2017-18 Catalog

Bio Engineering (BIOE)

Courses

BIOE 001 Freshman Seminar 1, Introduction to Bioengineering 1: Philosophy to Practice 1 Credit

Overview of the bioengineering field, the advancements of related topics in sciences, technology, engineering and applications for health care and medicine. Humanity and ethical issues. Pass/Fail.

BIOE 002 Freshman Seminar 2, Introduction to Bioengineering II: Current Topics 1 Credit

Overview of a broad spectrum of current topical areas in biotechnology and bioengineering and their applications in health care and medicine. Pass/Fail.

BIOE 020 Bioengineering Sophomore Research Seminar 1 Credit

Exposure to opportunities for on-campus research in bioengineering. Review of current literature on bioengineering topics through written reports and/or oral presentations. Preparation of written research proposal, including definition of topic, objectives, methodologies, research plans, and expected impact.

BIOE 110 Elements of Bioengineering 4 Credits

An introduction to the fields of biotechnology and biomedical engineering. The areas include biomechanics, biomaterials, bioinstrumentation, medical imaging, rehabilitation engineering, biosensors, biotechnology and tissue engineering.
Prerequisites: (BIOS 041 and BIOS 042)

BIOE 210 Introduction to Engineering Physiology 4 Credits

Mammalian physiology for bioengineering students, with an emphasis on control mechanisms and engineering principles. Basic cell function; biological control systems; muscle; neural; endocrine, circulatory, digestive, respiratory, renal, and reproductive systems; regulation of metabolism and defense mechanisms. Includes laboratory work.
Prerequisites: (BIOS 041 and BIOS 042) and (BIOE 110)

BIOE 225 GMP Good manufacturing practice and regulatory affairs for bioengineers 1 Credit

Review of the principles of the Food and Drug Administration including its history, mission and applied regulations. Understanding of how the FDA works with industry and is integral to the development of new products and technologies. Review and critique of case studies in various parts of the biomedical industry to see how FDA regulations are applied. Validation and analysis of products using failure mode analysis.
Prerequisites: BIOE 110

BIOE 226 Ethics in Bioengineering Practice 1 Credit

Introduction to ethical principles and role of critical thinking in ethical decision-making. Analysis of contemporary issues in bioengineering practice. Topics include biomedical device risk and failure, ethics of clinical trials, animal research, human enhancement, and research conduct.

BIOE 242 Bioengineering Research 1-4 Credits

Research on a topic chosen by students, with a faculty advisor typically from the three bioengineering tracks (biopharmaceutical engineering, bioelectronic/biophotonics or biomechanics and biomaterials). Independent meetings with advising professor will track progress. Includes written reports and/or oral presentations. Consent of instructor required.
Repeat Status: Course may be repeated.

BIOE 247 Biological Fluid Mechanics 4 Credits

Fluid and mass transport and their applications in biological systems. Mass conservation. Momentum and energy balances in fluid flow. Incompressible fluid flow with inviscid and viscous applications. Dimensional analysis. Fluid flow in pipes and porous media. Diffusion and convection.
Prerequisites: MATH 205

BIOE 257 Biomechanics and Biomaterials 3 Credits

Biomechanical analysis of tissues, microstructure of materials, force and mechanics in rigid and deformable bodies, analysis of biological response and biocompatibility, failure processes of implantable biomaterials/devices, strength of materials, and biomechanics of cells. Biomechanics and biomaterials concepts integrated (1) to examine the theoretical and practical implications of material properties and (2) to examine the biomechanical principles governing system behavior.
Prerequisites: MAT 033 and MECH 003 and MATH 205
Can be taken Concurrently: MATH 205

BIOE 290 Bioengineering Thesis 1-3 Credits

Thesis, guided by a faculty advisor, based on research and/or design projects. Independent meetings with advising professor to track progress. Consent of instructor required.
Prerequisites: BIOE 242 or TE 212

BIOE 307 (CSE 307) 3 Credits

Computational techniques and principles of structural biology used to examine molecular structure, function, and evolution. Topics include: protein structure alignment and prediction; molecular surface analysis; statistical modeling; QSAR; computational drug design; influences on binding specificity; protein-ligand, -protein, and -DNA interactions; molecular simulation, electrostatics. Tutorials on UNIX systems and research software support an interdisciplinary collaborative project in computational structural biology. Credit will not be given for both CSE 307 and CSE 407. Must have junior standing or higher.
Prerequisites: BIOS 120 or CSE 109 or CHM 113 or MATH 231

