CV 711 - GIS Applications in Water Resources Engineering

• See Graduate Catalog

CV 712 - Water Quality Analysis and Modeling

• See Graduate Catalog

CV 730 - Pollution Prevention and Waste Minimization

• See Graduate Catalog

CV 740 - Air Permitting

• See Graduate Catalog

CV 752 - Risk Assessment and Environmental Auditing

• See Graduate Catalog

CV 756 - Environmental Project Management/ Life Cycle Cost Analysis

• See Graduate Catalog

CV 760 - Environmental Law

• See Graduate Catalog

CV 799 - Civil Engineering Independent Study

• Determined by faculty member and student

• None

• Determined by faculty member and student

CV 1001 - Freshman Seminar I

• Describe the program options within the CAECM Department with an emphasis on architectural engineering with one of the three specialties (structural, mechanical, and electrical systems), civil engineering with one of the three specialties (structural, environmental/water resources, construction management) and construction management.
• Give examples of architectural engineering, civil engineering, and construction management career opportunities.
• Understand the professional responsibilities and ethical conduct expectations for registered professional engineers and certified construction managers.
• Understand the building design process and the roles that both architectural engineers, civil engineers, and construction managers play in the development and execution of building projects.
• Be proficient in the use of AutoCAD and REVIT software
• Have experience working as an effective team member.
• Develop academic, personal, and interpersonal skills that will help the student succeed in college and create a sense of campus involvement.
• Enhance skills in oral presentation, written expression, graphic communication and class participation with practice and feedback.
• Raise awareness of the student conduct and ethics code

• None

•  Introduction of CAECM department and programs
• Active learning and professionalism
• GE hours and the process for submission
• The architectural and engineering design process
• Introduction of the Construction Management program and specialty
• Introduction of the Environmental/Water Resources specialty
• Introduction of Transportation and Geotechnical Engineering
• Introduction of the Structural specialty
• Introduction of the Electrical specialty
• Introduction of the Mechanical specialty
• Ethics for engineers and construction managers
• MSOE policies and procedures

• AutoCAD menu structure, entity creation, saving drawings
• Creating circles and arcs, using object snaps, using layers
• Adding dimensions, dimensioning options, adding text, crosshatching
• Moving and copying entities, creating blocks
• Block attributes, prototype drawings, title blocks, use of viewports
• Getting started with REVIT
• Wall types, doors, windows, elevators
• Floors, floor to floor height, common walls
• Roof types, skylights
• Floor and ceiling systems

CV 1001L - Freshman Seminar I (Lab Only)

• Be proficient in the use of AutoCAD and REVIT software

• None

• AutoCAD menu structure, entity creation, saving drawings
• Creating circles and arcs, using object snaps, using layers
• Adding dimensions, dimensioning options, adding text, crosshatching
• Moving and copying entities, creating blocks
• Block attributes, prototype drawings, title blocks, use of viewports
• Getting started with REVIT
• Wall types, doors, windows, elevators
• Floors, floor to floor height, common walls
• Roof types, skylights
• Floor and ceiling systems

CV 1002 - Freshman Seminar II

• Understand how construction documents (drawings and specifications) are organized and their importance in building safe buildings and infrastructure
• Understand the building design process and the roles that both architectural engineers, civil engineers, and construction managers play in the development and execution of building projects
• Be proficient in the use of AutoCAD and REVIT software
• Develop academic, personal and interpersonal skills that will help the student succeed in college and create a sense of campus involvement

• Autodesk Revit

• Humanitarian engineering
• Orthographic projection drawing
• Engineering history
• Surveying/GIS Introduction
• Building elevation drawings
• Organization of construction documents
• CSI formats & RS means introduction
• Drawing stair plans
• Engineering drawings and symbols
• Civil engineering graphics
• Using the International Building Code
• Types of construction specifications
• Specification writing
• ADA code restrooms
• Engineering public policy
• Site plan drawings
• Engineering material selection
• Engineering economics

CV 2001 - Civil 3D

• Create models in Civil 3D
• Import surveying field data
• Create topography models and contour maps
• Subdivide property into lots
• Layout an alignment both horizontally and vertically
• Create models of roadways

• None

• Introduction to CAD
• Program interface
• Import survey data
• Modeling surfaces
• Designing horizontal alignments
• Designing vertical profiles
• Creating corridors and road cross-sections
• Subdividing parcels
• Designing pipe networks

CV 3310 - Geometric Design of Roadways

• Differentiate between functional highway classifications
• Design horizontal and vertical alignment of a roadway segment to fit existing topography
• Analyze intersection design conditions and choose appropriate control
• Identify and analyze the pros and cons of the general interchange types

• Civil 3D
• Transportation engineering

• Functional classification of highway systems
• Traffic characteristics and highway capacity as applicable to design decision-making
• Horizontal alignment of roadways
• Vertical alignment of roadways
• Access, pedestrians and bicycles
• Combination curves in highway design
• Design elements of cross sections
• Civil 3D applications in transportation engineering
• Freeway and interchange design

CV 3320 - Traffic Engineering

• Utilize statistical techniques to assess traffic conditions
• Model traffic flow conditions
• Design and analyze weaving, merging and diverging highway segments
• Appropriately sign and mark highway facilities
• Analyze and properly design signalized and non-signalized intersections

• Transportation engineering
• Probability and statistics

• Human factors in transportation design
• Traffic control devices
• Traffic flow theory and analysis
• Statistical testing in traffic applications
• Data collection and reduction techniques
• Volume, speed, travel-time and delay studies
• Weaving, merging, and diverging roadway segments
• Signing and marking
• Intersection design and warrants

CV 3500 - Geotechnical Engineering

• Conduct particle size analysis and determine Atterberg limits and use the results to classify soils per the USCS and AASHTO soil classification systems
• Calculate various soil parameters using an understanding of a three-phase diagram
• Calculate soil relative density and specify field compaction
• Calculate the hydraulic conductivity of various soils
• Calculate the total stress, pore water pressure, and effective stress at various points I the soil profile of a saturated soil without seepage
• Explain the process of settlement and consolidation in both sandy and clay soils
• Calculate the shear strength of cohesive and cohesionless soils
• Conduct typical geotechnical engineering laboratory tests and understand the application of their results in civil engineering
• Interpret the results from a geotechnical report for use in various aspects of civil engineering

• Construction materials
• Mechanics of materials

• Weight-volume relationships
• Clay minerals and clay chemistry
• Grain size analysis
• Atterberg limits
• Classification of soils (USCS and AASHTO)
• Compaction
• Water content and organic matter content
• Permeability
• Effective stress
• Subsurface stress in soils
• Relative density
• Compressibility of soil
• Proctor compaction test
• Shear strength
• Hydraulic conductivity test
• Footings
• Direct shear strength
• Retaining walls
• Soil sampling and investigation
• Soil reports
• Bridge pier foundation design

CV 3900 - Humanitarian Engineering

• Summarize the current status of development and examine some perspectives from the poor
• Relate the history of development and evaluate various theories of development
• Evaluate and judge different development models
• Explain various development principles
• Apply lessons from the course to concrete opportunities in various fields of engineering

• None

• Context
• History of development
• Development models
• Development principles
• Opportunities for engineers
• Student presentations

CV 4100 - Hydrology

• Develop design flow rates (low flow, peak flow, flow duration, firm yield, design hydrographs) for engineering designs  
• Calculate infiltration, evapotranspiration, snowmelt, and runoff using various methods.
• Disaggregate hydrographs into base and wet weather flow components
• Apply appropriate methods to determine time of concentration
• Develop synthetic hydrographs
• Apply unit hydrographs to develop storm hydrographs
• Characterize, using statistical methods, raw river flow and precipitation data
• Estimate return intervals of extreme hydrologic phenomena
• Perform hydrologic routing of flow through reservoirs and streams
• Perform hydrologic modeling of a watershed using a computer model (i.e. HEC-HMS)
• Estimate erosion potential of soils and impacts of sedimentation on reservoirs
• Use geographic information systems to obtain hydrologic data

• None 

• Hydrologic principles 
• Hydrologic analysis
• Frequency analysis 
• Hydrologic Flood routing 
• Hydrologic simulation (HEC-HMS) 
• Urban hydrology 
• GIS applications in hydrology 
• Radar rainfall applications in hydrology 
• Erosion and sedimentation 
• Severe storm impacts and flood management 

