M.Eng. Research Projects

Project Area/Concentration
Interaction of systems and synthetic biology and sustainable energy, background in systems, synthetic or molecular biology; mathematics; physics; or electrical or computer engineering

Project Description
Photosynthesis gives a first draft template for capturing sunlight and storing it with CO2 as biomass at enormous scale, at low or even negative cost, with almost no human intervention. However, this scale belies its inefficiency (0.1% on average). Micro-algae are capable of the most efficient form of photosynthesis (conversion of CO2 and sunlight to carbohydrates) yet seen in nature. However, this efficiency is far from its theoretical maximum, nor has it been fully leveraged for the production of biofuels. A big barrier to improving algal photosynthesis further is the lack of genetic tools to characterize and then engineer the genomes of micro-algae. We have developed Knockout Sudoku, a new technology for rapid, ultra-low-cost construction of whole genome knockout collections: a collection of single-gene knockout mutants for every non-essential in an organism’s genome. We want to construct a whole genome knockout collection for micro-algae to fully leverage their potential.

Possible Courses

• AEP 5200 Intermediate Mathematical Physics
• AEP 5300 Advanced Mathematical Physics
• BEE 5600 Molecular and Cellular Bioengineering
• BME 6130 Advanced Microbiome Engineering

Project Area/Concentration
Intersection of energy and synthetic biology, background in chemistry; electrical or computer engineering; physics; or synthetic biology

Project Description
Batteries have the perfect combination of energy, power density and scalability for automotive and grid-scale energy storage. However, their short calendar and cycle lifespans seriously limits their potential on the future smart grid. Irreversible formation of oxides on battery electrodes causes a gradual degradation of storage capacity. However, electroactive microbes such as Shewanella oneidensis have the potential to reduce and solubilize these oxides, restoring battery capacity at much lower financial, energy and carbon costs than replacement and recycling. However, most electroactive microbes, are unable to operate in harsh battery electrolytes. We aim to use Knockout Sudoku, a new technology for gene discovery developed by my lab, to discover the genetic mechanisms of microbes that thrive in highly alkaline environments and organic solvents. We will use this to build an electroactive microbe capable of operating inside battery electrolytes and restoring energy storage capacity.

Possible Courses

• AEP 5200 Intermediate Mathematical Physics
• AEP 5300 Advanced Mathematical Physics
• BEE 5600 Molecular and Cellular Bioengineering
• BME 6130 Advanced Microbiome Engineering

Project Area/Concentration
Intersection of energy and synthetic biology, background in systems, synthetic or molecular biology; chemistry; electrical or computer engineering; or physics

Project Description
Recent advances in cellulose degradation have yielded dramatic increases in the availability of feedstocks for carbon neutral biofuels. However, the low energy density and poor distribution infrastructure compatibility limits the amount of gasoline that can be displaced by first generation biofuels like ethanol to only ? 10%. This problem is even more acute in aviation where fuel energy density and safety requirements are even more stringent. Unfortunately, the dominant microorganism used for biofuel production, Saccharomyces cerevisiae, is limited in its ability to produce fuels other than ethanol. The oil-producing yeast Yarrowia lipolytica is one of the most promising microorganisms for the sustainable production of advanced biofuels, including gasoline, diesel, and jet fuel. We are using our new technology for gene characterization, Knockout Sudoku, to build a knockout collection for Y. lipolytica and with this learn how to tailor it for advanced biofuel production.

Possible Courses

• AEP 5200 Intermediate Mathematical Physics
• AEP 5300 Advanced Mathematical Physics
• BEE 5600 Molecular and Cellular Bioengineering
• BME 6130 Advanced Microbiome Engineering

Project Area/Concentration
Intersection of energy and synthetic biology, background in chemistry; electrical or computer engineering; physics; or synthetic biology

Project Description
Biology gives a first draft template for capturing and storing the power of the Sun at planetary scale with zero or even negative cost, from Earth abundant elements, and with no human intervention. However, the efficiency of natural photosynthesis is incredibly low (? 0.1%). This means that energy crops have to compete with land for wilderness, and land for agriculture. Electroactive microbes provide the tools to merge the efficiency of solar electricity with the flexibility and efficiency of biological metabolism. However, very little is known about the genomics of these microbes. We are seeking students to help us characterize the genomes of electroactive microbes with Knockout Sudoku, a new technology developed by my team for rapid, ultra-low-cost gene discovery. We aim to find genomic control points in these microbes that will enable engineering through targeted whole genome evolution; and to discover new parts for de novo organisms made through chemical synthesis.