BIOE 308 (CSE 308) Bioinformatics: Issues and Algorithms 3 Credits

Computational problems and their associated algorithms arising from the creation, analysis, and management of bioinformatics data. Genetic sequence comparison and alignment, physical mapping, genome sequencing and assembly, clustering of DNA microarray results in gene expression studies, computation of genomic rearrangements and evolutionary trees. Credit will not be given for both BIOE 308 (CSE 308) and BIOE 408 (CSE 408). No prior background in biology is assumed.
Prerequisites: CSE 017 or CSE 018
Attribute/Distribution: ND

BIOE 315 (ME 315) Bioengineering Statistics 3 Credits

Advanced methods in probability and statistics applied to bioengineering problems focusing on modeling and data analysis. Topics include the following: types of data, types of distributions, parametric and nonparametric analyses, goodness-of-fit, regression, power analysis, and multivariate analysis, life models, simulation, cluster analysis, and Bayesian statistics. Special emphasis is placed on projects and case studies.
Prerequisites: MATH 231

BIOE 320 (CSE 320) Biomedical Image Computing and Modeling 3 Credits

Biomedical image modalities, image computing techniques, and imaging informatics systems. Understanding, using, and developing algorithms and software to analyze biomedical image data and extract useful quantitative information: Biomedical image modalities and formats; image processing and analysis; geometric and statistical modeling; image informatics systems in biomedicine. Credit will not be given for both BioE 320 and BioE 420.
Prerequisites: (MATH 205 or MATH 043) and CSE 017
Attribute/Distribution: ND

BIOE 321 (PHY 321) Biomolecular & Cellular Mechanics 3 Credits

Mechanics and physics of the components of the cell, ranging in length scale from fundamental biomolecules to the entire cell. The course covers the mechanics of proteins and other biopolymers in 1D, 2D, and 3D structures, cell membrane structure and dynamics, and the mechanics of the whole cell.
Prerequisites: MATH 205 and MATH 231 and PHY 022 and (PHY 013 or PHY 021 or PHY 023)
Attribute/Distribution: NS

BIOE 324 (MAT 324) Introduction to Organic Biomaterials 3 Credits

Property, characterization, fabrication and modification of organic materials for biomedical and biological applications; host responses to biomaterials on the molecular, cellular and system level; general introduction to biosensors, drug delivery devices and tissue engineering.
Prerequisites: BIOE 110

BIOE 325 (MAT 325) Inorganic Biomaterials 3 Credits

Fabrication methods for biomedical implants and devices. Selection of metals and ceramics with specific bulk and surface physical as well as chemical properties. The role of materials chemistry and microstructure. Biocompatibility. Case studies (dental and orthopedic implants, stents, nonporous ceramic filters for kidney dialysis).
Prerequisites: MAT 033

BIOE 326 (MAT 326) Biomimetic and Bio-enabled Materials 3 Credits

The structure, function, properties and use of biopolymers, biocomposites, and biominerals. Biomimetic materials design, including colloids, interfaces, macromolecules, and applications of such materials. Environmental and ethical considerations, such as degradation products when using biomimetic materials. Closed to students who have taken MAT 426 (BioE 426).
Prerequisites: MAT 033 or BIOE 110
Attribute/Distribution: ND

BIOE 331 (PHY 331) Integrated Bioelectronics/Biophotonics Laboratory 2 Credits

Experiments in design and analysis of bioelectronics circuits, micropattering of biological cells, micromanipulation of biological cells using electric fields, analysis of pacemakers, instrumentation and computer interfaces, ultrasound, optic, laser tweezers and advanced imaging and optical microscopy techniques for biological applications.
Prerequisites: (ECE 081 or PHY 190) and (PHY 013 or PHY 021 or PHY 023) and PHY 022 and ECE 121 and ECE 123
Can be taken Concurrently: ECE 121, ECE 123
Attribute/Distribution: NS

