Research Projects in Professor Korkin’s Lab
Infectious outbreaks in confined environments, such as buildings or passenger transport, present a tremendous risk of rapid infection spread due to the high concentration of infected individuals and a frequent number of contacts. Unfortunately, current epidemiological models aim to study large-scale infection dynamics and cannot benefit from detailed models of infection spread and population behavior. The goal of the project is to develop computational tools to study dynamics of infectious disease outbreaks in confined environments and apply those tools to study highly contagious infections, such as Ebola, influenza, and measles in schools, office spaces, transport, and other environments. In this project, students will leverage the agent-based technology developed in the Korkin Lab. They will model the confined environment as a geographic information system (GIS) and study how the infection spreads, and which containment protocols can efficiently prevent the spread of infection. Background in programming (Java, C or Python) is required.
Research Projects in Professor Harrison's Lab
Research Projects in Professor Olson's Lab
Movement is ubiquitous to cells and takes on many different modes, depending on the particular cell type and the surrounding environment. In the presence of no cues or sources, a cell will often move in a non-biased and non-persistent direction corresponding to a random walk. A bias in their motion would correspond to moving in the direction of a chemical or physical cue. In addition, there may be different cell states, representing different motility patterns or speeds of movement. In this project, students will utilize previously developed cellular automaton (CA) or agent based (AB) computational models to understand the collective motion of groups of cells. Collective motion is the emergence of large scale motions that differ from the motion of a single cell due to interactions and crowding dynamics. Common examples of collective motion include schools of fish and flocks of birds. In this project, we wish to understand the stability of collective motions where the movement of each individual or cell is based on local rules that determine movement and transitions between states. Results of these models can be used to understand pattern formation and dynamics of group behaviors, having applications in the area of bio-inspired artificial intelligence. A background in programming is required.
Research Projects in Professor Ruiz’s Lab
These projects involve the design, implementation and use of algorithms and computational tools that investigate human health behavior. These tools, including health-support mobile apps, enable users to track their own behavior, receive automatic context-sensitive feedback and advice, and adopt healthier behaviors. This set of projects covers a wide range of computational aspects (including the design and implementation of mobile apps, automatic data collection, data mining and predictive analytics), as well as medical and behavioral psychology aspects (including healthy behaviors, addictions, behavioral change, feedback and interventions). Human health behaviors under investigation include sleep habits and eating habits. Programming experience in Java or Python is expected.
Research Projects in Professor Servatius’s Lab
Proteins are large biomolecules, consisting of one or more long chains of amino acid residues. They fold into a so called native state to perform their functions. To describe this folding process mathematically is very difficult. Whenever mathematicians encounter a problem that is too complex to tackle with tools at hand, they consider a simplified model, such as the one introduced by Dill as a tractable model for protein folding. A string of H's and P's is considered. H wants to be close to H, no other force is considered. Moreover, H's and P's can only be placed on the points of a grid, this way one can start with a model in the plane before considering 3-space. This project will introduce you to applied research in the field of discrete mathematics. The goal is to examine interesting examples in the context of literature in biology, mathematics, and computer science. No background other than mathematical curiosity and interest in proteins is required.
Research Projects in Professor Shell’s Lab
Bacterial genomes contain many different genes that allow them to survive in diverse habitats and conditions. However, they don’t want to use all of these genes at any given time. They must turn on, or express, the genes that will help them in the particular environmental condition that they happen to be experiencing, and turn off other genes until they are needed. How do bacteria turn genes on and off in response to environmental cues? In the Shell lab we use next-generation sequencing to measure the expression of thousands of genes in different conditions. Analyzing the large resulting datasets requires computational approaches. Summer students will use computational approaches to analyze gene expression data and help in our quest to understand how bacteria respond to stress. Required background: AP Biology and basic programming experience, preferably with Python. Students without programming experience will be considered if they are willing to complete online training in programming prior to the start of the summer research experience.
Research Projects in Professor Vidali's Lab
Professor Vidali’s labs investigates how plants grow using a combination of microscopy, genetics, bio informatics, and computational simulations. For this summer project, students will develop computer simulations of plant growth using experimentally derived growth parameters. The goal is to re-create existing growth patterns and predict changes in plant shape when the growth parameters are altered. Only basic computer and biology skills are required to participate in this project.