CV 4900 - Civil Engineering Senior Design Project I

• Develop and present a proposal for the design and construction of a civil engineering project in response to the RFP 
• Demonstrate the ability to design a system, component, or process to meet desired needs in more than one civil engineering context and within realistic constraints such as customary standards of practice, costs, and sustainability
• Demonstrate expertise as a functional member of a multidisciplinary team
• Demonstrate the ability to identify, formulate, and solve ill-defined engineering problems in the student’s area of specialization
• Demonstrate an ability to organize and deliver effective verbal, written, and graphical communications
• Demonstrate an understanding of the broad education necessary to understand the impact of engineering solutions in a global, economic, environmental, and societal context.
• Demonstrate self-directed learning
• Demonstrate the ability to use the appropriate techniques, skills, and engineering tools necessary for modern engineering practice
• Develop simulated industry work relationships using a student and faculty team approach
• Identify and list the advantages and limitations of the team approach in a realistic design project environment
• Display an understanding of the basic tenets of sustainability
• Demonstrate the ability to cooperate with team-mates, coordinate workloads, and manage time effectively
• Demonstrate understanding of applicable code requirements and design guidelines
• Demonstrate the students’ knowledge of their specialty area in civil engineering:

a.    Construction Management

• Exhibit understanding of effective site mobilization and project safety requirements
• Show understanding of project cash flow requirements
• Prove understanding of construction scheduling
• Present complete line item and summary of construction costs
• Develop a Management Information Systems (MIS) plan that is effective and project appropriate
• Apply appropriate computer tools
• Apply value engineering and constructability
• Demonstrate understanding of the LEED certification process and how it affects overall project costs, coordination, and owner decisions
• Present quality oral presentations and demonstrate ability to answer questions during presentations

b.    Environmental Engineering

• Characterize potential wastestreams
• Identify applicable regulations
• Identify and analyze appropriate alternative systems, components, or processes to manage, treat, and dispose of the wastestreams while complying with applicable regulatory requirements
• Create order of magnitude cost estimates for alternatives
• Select alternative(s) for design development
• Communicate graphically, verbally, and in writing to the client describing the selected alternatives
• Perform mass and energy balances on environmental systems
• Utilize the LEED and/or Envision rating systems for the assigned project
• Consider building sustainability issues with respect to appropriate electrical, HVAC, plumbing, and environmental design
• Consider emergency systems, egress lighting, exit signs, and fire alarm systems/pumps in relation to appropriate design

c.    Structural Engineering

• Develop structural systems compatible with Civil Engineering design and other engineering disciplines
• Understand structural loadings and other structural design criteria
• Understand lateral force resisting systems
• Understand structural design evident in structural plans
• Understand structural design evident in structural details
• Appropriately use knowledge of structural analysis by hand
• Appropriately use knowledge of structural analysis by computer programs
• Appropriately use knowledge of structural design calculations
• Discuss structural design and human behavior issues in meetings and presentations

d.    Water Resources Engineering

• Identify the relevant hydrologic and hydraulic features of the project requiring design
• Identify options for stormwater management applicable to the project
• Create order of magnitude cost estimates for each stormwater management option considered
• Identify options for relevant hydraulic systems (e.g., hydraulic profiles, water supplies, wastewater drainage) on the project
• Create order of magnitude cost estimates for hydraulic system options

• Must have completed all prior courses in specialization to start of course
• Approval of curriculum coordinator

• Introduction to course and scoping of project
• Problem identification within specialization
• Solution alternative identification
• Alternative analysis
• Alternative selection
• Presentation to client

CV 4920 - Civil Engineering Senior Design Project II

1 lecture hours 6 lab hours 4 credits

• Develop and present a proposal for the design and construction of a civil engineering project in response to the RFP.  
• Demonstrate the ability to design a system, component, or process to meet desired needs in more than one civil engineering context and within realistic constraints such as customary standards of practice, costs, and sustainability.
• Demonstrate expertise as a functional member of a multidisciplinary team.
• Demonstrate the ability to identify, formulate, and solve ill-defined engineering problems in the student’s area of specialization.
• Demonstrate an ability to organize and deliver effective verbal, written, and graphical communications.
• Demonstrate an understanding of the broad education necessary to understand the impact of engineering solutions in a global, economic, environmental, and societal context.
• Demonstrate self-directed learning.
• Demonstrate the ability to use the appropriate techniques, skills, and engineering tools necessary for modern engineering practice.
• Develop simulated industry work relationships using a student and faculty team approach.
• Identify and list the advantages and limitations of the team approach in a realistic design project environment.
• Display an understanding of the basic tenets of sustainability.
• Demonstrate the ability to cooperate with team-mates, coordinate workloads, and manage time effectively
• Demonstrate understanding of applicable code requirements and design guidelines
• Demonstrate the students’ knowledge of their specialty area in Civil Engineering:

a.     Construction Management

• Exhibit understanding of effective site mobilization and project safety requirements
• Show understanding of project cash flow requirements
• Prove understanding of construction scheduling
• Present complete line item and summary of construction costs
• Develop a Management Information Systems (MIS) plan that is effective and project appropriate
• Apply appropriate computer tools
• Apply value engineering and constructability
• Demonstrate understanding of the LEED certification process and how it affects overall project costs, coordination, and owner decisions
• Present quality oral presentations and demonstrate ability to answer questions during presentations

b.    Environmental and Water Resources Engineering

• Characterize potential wastestreams
• Identify applicable regulations
• Identify and analyze appropriate alternative systems, components, or processes to manage, treat, and dispose of the wastestreams while complying with applicable regulatory requirements
• Create order of magnitude cost estimates for alternatives
• Select alternative(s) for design development
• Communicate graphically, verbally, and in writing to the client describing the selected alternatives
• Perform mass and energy balances on environmental systems
• Utilize the LEED and/or Envision rating systems for the assigned project
• Consider building sustainability issues with respect to appropriate electrical, HVAC, plumbing, and environmental design
• Consider emergency systems, egress lighting, exit signs, and fire alarm systems/pumps in relation to appropriate design

• Identify the relevant hydrologic and hydraulic features of the project requiring design
• Identify options for stormwater management applicable to the project
• Create order of magnitude cost estimates for each stormwater management option considered
• Identify options for relevant hydraulic systems (e.g., hydraulic profiles, water supplies, wastewater drainage) on the project
• Create order of magnitude cost estimates for hydraulic system options

c.    Structural Engineering

• Develop structural systems compatible with Civil Engineering design and other engineering disciplines
• Understand structural loadings and other structural design criteria
• Understand lateral force resisting systems
• Understand structural design evident in structural plans
• Understand structural design evident in structural details
• Appropriately use knowledge of structural analysis by hand
• Appropriately use knowledge of structural analysis by computer programs
• Appropriately use knowledge of structural design calculations
• Discuss structural design and human behavior issues in meetings and presentations

• Must have completed all prior courses in specialization prior to start of course
• Approval of curriculum coordinator

• Modification of project plan as needed
• Perform final design calculations and design sketches
• Prepare draft design drawings and details
• Prepare final construction cost estimate
• Prepare draft construction documents
• Finalize documents and drawings
• Presentation of design to committee

CV 5210 - Matrix Structural Analysis

• See Graduate Catalog

CV 5220 - AISC Steel Design

• See Graduate Catalog

CV 5232 - Prestressed Concrete Design

• See Graduate Catalog

CV 5234 - Foundation Design

• See Graduate Catalog

CV 5240 - Masonry Design

• See Graduate Catalog

CV 5250 - Wood Design

• See Graduate Catalog

CV 5260 - Bridge Design

• See Graduate Catalog

CV 5262 - Modern Structural Systems

• See Graduate Catalog

CV 5263 - Retaining Structures and Slope Stability

3 lecture hours 0 lab hours 3 credits

• Understand various soil mechanics properties and lateral earth pressure theories applicable to retaining structures and slope stability
• Analyze and design various earth retaining structures for internal and external stability
• Analyze the stability of slopes using various hand calculation and computer methods

• Soil mechanics

CV 5800 - Research and Writing

• See Graduate Catalog

CV 6210 - Applied Finite Elements

• See Graduate Catalog

CV 6212 - Structural Dynamics

• See Graduate Catalog

CV 6214 - Lateral Loads on Structural Systems

• See Graduate Catalog

CV 6216 - Structural Stability

• See Graduate Catalog

CV 6222 - AISI Steel Design

• See Graduate Catalog

CV 6224 - Connection Design

• See Graduate Catalog

CV 6230 - Reinforced Concrete Structure Design

• See Graduate Catalog

CV 6370 - Facilities Planning

• See Graduate Catalog

CV 6461 - Life Cycle Assessment of Building and Infrastructure Systems

• Understand the basic elements required when performing an ISO 14040 compliant Life Cycle Impace Assessment (LCIA)
• Understand the basic elements of the Economic Input Output (EIO) method for quantifying environmental life cycle impacts
• Perform a Life Cycle Inventory (LCI) on a building or infrastructure system
• Perform a Life Cycle Impacts Assessment (LCIA) on a building or infrastructure system
• Identify common risks and liabilities associated with a green building or infrastructure project and assign costs associated with such risks and liabilities
• Perform a Life Cycle Cost Assessment on a building or infrastructure project, accounting for uncertainties associated with future costs and discount rates

• None

• Introduction to the ISO 14040 Life Cycle Assessment protocols
• Introduction to the Economic Input Output (EIO) method
• Review of life cycle cost modeling using the net present value technique
• Survey of green rating systems such as LEED, Green Globes, and Envision
• Introduction to risk management as applied to green building and infrastructure projects
• Strategies for quantifying uncertainties in the life cycle cost modelling of green building and infrastructure projects
• Introduction to software packages used to assist in LCA modeling
• Building and infrastructure case studies of life cycle assessment and life cycle cost modeling

CV 7100 - Applied Statistics and Modeling

• See Graduate Catalog

CV 8000 - Research and Presentation

• See Graduate Catalog

CV 8900 - Capstone Project I

• See Graduate Catalog

CV 8910 - Capstone Project II

• See Graduate Catalog

CV 8920 - Capstone Project III

• See Graduate Catalog

EB 401 - Topics in Biomolecular Engineering

• Varies

• Varies

EB 499 - BioMolecular Engineering Independent Study

• Varies

• Varies

• Varies

EB 1001 - Intro to BioMolecular Engineering

• Gain an understanding of both the engineering profession and what biomolecular engineers do
• Distinguish macro scales from micro scales. Should be able to perform unit and scale conversions
• Gain an understanding of the importance of project participation
• Ethics and rules of teamwork in a working environment for a lifelong learning approach
• Demonstrate the use of basic biomolecular engineering terminology
• Be familiar with the performance of selected engineering techniques and applications of biomolecular engineering discipline