Possible Courses

• AEP 5200 Intermediate Mathematical Physics
• AEP 5300 Advanced Mathematical Physics
• BEE 5600 Molecular and Cellular Bioengineering
• BME 6130 Advanced Microbiome Engineering

Project Area/Concentration
Systems and synthetic biology, background in systems, synthetic or molecular biology; mathematics; physics; or electrical or computer engineering

Project Description
Genomes could hold the keys to making it as easy to manipulate matter and energy as it is to manipulate information today. However, despite enormous advances in gene sequencing, we know very little about what most genes actually do, making exploiting them a tough challenge. Genetic network analysis has the potential to reveal the function of many more genes. However, the most useful tool for genetic network analysis, a double-gene knockout collection, requires a phenomenal amount of time and money to construct, and so far only exists for the baker’s yeast Saccharomyces cerevisiae. My lab has built Knockout Sudoku, a new technology for constructing that drops the cost of whole genome single-gene knockout collection construction from millions of dollars and years of work to only a few thousand dollars and a few weeks. We need help to upgrade Knockout Sudoku to build a rapid, generalizable low-cost method to democratize building double-gene knockout collections.

Possible Courses

• AEP 5200 Intermediate Mathematical Physics
• AEP 5300 Advanced Mathematical Physics
• BEE 5600 Molecular and Cellular Bioengineering
• BME 6130 Advanced Microbiome Engineering

Project Area/Concentration
Synthetic biology, backgrounds in synthetic, systems or molecular biology; physics; chemistry; or electrical or computer engineering

Project Description
Microbes offer one of the most promising routes for the low-cost capture of unconcentrated carbon dioxide from the atmosphere and its storage as a range of dense, non-volatile storage compounds. However, the efficiency and speed of naturally occurring CO2-fixing metabolism are far lower than the requirements of a practical system. We are looking for students to help us develop new rapid whole genome modification tools that leverage data from our Knockout Sudoku gene discovery tool to evolve CO2-fixing metabolism.

Possible Courses

• AEP 5200 Intermediate Mathematical Physics
• AEP 5300 Advanced Mathematical Physics
• BEE 5600 Molecular and Cellular Bioengineering
• BME 6130 Advanced Microbiome Engineering

Project Area/Concentration
High technology and synthetic biology, especially those with a background in electrical or computer engineering; systems, synthetic or molecular biology; physics; or chemistry

Project Description
Biology could make the control of matter and energy as easy as the control of information is today. In particular, biology offers an enormous range of capabilities for sustainable energy from artificial photosynthesis, to the extraction and purification of elements like rare earths that are critical for sustainable energy technologies. However, we don’t know nearly enough about how natural biology works to make this a reality. We have built Knockout Sudoku, a new technology that democratizes the creation of the most important genetic characterization tool for any organism: a whole genome knockout collection, a collection of single gene knockout mutants for every non-essential in an organism’s genome. This is enabling to fully explore, and then exploit the genomes of exotic microbes for solving challenges in energy. To make full use of Knockout Sudoku, we are building a custom automated workflow around Knockout Sudoku.

Possible Courses

• AEP 5200 Intermediate Mathematical Physics
• AEP 5300 Advanced Mathematical Physics
• BEE 5600 Molecular and Cellular Bioengineering
• BME 6130 Advanced Microbiome Engineering

Project Area/Concentration
Synthetic biology and the future of technology, background in electrical and computer engineering, mathematics, physics, chemistry or synthetic or molecular biology

Project Description
Biology could make the control of matter and energy as easy at the control of information is today. The most advanced artificial organisms of tomorrow could have completely synthetic de novo genomes. Whole genome synthesis is possible today, but it’s extremely high cost places it out reach for almost all synthetic biologists. This makes iterative design, and garage synthetic biology almost impossible. We developed Knockout Sudoku, a new technique for making whole genome knockout collections. Knockout Sudoku drops the cost of making a knockout collection from millions of dollars to only thousands, and the construction time from years to weeks. We aim to use the same approach to develop a new technology for rapid, ultra-low-cost whole genome assembly.

