2026-2027 Academic Catalog

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Biological Systems Engineering (BSE)

BSE 1004 - Engineering Biological Systems for the Global Good (1 credit)

Survey of global societal and technological issues that engage biological systems engineers in the areas of health, environment, food and energy. Application of systems-level approaches to meet engineering challenges that intersect with crucial societal issues, including sustainability and equity. Evaluation of key factors that affect the design, communication, and public acceptance of engineered solutions. Analysis of cultural intelligence, with a specific focus on personality and problem solving styles amongst individuals and teams and productive conflict resolution.

Instructional Contact Hours: (1 Lec, 1 Crd)

BSE 1984 - Special Study (1-19 credits)

Instructional Contact Hours: Variable credit course

BSE 2004 - Introduction to Biological Systems Engineering (3 credits)

Introduction to the fundamental concepts of Biological Systems Engineering, including statistics and material and energy balances, through applications in protein separation, hydrology, sediment/nutrient transport, and microbial metabolism. Engineering design process. Engineering problem-solving tools and techniques. Resolving ethical dilemmas. Development of oral and written communication skills; introduction to job searching resources; strategies for career development, and the importance of teamwork and ethics in Biological Systems Engineering.

Prerequisite(s): ENGE 1215 or ENGE 1414

Instructional Contact Hours: (2 Lec, 3 Lab, 3 Crd)

BSE 2304 - Landscape Measurements and Modeling (3 credits)

Introduction to land surveying, computer-aided design, and drafting for land and water resources engineering. Representation of features in two and three dimensions for documentation and visualization of watershed engineering projects. Create plans, cross sections, detail drawings, and three dimensional visualizations using computer-aided design and drafting tools.

Prerequisite(s): MATH 1206 or MATH 1226

Instructional Contact Hours: (2 Lec, 3 Lab, 3 Crd)

BSE 2504 - Introduction to Fluid Mechanics (3 credits)

Fluid properties. Hydrostatics. Bernoulli’s equation. Derivation and application of the mass, momentum, and energy conservation equations for calculating flow rates, fluid forces, and head losses. Analyses of pipe flows and piping systems, and open channel flows. Pumps. Lift and drag. Application to biological and ecological systems.

Prerequisite(s): PHYS 2305 and ESM 2104

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 2974 - Independent Study (1-19 credits)

Instructional Contact Hours: Variable credit course

BSE 2984 - Special Study (1-19 credits)

Instructional Contact Hours: Variable credit course

BSE 2994 - Undergraduate Research (1-19 credits)

Instructional Contact Hours: Variable credit course

BSE 3144 - Engineering Analysis for Biological Systems using Numerical Methods (2 credits)

Solving engineering problems related to biological systems using numerical analysis including root finding, numerical integration, differentiation, interpolation and numerical solution of ordinary differential equations. Error analysis and programming with engineering software. Course requirements may be satisfied by taking MATH 2214 prior to or concurrent with course.

Prerequisite(s): MATH 1226

Instructional Contact Hours: (2 Lec, 2 Crd)

BSE 3154 - Thermodynamics of Biological Systems (3 credits)

Description of biological, chemical and mechanical mechanisms of energy storage and conversion to work. Derivation and use of the first and second laws of thermodynamics (energy and entropy) to analyze processes found in biotechnology, ecological engineering, and living systems. Analysis of thermodynamic cycles and their relevance to biological systems. Introduction of Gibbs energy, equilibrium at specified pH, and calorimetry of biological reactions.

Prerequisite(s): CHEM 1036 and PHYS 2305 and (MATH 2204 or MATH 2204H)

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 3324 - Small Watershed Hydrology (3 credits)

Precipitation, soil physics, infiltration, evapotranspiration, groundwater hydrology, overland flow, open channel flow, flow routing, hydraulic analysis.

Prerequisite(s): PHYS 2305

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 3334 - Nonpoint Source Pollution Assessment and Control (3 credits)

Erosion prediction and control; transport and fate of sediment, nutrients, and microorganisms; design of nutrient management plans, wetlands, detention facilities and other management practices for rural and urban nonpoint source pollution control.

