REU Site Summer Research Program

Program Overview

This NSF-funded project establishes a Research Experience for Undergraduates (REU) in Interdisciplinary, Multiscale Materials Modeling (I3M) at the University of Louisville (UofL) specifically focusing on Computational Chemistry and Molecular Dynamics methods and their application to materials and biological and biomimetic systems. This site will host 9 undergraduate students (Fellows) each summer from 2021 to 2023 at the University of Louisville located in Louisville. KY. It is not expected that REU fellows would have this background prior to their summer internship. Fundamentals of computational chemistry and molecular simulations coupled with hands-on computer laboratory training will be provided at the start of the REU program. Additional training will be provided by faculty mentors and participating graduate students as pertains to the specific REU project. Eighteen faculty members from the SPEED School of Engineering (Chemical Engineering, Mechanical Engineering, Bioengineering), Chemistry, Physics, and Medicine have provided 15 projects from which the REU Fellows can select. Participating Faculty Mentors are identified in the section on REU Faculty Mentors and Departmental Affiliations.  All 15 projects are listed in the following section on Available REU Projects. REU Fellows will have the opportunity to become proficient in a particular method associated with their selected project.

Multiscale Materials Modeling
Computational methods and their location on the multi-scale map

Figure 1. Computational methods and their location on the multi-scale map

The research focus of our REU Site is Multiscale Materials Modeling. The 15 projects utilize different computational approaches to address focused projects offered by experienced faculty members representing multiple disciplines. In addition to working with project faculty, REU Fellows will interact with graduate students pursuing PhD degrees. The REU Fellows will be introduced to a variety of different computational methods such as Computational Chemistry (quantum mechanics), Molecular Dynamics, and Finite Elements that span the range of size and time domains as illustrated in Figure 1 and discussed briefly in the following sections. Individual REU Projects that utilize one or more specific computational approach are identified in each of the following sections.

Figure 2. H-bonding between a drug and polymer nanoparticle

Figure 2. H-bonding between a drug and polymer nanoparticle

Computational Chemistry

uses different approaches to obtain an approximate solution to the classical SchrÖdinger wave equation that can provide valuable information about individual molecules or small molecular clusters (small scale). Computational Chemistry methods include atomistic approaches such as first principles or ab initio methods, density function theory (DFT), and semiempirical approaches that require experimental parameterization but have the advantage of being computationally quicker and can be used to characterize larger molecules, such as proteins; however, results may be less accurate than achieved using ab initio methods. Molecular properties that can be obtained using Computational Chemistry include molecular geometry, conformation energies, band gaps, UV and IR spectra, dipole and quadrupole moments, and charge distribution. Programs such as Gaussian provide a graphical user interface (GUI) that facilitates computations. Gaussian and its graphical user interface (GUI), GaussView, will be discussed with hands-on training during the first week of the REU program. Projects: 1, 2, 6, 11, 15


Figure 3. MD simulation (side & top views) of a gramicidin channel (purple) in a lipid membrane

Figure 3. MD simulation (side & top views) of a gramicidin channel (purple) in a lipid membrane

Molecular Dynamics Simulation

(MD) lies at the next level of scale. MD simulations enables study of larger molecular structures whose conformational and diffusional properties cover a longer size and time range as was illustrated in Figure 1. In contrast to Computational Chemistry methods, Molecular Dynamics and related Monte Carlo methods can model a broad range of molecular size to enable molecular level characterization of polymers, zeolites, DNA, and proteins. Figure 3 shown a MD simulation of a gramicidin channel (colored purple) sitting in a lipid bilayer membrane (colored green). The solid spheres show water molecules passing through the membrane channel.

Projects: 1, 2, 3, 5

Finite Element

Methods lie at the far range of size and time domains as was illustrated in Figure 1.  These methods provide a bridge between Molecular Dynamics and experiment. They use computational methods distinct from Computational Chemistry and Molecular Dynamics. Figure 4 illustrates how medical imaging of arteries can be used to develop system models to study blood flow using Computational Fluid Dynamics.

Project: 12

Steps in the development of a model of an artery in which blood flow can be investigated using Computational Fluid Dynamics

Figure 4. Steps in the development of a model of an artery in which blood flow can be investigated using Computational Fluid Dynamics

REU Faculty Mentors and Departmental Affiliations

Faculty MemberDepartmentRank
Delaina AmosChemical EngineeringAssociate Professor
Eric BersonChemical EngineeringProfessor
Albert R. CunninghamMedicineAssociate Professor
Hermann B. FrieboesBioengineeringAssociate  Professor
Joel R. FriedChemical EngineeringProfessor
Gautam GuptaChemical EngineeringAssociate Professor
Vance W. JaegerChemical EngineeringAssistant Professor
Chakram S. JayanthiDepartment of Physics and AstronomyChair Person & Professor
Pawel M. KozlowskiChemistryChair Person & Professor
Jinjun LiuChemical EngineeringAssociate Professor
Badri NarayananMechanical EngineeringAssistant Professor
Joshua SpurgeonConn Center for Renewable Energy ResearchTheme Leader, Solar Fuels
Jill Steinbach-RankinsBioengineeringAssociate Professor
Lee ThompsonChemistry, College of Arts & ScienceAssistant Professor
John O. TrentJames Graham Brown Cancer Center, School of MedicineProfessor
Stuart WilliamsMechanical EngineeringAssociate Professor
Jerry WillingChemical EngineeringInterim Chairperson & Professor
Ming YuPhysicsAssociate Professor


Orientation and Introductory Courses in Week One

May 24Students Check in ElectronicallyReceptionIntroductions & Orientation
May 25Introduction to Multiscale Modeling and Quantum ChemistryLunchIntroduction to Gaussian and Practice Simulations
May 26Molecular Mechanics and Dynamics Monte Carlo MethodsLunchIntroduction to MAPS and Practice Simulations
May 27Coarse Graining

Finite Elements

Transport Models

LunchPractice Simulations
May 28Lab Safety

Tour of Campus & Computer Center

LunchMeet with Mentors and Research Team

Listing of Seminar Presentations, Site Visit, and Poster Schedule

WeekSeminar TopicInvited Speakers
2Ethical ScienceAvery Kolers, Instructor of Ethics Course
3Peer Review ProcessPanel of Mentors
4Data ReproducibilityDoug Lorenz, Director Statistical Consulting Ctr
5Academic CareersPanel of Mentors
6Visit to ORNLJeremy Smith, Center for Molecular Biophysics
7Diversity in ScienceHeidi Neal, Asst. Dean of Student Affairs
8Presentation of DataPanel of Mentors
9Intellectual PropertyJohn Cross, Esq., IP expert
10Poster SessionEmmanuel Collins, Dean of Engineering
  • Delivery of poster presentations will be hybrid
  • Tour of Oak Ridge National Laboratory (ORNL) will be held virtually; others available as hybrid

Important Dates

Application DeadlineMonday, May 3, 2021
Notification of SelectionMonday, May 10, 2021
REU Program StartsMonday, May 24, 2021
Research Poster Competition WeekFriday, July 30, 2021

Eligibility & Deadlines

Required Application Materials

  • 2021 13M REU application (see application link at the end)
  • Official college transcript(s) or recent copy
  • Resume (2-page limit)
  • Personal Statement (1-page limit) indicating what interests you about your top three chosen projects. Tell us if you already have experience in any of the areas involving these projects.
  • Two Letters of Recommendation

Applications are now closed for the 13M REU Site Summer Research Program!