Possible Courses

• AEP 5200 Intermediate Mathematical Physics
• AEP 5300 Advanced Mathematical Physics
• BEE 5600 Molecular and Cellular Bioengineering
• BME 6130 Advanced Microbiome Engineering

Project Area/Concentration
Synthetic biology, energy and high technology with backgrounds in molecular or synthetic biology, microbiology, chemistry, physics or electrical or computer engineering

Project Description
Rare earth elements (REEs) are essential ingredients of modern electronics and sustainable energy technologies like automotive electric motors, wind turbines, and solid-state lighting. However, they are diffuse in the Earth’s crust, requiring extraction from extremely large volumes of ore, while their chemical similarity makes purification extremely challenging. These processes are expensive, difficult, and environmentally challenging, creating geopolitical risk for the supply of these elements.Microbes offer a route to the extraction of REEs from ore and their purification under benign conditions. However, naturally occurring microbes do this with far lower efficiency than thermochemical methods. We will use Knockout Sudoku, a new ultra-low-cost gene discovery tool developed by my lab to discover control points in the genomes of REE solubilizing microbes to enhance REE extraction and purification, with the aim of matching or even exceeding the performance of thermochemical methods.

Possible Courses

• AEP 5200 Intermediate Mathematical Physics
• AEP 5300 Advanced Mathematical Physics
• BEE 5600 Molecular and Cellular Bioengineering
• BME 6130 Advanced Microbiome Engineering

Project Area/Concentration
Synthetic biology, and a background in one or more of molecular, micro or synthetic biology; physics; or chemistry

Project Description
Vibrio natriegens is a new genomic powerhouse for synthetic biology and directed evolution. However, it currently lacks the most useful tool for gene characterization for any organism: a whole genome knockout collection: a collection of single-gene knockout mutants for every non-essential in an organism’s genome. We will use Knockout Sudoku, a new technology developed by our team for making knockout collections at ultra-low-cost and high speed, to build a knockout collection for V. natriegens to learn how to fully leverage its potential.

Possible Courses

• AEP 5200 Intermediate Mathematical Physics
• AEP 5300 Advanced Mathematical Physics
• BEE 5600 Molecular and Cellular Bioengineering
• BME 6130 Advanced Microbiome Engineering

Project Area/Concentration
Material Properties, Database, Prediction, Visualization, Crowdsourcing

Project Description
While engineering properties for biomaterials exist in research papers, their access is difficult, and predictability is limited. Researchers at Cornell BEE are currently developing a database which enables easy access and convenient visualization of diverse engineering and manufacturing properties through a crowd-sourced website. A prototype of the website has been built with a sound foundation and basic functionalities—it is able to store, extract and visualize properties for a very large collection of materials. The most significant physical engineering aspect is building frameworks for material properties and ways to make sense of material properties from theoretical, semi-empirical, and empirical sources. The computer science aspects are: enabling crowdsourcing with effective oversight by a community, building user-friendly interface and visualization capabilities that better engages the audience, and improving the backend database and analysis capabilities.

Possible Courses
Transport Processes and Computation

• BEE 5500 Heat and Mass Transfer in Biological Engineering
• BEE 5530 Computer-Aided Engineering: Applications to Biological Processes
• BEE 6880 Applied Modeling and Simulation for Renewable Energy Systems
• MAE 6230 Computational Fluid Dynamics
• MAE 6510 Advanced Heat Transfer

Food Science and Biological Engineering

• FDSC 5230 Unit Operations and Food Packaging
• FDSC 6250 Food Processing: Conventional and Emerging Technologies
• FDSC 6650 Food and Bioprocessing Systems

Project Area/Concentration
Database, Visualization, Animation, Crowdsourcing, Complex Systems

