2019 Summer REU Program

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Undergraduate students examining falcon during biodiversity lab tour
June 10 - August 8, 2019
8:00AM - 5:00PM
Location
MBI Auditorium, Jennings Hall 355

Date Range
Add to Calendar 2019-06-10 08:00:00 2019-08-08 17:00:00 2019 Summer REU Program

MBI administers a multi-institution summer REU (Research Experiences for Undergraduates) program in the mathematical biosciences each year. The objectives of the program are: (1) to introduce a diverse cohort of undergraduate students to the mathematical biosciences, broadly interpreted to include areas such as biostatistics, bioinformatics, and computational biology, in addition to biologically-inspired mathematical modeling; (2) to encourage students to pursue graduate study in the mathematical biosciences; and (3) to increase the number of students who enter the workforce with training in this field.

REU participants work on projects in areas such as molecular evolution, neuronal oscillatory patterning, cancer genetics, epidemics and vaccination strategies, and animal movement.  Participants work individually or in pairs under the guidance of expert mentors to make specific research contributions in these areas, often leading to a peer-reviewed publication and conference presentations. The REU program incorporates various professional and research-skills development activities throughout the summer to help ensure the participants’ success in completing their summer project and to prepare them for graduate study or entering the workforce.

The program consists of three parts:

  • Mathematical Biosciences Bootcamp (June 10th-14th, 2019) at MBI
    Participants are introduced to various areas of the mathematical biosciences via lectures, computer labs, and visits to biological labs on campus.
     
  • Mentored Research Experience (June 17th-August 2nd, 2019) at the REU host sites
    Participants complete a mentored research project individually or in pairs at one of MBI's partner institutions. Participants also attend a weekly online seminar series and virtual all-program meeting.
     
  • Capstone Week (August 5th-8th, 2019) at MBI
    Participants return to MBI for a wrap-up week featuring student talks and posters, keynote talks by prominent mathematical and biological scientists, and Q&A panels.
MBI Auditorium, Jennings Hall 355 Mathematical Biosciences Institute mbi-webmaster@osu.edu America/New_York public
Description

MBI administers a multi-institution summer REU (Research Experiences for Undergraduates) program in the mathematical biosciences each year. The objectives of the program are: (1) to introduce a diverse cohort of undergraduate students to the mathematical biosciences, broadly interpreted to include areas such as biostatistics, bioinformatics, and computational biology, in addition to biologically-inspired mathematical modeling; (2) to encourage students to pursue graduate study in the mathematical biosciences; and (3) to increase the number of students who enter the workforce with training in this field.

REU participants work on projects in areas such as molecular evolution, neuronal oscillatory patterning, cancer genetics, epidemics and vaccination strategies, and animal movement.  Participants work individually or in pairs under the guidance of expert mentors to make specific research contributions in these areas, often leading to a peer-reviewed publication and conference presentations. The REU program incorporates various professional and research-skills development activities throughout the summer to help ensure the participants’ success in completing their summer project and to prepare them for graduate study or entering the workforce.

The program consists of three parts:

  • Mathematical Biosciences Bootcamp (June 10th-14th, 2019) at MBI
    Participants are introduced to various areas of the mathematical biosciences via lectures, computer labs, and visits to biological labs on campus.
     
  • Mentored Research Experience (June 17th-August 2nd, 2019) at the REU host sites
    Participants complete a mentored research project individually or in pairs at one of MBI's partner institutions. Participants also attend a weekly online seminar series and virtual all-program meeting.
     
  • Capstone Week (August 5th-8th, 2019) at MBI
    Participants return to MBI for a wrap-up week featuring student talks and posters, keynote talks by prominent mathematical and biological scientists, and Q&A panels.
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Project Descriptions

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Project 1 (Mentor: Dr. Jared Barber): Characterizing interactions between pairs of cells in tube/vessel flow: Blood is composed of mainly red blood cells (45%) and plasma. As blood flows through vessels, cells near walls are pushed towards the vessel center by wall interactions but pushed away from the vessel center by interactions with other cells. These competing effects have a primary role in how cells are distributed across the vessel which, in turn, affect distribution of other important quantities like oxygen. We have developed a two-dimensional computational model of red blood cell motion to use to consider how two isolated cells interact near vessel walls. The project, based on past work, will be to use the model to consider different types of interactions that pairs of cells undergo in this environment, how flexibility and vessel width affect the strength of these interactions, and the implications of such findings on red blood cell distribution across the vessel lumen.

