potential for profitability improvement through incremental changes in the process. Students work in small teams to complete a major project demonstrating their understanding of and proficiency in the primary objectives of the course. Students report several times both orally and in writing on their accomplishments.

Sec. 01

02

03

WF TTh 9-11:50 TTh 9:30-11:50

MW 1:30-4:20

TTh 1:30-4:20

540.404 (E)

THERAPEUTIC AND DIAGNOSTIC COLLOIDS (3) Hanes/ Wirtz   Limit 50
The inefficient or inappropriate transport of particles in complex biological fluids in the body currently limits the effectiveness of nanoparticle-based strategies aimed at providing a variety of breakthroughs in medicine, from highly targeted drug and gene delivery systems to improved particles for advanced imaging and diagnostics. Many bodily fluids serve as barriers to particle transport to desired locations, and some are microporous, highly viscous and/or elastic in nature. This course seeks to provide a fundamental understanding of the phenomena, including fluid micro-, meso- and macrorheology, that governs nano- and microparticle transport in important biological fluids, including the blood, airways, mucus, and living cells. A comparison of macroscopic and microscopic particle transport behavior, including comparisons of ensemble-average transport behavior to that of individual particle behavior, is a common thread that runs throughout the course. The importance of particle physicochemical properties in achieving desired particle transport through biological barriers to desired sites of action will be addressed. The course will include a case study involving the design criteria of efficient synthetic systems for gene delivery in the lung airways.
Same as 540.604

 Sec. 01

MW 4:30-5:45pm

540.406 

MOLECULAR SUMULATIONS AND MUTISCALE MODELING (3)  Drazer/Gray   Limit 30 This course provides an introduction to modern numerical methods for calculating thermodynamics, transport and structural properties of complex systems in chemical and biomolecular engineering. The first part of the course will focus on molecular level simulations, from ab initio methods to Molecular Dynamics and Monte Carlo simulations, their applications and limitations. The second part of the course will emphasize the need of multiscale models to address the multiplicity of length and time scales present in complex systems. Mesoscopic models will be investigated as a first step into multiscale models. Then, current methods to bridge the gap between atomistic simulations and macroscopic methods will be presented in case studies.

Sec. 01

MWF 11-11:40

360.404 (E)

INTERFACIAL PHENOMENA IN NANOSTRUCTURED MATERIALS
Erlebacher/ Frechette   Limit  25
All materials properties of materials change when encountered or fabricated with nanoscale structure.  In this class, we will examine how the properties of nanostructured materials differ from their macroscopic behavior, primarily due to the presence of large interfacial areas relative to the characteristic volume scale.  General topics include the structure of nanostructured materials (characterization and microscopy), thermodynamics (effects of high curvatures and surface elasticity), kinetics and phase transformations (diffusion and morphological stability), and electronic properties (quantum confinement and effects of dimensionality).       
Cross-listed with Materials Science and Interdepartmental   Same as 360.644

Sec. 01

TTh 1:30-2:45

540.412 (E)

HYDRATION IN MOLECULAR BIOPHYSICS (3)  Asthagiri Limit 25 Prereq: A good background in thermodynamics is essential. Water is the solvent matrix for all terrestrial life processes. Understanding protein structure and function is predicated on understanding the nature of water and protein-water interactions. Proteins are poly-electrolytes with a surface that has charged, polar, and neutral residues. For instance, charged species interact with strengths comparable to those found in chemical bonds, whereas neutral species interact much less strongly. Yet it is the delicate balance of all these interactions that results in a functioning molecule. Our specific interests are in addressing: What is the nature of water and how does it influence protein structure? How is it modeled in studies on protein hydration? What are the physical principles underlying these models? (Some of these models are used in the industry in, for example, computer aided drug design.) What is the chemical role of water and the modern view of the ionic constituents of water? And what are some of the current developments that inform us about the process of hydration? These are some of the questions that we will try to address in this course. Many of the ideas to be discussed in the course are actively debated in the literature, and we will attempt to better understand these debates. The course will be primarily based on research papers and, when appropriate, hands-on computer simulations. It is appropriate for both advanced UG and Grad students wanting to familiarize themselves with an important area in molecular biophysics and chemical engineering. A good background in thermodynamics is necessary. All the necessary statistical thermodynamics ideas will be developed within the course. Course added 10/26/07

Sec. 01

TTh 3-4:15

540.420 (E,N)