Project Description
Short, concise and annotated video are an effective medium to convey complex ideas to its audience. This project aims to employ the convenience of such a medium to illustrate critical scientific insights into the visual changes occurring during a food processing operation. The central idea is to build a crowdsourced video repository which includes video demonstration and synchronized text-based annotations from the scientific community on the physics, chemistry and biology of the changes that occur in a food during its processing. The challenges in implementing a crowdsourced video system are numerous: How should the platform incentivize submissions and bootstrap a community around the site? What sorts of adjudication, annotation, and tagging are necessary for the user-contributed content, and how can that be scaled up? How does a site encourage a broad collection of users to contribute useful knowledge for a variety of levels of expertise? We already have a working prototype but we are looking for major enhancements in all areas.

Possible Courses
Transport Processes and Computation

• BEE 5500 Heat and Mass Transfer in Biological Engineering
• BEE 5530 Computer-Aided Engineering: Applications to Biological Processes
• BEE 6880 Applied Modeling and Simulation for Renewable Energy Systems
• MAE 6230 Computational Fluid Dynamics
• MAE 6510 Advanced Heat Transfer

Food Science and Biological Engineering

• FDSC 5230 Unit Operations and Food Packaging
• FDSC 6250 Food Processing: Conventional and Emerging Technologies
• FDSC 6650 Food and Bioprocessing Systems

Project Area/Concentration
Simulation, Modeling, Digital Twin, App, Database, Crowdsourcing, Complex Systems

Project Description
The application of physics-based simulation is prevalent in various industrial sectors starting from the aircraft industry to the electronic chip manufacturing industry.  In the food manufacturing sector, the idea is slowly gaining traction but the greatest inhibitor to large scale application of the concept is its innate complexity and the absence of user-friendly tools. We are developing some of the simulation tools that lets the user perform quick calculations without much technical knowledge. For the idea of simulation-based design to take off in the food industry, we need to make this tool available to others and we need a build an effective repository where others can submit the tools they are building, i.e., crowdsource the simulation app repository. The success of the repository will be hinged on sustainability and convenience. The challenge is to ensure sustainability through encouraging contribution from external sources and make the simulation cost affordable by using latest server tools.

Possible Courses
Transport Processes and Computation

• BEE 5500 Heat and Mass Transfer in Biological Engineering
• BEE 5530 Computer-Aided Engineering: Applications to Biological Processes
• BEE 6880 Applied Modeling and Simulation for Renewable Energy Systems
• MAE 6230 Computational Fluid Dynamics
• MAE 6510 Advanced Heat Transfer

Food Science and Biological Engineering

• FDSC 5230 Unit Operations and Food Packaging
• FDSC 6250 Food Processing: Conventional and Emerging Technologies
• FDSC 6650 Food and Bioprocessing Systems

Project Area/Concentration
Process simulation, CFD, Risk, Food Safety, Educational simulation

Project Description
The overall mission of the project is to enhance teaching and learning through the use of simulation. We are working toward enhancing food safety (and quality) education by developing multi-disciplinary (predictive microbiology, engineering, risk analysis), multi-level, quantitative, simulation-based learning modules that are easily incorporated into existing courses. The MEng student will develop Computational Fluid Dynamics (CFD)-based and the software R-based simulations of processes. The student will need knowledge of and interest in engineering simulations and applications to food processes.

Possible Courses
Transport Processes and Computation

• BEE 5500 Heat and Mass Transfer in Biological Engineering
• BEE 5530 Computer-Aided Engineering: Applications to Biological Processes
• BEE 6880 Applied Modeling and Simulation for Renewable Energy Systems
• MAE 6230 Computational Fluid Dynamics
• MAE 6510 Advanced Heat Transfer

Food Science and Biological Engineering

• FDSC 5230 Unit Operations and Food Packaging
• FDSC 6250 Food Processing: Conventional and Emerging Technologies
• FDSC 6650 Food and Bioprocessing Systems

Project Area/Concentration
Biomechanics, sustainable engineering

Project Description
Fish produce vocal sounds using their swim bladder at low frequencies. Some fishes have a very specialized shape of the swim bladder, presumably to enhance the performance of sound production and source localization. Such a tiny & efficient underwater device in source localization can be adapted into sonar sensing in ocean or lakes. In this project, we plan to understand the functional relation between the sound source localization and the swim bladder shape.