Project 2 (Mentor: Dr. Julia Arciero): The role of blood flow regulation and oxygen transport in glaucoma: Dysfunctional blood flow regulation and impaired oxygenation of the retina have been identified as potential factors contributing to glaucoma.  In this project, students will adapt a theoretical model to simulate flow regulation in a heterogeneous retinal arteriolar network obtained from confocal microscopy images.  Blood flow regulation will be modeled using the length-tension characteristics of vascular smooth muscle that are assumed to depend on myogenic, shear-dependent, and conducted metabolic responses.  Oxygen transport will be simulated in the vasculature and surrounding tissue using a Green’s function model that allows for a non-uniform network structure.  The impact of the regulatory mechanisms will be assessed by simulating responses independently and in combination.  Overall, this model will allow for spatial predictions of tissue oxygenation in the retina, which is an important feature for identifying hypoxic regions in a realistic, heterogeneous retinal vascular network and for providing insight into glaucoma risk factors.

Project 3 (Mentor: Dr. Jared Barber): Using a computational model to investigate breast cancer cell translocation: Breast cancer deaths are usually not due to the site of primary infection but rather by metastases at other locations. Preventing breast cancer cells from entering blood vessels (intravasation), traveling to other potential tumor sites (translocation), and migrating into the tissues at those sites (extravasation) could help mitigate the effects of cancer on the estimated 3.5 million people with a history of breast cancer. Experiments suggest that prevention of these metastatic events can depend on cell physical properties such as elastic and viscous coefficients as well as physical forces acting on the cells that can instigate mechanotransduction of cellular processes such as apoptosis, division, and others. To study these physical properties and forces, we have constructed a mechanical model of an individual cancer cell in a microfluidic device. The project is to investigate the numerical stability of our model by considering the numerical stability associated with a couple of simpler problems. Numerical stability corresponds with the step size one can take when running a simulation which corresponds with the overall speed with which one can produce a simulation. Understanding what parameters significantly affect the numerical stability of our model will help us as we calibrate and improve the current model so that we can use it to investigate how cell properties and mechanotransduced processes may contribute to the metastatic potential of breast cancer cells.

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Project 1 (Mentors: Dr. Simon Garnier (NJIT), Dr. Jason Graham (U of Scranton)): Models of pattern formation and decision making in slime mold: In a complex and dynamic world, how do you navigate your environment when you do not possess a brain, or even the beginnings of a nervous system? From bacteria and immune cells to fungi and plants, the large majority of living beings face this problem every day. Nevertheless our knowledge of decision-making mechanisms is mostly limited to those of neuronal animals, and in particular vertebrates. The goal of this project is for students to explore with University of Scranton Associate Professor Jason Graham and NJIT Associate Professor Simon Garnier the navigational abilities of a non-neuronal model organism: the slime mold Physarum polycephalum. Using models of morphogenesis, the students will study (1) how external and internal stimuli modify the morphology of this giant cell as it moves through its environment and (2) how this morphological changes result in the integration of noisy and contradictory information during decision-making by P. polycephalum. The students will also compare their results to experimental data collected by Garnier’s lab as part of an IOS NSF-funded research effort. The results of this work will help understand information processing in organisms without a brain, thereby advancing our comprehension of the emergence of cognitive processes in biological systems.

Project 2 (Mentors: Dr. Anand U. Oza): Hydrodynamic interactions in animal schools and flocks: The complexity and beauty of fish schools and bird flocks have long fascinated scientists, as their complex collective dynamics are readily observed in nature. Recent experiments have suggested a hydrodynamic function for orderly formations in schools and flocks, but hydrodynamic interactions between fast-moving animals remain poorly understood. The goal of this project is for students to develop and analyze a mathematical model for schooling and flocking that accounts for the vortices shed by flapping wings. The model accounts for the temporally nonlocal hydrodynamic interactions between constituents, wherein the forces between bodies at a given time depend on their past positions and velocities. The project will combine mathematical analysis and computation to shed light on the role of hydrodynamics in stabilizing schooling formations, and the potential speed and energetic benefits of such formations.

Project 3 (Mentor: Dr. Enkeleida Lushi): Coupled dynamics of predator and prey plankton: Bdellovibrio bacteriovorus (BV) is a predator bacterial species found in the environment and within the human gut which preys and hunts other pathogen bacteria like Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus. Due to this remarkable ability, it is suggested that BV may serve as a biocontrol agent and a living antibiotic. We will explore a simple mathematical model of BV sensing and hunting pathogen bacteria with various shapes and surface attachment properties, to explore how BV proliferates whether it manages to eradicate a pathogen colony.