BIOE 335 BioFluid Mechanics of Physiological Systems 3 Credits

Application of advanced fluid dynamic principles to physiological systems with emphasis on micron sized structures such as pulmonary airway/alveoli, small blood vessels and biological cells. Introduction to advanced topics relevant to the human body including a) oscillatory and transient flows in the cardiovascular and pulmonary systems b) non-Newtonian flows, c) surface tension driven flows, d) fluid-structure interactions, and e) cellular fluid mechanics.
Prerequisites: (MATH 205 and ME 231 and MATH 231)

BIOE 339 Neuronal Modeling and Computation 3 Credits

Neuroscience in a computational, mathematical, and engineering framework. Literature surveys and case studies with simulations. Computational aspects of information processing within the nervous system by focusing on single neuron modeling. Single neurons and how their biological properties relate to neuronal coding. Biophysics of single neurons, signal detection and signal reconstruction, information theory, population coding and temporal coding.
Prerequisites: ENGR 010 and MATH 205

BIOE 341 (CHE 341) Biotechnology I 3 Credits

Applications of material and energy balances; heat, mass, and momentum transfer; enzyme and microbial kinetics; and mathematical modeling to the engineering design and scale up of bioreactor systems. Closed to students who have taken BioE 441 (CHE 441).
Prerequisites: (MATH 205 and CHE 031 and CHM 031)

BIOE 342 (CHE 342) Biotechnology II 3 Credits

Engineering design and analysis of the unit operations used in the recovery and purification of products manufactured by the biotechnology industries. Requirements for product finishing and waste handling will be addressed. Consent of instructor required. Closed to students who have taken BIOE 442 (CHE 442).
Prerequisites: CHE 031 and CHM 031

BIOE 343 Integrated Biotechnology Laboratory 3 Credits

Biosafety, sterilization, media formulation, biochemical and enzyme assays, recombinant DNA technique, protein and DNA isolation and purification, for microbial fermentation and animal cell culture. Integration of biotechnology techniques for biopharmaceutical production. Consent of instructor required.
Prerequisites: BIOE 110 and (CHE 341 or BIOE 341)

BIOE 344 (CHE 344) Molecular Bioengineering 3 Credits

Kinetics in small systems, stochastic simulation of biochemical processes, receptor-mediated adhesion, dynamics of ion-channels, ligand binding, biochemical transport, surface Plasmon resonance, DNA microarray design, and chemical approaches to systems biology. Senior standing in BIOE.
Prerequisites: (MATH 205 and MATH 231)

BIOE 345 (CHE 345) Quantitative Biology 3 Credits

Basic concepts in molecular and cellular biology as well as biochemistry. Connects these to engineering principles in order to (1) develop a quantitative understanding of biological systems and (2) understand how applications of methods and principles in biology are used in modern engineering. Topics include protein structure and function, enzymology, membrane transport and trafficking, transcription/translation, signal transduction and models for cellular processes. An important part of this course is also taking topics discussed in lecture and translating them into practice.
Prerequisites: MATH 205

BIOE 349 Metabolic Engineering 3 Credits

Quantitative perspective of cellular metabolism and biochemical pathways. Methods for analyzing stoichiometric and kinetic models, mass balances, flux in reaction networks, and metabolic control. Solving problems using advanced mathematics and computer programming.
Prerequisites: MATH 205 and MATH 231

BIOE 350 Special Topics 1-4 Credits

Special topics of study in bioengineering. Permission of Instructor.
Repeat Status: Course may be repeated.

BIOE 357 Integrated Biostructural Mechanics Laboratory 2 Credits

Experimental manipulation and analysis of mammalian cells, with a focus on the biomechanical properties of cells, the interface of living and non-living materials, and on bioengineering applications. Experimental techniques include mammalian cell culture, advanced microscopy techniques, preparation of bioactive substrates, microfluidic device fabrication, micropatterning of cells and cell growth in 3D matrices. Consent of instructor required.
Prerequisites: BIOE 110

BIOE 358 Biomechanics 3 Credits

Applications of mechanics to study behavior of anatomical structures and biological tissues of the musculoskeletal system. Specific topics include structure and function of biological tissues, mechanical properties of biological tissues, and analysis of specific tissues (i.e. bone, muscle, and soft connective tissues).
Prerequisites: MECH 003
Can be taken Concurrently: MECH 003