This study will include multiple sub-systems to tackle the underlying mechanism. First, we need to create an artificial swim bladder with a thin flexible membrane. Second, we will design electronic components to generate and capture sound at different locations. Third, students will learn how to use multiple high-speed cameras to reconstruct 3D vibrational modes on the swim bladder. Lastly, we will develop theoretical models to understand the acoustic mechanism on the swim bladder.

Possible Courses

• BEE 5310 Bio-Fluid Mechanics
• BEE 5900 Biorobotics
• MAE 5650 Biofluid Mechanics
• MAE 5230 Intermediate Fluid Dynamics with CFD
• MAE 6270 Experimental Methods in Fluid Dynamics

Project Area/Concentration
Biomechanics, human injuries

Project Description
Diving is common activity for animals including humans. However, the water-entry process and mechanism of such complex body shapes is poorly understood and difficult to study, but is of great importance in their injuries. Furthermore, heights greater than 30 feet (~ 10 meters) is arbitrary set for the injury risk of diving into water by governments. However, the Redbull Cliff Diving competition regularly tests people’s abilities to dive from 90 feet.

The goal of this project is to understand the mechanics of human diving by investigating the interplay amongst the overall diving kinematics and their bone structures, muscles, and skin properties. Furthermore, this study will allow us to understand the significance of mechanical forces during diving at different postures. Our proposed research approaches will involve the structural characterizations, reduced-order experimentation, force-measuring electronics, high-speed imaging, and mathematical modeling.

Possible Courses

• BEE 5310 Bio-Fluid Mechanics
• BEE 5900 Biorobotics
• MAE 5650 Biofluid Mechanics
• MAE 5230 Intermediate Fluid Dynamics with CFD
• MAE 6270 Experimental Methods in Fluid Dynamics

Project Area/Concentration
Sustainable engineering, Bio-fluid mechanics

Project Description
The dynamics of drop impact on soft surfaces has drawn a lot of attention for its application, and an analogous natural example is when a raindrop impacts on a leaf. In nature, a leaf deforms and vibrates a lot when a drop impacts at high speeds (2~10 m/s).

Our group aims to develop and explore engineering devices inspired by (1) a natural system in which an elastic leaf interacts with an impacting raindrop. Pedagogically, this study will enable us to understand the fundamental mechanism of how an impulsive fluid drop couples with and drives a beam’s bending. Here, we suggest three innovative suitably engineered systems inspired by natural mechanism of elastic beams coupled with fluid drops. An underlying strategy is to use a piezo-electric material for the elastic beam, and then an electric output is recorded and stored due to mechanical vibrations subject to drop impact. This leads to (2) an innovative energy-harvesting device from raindrops. Moreover, by measuring and analyzing the electric signal, we can infer the size, speed, and other hydrodynamic properties of impacting drops or jets.

Possible Courses

• BEE 5310 Bio-Fluid Mechanics
• BEE 5900 Biorobotics
• MAE 5650 Biofluid Mechanics
• MAE 5230 Intermediate Fluid Dynamics with CFD
• MAE 6270 Experimental Methods in Fluid Dynamics

Project Collaborators
Dr. Anupam Pandey

Project Area/Concentration
Environmental fluid mechanics

Project Description
Waves not only excite surfers, but also captivate artists and scientists alike. For example, The Great Wave by Japanese artist Katsushika Hokusai has become one of the most influential work of art in the world (see figure 1(a)). Looking at it closely, one realizes that the painting remarkably captures the phenomenon of wave breaking into droplets of different sizes.  These tiny droplets remain suspended in air for long times, potentially carrying harmful toxins and pathogens to large distances.

In this project, we will study the generation of tiny droplets and bubbles as a surface wave smash onto rigid surfaces. In particular, we will look into how different surfaces like sand beds and rocky terrains influence this process. This project will combine designing and prototyping of automated components and fundamental understanding of fluid mechanics. The first part of the project will be to design and construct a wave maker with a rotating piston (see figure 1(b)) that can generate long surface waves in a shallow pool of water. The second part will involve full characterization of wave breakup including measurement of droplets/bubble size distribution and their dynamics.