BUILD-A-GENOME (4) Boeke/Bader/Ostermeier  Limit 16 Perm Req'd Must understand fundamentals of DNA structure, DNA electrophoresis and analysis, Polymerase Chain Reaction (PCR) and must be either a) Experienced with molecular biology lab work or b) Adept at programming with a biological twist. In this combination lecture/laboratory "Synthetic Biology" course students will learn how to make DNA building blocks used in an int'l. project to build the world's first synthetic eukaryotic genome, Saccharomyces cerevisiae v. 2.0. Please study the wiki www.syntheticyeast.org for more details about the project. Following a biotechnology boot-camp, students will have 24/7 access to computational and wet-lab resources and will be expected to spend 15-20 hours per week on this course. Advanced students will be expected to contribute to the computational and biotech infrastructure. Co-listed with 580.420 & 020.420 Successful completion of this course provides 3 credit hours toward the supervised research requirement for Molecular and Cellular Biology majors, or 2 credit hours toward the upper level elective requirement for Biology or Molecular and Cellular Biology majors. Course added 12/20/07

Sec. 01

MWF 5-6:30pm

540.433

ENGINEERING ASPECTS OF CONTROLLED DRUG DELIVERY (3)  HanesCourse canceled 10/26/07

Sec. 01

MW 4:30-5:45pm

540.440 (E)

MICRO & NANOTECHNOLOGY (3)
Gracias    Limit 50 30 Prereq: An undergraduate course in Biochemistry and/or Cell Biology.   Micro/Nanotechnology is the field of fabrication, characterization and manipulation of extremely small objects (dimensions on the micron to nanometer length scale). Microscale objects, because of their small size are expected to be at the frontier of technological innovation for the next decade. This course will include a description of the materials used in microtechnology, methods employed to fabricate nanoscale objects, techniques involved in characterizing and exploiting the properties of small structures, and examples of how this technology is revolutionizing the areas of Electronics & Medicine. Same course as 540.640 This course provides details of the latest advances in cellular and molecular biology for mammalian systems, with special implications for biotechnology. Topics covered include tissue organization, gene expression, signal transduction, immunology, proteomics, genomics, and post-transnational processing.  Special emerging areas in biotechnology involving mammalian cells will be described including nanobiotechnology for mammalian cells, metabolic and cellular engineering, stem cell therapies, and tissue engineering.

Sec. 01

MW 5:30-6:20
Th 5-8pm

540.442 (E)

ADVANCED TOPICS IN BIOCHEMICAL KINETICS (3) Betenbaugh/Ostermeier/Hanes  Limit 40  Survey of kinetic/reactor phenomena of high relevance to industry and cutting-edge biomolecular engineering research. Topics to be covered include: reactions with phase changes for the microelectronics industry, computational modeling of complex multiple reaction systems, enzyme kinetics (including inhibition, allostery and cooperativity), pharmacokinetics, cell bioreactors, and intracellular kinetics relevant to metabolic engineering. Course canceled 11/26/07

Sec. 01

TTh 4:30-5:45pm

540.460 (E)

DESIGN OF BIOLOGICAL MOLECULES AND SYSTEMS COMPUTATIONAL AND EXPERIMENTAL DESIGN OF BIOMOLECULES (3)  Ostermeier/Gray  Limit 50 20  Prereq:  020.305 & 020.306 or permission of instructor.  This course reviews current research problems in biomolecular design both from computational and experimental approaches. Current methods in structure prediction and design will be used to illustrate fundamental concepts in protein structure, biophysics, and optimization (i.e. protein folding and docking, design of ligand-binding sites, design of turns and folds, design of protein interfaces). Current research problems in evolution-based biomolecular engineering will be used to illustrate principles in the design of biomolecules (i.e. protein engineering, RNA/DNA engineering), metabolic pathways, signaling pathways, genetic circuits and complex biological systems including cells. engineering will be used to illustrate principles in the design of biomolecules (i.e. protein engineering, RNA/DNA engineering), metabolic pathways, signaling pathways, genetic circuits and complex biological systems including cells. Emphasis will be placed on experimental approaches to design (especially those approaches that employ the principles of evolution).