Prerequisite(s): BSE 3324

Instructional Contact Hours: (2 Lec, 3 Lab, 3 Crd)

BSE 3504 - Transport Processes in Biological Systems (3 credits)

Introduction to material and energy balances in biological systems. Fundamentals of heat and mass transfer in biological systems. One and two dimensional conduction, convection, and diffusion of thermal energy and mass. Heat and mass transfer rates, steady and unsteady state conduction, convection, diffusion; design of simple heat exchangers. Application of these topics and fluid mechanics to fluid handling, bacterial growth, plant nutrient uptake, enzymatic reactions.

Prerequisite(s): BSE 3154 and ESM 3024 and MATH 2214

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 3524 - Unit Operations in Biological Systems Engineering (3 credits)

Description of unit operations for processing biological materials including evaporation, drying, gas-liquid separations, adsorption, membrane separation, and mechanical separation.

Prerequisite(s): BSE 3154 and MATH 2214

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 3534 - Bioprocess Engineering (3 credits)

Engineering concepts for biological conversion of raw materials to food, pharmaceuticals, fuels, and chemicals. Metabolic pathways leading to products, enzyme kinetics, cell growth kinetics, and analysis of bioreactors and fermenters.

Prerequisite(s): BSE 3154

Corequisite(s): BIOL 2604, BSE 3504

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 3954 - Study Abroad (1-19 credits)

Instructional Contact Hours: Variable credit course

BSE 3984 - Special Study (1-19 credits)

Instructional Contact Hours: Variable credit course

BSE 4014 - Engineering Biology Course-based Research Experience (2 credits)

A hands-on introduction to the fundamental concepts of recombinant DNA technology and how it can be used to engineer molecular, cellular, and organismal systems to sustainably produce food, fuel, fibers, pharmaceuticals, and industrial chemicals through a course-based research and career development experience. Using engineering design cycles of learn->design->build->test->learn, we will construct DNA plasmids and explore and experience the fields of quantitative and synthetic biology, the current capabilities and limitations of engineering biology, and the application of lab automation.

Prerequisite(s): BIOL 1105

Instructional Contact Hours: (1 Lec, 3 Lab, 2 Crd)

BSE 4125 - Comprehensive Design Project (2 credits)

Prerequisite(s): (BSE 3534 and BSE 3524) or (BSE 3324 and BSE 3334)

Instructional Contact Hours: (1 Lec, 3 Lab, 2 Crd)

BSE 4126 - Comprehensive Design Project (3 credits)

4125: Identify and develop an engineering design project using the team approach; use of literature resources to define project objectives and approach; present project proposal in a professional written and oral manner; engineering ethics, professionalism and contemporary issues. Pre: Completion of 96 hours, overall GPA of 2.0 or better. 4126 Complete a comprehensive design project using the team approach, test prototype, and prepare and present a professional engineering design report.

Prerequisite(s): BSE 4125

Instructional Contact Hours: (1 Lec, 6 Lab, 3 Crd)

BSE 4224 - Field Methods in Hydrology (3 credits)

Site characterization: surveying, channel and floodplain mapping, land use, electronic data acquisition. Techniques for measuring surface and subsurface hydrologic processes: water flow, hydrologic conductivity, precipitation, evaporation. Sampling techniques: surface water, groundwater, and soil pore water sampling. In-situ monitoring: automatic samplers, dataloggers, water quality sondes. Laboratory analyses: good laboratory practices, selection of analytical method, calibration, quality assurance/quality control.

Prerequisite(s): BSE 3324 or FREC 3104 or WATR 3104 or CEE 3314

Instructional Contact Hours: (2 Lec, 3 Lab, 3 Crd)

BSE 4304 - Introduction to Watershed Modeling (3 credits)

Fundamental modeling principles used to quantifywatershed hydrology, energy budgets,and associated ecosystem functions, such asplant dynamics and biogeochemical processes, at scales ranging from soil poresto watersheds. Code development and model integration to simulate watershed hydrologyandnutrient and sediment transport. Model calibration and performance assessment. Data discovery, acquisition, and processing of data relevant to hydrologic/watershed modeling.