Possible Courses

• BEE 5310 Bio-Fluid Mechanics
• BEE 5900 Biorobotics
• MAE 5650 Biofluid Mechanics
• MAE 5230 Intermediate Fluid Dynamics with CFD
• MAE 6270 Experimental Methods in Fluid Dynamics

Project Collaborators
Dong Wang

Project Area/Concentration
Biomaterials, Hydrogels, Polymer sciences and engineering, Biological Engineering

Project Description
Hydrogels are playing an increasingly important role in a wide variety of applications, especially in the biological and biomedical fields. DNA, as an essential genetic macromolecule and also a generic construction material, has provided unique multifunctionality and programmability for the development of novel hydrogels. Design and preparation of DNA hydrogels have since become an extremely attractive research area because there are exciting possibilities including unexpected properties and functions. This project aims to develop DNA hydrogels with fascinating performance by employing interdisciplinary methodology combing chemical and biological ways, from polymeric to enzymatic techniques. Real-world applications of these novel DNA hydrogels will be explored.

Possible Courses

• BEE 5900 Biorobotics
• MSE 5210 Properties of Solid Polymers

Project Collaborators
Dan Luo

Project Area/Concentration
Biosensing, Biological Engineering, Point of care, Biosensor

Project Description
Rapid sensing of DNA/RNA at Point-of-care (i.e. detection on site) has a significant impact in various fields, from preventing widespread outbreaks of infectious diseases to monitoring environmental pollutions. You will be a member of our team to develop the next generation of POC detection device based on the technologies recently developed in our lab. The research involves an integration of bionanotechnology, microfluidics, image processing, and 3-D printing to design and build a prototype for the real-world applications.

Possible Courses

• BEE 5530 Computer-Aided Engineering: Applications to Biomedical Processes
• BEE 5900 Biorobotics

Project Collaborators
Filipe Espinheira

Project Area/Concentration
Biomaterials

Project Description
Many different types of biomaterials have been used for contact lenses, but there are still challenges. For example, silicone elastomer is highly permeable to oxygen and therefore provides minimal interference to corneal respiration. However, its hydrophobic surface must be treated to allow comfortable wear. Hydrogel lenses (e.g. HEMA based hydrogels) have a high water content and are more comfortable. However, for hydrogel-based lenses, oxygen permeability is low, much lower than the silicone lenses. Another type of contact lenses are the silicone-hydrogel hybrid ones (such as AerGel, a co-blocked silicone-hydrogel with water content of over 40%, Bausch & Lomb), but their manufacturing becomes more complex and expensive. Furthermore, the silicone hydrogels still have lower water content than traditional hydrogel materials. In this project, we aim to develop a new class of contact lenses that have both high oxygen permeability and high water content or wear comfort.

Possible Courses

• BEE 5500 Heat and Mass Transfer in Biological Engineering
• BEE 6400 Advanced Topics in Biomaterials
• CHEME 6400 Polymeric Materials
• MSE 6010 Chemistry of Materials

Project Advisors
Professor Minglin Ma
Professor Michael Timmons

Project Area/Concentration
Fish, diabetes, encapsulation

Project Description
In type 1 diabetes, insulin-producing pancreatic beta-cells are destroyed or impaired. Our lab has been developing encapsulation devices that can allow for donor or stem cell-derived beta cells to be successfully implanted in recipients without immunosuppression, freeing them of diabetes and its related complications. This project will involve investigation of the use of new and inexpensive sources of beta-cells in encapsulation devices. One of the options under study is tilapia islets. In research, tilapia are relatively more sustainable alternative tissue source when compared to traditional animals, given that they are much more inexpensive to obtain and raise, reach maturity more quickly, and have much larger numbers of offspring. Islet cell procurement from tilapia is simpler than from rodents or pigs, and the cells themselves are resistant to hypoxia. It is also thought that tilapia islets do not trigger as strong immune system attack during transplantation as other foreign cells such as porcine islets. Tilapia as an islet source could therefore resolve a multitude of current islet transplant issues.