• No prerequisites by topic appended

• Syllabus, intro, pre-test, survey, history and intro to BioE (2 classes)
• Intro to BioE program, curriculum and the CBM (3 classes)
• Difference between macro and micro scale. Interchangeable use and applications (3 classes, practice in class)
• Diversity and extent of the biomolecular engineering (2 classes)
• Think out of the box activity (2 classes)
• Reading, understanding and discussing a scientific/engineering paper (5 classes)
• T-shirt design discussions (5 classes)
• Introduction to the design process, maintenance of the engineering logbook, and an introduction to time management and time logs (3 classes)
• ​Introduction to Word, Excel, PowerPoint (3 classes, practice in class)
• Exam and quiz (2 classes)

EB 2001 - Laboratory and BioProcess Safety and Ethics

• Recognize potential hazards in the laboratory and manufacturing settings and learn how to avoid them by utilizing safety measures including basic guidelines of proper laboratory and large-scale practice and engineering controls, as well as picking up and using the appropriate kind of personal protective equipment properly 
• Use MSDS to obtain information about potential material toxicity and appropriate safety measures
• Research the information in regard to the safety guidelines and regulations to comply with them
• Apply safety measures in the design and performance of biomolecular engineering experiments and large-scale bioprocessing
• Apply various methods of hazards analysis to bioprocessing
• Recognize the impact of the work of the biomolecular engineer on the environment and on society, as well as potential ethical questions connected to this work and be prepared to discuss them in a professional manner, supported by related professional organizations’ guidelines
• Recognize the need and value of life-long learning in regard to the safety and ethical problems in the continuously developing field of biomolecular engineering
• Recognize the hazards associated with the physical, chemical, and biological products and processes designed by biomolecular engineers
• Recognize the role of safety in various aspects of bioprocess design and operations
• Apply various methods of hazards analysis to bioprocessing
• Identify design considerations for various unit operations and production facilities for safe design and operation
• Analyze process hazards using a suitable methodology

• None

• Introduction and guidelines
• General laboratory safety rules
• Personal protection equipment
• Protection layering
• Use of laboratory equipment
• Physical, chemical, fire, electrical, and radiation safety and hazards
• Chemical safety data sheet
• Biological safety and hazards
• Biosafety guidelines
• Good microbiological techniques
• Engineering controls
• Safe experimental design
• Safety regulations:  institutional, local, and national
• Need for bioprocess safety, past incidents
• Overview of the bioprocessing industry
• The bioprocess lifecycle
• Bioprocessing safety management practices
• Identifying bioprocess hazards
• Hazard analysis methods
• Bioprocess design considerations
• Bioprocess unit operations
• Risk management and emerging technologies
• Selected regulations
• Large scale biosafety guidelines
• A generic biosafety checklist
• Biological assessment questionnaire
• Bioprocess facility audit checklist
• Life-long learning
• Ethics in the workplace
• Ethics in research
• Paper discussions
• BioE lab tour
• Group work
• Speakers

EB 2100 - BioMolecular Engineering Sophomore Seminar

• Apply knowledge of mathematics, science, and engineering
• Start understanding professional and ethical responsibility
• Start understanding the impact of engineering solutions in a global, economic, environmental, and societal context
• Start recognizing the need for, and an ability to engage in, life-long learning
• Start having knowledge of contemporary issues
• Learn more about biomolecular engineering applications in today’s society
• Be introduced to professional communication in the form of formal presentations by invited speakers
• Learn what professional routes exist for graduates with a B.S. in biomolecular engineering, including careers in industry, research academia and graduate school
• Be able to relate to program alums as role models

• No prerequisites by topic appended

• Introduction to the course and team formation
• Pre-seminar discussion on reading and concepts relevant to the seminars
• Invited speakers-topics vary from year to year
• Post-seminar discussion on reading and concepts relevant to the seminars
• Open group discussions
• Course learning assessment survey and questionnaires

EB 2240 - Engineering Applications in Biochemistry

• Gain knowledge of engineering applications of biochemistry concepts
• Perform experimentation related to biomolecular engineering, including hypothesis formulation, model development, measurements with positive and negative controls, and data analysis
• Gain knowledge to design, analyze and control physical, chemical, and biological processes
• Learn to apply basic science engineering concepts knowledge to new situations

• Material taught in CH 200 , CH 222  and CH 223  
• Material taught in MA 136 , MA 137 , PH 2011 , BI 102 , and EB 2001  
• Definitions and nomenclature of basic organic and biomolecules
• Organic functional groups
• Monomers of basic biomolecules, proteins, enzymes, nucleic acids, lipids, carbohydrates
• Directionality of biomolecules, properties of biomolecules
• Key points of metabolism
• Nucleophiles and electrophiles, hydrophobicity and hydrophilicity

• Introduction to the syllabus
• Enzyme catalysis
• Enzyme kinetics
• Applications commercial/industrial use of proteins and enzymes
• Regulations (enzymes) and applications
• A great engineering example-the cell and applications
• H-fuel cell and microbial fuel cell
• Bioenergetics
• Design of metabolism and aerobic metabolism
• Photosynthesis and engineering aspects of metabolism
• Designing of proteins and enzymes and applications

• Lab 1: Log notebook, good lab practices, dos and don’ts of LMPS
• Lab 2: Fuel cells: H and microbial fuel cell
• Lab 3: Diffusion measurement in a two-compartment model
• Lab 4, 5, 6: Model trays for the electron pathway and energy transfer during respiration and photosynthesis
• Lab 7: Measurement of enzymatic reaction rate
• Lab 8: Measurement of enzymatic reaction rate with inhibitor
• Lab 9: Fuel cell challenge design

EB 2250 - Biopolymer Engineering

• Categorize different kinds of natural and synthetic biopolymers
• Understand and discuss the step-growth and chain-growth polymerization and biopolymer processing
• Discuss the methods for polymers and biopolymers characterization, and analyze the characterization data using their science and engineering skills
• Understand and discuss the importance of the biopolymer properties: biocompatibility and biodegradability
• Discuss industrial applications of biopolymers and biopolymer marketing and regulations

• Biokinetics and biocatalysis
• Industrial use of proteins and enzymes
• Design and applications of proteins and enzymes

• Introduction to polymers and biopolymers
• Natural biopolymers in life science
• Principles of polymerization
• Polymer and biopolymer processing
• Polymer and biopolymer characterization: Physics
• Polymer and biopolymer characterization: Chemistry
• Biocompatibility
• Biopolymers: biomedical applications
• Biopolymers: environmental applications
• Project I (biopolymers: agricultural applications)
• Project I (biopolymers: cosmetic applications)
• Biopolymers: food industry applications
• Bioplastics (green plastics): science of biodegradable plastics
• Engineering biopolymers: market
• Engineering biopolymers: regulations
• Project II

EB 2410 - Principles of Biotechnology

• Discuss the history, impacts, and implications of biotechnology
• Discussion pros and cons of the different aspects of the field
• Discuss the underlying principles of several bio-techniques
• Perform several molecular level biotechnology experimental techniques including hypothesis formulation and measurements with positive and negative controls
• Perform data analysis using knowledge of basic sciences and engineering
• Practice at least three different techniques of biotechnology independently
• Identify several biomolecular engineering applications of biotechnology
• Integrate molecular knowledge into analysis and design experiments

• Basic terminology of nucleic acids, proteins, and other biomolecules

• Syllabus, history, safety and ethics in biotechnology (1 class)
• Lifelong learning in biotechnology (1 class)
• Different types of biotechnology (1 class)
• Impact of biotechnology on engineering (1 class)
• Basic skills - doing, speaking, thinking biotech (2 classes)
• Isolating and manipulating biomolecules, DNA, proteins (2 classes)
• Genetic engineering/cloning (3 classes)
• Transformations/fermentations (2 class)
• Operons and transformations (1 class)
• Infections/transfections (1 class)
• Polymerase chain reaction (2 classes)
• Forensics (2 classes)
• Design project presentation and reevaluation (outside class time half a day Saturday)
• Advanced topics (if time allows)
• Review

• Intro to biotechnology methods
  • Setting up a legal scientific notebook
  • Laboratory safety and ethics
• Chemistry needed for biotechnology methods
  • Measuring very small volumes
  • Measuring mass
  • Making solutions
  • Making dilutions
  • Basic biotechnology calculations
• Role of biomolecules in biomolecular engineering
  • Understanding design of two strands of DNA
  • DNA resolving gels
  • DNA isolation
  • Quantitation of DNA via gel electrophoresis
  • Quantitation of DNA via spectrophotometer
• Manipulations of biomolecules models for molecular engineering
  • Transformation of bacteria with plasmid (model of switches at work)
  • Restriction analysis of pre cut DNA sequence (phage)
  • Crime scene MSOE - DNA fingerprinting
  • Visiting a crime lab
  • Data analysis
• Amplification models for molecular engineering
  • Polymerase chain reaction
  • Extended activities

EB 2420 - Informatics Computing I

• Understand the programming concepts and logics
• Understand the syntax and structure of C
• Understand the basics of MATLAB and Perl
• Use HTML and JavaScript to create Web pages
• Understand the basics of Python

