Program Overview

Research in Computational Science

The COMS-REU program provides prospective undergraduates with a 8-week program of study focused on developing practical research skills in the area of computational science. Students learn a blend of computational approaches from the fields of computer science and mathematics with a focus on solving problems in the applied sciences (in particular, biology and physics). Accepted applicants are provided on-campus housing for the duration of the 8-week program (during the summer) along with a $4K stipend.

Students develop skills in computer programming (Python, GitHub, JupyterLab), high-performance computing (Linux, Torque, MPI) and mathematical modeling (differential equations - numpy/scipy/COMSOL, machine learning - SciKitLearn/Keras, and model validation) during the first half of the program. During the second half of the program, students develop practical research skills including experiment/simulation design/testing and data generation/presentation by working closely with program faculty on applied research projects from scientific domains.

How to apply

Please use the link below to complete an REU application. After you click the link, you will need to create an account by selecting the "Create New Account" option displayed beneath the Log In button. Attention MTSU students: when creating the account, do NOT use your MTSU email account. You must use a non-MTSU (personal) email account.

Click here to apply for Summer 2019 Click here for additional program information [PDF]

Schedule

Dates Activity Responsible
Sunday, June 2Orientation: Check in to dorm, connect to WiFi and learn about food optionsDr. Leander
Monday, June 3Orientation: Meet with project mentors and other REU students, complete paperwork, and tour campus facilitiesFaculty Mentors
Regular Weekdays
Monday-FridayResearch with mentorsStudent Teams and Faculty Mentors
Tuesdays & ThursdaysWorkshops on research methods and professional developmentFaculty Mentors
WednesdaysLunch with research groupsResearch Groups
FridaysProject team meeting (progress checks)Faculty Mentors

Location

Middle Tennessee State University

The COMS-REU program takes place on the campus of Middle Tennessee State University in Murfreesboro, TN. Dormitory housing for students is provided on the campus, and the city bus system provides access to restaurants, shopping, etc. throughout the city of Murfreesboro. Some of these options are within walking distance of the campus. From the campus, it is a 45-minute drive to the capital city of Nashville and planned social events provide opportunity for students to visit Nashville while in the area.

Click below to obtain more information about our campus, city, and the surrounding region:

MTSU Directions Interactive Map Murfreesboro Nashville State Parks

Timeline

Date Activity
January-MarchRecruit Participants
January-MarchDevelop workshop materials, design surveys
MarchContact accepted applicants and arrange travel
AprilConduct pre-REU surveys
MayMentor training
June 2Student orientation
June 3 - June 7Python bootcamp 9:00-11:00, 1:00-4:30 research meeting
June 8 - July 26Research investigations
July 1Conduct midpoint survey
July 26Research celebration and conduct post-survey
August-Prepare results for publication and present results at professional meetings

Workshops

Title Speaker Topics
Python Boot Camp Part 1: Introduction to programming in Python Dr. Phillips Object-oriented programming, functional programming, logic, structuring code, readability, sharing code, plotting, Python libraries, Jupyter notebooks
Python Boot Camp Part 2: Direct optimization and analysis in Python Dr. Robertson Motion prediction using Euler and Euler-Cromer method, simulated annealing, neural networks, data classification
Modeling with differential equations Dr. Ding Interpreting ODE models, parameterization, model fitting, stability analysis, sensitivity analysis, model comparison, and numerical simulation
Modeling with stochastic differential equations Dr. Leander Stochastic integration, deriving an SDE from a discrete stochastic model, and computational methods for solving SDEs
Molecular modeling Dr. Phillips Molecular modeling and simulation (GROMACS, bash), post-simulation analysis with statistical and machine learning techniques (MDAnalysis, Keras/TensorFlow, and SciKitLearn), and visualization of molecular models and simulations (Pymol, VMD)
Documentation and reproducibility in computational research Dr. Phillips Collaborative coding, code versioning and code repositories
Tips for preparing a research article for publication Dr. Brinthaupt (LT&ITC) Finding the appropriate journals and writing the manuscript in a professional way
Tips for building and maintaining professional collaborations Dr. Brinthaupt (LT&ITC) Finding collaborators and resolving problems
Tips for getting the most from professional meetings Dr. Brinthaupt (LT&ITC) Creating a professional presentation, presenting and networking
Machine Learning Molecular Dynamics Optmization Differential Equations Scientific Computing

MTSU-COMS REU

Faculty Mentors

Dr. Wandi Ding

Dr. Wandi Ding

Mathematics (PI)

Website

Dr. Ding's research interests include mathematical biology, computational biology, mathematical modeling, ordinary and partial differential equations, difference equations and hybrid systems. Applications include population dynamics, disease modeling, natural resource management, systems biology and quantum biology.

Dr. Ding's research focuses on understanding the spatial and temporal patterns that arise in dynamic biological systems and, when possible, finding the best way to control the system.

Dr. Rachel Leander

Dr. Rachel Leander

Mathematics (co-PI)

Website

Dr. Leander uses mathematical modeling and data analysis to study cellular processes. She is especially interested in the analysis of cellular decisions, including division and death. She collaborates with biologists to build detailed, mechanistic models of intracellular processes as well as top-down, qualitative models of processes occurring at the level of an individual cell or population. In coupling these models to biological data, she develops custom numerical methods.

Dr. Joshua L. Phillips

Dr. Joshua L. Phillips

Computer Science (co-PI)

Website

Dr. Phillips' research interests are in computational biophysics and cognitive science, but primarily on the development of novel computational methods for addressing existing scientific or engineering problems related to molecular or structural biology. His background is in machine learning and neural networks, so his work often employs or is inspired by algorithmic approaches from these fields.

Dr. William Robertson

Dr. William Robertson

Physics (co-PI)

Website

Dr. Robertson's research interests cover a broad range of subjects in optics and acoustics explored both experimentally and through numerical simulation. Some key areas of current interest are acoustic and photonic band gap materials, acoustic metamaterials, fast and slow wave phenomena (including superluminal sound), surface electromagnetic excitations including surface plasmons and surface waves on photonic crystals, label-free biosensing, signal processing of speech and musical sound manipulation, and the design of innovative diffractive optics.

Funding

Funding for the COMS REU program is provided by the National Science Foundation (Award #1757493).