Possible Courses

• BEE 5500 Heat and Mass Transfer in Biological Engineering
• BEE 6400 Advanced Topics in Biomaterials
• CHEME 6400 Polymeric Materials
• MSE 6010 Chemistry of Materials

Project Area/Concentration
In vitro tissue models

Project Description
The intestinal tract serves as a primary vehicle for exposing humans and other animals to their surroundings. Technically, the length of the GI tract is outside the body and therefore has many mechanisms of both interacting with and protecting against the outside world. Research in understanding the GI tract and the microorganisms that live along its length is limited to animal and very simple in vitro models. This project will work on building a more realistic intestinal model, complete with the peristaltic motions that allow intestinal content to move through the body and that also serve to protect the host from bacterial invasion. Students with interests in mechanical models, the computer/model interface and intestinal biology should consider applying.

Possible Courses

• BME 5390 Circuits, Signals and Sensors: Instrumentation Laboratory
• BME 5850 Current Practice in Tissue Engineering

Project Collaborators
Justine Vanden Heuvel

Project Area/Concentration
Agricultural Biotechnology

Project Description
There are over 1,043,000 acres of bearing grapes in the United States (National Agricultural Statistics, 2012). With the exception of approximately 67,000 acres being grown in Washington state, the vast majority of the remaining >900,000 acres don’t grow on their own roots; they are grafted onto rootstocks that are either tolerant or resistant to Phylloxera vastatrix – a microscopic insect related to aphids that feeds on the roots of most commercially-grown grapevines. We are trying to determine the factors that play into selection of grapes by phylloxera. Students with interest in chemical ecology or interspecies communication should consider applying. Our focus will be on first understanding then manipulating crosstalk between phylloxera and their hosts.

Possible Courses

• ENTOM 5200 Grape Pest Management

Project Collaborators
Mary Austerman

Project Area/Concentration
Flood risk assessments

Project Description
In this project, students will conduct work to support the development of a quantitative flood risk assessment tool for shoreline communities along Lake Ontario that is part of an ongoing collaboration between Cornell University and New York Sea Grant. This project will consist of two primary objectives: 1) compare FEMA flood hazard maps to those developed by the Cornell tool to help determine how these approaches differ in their quantification of flood risk; and 2) develop a statistical model that can help predict areas of the shoreline where flood risk estimated by these tools most likely diverges.

Possible Courses

• BEE 6110 Hydrologic engineering in a changing climate
• BEE 6310 Multivariate statistics for environmental applications
• BEE 5730 Watershed engineering
• CEE 6200 Water resources systems engineering
• CRP 5080 Introduction to GIS for planners

Detailed Description
Over the last 3 years, shoreline communities on Lake Ontario have experienced two major flood events. In June 2017, water levels reached 75.88 m, the highest in the 100-year record. This record was again broken in May 2019, when water levels reached 75.92 m. These floods occurred soon after the establishment of a new lake level management plan (Plan 2014) that influences water levels on the lake through releases at the Moses Saunders dam on the St. Lawrence River. These floods also followed record setting precipitation in the Great Lakes basin.

Shoreline communities blame the flooding on new operations under Plan 2014, while the international board that manages the lake argues that the flooding was caused by unprecedented precipitation and would have occurred under the previous management plan. Regardless of the cause, the recent flooding has introduced a heightened urgency among municipal, county, and state officials to better prepare shoreline communities for an evolving and uncertain flood regime.

In parallel to the above developments, FEMA has been updating the flood hazard maps used to establish floodplains along the lakeshore and set flood insurance requirements for new construction. FEMA’s Great Lakes Coastal Flood Study uses state-of-the-art hydrodynamic modeling to integrate water level, storm surge, and wave runup processes into aggregate measures of flood risk. However, it is unclear whether and how the updated FEMA maps have accounted for shifts in flood risk under new lake level management or recent changes in basin-scale climate.  