Sec. 01

MW 3-4:15

540.502

INDEPENDENT STUDY

540.522

INDEPENDENT RESEARCH

540.601

CHEMICAL ENGINEERING  SEMINAR  Gray Limit 75

 Sec. 01

Th 11-11:50

540.604

THERAPEUTIC AND DIAGNOSTIC COLLOIDS Hanes/ Wirtz  Limit 50
see 540.404 for description  Same course as 540.404 

 Sec. 01

MW 4:30-5:45pm

540.606

MOLECULAR SUMULATIONS AND MUTISCALE MODELING Drazer/Gray  Limit 30 This course provides an introduction to modern numerical methods for calculating thermodynamics, transport and structural properties of complex systems in chemical and biomolecular engineering. The first part of the course will focus on molecular level simulations, from ab initio methods to Molecular Dynamics and Monte Carlo simulations, their applications and limitations. The second part of the course will emphasize the need of multiscale models to address the multiplicity of length and time scales present in complex systems. Mesoscopic models will be investigated as a first step into multiscale models. Then, current methods to bridge the gap between atomistic simulations and macroscopic methods will be presented in case studies.

Sec. 01

MWF 11-11:40

540.612

HYDRATION IN MOLECULAR BIOPHYSICS (3)  Asthagiri Limit 25 Prereq: A good background in thermodynamics is essential.
See 540.412 for description  Same course as 540.412  Course added 10/26/07

 Sec. 01

TTh 3-4:15

540.640

MICRO & NANOTECHNOLOGY
Gracias   Limit 50  Micro/Nanotechnology is the field of fabrication, characterization and manipulation of extremely small objects (dimensions on the micron to nanometer length scale). Microscale objects, because of their small size are expected to be at the frontier of technological innovation for the next decade. This course will include a description of the materials used in microtechnology, methods employed to fabricate nanoscale objects, techniques involved in characterizing and exploiting the properties of small structures, and examples of how this technology is revolutionizing the areas of Electronics & Medicine. Same class as 540.440

Sec. 01

MW 5:30-6:20
Th 5-8pm

540.642

ADVANCED TOPICS IN BIOCHEMICAL KINETICS  Betenbaugh/Hanes/Ostermeier Limit 15 Survey of kinetic/reactor phenomena of high relevance to industry and cutting-edge biomolecular engineering research. Topics to be covered include: reactions with phase changes for the microelectronics industry, computational modeling of complex multiple reaction systems, enzyme kinetics (including inhibition, allostery and cooperativity), pharmacokinetics, cell bioreactors, and intracellular kinetics relevant to metabolic engineering. Course canceled 11/26/07

 Sec. 01

 TTh 4:30-5:45pm

360.644

INTERFACIAL PHENOMENA IN NANOSTRUCTURED MATERIALS
Erlebacher/ Frechette   Limit  25 All materials properties of materials change when encountered or fabricated with nanoscale structure.  In this class, we will examine how the properties of nanostructured materials differ from their macroscopic behavior, primarily due to the presence of large interfacial areas relative to the characteristic volume scale.  General topics include the structure of nanostructured materials (characterization and microscopy), thermodynamics (effects of high curvatures and surface elasticity), kinetics and phase transformations (diffusion and morphological stability), and electronic properties (quantum confinement and effects of dimensionality).       
Cross-listed with Materials Science and Interdepartmental   Same as 360.404

Sec. 01

TTh 1:30-2:45

540.660

DESIGN OF BIOLOGICAL MOLECULES AND SYSTEMS COMPUTATIONAL AND EXPERIMENTAL DESIGN OF BIOMOLECULES (3)  Ostermeier/Gray  Limit 50 20  Prereq:  020.305 & 020.306 or permission of instructor.  This course reviews current research problems in biomolecular design both from computational and experimental approaches. Current methods in structure prediction and design will be used to illustrate fundamental concepts in protein structure, biophysics, and optimization (i.e. protein folding and docking, design of ligand-binding sites, design of turns and folds, design of protein interfaces). Current research problems in evolution-based biomolecular engineering will be used to illustrate principles in the design of biomolecules (i.e. protein engineering, RNA/DNA engineering), metabolic pathways, signaling pathways, genetic circuits and complex biological systems including cells. engineering will be used to illustrate principles in the design of biomolecules (i.e. protein engineering, RNA/DNA engineering), metabolic pathways, signaling pathways, genetic circuits and complex biological systems including cells. Emphasis will be placed on experimental approaches to design (especially those approaches that employ the principles of evolution).Graduate level of 540.460

Sec. 01

MW 3-4:15

540.801

GRADUATE RESEARCH

540.811

INDEPENDENT STUDY