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Project 1 (Mentor: Dr. Chuan Xue): Mathematical models for intracellular transport: A biological cell is like a city, and it has an internal transportation system that connects different parts of the cell. Nearly all cellular functions rely on the active transport of various cargoes, including proteins and organelles, inside the cell. Microtubules are long, dynamic polymers that serve as highway tracks for intracellular transport. Kinesin and dynein are motor proteins that move cargoes back and forth along microtubules. Disruptions of intracellular transport in nerve cells can cause local swelling of the axon, similar to a traffic jam that we see in real life, leading to nerve cell degeneration in severe situations. These phenomena have been found in many neurodegenerative diseases, such as ALS, Alzheimer’s and Parkinson’s. In this project, we will use mathematical models to investigate how intracellular traffic is regulated under normal conditions and how intracellular traffic jams arise under abnormal conditions. Sponsored in part by NSF CAREER Award 1553637.

Project 2 (Mentors: Dr. Oksana Chkrebtii, Dr. Amir Asiaeetaheri): Approximate Inference of Cancer Progression Network from Cross-sectional Data: We are interested in modeling the way cancer progresses. The observations that we usually have are outcomes of life long gain of genetic aberrations and therefore it is very challenging to use them to reverse engineer the sequence of events that caused cancer. For each type of cancer, genetic aberrations will progress differently and understanding the order of such events are of interest for early detection and targeted therapy. We assume that there is an underlying network structure (summarized by a directed acyclic graph, or DAG) that determines the order of events. We then assume that sample patient cancers are generated probabilistically by the DAG. Realization of the underlying progression network in each patient is different, which results in various clones. We have developed a probabilistic engine that generates aberrations for different clones and returns the superposition of those aberrations as a synthetic sample. This model is written in terms of several unknown parameters, and a primary goal of this project is to simultaneously infer the cancer progression network and parameters of the sample generating engine from cross-sectional samples.

Project 3 (Mentors: Dr. Adrian Lam, Dr. Rachidi Salako): Phytoplankton Competition in Water Columns: Human activities have accelerated the eutrophication of many freshwater lakes and coastal ecosystems, including Lake Erie in the US and the Baltic Sea in Europe, causing harmful algal blooms (HABs) to emerge. This phenomenon can be explained by the competitive reversal between diatoms and cyanobacteria (or blue-green algae). Several ways of mitigating the phenomenon, involving physical mixing of the lake, has proved effective. In this project we will use a spatial model to study the competition dynamics among multiple phytoplankton species, to better understand HABs, and to weigh the cost and benefit of each mitigating method. This project will have a numerical component using Matlab programming, and an analysis component based on simplified models.

Project 4 (Mentors: Dr. Adrian Lam, Dr. Rachidi Salako): Spreading Phenomena of Interacting Species with Multiple Speeds: While the spreading of a single species in an unoccupied habitat is well understood, the question has been largely open in case of multiple species. The latter question has the potential to explain, for instance, the spreading of plant species in the de-glaciated North American continent after the last ice-age. In this project we will use the Lotka-Volterra model to study how multiple species spread into an empty habitat with multiple spreading speeds, and to recover the different speeds from model parameters. This project will have a numerical component using Matlab programming, and an analysis component based on simplified models.

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Mathematical Biosciences Bootcamp Schedule 