BIOE 359 Biomechanics Laboratory 1 Credit

Applications of mechanics to study behavior of anatomical structures and biological tissues of the musculoskeletal system. Specific topics include structure and function of biological tissues, mechanical properties of biological tissues, and analysis of specific tissues (i.e. bone, muscle, and soft connective tissues).
Prerequisites: MECH 003 and BIOE 358
Can be taken Concurrently: MECH 003, BIOE 358

BIOE 366 (ECE 366) Neural Engineering 3 Credits

Neural system interfaces for scientific and health applications. Basic properties of neurons, signal detection and stimulation, instrumentation and microfabricated electrode arrays. Fundamentals of peripheral and central neural signals and EEG, and applications such as neural prostheses, implants and brain-computer interfaces. Closed to students who have taken BIOE 466, ECE 366, or ECE 466.
Prerequisites: ECE 081

BIOE 368 (ECE 368) Introduction to Biophotonics and Optical Biomedical Imaging 3 Credits

Optical principles, techniques, and instruments used in biomedical research and clinical medicine. Fundamental concepts of optical imaging and spectroscopy systems, and details of light-tissue interaction. Commercial devices and instruments, as well as novel optical imaging technologies in development. Closed to students who have taken BIOE 468, ECE 368, or ECE 468.
Prerequisites: ECE 202 or PHY 212

BIOE 380 (BIOS 380) Biomolecular & Cellular Biophysics 3-4 Credits

Physical principles of biomolecular and cellular organization. Biomolecular interactions and recognition, molecular motors, physical organization and functioning of cellular membranes, electrical signaling in live cells. Modern techniques in biophysics, molecular spectroscopy, molecular modeling, florescence imaging, electrophysiology, electron microscopy.
Prerequisites: (BIOS 115) and (PHY 013 or PHY 021)

BIOE 407 (CSE 407) 3 Credits

Computational techniques and principles of structural biology used to examine molecular structure, function, and evolution. Topics include: protein structure alignment and prediction; molecular surface analysis; statistical modeling; QSAR; computational drug design; influences on binding specificity; protein-ligand, -protein, and –DNA interactions; molecular simulation, electrostatics. This course, a version of 307 for graduate students, requires advanced assignments and a collaborative project. Credit will not be given for both BIOE 307 and 407. Consent of instructor required.

BIOE 408 (CSE 408) Bioinformatics: Issues and Algorithms 3 Credits

Computational problems and their associated algorithms arising from the creation, analysis, and management of bioinformatics data. Genetic sequence comparison and alignment, physical mapping, genome sequencing and assembly, clustering of DNA microarray results in gene expression studies, computation of genomic rearrangements and evolutionary trees. This course, a version of 308 for graduate students requires advanced assignments. Credit will not be given for both BIOE 308 (CSE 308) and BIOE 408 (CSE 408). No prior background in biology is assumed.
Prerequisites: CSE 017 or CSE 018
Attribute/Distribution: ND

BIOE 420 (CSE 420) Biomedical Image Computing and Modeling 3 Credits

Biomedical image modalities, image computing techniques, and imaging informatics systems. Understanding, using, and developing algorithms and software to analyze biomedical image data and extract useful quantitative information: Biomedical image modalities and formats; image processing and analysis; geometric and statistical modeling; image informatics systems in biomedicine. This course, a graduate version of BioE 320, requires additional advanced assignments. Credit will not be given for both BioE 320 and BIOE 420.
Prerequisites: MATH 205 and CSE 109
Attribute/Distribution: ND

BIOE 421 (CHE 421) Biomolecular & Cellular Mechanics 3 Credits

Mechanics and physics of cell components, from fundamental biomolecules to the entire cell. The mechanics of proteins and other biopolymers in 1D, 2D, and 3D structures, cell membrane structure and dynamics, and the mechanics of the whole cell. This course is a graduate version of ChE 321 (BioE/Phy 321). The lecture content will be the same as in ChE 321 (BioE/Phy 321), but students enrolled in ChE 421 (BioE 421) will have more advanced assignments. Closed to students who have completed ChE 321 (BioE/Phy 321). Must have graduate standing.