• None

EB 2430 - Informatics Computing II

• Understand object-oriented programming concepts
• Write Java programs using object-oriented concepts
• Understand various basic sorting and searching algorithms
• Understand abstract data types (ADTs)
• Understand basic concepts of data structures
• Perform Monte Carlo simulations

• None

• Object-oriented concepts
• Data types and operators
• Variables, declarations, and assignments
• Decision making and iterations
• Recursion
• Input and output
• Arrays and ArrayLists
• Search and sorting algorithms
• Time and space complexity
• Random number generation and simulations
• Abstract data types (ADTs)
• LinkedLists
• Stacks and queues
• Hashing
• Graphs and trees

• Introduction to Java Programming (1 lab)
• Data types and operators (1 lab)
• Decision making and iteration (1 lab)
• Recursion (1 lab)
• Arrays and ArrayLists (1 lab)
• Time and space complexity (1 lab)
• Random simulation (1 lab)
• Stacks, Queues, and LinkedLists (1 lab)

EB 2510 - Thermodynamics I

• Gain a fundamental understanding of the first and second laws of thermodynamics and their relevance in the biomolecular world
• Develop a fundamental understanding of concepts such as: entropy, enthalpy, free energy, internal energy, the conservation of energy, etc. and their relevance in biomolecular engineering
• Identify problems, formulate solutions and solve using thermodynamic principles
• Understand fundamental equations of state applied to ideal/real gases
• Apply fundamental thermodynamic relationships at the molecular level
• Use thermodynamic properties of fluids to solve problems

• Differential equations, basic principles of thermodynamics

• Thermodynamics-basic definitions: heat, work, energy, pressure, temperature, force
• First Law of Thermodynamics: Conservation of energy principle and its application to real world problems
• Ideal and Real Gas Laws
• Heat effects–Exothermic and endothermic chemical reactions
• Second Law of Thermodynamics: Entropy, free energy
• Thermodynamic properties of fluids
• Flow processes
• Refrigeration
• Equilibrium

EB 3100 - BioMolecular Engineering Junior Seminar

• Apply knowledge of the basic sciences and engineering to understand the materials being presented by speakers
• Understand the importance of a biomolecular engineer on multidisciplinary teams with professional ethics
• Define and describe professional and ethical responsibility of a biomolecular engineer
• Communicate effectively with colleagues and with nontechnical audiences, in oral, written and graphical forms
• Compose an effective seminar logbook
• Communicate professionally by participating in active discussions with the various speakers
• Learn professional presentation skills by presenting to the senior BioE students
• Define and identify contemporary engineering/scientific issues of the field
• Understand the direct and/or indirect impact of biomolecular engineering on the identified contemporary scientific issues in a global, economic, environmental and societal context
• Define lifelong learning
• Recognize the need for lifelong learning approaches towards new professional ideas
• Learn what professional routes exist for graduates with a B.S. in biomolecular engineering, including careers in industry, research, academia and graduate school

• Knowledge of the terminologies in chemistry, physics, and biology
• Basic understanding of organic chemistry, biochemistry, and biotechnology
• Basic understanding of biomolecules and their structure including proteins, nucleic acids, lipids, and carbohydrates
• Knowledge of basic presentation skills

• Introduction
• BioE faculty senior design project idea presentations for the upcoming year
• Presentation by invited speakers (topic will change from year to year)
• BioE junior presentations to BioE seniors
• BioE senior presentations to BioE freshmen and sophomores
• Course learning assessment survey and questionnaire (will be done in groups)

EB 3200 - Bioanalytical Instrumentation

• Identify key components of several machines used for probing and analysis of biomolecules
• Demonstrate understanding of concepts, principles of operations and applications of the field
• Recognize the vital components of sample preparation for the probing and analysis
• Distinguish between the principles and constraints of high and low throughput
• Recognize that bioprobing and bioanalysis need constant practice and discipline
• Practice safety and ethics involved with the field of bioprobing and bioanalysis
• Recognize and list the hazards associated with the field of bioprobing and bioanalysis

• Biomolecules structure and function. Physics of mechanics, Physics of electricity and magnetism and modern physics

• Atomic Force Microscopy (AFM)-the basics
• AFM-beyond the basics - using AFM to characterize individual biomolecules, such as DNA
• Fourier-Transform Infrared Spectroscopy (FT-IR). Theoretical foundations of vibrational spectroscopy. Principles of operation of IR and FT-IR
• FT-IR in biomolecular engineering: spectra of functional groups, application of FT-IR to secondary structure of proteins
• Safety, hazards, discipline, sample prep
• Principles of plate reading/immunolabeling
• Applications/constrains of plate reading/immunolabeling
• Electron microscopy-principles and applications
• Mass spectroscopy-principles and applications
• Basic principles of operation of Palpator^TM and the range of its possible applications in the biomolecular engineering field
• Using the Palpator^TM for high-throughput cellular characterization and cellular treatment efficiency, i.e. pharmaceutical efficacy or toxicity testing

• Laboratory safety, hazards, discipline
• Hands on AFM-contact and tapping mode imaging of objects of known morphology. Basic use of nanoscope
• Analysis software
• Hands on AFM. Preparation of biological samples: DNA on mica. Contact and tapping mode AFM of DNA on mica
• Protein sample preparation. Acquiring spectra of buffer and BSA in buffer
• Analysis of FT-IR spectra of BSA in buffer and determination of changes in the secondary structure of proteins
• Hands on sample prep and Plate reader principle and application
• Tour to Mass Spec facility at MCW
• Hands on sample prep and Palpator^TM application to cell characterization

EB 3300 - Molecular Nanotechnology

3 lecture hours 0 lab hours 3 credits

• Define terms like nanotechnology, bionanotechnology and nanobiotechnology
• Discuss the nanofabrication methods
• Characterize nanomaterials/nanodevices and analyze data
• Discuss molecular nanotechnology applications in food safety, agriculture, medicine, pharmaceuticals, environment, as well as other bio-based engineering disciplines; and, be able to apply molecular nanotechnology into these fields
• Discuss the philosophy and ethics of molecular nanotechnology

• Introduction to nanoscience
• The nature of nanotechnology (from nanoscience to nanotechnology)
• Nanomaterials and nanostructures
• Nanofabrication: top-down versus bottom-up
• Nanofabrication: chemical synthesis and modification
• Characterization at the nanoscale
• Demonstration: nanofabrication and nano-characterization
• Bionanotechnology and nanobiotechnology
• Medical nanotechnology and nanomedicine
• Special topic I: Design of nanoparticles for cancer treatment
• Nanotechnology in the agri-food sector
• Special topic II: nanoparticle interactions with plants
• Nanotechnology and environment
• Philosophy and ethics of nanotechnology

EB 3400 - Food Engineering

• Understand and design basic food manufacturing processes
• Understand the food storage mechanism and methods, and design food storage processes
• Understand and discuss the importance of food quality and safety control, especially HACCP and cGMP systems; and design food products/processing processes under the HACCP and cGMP guidelines.

• None

• None

EB 3410 - Applications of Biotechnology

• Discuss the applications of biotechnology
• Discuss the biotechnology tools in regard to their application in biomolecular engineering
• Design and perform simple biotechnology experiments, including hypothesis formation, measurements, and positive and negative controls
• Demonstrate the laboratory skills related to basic biotechnology techniques
• Analyze the experimental data using basic science and engineering skills
• Discuss the new developments in biotechnology in regard to the biomolecular engineering field
• Apply their knowledge of biology, chemistry, and biotechnology to solve basic problems in the biotechnology and biomolecular engineering field

• None

• Biotechnology: science and technology
• Manipulating biomolecules: DNA
• Polymerase chain reaction
• Manipulating biomolecules: protein
• Protein electrophoresis
• Western blotting
• Immunological applications
• ELISA
• Plant biotechnology
• Biological engineering and scale up of industrial process
• Impact of biotechnology on economic and societal issues
• Student presentations
• Exam

• Nucleic acid applications: polymerase chain reaction
• Protein applications: protein isolation and purification
• Protein applications: PAGE
• Protein applications: Western blot
• Immunological applications: ELISA
• Plant biotechnology
• Lab exam

EB 3411 - Applications of Biotechnology II

• Apply the biotechnology tools previously learned toward applications in biomolecular engineering
• Discuss new developments in a variety of biotechnology fields in regard to the biomolecular engineering field
• Discuss the components necessary for founding a biotechnology company
• Apply their knowledge of biology, chemistry, and biotechnology to solve basic problems in the biotechnology and biomolecular engineering field. 