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Time Session
09:00 AM
10:00 AM
Welcome and Introductions
10:00 AM
11:00 AM
Project Introductions - Jared Barber, IUPUI
11:00 AM
12:00 PM
Project Introductions - Enkeleida Lushi, NJIT
12:00 PM
01:30 PM
Lunch Break
01:30 PM
02:00 PM
Remote Desktop Connection Testing
02:00 PM
04:00 PM
Software Tutorials - MATLAB and XPP
04:00 PM
05:00 PM
Project Introductions - Anand Oza, NJIT
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Time Session
9:00 AM
10:00 AM
Project Introductions - Julia Arciero, IUPUI
10:00 AM
11:00 AM
Project Introductions - Oksana Chkrebtii, OSU
11:00 AM
12:00 PM
How to Write Scientific Papers
12:00 PM
01:30 PM
Lunch Break
01:30 PM
03:00 PM
Software Tutorial - R
03:00 PM
05:00 PM
Lab Tour - Aquatic Ecology Lab
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Time Session
9:00 AM
11:00 AM
Lab Tour - Dawes Lab, Molecular Genetics
11:00 AM
11:30 AM
Work Time
11:30 AM
01:00 PM
Lunch Break
01:00 PM
01:30 PM
Postdoc Breakout Session - Working with an Advisor
01:30 PM
03:00 PM
Software Tutorial - LaTeX
03:00 PM
05:00 PM
Lab Tour - Wetlands Research Park
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Time Session
9:00 AM
10:00 AM
Postdoc Panel - Career Paths
10:00 AM
11:30 AM
Work Time
11:30 AM
01:00 PM
Lunch Break
01:00 PM
02:00 PM
Presentation Reviews with Postdocs and Mentors
02:00 PM
03:00 PM
The Academic Publishing Process
03:00 PM
05:00 PM
Lab Tour - Museum of Biological Diversity
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Time Session
09:00 AM
09:30 AM
Henry Fessler - Information Transfer During Slime Mold Food Decisions
09:30 AM
10:15 AM
Mandy Abernathy & Hannah Scanlon - The Role of Blood Flow Regulation and Oxygen Transport in Glaucoma
10:15 AM
11:00 AM
Courtney Deaver & Phil Nicol - Approximate Inference of Cancer Progression Networks
11:00 AM
12:00 PM
Research Talk - Omar Saucedo
12:00 PM
01:30 PM
Lunch Break
01:30 PM
02:00 PM
Francesca Zumpano - Modeling a Predator Prey Reaction Between Bdellovibrio Bacteriovorus (BV) and E. Coli
02:00 PM
02:30 PM
Laynie Jensen - The U-Shaped Trap Problem: Modeling Decision Making in Slime Mold
02:30 PM
03:00 PM
Alan Gan - Modeling Breast Cancer Cell Motion Through a Microfluidic Channel
03:00 PM
03:30 PM
Joe Huang - Homeostasis in Gene Networks
03:30 PM
04:15 PM
Emily Mader & Kay Pontarelli - Phytoplankton Competition in Water Columns
04:15 PM
05:00 PM
Postdoc Poster Session and Reception
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Capstone Week Schedule 

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Time Session
09:30 AM
09:45 AM
Daily Introduction
09:45 AM
11:15 AM
Elizabeth Marschall
Aquatic Ecology Laboratory, The Ohio State University

Combining Field, Laboratory, and Modeling Approaches in Ecological Research
11:30 AM
01:00 PM
Lunch Break
01:00 PM
02:00 PM
Talks and Slides Advice Session
02:00 PM
03:30 PM
Panel on Topics Related to Graduate School
03:30 PM
05:00 PM
Poster Session and Pizza Reception
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Time Session
09:30 AM
09:45 AM
Daily Introduction
09:45 AM
11:15 AM
Nina Fefferman
Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville

Evolving Efficient Solutions: How Simple Natural Systems Solve the Most Complicated Problems
11:30 AM
01:00 PM
Lunch Break
01:00 PM
02:00 PM
Panel on Career Opportunities
02:00 PM
02:30 PM
Informal Discussion with Panelists
02:30 PM
02:55 PM
Henry Fessler - Discrete Shuttle Streaming of Slime Mold
02:55 PM
03:20 PM
Laynie Jensen - Modeling Slime Mold Decision-making: The U-Shaped Trap Problem
03:25 PM
04:00 PM
Mandy Abernathy & Hannah Scanlon - Developing Mathematical Models of the Retinal Microvasculature
06:30 PM Columbus Clippers Baseball Game
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Time Session
09:30 AM
09:45 AM
Daily Introduction
09:45 AM
10:10 AM
Francesca Zumpano - Separating Motile and Immotile Bacteria Through Confined Chemotaxis
10:10 AM
10:35 AM
Joe Huang - Homeostasis in Network Based on Simple Path
10:40 AM
11:15 AM
Courtney Deaver & Phillip Nicol - Inferring Cancer Progression Networks from Cross-Sectional Data
11:30 AM
01:00 PM
Lunch Break
01:00 PM
02:30 PM
Ralf A. Bundschuh
Department of Physics, The Ohio State University

Prediction of Protein-RNA Interactions
02:30 PM
02:45 PM
Break
02:45 PM
03:10 PM
Alan Gan - Steady and Near-Steady State Cancer Cell Model
03:10 PM
03:35 PM
Greg LeVay - Modeling mRNA Localization in the Vegetal Cortex
03:40 PM
04:15 PM
Emily Mader & Katherine Pontarelli - Principal Eigenvalues for Phytoplankton Populations
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Time Session
09:30 AM
09:45 AM
Daily Introduction
09:45 AM
11:15 AM
Adriana Dawes
Department of Mathematics, The Ohio State University

Patterns, Patterns Everywhere! Using Math to Understand the World Around Us
11:15 AM
11:45 AM
Group Photo and Wrap-Up
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National Science Foundation Logo
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This program is supported by the National Science Foundation Division of Mathematical Sciences (DMS) award number DMS-1757423.

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