BIOE 424 (MAT 424) Introduction to Organic Biomaterials 3 Credits

Property, characterization, fabrication, and modification of organic materials for biomedical and biological applications; host responses to biomaterials on the molecular, cellular, and system level; general introduction to biosensors, drug delivery, and tissue engineering. Graduate version of BioE 324 requiring additional assignments. Credit is not given for both BioE 324 (MAT 324) and BioE 424 (MAT 424).
Prerequisites: MAT 033

BIOE 425 (MAT 425) Inorganic Biomaterials 3 Credits

Fabrication methods for biomedical implant and devices. Selection of metals and ceramics with specific bulk and surface physical as well as chemical properties. The role of materials chemistry and microstructure. Biocompatibility. Case studies (dental and orthopedic implants, stents, nonporous ceramic filters for kidney dialysis). Graduate version of MAT 325; credit will not be given for both MAT 325 and MAT 425.
Prerequisites: MAT 033

BIOE 426 (MAT 426) Biomimetic and Bio-enabled Materials 3 Credits

This course is a graduate version of BIOE 326 (MAT 326). While the lecture content will be the same as the 300-level course, students enrolled in BIOE 426 (MAT 426) will have more advanced assignments. Closed to students who have taken BIOE 326 (MAT 326). Must have graduate standing in Bioengineering or Materials Science and Engineering.
Attribute/Distribution: ND

BIOE 439 (CHE 439) Neuronal Modeling and Computation 3 Credits

This course is a graduate version of BIOE 339 (CHE 339). While the lecture content will be the same as the 300-level course , students in the 400-level class will be expected to complete an independent term project. Closed to students who have completed BIOE 339 (CHE 339). Must have graduate standing in Bioengineering or Chemical Engineering.

BIOE 441 (CHE 441) Biotechnology I 3 Credits

See the course description listed for BioE 341. In order to receive 400-level credits, the student must do an additional, more advanced term project, as defined by the instructor at the beginning of the course. Closed to students who have taken BioE 341 (CHE 341).

BIOE 442 (CHE 442) Biotechnology II 3 Credits

See the course description listed for BIOE 342 (CHE 342). In order to receive 400-level credit, the student must do an additional, more advanced term project, as defined by the instructor at the beginning of the course. Closed to students who have taken BIOE 342 (CHE 342).

BIOE 447 (CHE 447) Molecular Bioengineering 3 Credits

This course is a graduate version of CHE 344 (BioE 344). While the lecture content will be the same as the 300-level course, students enrolled in CHE 447 will have more advanced assignments. Closed to students who have completed BioE 344 (CHE 344).

BIOE 449 (CHE 449) Metabolic Engineering 3 Credits

This course is a graduate version of BIOE 349. While the lecture content will be the same as the 300-level course, students enrolled in BIOE 449 (CHE 449) will have more advanced assignments. Closed to students who have completed BIOE 349. Must have graduate standing in Chemical Engineering or Bioengineering.

BIOE 450 Special Topics 1-3 Credits

Special topics of study in bioengineering. Permission of instructor.

BIOE 466 (ECE 466) Neural Engineering 3 Credits

Neural system interfaces for scientific and health applications. Basic properties of neurons, signal detection and stimulation, instrumentation and microfabricated electrode arrays. Fundamentals of peripheral and central neural signals and EEG, and applications such as neural prostheses, implants and brain-computer interfaces. Closed to students who have taken BIOE 366, ECE 366, or ECE 466. Students enrolled in the course at the 400-level must complete additional advanced assignments, as defined by the course instructor.

BIOE 468 (ECE 468) Introduction to Biophotonics and Optical Biomedical Imaging 3 Credits

Optical principles, techniques, and instruments used in biomedical research and clinical medicine. Fundamental concepts of optical imaging and spectroscopy systems, and details of light-tissue interaction. Commercial devices and instruments, as well as novel optical imaging technologies in development. Closed to students who have taken BIOE 368, ECE 368, or ECE 468. Students enrolled in the course at the 400-level must complete additional advanced assignments, as defined by the course instructor.

BIOE 490 Thesis 1-6 Credits

Repeat Status: Course may be repeated.

BIOE 499 Dissertation 1-12 Credits