Prerequisite(s): BSE 3334

Instructional Contact Hours: (2 Lec, 3 Lab, 3 Crd)

BSE 4324 - Applied Fluvial Geomorphology (3 credits)

Introduction to landscape evolution. Influence of geology and climate on stream form and processes. Fundamental river mechanics and sediment transport. Stream surveying and classification. River system response to changes in hydrology and sediment supply. Interactions between ecosystems and fluvial systems. Human impacts on stream systems.

Prerequisite(s): BSE 3324 or CEE 3314 or FREC 3104 or WATR 3104

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 4344 - Geographic Information Systems for Engineers (3 credits)

Conceptual, technical, and operational aspects of geographic information systems (GIS) as a tool for storage, analysis, and presentation of spatial information. Focus on data and applications relevant to watershed and ecological engineering and analysis. Access public sources of spatial data including: hydrography, political boundaries, aerial photos, land cover, soil, and elevation (lidar). Digitize new data features from aerial photos. Delineate watersheds. Integrate Global Positioning System data into GIS to create topographic cross sections. Implement GIS to solve an independent watershed engineering problem.

Prerequisite(s): BSE 3324 or CEE 3314 or FREC 3104 or WATR 3104

Instructional Contact Hours: (2 Lec, 3 Lab, 3 Crd)

BSE 4394 - Water Supply and Sanitation in Developing Countries (3 credits)

Social, economic and engineering principles of water supply and sanitation in developing countries as affected by climate, cultural and sociological factors, and material and financial resources. Pre: Junior or Senior standing.

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 4524 - Biological Process Plant Design (3 credits)

Engineering principles for design of systems for processing biological materials into primary and secondary products. Construction and analysis of process flow diagrams. Delivery, scheduling, storage requirements, and profitability and economic analysis. Process control and instrumentation of bioprocessing plants.

Prerequisite(s): BSE 3524

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 4534 - Bioprocess Engineering Lab (1 credit)

Unit operations commonly used in processing biological materials, including filtration, heat transfer, ultrafiltration, crystallization, and protein expression by fermentation, purification by chromatography, and characterization by gel electrophoresis.

Prerequisite(s): BSE 3524 and BSE 3534

Instructional Contact Hours: (3 Lab, 1 Crd)

BSE 4544 - Protein Separation Engineering (3 credits)

Concepts, principles and applications of various unit operations used in protein separations. Properties of biological materials, such as cells and proteins, and their influences on process design. Design of processes for protein purification based on the impurities to be eliminated. Concepts and principles of scale-up of unit operations. Case studies in practical protein recovery and purification issues, with a focus on enhanced protein purification by genetic engineering. Protein purification process simulation and optimization using process simulation software.

Prerequisite(s): BSE 3504 or CHE 3144

Instructional Contact Hours: (3 Lec, 3 Crd)

Course Crosslist: CHE 4544

BSE 4554 - Creating the Ecological City (3 credits)

Multidisciplinary, team oriented, problem-solving approaches to creating cities that foster healthy interconnections between human and ecological systems. Analysis of problems from practical and ethical perspectives in the context of the diverse knowledge bases and values of decision-makers. Formation and utilization of integrated design teams to address complex ecological city design and planning problems at a variety of scales. Pre: Senior standing.

Prerequisite(s): HORT 2134 or FREC 2134

Pathway Concept Area(s): 3 Reasoning in Social Sciences, 6A Critique & Practice in Arts, 6D Critique & Prac in Design, 10 Ethical Reasoning

Instructional Contact Hours: (3 Lec, 3 Crd)

Course Crosslist: FREC 4554, HORT 4554, LAR 4554, SPIA 4554

BSE 4564 - Metabolic Engineering (3 credits)

Engineering concepts for analyzing, designing, and modifying metabolic pathways to convert raw materials to food, pharmaceuticals, fuels and chemicals. Cell metabolism, pathway design, bioenergetics, regulatory mechanisms, metabolic modeling, and genetic tools.

Prerequisite(s): BSE 3534 or BCHM 4115 or BIOL 3774

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 4604 - Food Process Engineering (3 credits)

Analysis and design of food processing operations including thermal pasteurization and sterilization, freezing, extrusion, texturization, and mechanical separation.