• Knowledge of core biotechnology applications such as bacterial transformation, cloning, forensic analysis, DNA extraction, PCR, protein extraction, Western blotting, ELISA and plant biotechnology
• Ability to apply the core biotechnology applications to biomolecular engineering in a manufacturing setting, i.e. scale-up
• Knowledge of how biotechnology is used in current practice and in the field of biomolecular engineering
• Ability to use biology, chemistry and biotechnology to solve basic problems in the biotechnology and biomolecular engineering field

• Emergence of a biotechnology industry
• Applications in animal biotechnology
• Applications in agricultural biotechnology
• Applications in medical biotechnology
• Applications in industrial biotechnology
• Applications in environmental biotechnology
• Patents in molecular biotechnology industry: legal and ethical issues
• Founding a biotech company
• Marketing a biotech product
• Biotechnology opportunities
• Ethics in biotechnology
• The future of biotechnology
• Student presentations

EB 3420 - Bioinformatics I

• Acknowledge various contemporary issues and appreciate the impact of bioinformatics in genomics, proteomics, human disease research, and drug development
• Apply knowledge of chemistry to understand the structures and physicochemical properties of the basic building blocks of biomolecules and, in turn, to understand biomolecular structure and function
• Navigate the human genome to locate a gene of interest on a chromosome and interpret its results
• Understand the computational algorithms/approaches pertinent to similarity search for an RNA or protein sequence query
• Search against various specialized biological databases for a query and analyze/interpret the hits
• Understand the basic principles and strategies of comparative analysis of protein sequences
• Apply knowledge of mathematics, science, and engineering to bioinformatics

• None

EB 3430 - Bioinformatics II

• Search, collect, and align homologous biological sequences of interest
• Create a quality alignment of biological sequences
• Build and interpret a phylogenetic tree based on well-aligned biological sequences
• Derive sequence-structure relationships by comparing biological sequences and their structure data
• Compare the 3D structures of homologous biomolecules
• Visualize and appreciate the detailed 3D structures of very complex biomolecules using various molecular visualization tools
• Identify and characterize various sequence and structural motifs from a detailed cross-analysis of biological sequences and their corresponding higher-order 3D structures
• Perform homology modeling to predict the 3D structure of a biological sequence whose structure is not yet available

• None 

• RNA sequence analysis
• The Tree of Life: phylogenetic relationships between organisms
• Sequence-Structure relationships of biological macromolecules
• 3D structure of protein and RNA
• 3D visualization of biomolecular structures and their analysis
• Sequence and structural motifs in biological macromolecules
• Homology modeling of novel biological macromolecules

• Comparative analysis of RNA sequences (2 labs)
• The Tree of Life and phylogenetic analysis (2 labs)
• Sequence-structure relationships of biomolecules (1 lab)
• Comparative analysis of 3D protein and RNA structures (1 lab)
• 3D visualization and analysis of biomolecular structure (1 lab)
• Sequence and structural motifs in biomolecules (1 lab)
• Homology molecular modeling (1 lab)

EB 3510 - Thermodynamics II

• Understand solution thermodynamics, chemical and bio-reaction equilibria and phase equilibria and be able to use thermodynamic properties of fluids to solve problems
• Gain a fundamental understanding of the thermodynamics principles and molecular thermodynamics and their relevance in the biomolecular world
• Develop a fundamental understanding of concepts such as: entropy, enthalpy, free energy, internal energy, the conservation of energy, etc. and their relevance in biomolecular engineering
• Identify problems, formulate solutions and solve using thermodynamic principles
• Understand fundamental equations of state applied to intramolecular and intermolecular interactions
• Apply fundamental thermodynamic relationships at the molecular level for such events as molecular cooperativity and binding

• None

• Solution thermodynamics
• Mixing processes
• Phase equilibria
• Chemical reaction equilibria
• Introduction to statistical thermodynamics
• Thermodynamic extremum principles to predict equilibria
• Entropy and Boltzmann distribution
• Driving forces and free energies
• Intermolecular interactions
• Binding

EB 3520 - Engineering of Controlled Drug Delivery

• Discuss basic pharmacology, pharmacokinetics and pharmacodynamics
• Discuss the principles of prodrug design and design prodrugs as drug delivery systems
• Discuss physiological and chemical barriers for drug delivery
• Discuss and design the carriers for drug delivery
• Discuss different controlled drug delivery systems and understand the FDA requirements for controlled release systems; and, be able to design controlled drug delivery systems under the FDA requirements
• Discuss targeted drug delivery, especially to the brain and tumor; and, be able to design targeted drug delivery systems

• None

• Introduction to drug delivery
• Pharmacology, pharmacokinetics and pharmacodynamics
• Physiological and biochemical barriers to drug delivery
• Prodrugs as drug delivery
• Engineered carriers and vectors in drug delivery
• Diffusion-controlled drug delivery systems
• Dissolution-controlled drug delivery systems
• Erodible drug delivery systems
• Osmotic-controlled drug delivery systems
• Oral controlled-release delivery
• Targeting approaches to drug delivery
• Site-specific drug delivery
• Bioconjugates and chemical drug delivery
• Market and FDA requirements for controlled release products

• Biopolymer purification to achieve pharmaceutical grade
• Drug stability
• Alginate-based microcapsules preparation
• Release profiles of encapsulated drugs

EB 3530 - Cell Culture Lab for BioMolecular Engineering

• Get BSL2+ trained
• Perform cell culture using mammalian cell lines
• Prepare media and recognize the vital components of media and perform aseptic techniques imperative for primary and immortalized mammalian cells
• Conduct cell count, design growth curve experiments, and formulate conditions for optimal transient transfection of cells
• Identify machines used in cell culture
• Recognize critical components of the mechanism of how cell culture reagents work and impact of cell culture on cell engineering
• Handle calculations associated with cell culture and be able to use those in new situations
• Recognize that the field of cell culture needs constant practice and discipline
• Recognize the engineering application of cell culture to the design, analysis and control of chemical, physical, and/or biological processes
• Practice safety and ethics involved with the field of cell culture
• Recognize the hazards associated with these processes

• Basic knowledge on cell, biomolecules and metabolism from BI 102 , CH 223 , and EB 2240  

• Syllabus, introduction to cell culture
• Aseptic techniques/passaging counting and housekeeping cells
• SAFETY AND HAZARDS guest speaker from EHS department
• Industrial use of plant and animal cell culture
• Transfer of foreign DNA into animal and plant cells
• Applications and scale-up
• Design of the projects discussion
• Immunostaining

• Aseptic techniques/counting cells/scopes and passaging
• Senior design mini project: (select and perform 1)
• Design and establish a process of cell healing (scratch assays). Can be done on all available cell lines, including stem cells
• Design transformation of embryonic stem cells into a different kind. Can be done on available embryonic rabbit stem cells
• Design cellular differentiation of cells, changing them into a tissue and establishing the mechanical properties using a palpator. Can be done on all cell line

EB 3561 - Unit Operations-Production Scale Bioseparations

• Apply the principles of transport phenomena and thermodynamics to design and characterize batch and continuous separation unit operations
• Describe the working of various unit operations
• Design and scale-up the equipment for various unit operations

• Differential equations

• Introduction to bioproducts and bioseparations
• Cell lysis and flocculation
• Filtration
• Sedimentation, centrifugation
• Extraction and distillation
• Liquid chromatography, adsorption
• Precipitation
• Crystallization
• Drying

EB 3570 - Kinetics and Bioreactor Design

• Derive and apply macroscopic mole and energy balances to size reactors
• Analyze lab data to ascertain the kinetics of a reaction and scale-up design of a bioreactor from lab data
• Distinguish between various types and arrangements of reactors and understand their operation
• Design or select a bioreactor for a specific purpose
• Use a mathematical tool to solve systems of equations

• Chemical and biochemical reaction kinetics
• Collection of reaction rate data
• MATLAB programming
• Mass and energy balances

• Mole balances and introduction to polymath
• Design equations, rate vs. conversion plots
• Types of reactors, reactor arrangement/staging, rate laws, and stoichiometry
• Isothermal reactor design-irreversible and reversible reactions
• Pressure drop, membrane reactors
• Batch, semi-batch, CTSR, recycle and aerated reactors
• Analysis of rate data, multiple reactions, heat effects/energy balance
• Enzymes, MM kinetics, enzyme inhibition, fermenters
• Bioreactors, cell growth kinetics/rate laws, scale up and operation
• Review of reactor design, selection, impeller selection as a function of cell type
• Problem solving using polymath

EB 3600 - -omics in Engineering

• Describe the principal aims, technologies, and statistical issues in genomics and proteomics
• Gain an understanding of the natural and artificial genome and proteome
• Describe instrumental methods used in genomics and proteomics
• Gain an understanding of the applications used in genomics, transcriptomics, proteomics, epigenomics, metagenomics, and interactomics
• Write a scientific report in standardized format

• Cellular biology
• Genetics
• Molecular biology
• Microbiology
• Biotechnology

• Introduction to -omics
• Genome sequencing acquisition and analysis
• Next gen sequencing
• Comparative genomics in evolution and medicine
• Genomic variation
• Transcriptomics
• Epigenomics
• Metagenomics
• Introduction & applications of microarrays
• Proteomics
• Systems biology and synthetic biology
• Student presentations

EB 3610 - Transport Phenomena I

• Derive and apply macroscopic mass, momentum and energy balances and solve engineering problems related to fluid flow
• Solve continuity and Navier-Stokes equations to analyze engineering problems related to Newtonian fluid flow
• Employ dimensional analysis in fluid flow analysis and experimentation
• Distinguish between Newtonian and various types of non-Newtonian fluids’ behavior
• Explain fluid flow behavior on a molecular as well as macroscopic level
• Describe flow parameters and forces acting on objects that are interacting with fluids
• Explain the flow in pipes and ducts and differences between laminar and turbulent flow and solve related engineering problems

• Differential equations
• Vectors

• Introduction to transport phenomena
• Viscosity and mechanisms of momentum transport
• Equations of change for isothermal systems- equation of motion and equation of continuity
• Navier-Stokes equation, Newtonian and non-Newtonian fluids
• Approximations of Navier-Stokes equation
• External flow, frictional and pressure drag
• Time dependent flow
• Laminar/turbulent flow in pipes, frictional losses, experimental devices used to measure fluid flow
• Friction factors for flow in various geometries
• Conservation laws of mass, momentum and energy with engineering applications, Bernoulli equation
• Dimensional analysis
• Flow in pipes, ducts, open channels, pumps and reactors
• Computational fluid dynamics simulation demonstration