In this project, M.Eng students will conduct work to support the development of a quantitative flood risk assessment tool for shoreline communities that is part of an ongoing collaboration between Cornell University and New York Sea Grant. This project will consist of two primary objectives: 1) compare FEMA flood hazard maps to those developed by the Cornell tool to help determine how these approaches differ in their quantification of flood risk; and 2) develop a statistical model that can help predict areas of the shoreline where flood risk estimated by these tools most likely diverges.

For Objective 1, students will collect a variety of existing data, including flood elevations for individual shoreline parcels estimated using legacy and updated FEMA mapping products, as well as the Cornell flood risk tool that accounts for water level variability under the updated lake level management plan. Students will also collect key attributes of these parcels, including nearshore and backshore slope, shoreline type, and the presence of shoreline protection structures. Students will use ArcGIS to determine the differences in key flood hazard elevations and will diagnose major discrepancies between the products.

This comparison will form the basis for Objective 2, in which students will use data analytics in the R statistical software environment to develop a model that can predict major discrepancies between the different flood risk products. Using standard statistical regression models and machine learning algorithms (e.g., regression trees), students will determine which shoreline attributes are most associated with differences in parcel-level estimates of flood hazard. This model will then be used to predict discrepancies between the FEMA and Cornell approaches at locations along the shoreline, including those without recent FEMA data.

Students will document data collection, model development, and prediction accuracy in a final project report. The results of this analysis will help NYSG understand the degree to which the Cornell tool can be used for screening level assessments of flood risk, particularly under different scenarios of water level management and climate change that are not accounted for in the FEMA assessments.

Project Area/Concentration
Environmental, Soil and Water

Project Description
Students will work in teams to collect stormwater infrastructure data and analyze the existing capacity of the system. Stormwater infrastructure refers to road culverts but may also include road ditches, stormwater catch basins and pipes, stormwater retention structures, and green infrastructure (e.g., bioswales). The capacities through the stormwater system will be compared to estimates of storm runoff under recent and projected climate conditions as well as current and projected land uses. All data and analyses will be incorporated into a regional database for use by communities and municipalities in prioritizing stormwater upgrades. In addition, a final report will be prepared for each watershed-based team and uploaded to the Internet.

Students will also receive formal training in the North Atlantic Aquatic Connectivity Consortium (NAACC) protocols for assessing potential aquatic barriers. These protocols will be used in field data collection and the data will be added to the regional NAACC database. Some students may choose to develop a project that utilizes these data.

Possible Courses
Hydrology and Aquatic Ecology

• BEE 6710 Introduction to Groundwater

Water Resources Engineering and Management

• BEE 5730 Watershed Engineering
• CEE 5980 Design Framing and Analytics
• CEE 6200 Water Resources Systems Engineering
• NTRES 6240 Sustainable, Ecologically Based Management of Water Resources

Applied Computational Tools

• CEE 6100 Remote Sensing Fundamentals
• PLSCS 5200 Geographic Information Systems (GIS): Concepts and Application

Project Area/Concentration
Microfluidics, environmental biology

Project Description
The occurrence of harmful algal blooms (HABs) has been increasing due to nutrient enrichment of waters by the run-off from urban, agriculture and industrial development. HABs are caused by sudden growth of cyanobacteria, that secret toxins causing severe health problems and endangering aquatic systems. Current assays for studying HABs are large scale, experimental ponds or test tubes, they are not designed to study multiple environmental cues on the growth of cyanobacteria. As a result, there is limited understanding for the onset condition of HABs. This project will introduce students to use nano- micro- technology to study single cell growth under well-controlled complex environmental conditions. The goal of the project is to find a sustainable solution for the management of HABs. Students who have either microfabrication or microbiology background is strongly encouraged to apply.

Possible Courses
I select a set of courses together with students depending on the research project and students career goal. Everyone is different, and there is no one set of courses that fit all. In general, I emphasize the physical aspect of biological engineering including cellular engineering and bioinstrumentation.

Core

• BEE 6550 Biologically Inspired Microsystems Engineering
• BME 6260 Optical Microscopy and Fluorescence Methods for Research

Optional and largely dependent on student background

• BME 5390 Circuits, Signal and Sensors: Instrumentation Laboratory
• MAE 6680 Cancer for Engineers and Physicists