Prerequisite(s): BSE 3504 and BSE 3524

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 4634 - Protein Engineering for Biotechnology (3 credits)

Provides theoretical and practical training in protein engineering, emphasizing rational design, computational modeling, and applications in biotechnology. Topics include protein structure and folding, rational and de novo design, noncanonical amino acids, and computational structure prediction. Consideration of ethical and societal implications. Pre: Junior Standing

Instructional Contact Hours: (2 Lec, 3 Lab, 3 Crd)

BSE 4964 - Field Study (1-19 credits)

Instructional Contact Hours: Variable credit course

BSE 4974 - Independent Study (1-19 credits)

Instructional Contact Hours: Variable credit course

BSE 4984 - Special Study (1-19 credits)

Instructional Contact Hours: Variable credit course

BSE 4994 - Undergraduate Research (1-19 credits)

Instructional Contact Hours: Variable credit course

BSE 5044 - Engineering Mathematics (3 credits)

Introduction to numerical solutions of partial differential equations using the finite element method in one-, two-, and three-dimensions with direct relevance to chemical engineering, biological systems engineering and biomedical engineering and sciences. Partial differential equations and ordinary differential equations using finite differences, model parameter sensitivity analysis, optimization, and data analysis. Pre-requisite: Graduate Standing required.

Instructional Contact Hours: (3 Lec, 3 Crd)

Course Crosslist: BMES 5044, CHE 5044

BSE 5124 - AI and Cyberbiosecurity in Water and Agriculture (3 credits)

An introduction to emerging technologies (AI & Cyber) as they are applied to water systems and agriculture. AI topics will include machine learning, neural networks, knowledge-based reasoning, probabilistic inference, and reinforcement learning. Cyberbiosecurity topics will include detecting and mitigating cyber-physical threats, cyber hygiene, protecting big data, cybercrime, and cyber policies. AI and cyber application examples are presented, such as addressing water security challenges, protecting water supply systems, optimizing smart-farming and precision agriculture, using sensors for data collection, and understanding the effects of outlier events on biological systems. While applying AI to biological systems, serious challenges arise, such as the need for AI assurance, bias mitigation, AI explainability, data poisoning, and imbalance challenges. Pre: Graduate standing.

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 5214 - Advanced Topics in Biological Systems Engineering (3 credits)

An in-depth exploration of advanced topics in biological systems engineering. Reading, discussion, summary and presentation of current research in the areas of biological systems engineering. Topics will vary by semester and may include Ecological Engineering for Urban Streams, Hydrometeorology and Water Management, Emerging Surface Water Contaminants of Human Health Concern, Biological Control Systems, Biosensors and Diagnostics, Advances in Engineering Biology, Biomaterials Engineering. May be repeated 3 times with different topics for a maximum of 12 credits. Pre: Graduate standing.

Instructional Contact Hours: (3 Lec, 3 Crd)

Repeatability: up to 12 credit hours

BSE 5224G - Advanced Field Methods in Hydrology (3 credits)

Site characterization: surveying, channel and floodplain mapping, land use, electronic data acquisition. Techniques for measuring surface and subsurface hydrological processes: water flow, hydrologic conductivity, precipitation, evaporation. Sampling techniques: surface water, groundwater, and soil pore water sampling. In-situ monitoring: automatic samplers, dataloggers, water quality sondes. Laboratory analyses: GLP practices, selection of analytical method, calibration, QA/QC. Pre: Graduate standing.

Instructional Contact Hours: (2 Lec, 3 Lab, 3 Crd)

BSE 5244 - Advanced GIS in Hydrologic Analysis (3 credits)

Advanced GIS course focusing on raster analysis with particular application to the issues associated with hydrologic analysis. Application and evaluation of algorithms for terrain analysis, watershed characterization, and hydrologic analysis and modeling as implemented in GIS. Digital elevation data sources and error assessment. Approaches to GIS/model integration and application. Course credit will not be awarded for both CEE 4364 and CEE 5244.