EB 3620 - Transport Phenomena II

• Apply knowledge of mathematics, science, and engineering
• Display a thorough foundation in the basic sciences and sufficient knowledge in the concepts and skills required to design, analyze, and control physical, chemical, and biological processes in the field of biomolecular engineering
• Gain a fundamental understanding of the modes of heat and mass transfer
• Use the governing equations and boundary conditions of heat transfer and understand their relevance in the biological world
• Gain a fundamental understanding of conductive and convection heat transfer and how it applies to biomolecular problems
• Develop a fundamental understanding of concepts such as thermal conductivity, thermal diffusivity, convective and radiative heat transfer, diffusion, dispersion, and convective mass transfer etc. and their relevance to biomolecular engineering
• Identify problems, formulate solutions, and solve using mass and heat transfer principles
• Apply fundamental heat and mass transfer relationships to processes such as heat exchange, evaporation, condensation, boiling and drying operations in biological and biomolecular systems

• None 

• Equilibrium, energy conservations, and temperature
• Modes of heat transfer
• Governing eqn and boundary conditions of heat transfer
• Conduction of heat transfer: Steady state
• Conduction heat transfer: Unsteady state
• Convection heat transfer
• Heat transfer with change of phase
• Radiative heat transfer
• Equilibrium, mass conservation, and kinetics
• Modes of mass transfer
• Governing eqns and boundary conditions of mass transfer
• Diffusion mass transfer: Steady state

EB 3800 - Drug Discovery and Development

• Describe drug discovery and development processes
• Understand the strategies for drug discovery and development
• Understand the molecular basis of diseases including orphan diseases
• Understand basics of drug metabolism
• Understand the strategies for drug discovery and development
• Understand drug target identification and validation
• Understand the identification and optimization of lead compounds
• Describe the mechanisms of drug action and resistance
• Know about the major lines of drugs under development
• Appreciate the impact of bioinformatics on modern drug discovery and development

• None

• Introduction to drug discovery and development - Past, current, and future
• Drug discovery and development pipelines - Problems and hopes
• Considerations in drug discovery and development
• Strategies in drug discovery and development
• Drug metabolism and pharmacokinetics
• Types of drugs under development

EB 3810 - Tissue Engineering

• Understand the molecular and cellular basis of tissue formation
• Understand various microfabrication technologies in tissue engineering
• Design scaffolds for tissue engineering
• Understand the strategies for tissue engineering in different organ/tissue systems: skin, bone/cartilage, cardiovascular and neural
• Understand and identify the regulatory requirements and ethical issues during clinical translation of tissue engineered products
• Integrate chemistry, biology, and biomaterials to provide potential tissue engineering products to human health problems

• Biocompatibility
• Biodegradation

• Cells for tissue engineering
• Clinical grade production of MSCs        
• Bioscaffold for tissue engineering
• Scaffold design and fabrication
• Bioreactors for tissue engineering                           
• Controlled release strategies in tissue engineering
• Tissue fabrication technology: Microfabrication 
• Scaffold Design and Fabrication: Organoids and organs-on-a-chip
• Scaffold design and fabrication: Bioprinting
• Scaffold design and fabrication: Decellularization  
• Scaffold design and fabrication: Vascularization
• Skin tissue engineering
• Bone and cartilage tissue engineering
• Neural tissue engineering
• Cardiovascular tissue engineering 
• Product and process design: Toward industrial TE manufacturing
• Clinical translation of tissue engineering
• Ethical issues in tissue engineering

EB 3820 - Molecular Biology for Engineering

• Apply the biotechnology tools previously learned toward applications in biomolecular engineering
• Discuss new developments in a variety of biotechnology fields in regard to the biomolecular engineering field
• Discuss the components necessary for founding a biotechnology company
• Apply their knowledge of biology, chemistry, and biotechnology to solve basic problems in the biotechnology and biomolecular engineering field

• Microbial cell structure
• Microbial growth
• Microbial genetics
• Viruses, viroids and prions
• Microbial mathematics/lab tools
• Food microbiology
• Water and sewage treatment
• Environmental microbiology
• Bioremediation
• Future microbial challenges

• Review basic information on DNA, RNA, and proteins
• DNA techniques:  cloning and vectors
• DNA techniques:  PCR
• DNA techniques:  Nucleic acid hybridization - southern blots and in-situ hybridization
• RNA techniques:   RNA isolation and purification
• RNA techniques:  nucleic acid hybridization - northern blots
• Molecular tools:  labeled tracers
• Protein techniques:  genome editing
• Protein techniques:  DNA-protein and protein-protein interactions
• Whole organism techniques:  knock-in, knock-out, and transgenic mice

EB 3830 - Heat Transfer Equipment in Process Engineering

• Gain fundamental understanding of heat transfer mechanism, applied methods, and working principles of heat transfer equipment used in bio and chemical industries
• Identify requirements of the equipment and formulate solutions
• Apply the momentum, heat, and mass transfer principles to find optimum design choice 
• Analyze the process data and interpret the performance of the equipment while considering the economic aspects of the process

• Conduction and convection heat transfer
• Mass and momentum transfer principles
• Mass and energy balances

• Heat transfer principles
• Design and analysis of heat exchangers
• LMTD and NTU methods
• Boilers and condensers
• Evaporation process principles and equipment
• Drying process principles and equipment

EB 3840 - Bioinformatics III

• Understand the complexity of biomolecular 3D structure and its complex intermolecular interactions
• Understand the implications of biomolecular folding and misfolding
• Identify and characterize sequence and structural motifs implicated in biomolecular 3D architecture
• Understand the impact of homology modeling on biomolecular structure prediction

• Biological databases
• Sequence analysis

• How a biomolecule folds and why
• Complexity of higher-order biomolecular structure/assembly
• Sequence and structural motifs and their roles
• Biomolecular structure prediction: Homology modeling
• Drug-receptor interactions: Molecular docking

EB 3850 - Cosmetics: Science, Engineering & Technology

• Understand the difference between cosmetics and makeup
• Identify and name different types of cosmetic ingredients and formulate and identify product biochemical functions
• Identify the impact of the cosmetic industry on society
• Analyze and apply the interrelationship of cosmetic technology with those of the human body and metabolic processes essential to body functions
• Participate in scientific conversations about science, engineering, and technology of cosmetics using correct terminology
• Identify the latest technologies and emerging and contemporary trends in the field-specific applications biotechnological mechanisms, and their impact on the personal care industry
• Understand challenges faced as the use of biotechnology expands in the personal care industry 
• Illustrate how personal care products are developed
• Understand the future of personal care product development and use 

• Names and structures of biomolecules
• Basic chemistry and biochemistry concepts

• Introduction
• Difference between make up and cosmetics
• History of cosmetics
• Basic cosmetic chemistry - Are cosmetics drugs, neutraceuticals or soaps, emulsion technology, chemical structure of oils and the form of emulsions, high and low polar oils with unique properties, connection of properties of the oil and emulsion with the organics, emulsion stabilized active ingredients for skin permeation and higher efficiency.
• Cosmeceuticals and common cosmetic ingredients
• Prohibited cosmetic ingredients, hypoallergenic cosmetics
• Color additives, shelf lives, hair, skin, and eye cosmetics
• Safety evaluation and assessment of cosmetics, labeling language vs labeling information, material facts, warning statements 
• Consumers and stake holders
• Packaging and marketing
• Industrial regulation and quality: Compliance with and enforcement of laws and related FDA regulations for cosmetics. Research related to cosmetic products, ingredients, and testing
• National and international activities; FDA’s involvement in international activities related to cosmetics, including imports and exports
• FD&C Act: Adulterated cosmetics, misbranded cosmetics, regulations making exemptions
• Formulation approaches and formulas
• Production and scale up
• Cosmetics surgery vs cosmetic dermatology vs cosmetic microbiology
• Future of cosmetics

EB 3860 - Prokaryotic Processes

• Express familiarity with prokaryotic metabolic diversity
• Describe the influence of various environmental factors on prokaryotic metabolism
• Evaluate microbial communities as engineered systems and make informed choices about microbial system design
• Make reasonable hypotheses about metabolic pathways for novel substrates/products
• Describe mechanisms of global regulation, signal transduction, and quorum sensing in bacteria
• Discuss current and future applications of prokaryotic control strategies to a variety of engineering challenges

• Fundamentals of cellular metabolism and bioenergetics
• Gene regulation and prokaryotic operons

• Introduction to bacterial physiology & metabolism
• Composition & structure of prokaryotic cells
• Biosynthetic pathways
• Growth strategies
• Aerobic metabolism of non-glucose substrates
• Anaerobic metabolism
• Chemolithotrophy
• Metabolic pathway prediction
• Fundamentals of metabolic regulation
• Methods of metabolic regulation
• Specific responses to environmental stimuli
• Microbial survival strategies

EB 3870 - Microfluidics

• Explain the benefits of microfluidics
• Describe the designs and working principles of basic components of microfluidic devices
• Recognize the varied applications of microfluidics
• Identify different microfabrication processes
• Design a microfluidic chip

• None

• Introduction to microfluidics 
• The benefits of small scale
• Separation of particles in microfluidics
• Mixing in microfluidics 
• Common components of microfluidic devices
• PCR with microfluidics
• Diagnostic microfluidic devices
• Microfluidics device companies
• Organ-on-chips
• Droplets on a chip
• Photolithography, soft lithography and other microfabrication methods

EB 3880 - Entrepreneurship in BioMolecular Engineering

• Understand the basic steps involved in entrepreneurship
• Understand entrepreneurship in BioE markets
• Understand the marketing of BioE products
• Understand angel and venture financing and investor motivations
• Be aware of regulatory approvals and compliances for biotech products

• None

• Introduction to entrepreneurship
• Building great teams and networks
• Defining your customer
• How does the customer acquire your product?
• How do you design and build your product?
• How do you scale your business?
• Introduction to BioE industry
• Markets and challenges in the BioE industry
• BioE business models
• Company formation, ownership structure
• Licensing technology, IP protection strategies
• Marketing and financing strategies
• Securing angel and venture capital
• Regulatory approval and compliance for biotech products
• Ethical considerations for BioE entrepreneurs

EB 4100 - BioMolecular Engineering Senior Seminar

• Learn about biomolecular engineering and its applications in today’s society
• Develop how to keep an effective seminar logbook
• Develop professional communication skills by asking critical and logical questions about the materials presented by various speakers
• Develop professional presentation skills through effective presentation to the BioE freshmen and sophomores
• Learn about post-graduate career options with a B.S. in Biomolecular Engineering, including jobs in research, industry, academia and graduate school

• No prerequisites by topic appended

• Introduction
• Take-home assignment for BioE faculty senior design project idea presentations
• Presentation by invited speakers (topics will vary from year to year)
• BioE junior presentations to BioE seniors
• BioE senior presentations to BioE freshmen and sophomores
• Course learning assessment survey and questionnaire (will be done in groups)

EB 4300 - Metabolic Engineering and Synthetic Biology

• Apply knowledge of mathematics, science, and engineering
• Design and conduct experiments, as well as to analyze and interpret data
• Design a system, component, or process to meet desired needs within realistic constraints such as economic, environmental, social, political, ethical, health and safety, manufacturability, and sustainability
• Identify, formulate, and solve engineering problems
• Gain knowledge of contemporary issues
• Use the techniques, skills, and modern engineering tools necessary for engineering practice
• Display a thorough foundation in the basic sciences and sufficient knowledge in the concepts and skills required to design, analyze and control physical, chemical and biological products and processes in the field of biomolecular engineering
• Gain a fundamental understanding of the definitions of metabolic engineering and the defining experiments in the field
• Understand and apply basic aspects of mass/material balances and flux analysis to a metabolic engineering problem
• Identify a metabolic problem, propose solutions, and analyze possible problems
• Gain a fundamental understanding of the definitions of synthetic biology and the defining experiments in the field
• Understand and apply basic aspects of parts, devices and systems analysis to a synthetic biology design
• Identify a problem and propose possible synthetic biology responses to the identified problem, including detailing the needed design, parts, and testing
• Identify ethical considerations related to synthetic biology, including both possible positive and negative aspects of the field
• Identify how metabolic engineering and synthetic biology have influenced the areas of production of pharmaceuticals, generation of novel drugs, and energy generation

• None 

• Synthetic biology: overview/foundations and engineering principles, BioBricks, designed genetic circuit examples, sensors, output, regulation, oscillations
• Metabolic engineering: foundations, growth nutrients, material/mass balance, regulation, network rigidity
• Applications: clinical, biofuels, pharmaceutical, food, environmental, and biotechnology
• Theoretical design and proposal of a new sensor and output device
• Laboratory experience with genetic devices, regulation (promoters and RBS sites), complex circuits, and cellular chassis
• Ethical considerations of metabolic engineering and/or synthetic biology research and development

EB 4511 - Bio-Process Control

• Identify common process instrumentation
• Design and analyze a process control strategy for a process requirement
• Choose an appropriate control strategy for a given process requirement
• Tune PID controllers
• Mathematically analyze control behavior of process control loops
• Design and implement appropriate control strategies for a given process requirement
• Synthesize the flowsheet/sequence of unit operations needed in a biomanufacturing process

• No prerequisites by topic appended

• Process instrumentation
• Process control
• Dynamic modeling
• Laplace transforms
• Transfer functions
• PID control
• PID tuning methods
• Advanced control strategies

EB 4561 - Process Engineering Lab

• Explain the working of each unit operation studied in the lab
• Use the equipment for each of the unit operations from the lab to achieve the desired output
• Use design equations to design the unit operations equipment
• Scale-up the lab equipment for the required output/thoroughput 
• Synthesize and analyze the sequence of unit operations needed to achieve the necessary final product specifications

• None

• Fermentation
• Homogenization
• Centrifugation
• Filtration
• Extraction
• Chromatography
• Drying
• Process simulation

• Fermentation
• Homogenization
• Centrifugation
• Filtration
• Extraction
• Chromatography
• Drying
• Process simulation

EB 4910 - BioMolecular Engineering Design I

• Formulate, analyze, and evaluate design solutions to determine the most feasible solution(s)
• Build, test and demonstrate a sub-system (product or process)
• Maintain an engineering design log
• Present a formal first design review

• None 

• Team building
• Conceptual thinking and problem definition
• Feasibility study
• Composing technical specifications
• Design aids and research techniques
• Industry standards
• Prototype development and testing
• Verbal and written communications
• Each student is required to keep a design log in a bound engineering logbook
• Substantial, continuous individual and team progress is expected
• Lab and process safety and hazards
• Creative problem solving

• Vary by the project

EB 4920 - BioMolecular Engineering Design II

• Complete the lab/practical work and determine feasibility of the project
• Complete and test the system, demonstrate prototype (product or process)
• Maintain an engineering design log
• Present a formal second design review
• Process control topics: effect of tuning parameters on P/PI/PID control, cascade, ratio and feedforward control and an introduction to MIMO systems and Model Predictive Control

• None 

• Team process evaluation
• Subsystem test plan
• Design review
• PAT, ObD, cGMP, SOP in bioprocessing
• Process simulation–SuperPro

• Vary by the design project

EB 4930 - BioMolecular Engineering Design III

• Complete the project report
• Maintain an engineering design log
• Present a formal final design review
• Present a poster
• Submit complete Senior Design Report

• None 

• Professional practices
• Annotated Bibliography
• Personal growth evaluation
• Compliance Test plan
• Peer review

• Vary by the design project

EE 201 - Linear Networks: Steady-State Analysis

• Write and solve KCL and KVL equations using mesh and nodal analysis, and utilize voltage and current dividers in DC circuit analysis
• Describe the electrical characteristics of the various passive circuit elements
• Write and solve KCL and KVL equations using branch and nodal analysis for the AC steady-state case
• Calculate average, apparent, and reactive powers for an AC circuit
• Simplify networks using Thevenin’s and Norton’s theorems
• Perform source transformations
• Use the superposition principle in circuit analysis
• Be adept at solving DC and AC circuits with dependent sources
• Use circuit simulation to analyze circuits

• Differentiation and integration of algebraic and transcendental functions
• Solution of systems of linear equations
• Complex number theory and algebraic manipulations

• DC network theorems and techniques (18 classes)
• Principles of Inductance/Capacitance (4 classes)
• AC steady-state circuit analysis techniques (10 classes)
• AC power concepts (4 classes)
• Circuit simulation analysis of steady state circuits (1 class)
• Tests and quizzes (3 classes)

EE 407 - Senior Design Project I

• Approach engineering design problems with an open and creative mind, and use various ideation techniques to explore a variety of alternative solutions
• Form a team to define and solve an open-ended engineering problem
• Use a variety of resources in researching the problem, including technical periodicals, trade journals, patent listings, manufacturers catalogs and application notes
• Keep a bound engineering logbook of all design activities
• Develop detailed design specifications
• Understand the impact of engineering solutions in a global, economic, environmental, and societal context
• Prepare a test plan and conduct a subsystem hardware test
• Make a formal oral presentation on the project

• Analysis and design of diode and transistor circuits
• Analysis and design of combinational and sequential logic circuits
• Design of microprocessor-based systems
• Electromagnetic field theory
• Basic AC and DC motors and generators
• Introduction to linear control systems analysis and design
• Computer aided design and familiarity with programs for analog and digital circuit analysis and design
• Technical communications

• Introduction to capstone design sequence and requirements (1 class)
• Team formation and team dynamics (1 class)
• Project selection (1 week)
• System design (1 week)
• System diagram (1 week)
• Test plan (1 week)
• Specifications (1 week)
• Subsystem test details (1 week)
• Subsystem hardware demonstration (1.5 weeks)
• Oral design review (1.5 weeks)

• Varies with team project

EE 408 - Senior Design Project II

• Define their team roles and evaluate their performance on a team
• Design to match a set of detailed specifications
• Utilize past coursework to generate a reasonable design
• Choose an appropriate prototype technique and begin constructing a prototype
• Select and order parts for implementing a prototype
• Give oral status reports on the design
• Define their team roles and evaluate their performance on a team
• Make a formal oral presentation on the project
• Prepare a formal design report and give a formal oral presentation of the report

• Completion of EE 407  topics

• Dependent on student projects

• Varies with team project

EE 409 - Senior Design Project III

• Work as part of a design team to completely design, prototype, and test a design
• Demonstrate the iterative nature of design
• Evaluate their behavior on their design team in the context of professional and ethical responsibility
• Utilize laboratory instrumentation for debugging and testing a prototype
• Prepare a compliance test plan and conduct the compliance test
• Prepare a complete project report documenting the design, prototype, and testing
• Present the project results to faculty and peers in a trade show setting
• Conduct a design review