Prerequisite(s): BSE 4344 or CEE 5204 or GEOG 4084 and BSE 3305 or CEE 4304

Instructional Contact Hours: (2 Lec, 3 Lab, 3 Crd)

Course Crosslist: CEE 5244

BSE 5304G - Advanced Watershed Modeling (3 credits)

Fundamental modeling principles used to quantify watershed hydrology, energy budgets, and associated ecosystem functions, such as plant dynamics and biogeochemical processes, at scales ranging from soil pores to watersheds. Code development and model integration to simulate watershed hydrology and nutrient and sediment transport. Model calibration and performance assessment. Data discovery, acquisition, and processing of data relevant to hydrologic/watershed modeling. Pre: Graduate standing.

Instructional Contact Hours: (2 Lec, 3 Lab, 3 Crd)

BSE 5324 - Applied Fluvial Geomorphology (3 credits)

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 5344G - Advanced Geographic Information Systems for Engineers (3 credits)

Instructional Contact Hours: (2 Lec, 3 Lab, 3 Crd)

BSE 5364 - Stream Restoration (3 credits)

Stream restoration practices related to channel dynamics, sediment transport, impact of human activities, aquatic habital improvements, and design and assessment. Inspecting, classifying, identifying and measuring river features of channel morphology to predict river reaction to human activities and watershed change.

Prerequisite(s): BSE 5324

Instructional Contact Hours: (2 Lec, 3 Lab, 3 Crd)

BSE 5404 - Agricultural Nonpoint Source Pollution (3 credits)

Assessment and management of agricultural nonpoint source pollution (NPS). Precipitation, runoff, erosion, pollutant fate and transport, and best management practices. Application of Total Maximum Daily Loads and water quality standards. Pre: Background in physical, chemical, biological, and soil factors affecting the environment and in environmental regulations.

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 5524G - Advanced Biological Process Plant Design (3 credits)

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 5534 - Biosensors (3 credits)

Biosensor fundamentals for animal and human health monitoring. Introduction to biosensors, history of biosensors, classification, characterization and immobilization of biosensors, manufacture of biosensors, nanotechnology, microfluidics, electrochemical biosensors, optical biosensors, enzymatic biosensors, immunosensors, DNA biosensors, implantable sensors, and in vitro biosensors. Pre:

Instructional Contact Hours: (3 Lec, 3 Crd)

Course Crosslist: APSC 5534

BSE 5544G - Advanced Protein Separation Engineering (3 credits)

Prerequisite(s): BSE 3504 or CHE 3144

Instructional Contact Hours: (3 Lec, 3 Crd)

Course Crosslist: CHE 5544G

BSE 5564G - Advanced Metabolic Engineering (3 credits)

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 5614 - Advances in Recombinant Protein Production (3 credits)

Concepts, principles and applications of various expression systems for protein and enzyme production, and the principles and applications of the most current unit operations used in bioseparations. Principles and applications of various methods for protein molecular modification to facilitate its downstream processing. Protein engineering by directed evolution and rational design. Mutant selection and identifications, and establishment of mutant library for protein expression. In vitro synthetic enzymatic biosystems for biomanufacturing. Pre: Graduate standing.

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 5634G - Advanced Protein Engineering for Biotechnology (3 credits)

Instructional Contact Hours: (2 Lec, 3 Lab, 3 Crd)

BSE 5894 - Final Examination (3 credits)

Instructional Contact Hours: (3 Lec, 3 Crd)

BSE 5904 - Project and Report (1-19 credits)

Instructional Contact Hours: Variable credit course

BSE 5944 - Seminar (1 credit)

Selected presentations and discussions by graduate students and faculty.

Instructional Contact Hours: (1 Lec, 1 Crd)

BSE 5954 - Study Abroad (1-19 credits)

Instructional Contact Hours: Variable credit course

BSE 5974 - Independent Study (1-19 credits)

Instructional Contact Hours: Variable credit course

BSE 5984 - Special Study (1-19 credits)

Instructional Contact Hours: Variable credit course

BSE 5994 - Research and Thesis (1-19 credits)

Instructional Contact Hours: Variable credit course

BSE 7994 - Research and Dissertation (1-19 credits)

Instructional Contact Hours: Variable credit course