• Completion of EE 408  topics

• Dependent on student projects

• Varies with team project

EE 421 - Digital Communication Systems

• Make fundamental decisions involved in the design of a digital communication system by weighing the performance factors associated with digital communication systems
• Describe various pulse modulation methods
• Determine required bandwidths for various digital modulation methods
• Determine the signal-to-noise ratio needed to achieve a specified bit-error rate for various digital modulation methods
• Design an optimal detection filter or correlation receiver
• Explain the properties and features of various error detection and error correction codes

• Fourier methods
• Fundamental analog and digital communications principles
• Fundamental probability and random signal concepts

• Signaling, including sampling and random signal characteristics (7 classes)
• Pulse modulation, baseband digital communication, line coding, and pulse shaping (5 classes)
• Digital modulation and detection, including spread spectrum (5 classes)
• Information theory, source coding and error-correction coding (6 classes)

EE 423 - Applications of Digital Signal Processing

• Determine the appropriate system design for DSP applications
• Be proficient in the C programming language of a DSP chip

• Sampling theorem
• FIR/IIR transfer function design and analysis
• Discrete/fast Fourier transform
• Communications systems
• Computer programming in C

• DSP system architecture and C programming language (4 classes)
• Modulation, demodulation (3 classes)
• FIR, IIR, adaptive, multirate digital filter implementation (6 classes)
• Discrete and fast Fourier transform implementation (2 classes)
• Auto- and cross correlation methods (3 classes)
• Phase locked loop (2 classes)

• Operation of evaluation module
• FIR or IIR filter
• Demodulator (QAM)
• Modulator (ISB)
• Adaptive filter
• Design project

EE 425 - Radio Frequency Circuit Design

• Analyze and design RF inductors and tank circuits
• Diagnose and address shield current issues
• Design lumped component matching networks
• Design transmission line matching networks
• Analyze and design a class-C amplifier
• Design microstrip filter circuits
• Analyze and design a single stage RF amplifier
• Learn how to use basic RF test equipment

• Electromagnetic field theory
• Electronic devices and circuits
• Transmission line theory

• Resonant circuits and applications (3 classes)
• RF models of inductor, capacitor, and resistor (2 classes)
• Lumped element matching networks (3 classes)
• Transmission lines, S-parameters, and Smith chart review (3 classes)
• Transmission line matching networks (2 classes)
• Class-C amplifier analysis (2 classes)
• Microstrip filters (2 classes)
• Noise figure (1 class)
• Examinations (2 classes)

• RF/Microwave CAD software (2 sessions)
• Demonstration and practice the modern test equipments (2 sessions)
• Resonant circuits
• Coupled resonant circuits
• Class-C amplifier
• Baluns
• PIN diodes

EE 426 - Advanced Electromagnetic Fields

• Develop analytic solutions to electromagnetic problems, such as two-dimensional electrostatic boundary value problems, skin depth, plane waves in ferrite media, and the Hertzian dipole antenna
• Apply scalar and vector potential functions in electromagnetic problems
• Interpret the analytic solutions to electromagnetic problems

• Electromagnetic fields
• Transmission line theory
• Scattering parameters
• Basic plane wave and antenna concepts

• Lecture topical emphasis intended to be at the discretion of the instructor; typical course topics:
• Scalar electrostatic potential, Poisson’s and Laplace’s equations, two dimensional boundary value problems
• Time varying fields / Maxwell’s equations (especially in differential form)
• Wave equation, uniform plane wave solution, propagation, and reflection
• Skin depth
• TEM solution in coax
• Plane wave propagation in ferrite media
• Magnetic vector potential
• Hertzian dipole electromagnetic field solution
• Electromagnetic field simulation

EE 429 - Microwave Engineering

• Describe the operation of and calculate key properties of microstrip characteristics and microstrip components
• Utilize RF/microwave simulation software in high frequency circuit analysis
• Describe and sketch field patterns in common high frequency transmission media, especially microstrip, stripline, and rectangular and circular waveguides
• Determine the analytic expressions for the electromagnetic fields inside rectangular and circular waveguides
• Describe the operation of and key specifications of microwave resonators and ferrite devices

• Electromagnetic fields
• Transmission line theory and Smith charts
• Scattering parameters
• Plane waves

• Transmission lines and Maxwell’s equations review (2 classes)
• TEM, especially microstrip, media and components (4 classes)
• Rectangular and circular waveguides (7 classes)
• Microwave resonators (2 classes)
• Microwave ferrite and other components (3 classes)
• Homework sessions. (2 classes) [exams are typically take-home]

• Laboratory topics and schedule intended to be at the discretion of the instructor; typical laboratory topics:
• RF/microwave simulation
• Measurements of RF/microwave components
• RF/microwave project (usually in microstrip)

EE 444 - Power Electronics

• Demonstrate an understanding of the electrical characteristics of power semiconductor devices
• Analyze power semiconductor circuits operating at high power levels under transient and steady state conditions
• Develop the skills necessary to use the computer to analyze and design power conversion circuits
• Develop the understanding of important considerations in the design of power conversion and switching circuits

• Steady state and transient circuit analysis
• Electrical characteristics of diodes, bipolar junction transistors, and field effect transistors
• Analysis of circuits with diodes and transistors
• Frequency response of electrical circuits

• Power Electronics applications (2 classes)
• Power Electronics semiconductor devices (3 classes)
• Rectifiers (2 classes)
• Line-controlled converters (2 classes)
• DC-DC converters (3 classes)
• DC power supplies (2 classes)
• Square-wave inverters (2 classes)
• PWM inverters (2 classes)
• Resonant converters (3 classes)
• Practical circuit techniques (3 classes)
• Review (3 classes)
• Exams (2 classes)

• MOSFET switch application
• SCR application
• AC voltage control application
• Buck and boost converters
• Inverters

EE 447 - Power System Analysis I

• Describe the elements that make up a power system
• Understand the basic concepts of real and reactive power, direction of power flow, conservation of complex power and power factor correction
• Understand the per-phase representation of the three-phase systems and computations
• Calculate the inductance and capacitance of a transposed transmission line
• Use line models to obtain the transmission line performance
• Determine the series and shunt capacitors and shunt reactors required for line compensation
• Understand the basic models of transformers and synchronous generators for the steady-state analysis
• Develop a program for formation of the bus admittance matrix
• Understand the computer techniques and algorithms used to obtain the transmission line parameters, line performance, compensation and solution of the load flow problems

• Linear circuit analysis
• Three-phase circuits
• Basic knowledge of electrical machines and transformers
• Computer programming

• Power in AC circuits, complex power (1 class)
• Review of three-phase systems (2 classes)
• Simple models of transformers and generators for steady-state analysis (3 classes)
• The per-unit systems and impedance diagrams (2 classes)
• Transmission line parameters. Electromagnetic and electrostatic induction (5 classes)
• Transmission line models, performance and compensation (5 classes)
• Network solution and the bus admittance matrix. (2 classes)
• Iterative solution of nonlinear algebraic equations (1 class)
• Load flow problem and solution by the Gauss-Seidel iterative method (3 classes)
• Load flow solution by the Newton-Raphson method (2 classes)
• Tap changing transformers, real and reactive power control (2 classes)

EE 449 - Power System Analysis II

• Understand the nonlinear function optimization with constraints
• Obtain the economical scheduling of real power generation neglecting line losses
• Determine the loss coefficients of a power system network
• Obtain the economical scheduling of real power generation including line losses
• Understand the simplified models of the synchronous machines for fault analysis and transient stability problems
• Calculate the internal voltages of loaded machines under transient conditions
• Understand and be able to evaluate the currents in the network for a balanced three-phase fault
• Transform unbalanced phasors to their symmetrical components
• Use symmetrical components for short-circuit analysis of unsymmetrical faults
• Understand the general problem of power system stability
• Apply the equal-area criterion for stability to system of one machine against an infinite bus bar
• Obtain the time-domain solution of the swing equation for a one-machine system against an infinite bus
• Develop computer programs to determine optimal load flow and balanced faults on an interconnected power system

• Per unit systems
• Power systems components and models
• Load flow analysis

• Optimal dispatch of generation (5 classes)
• Generator modeling (2 classes)
• Direct formation of the bus impedance matrix (2 classes)
• Symmetrical three-phase faults (3 classes)
• Symmetrical components (4 classes)
• Unbalanced fault analysis (5 classes)
• Power system stability (7 classes)

EE 484 - Neural Networks

• Describe the basic configurations of neural networks
• Describe and implement neural networks
• Formulate engineering problems for which neural networks may be a suitable solution
• Evaluate the suitability of neural network architectures and learning algorithms for engineering problems
• Use commercially available neural network development tools
• Interpret and critique scholarly articles in the area of neural networks

• High-level language programming with objects or structures
• Calculus (gradients, series expansions)
• Matrix arithmetic

• Introduction to neural networks, problems, terminology, MATLAB toolbox (2 classes)
• Data gathering and formatting (2 classes)
• Linear perceptron and multilayer backpropagation networks (4 classes)
• Training algorithms and associated mathematics (4 classes)
• Radial basis networks (3 classes)
• Self-organizing maps (1 class)
• Time series networks, control systems, and adaptive filtering (4 classes)
• Deep learning (3 classes)
• Special topics (2 classes)
• Project workshops (5 classes)

EE 499 - Independent Study

• Carry out an in-depth independent investigation on a technical topic with minimal supervision
• Write a formal report which clearly presents a new body of knowledge learned

• Varies

• Course topics to be selected