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Molecular Dynamics Simulations of Diffusion in Polymers. Zach Eldridge Department of Mechanical Engineering University of Arkansas Fayetteville, AR 72701 USA REU 2 nd Week Seminar – Friday May 29 th , 2009. Background. What is Molecular Dynamics?

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Molecular dynamics simulations of diffusion in polymers

Molecular Dynamics Simulations of Diffusion in Polymers

Zach Eldridge

Department of Mechanical Engineering

University of Arkansas

Fayetteville, AR 72701 USA

REU 2nd Week Seminar – Friday May 29th, 2009


  • What is Molecular Dynamics?

    • Molecular dynamics is a form of computer simulation used to observe the behavior of atoms and molecules, which cannot be easily observed during experiments.

    • Through the use of computer algorithms and known laws of physics, mathematics, and chemistry we are able conduct an experiment and model it through a simulation.

    • Through analysis of the simulation we are able to study the behavior of the material.

Nano Indention

My project
My Project

  • Methodology

    • The main objective of the research is to study diffusion of gas penetrates through PDMS (Polydimethylsiloxane)

      • PDMS – the most widely used silicon based organic polymer. It is composed of Oxygen, Siliocon and a methly, a CH2 or CH3. Common uses include contact lenses and shampoo.

      • Penetrates – for the most part we will be studying CH4, methane, and its effects.

        PDMS 1 PDMS 2

    • Molecular dynamics simulation will allow us to calculate the diffusion coefficients of the penetrate through the PDMS and evaluate the role of concentration and distribution of penetrates

My project objectives
My Project Objectives

  • Short Term Objectives (1-3 weeks)

    • Become familiar with Lammps, Ensight, and Linux

    • Read to understand diffusion and polymers

  • Long Term Objectives (4-10 weeks)

    • Perform simulations that model the diffusion of methane through a PDMS polymer.

    • Analyze the results of the simulation to determine the diffusion coefficient of methane, and the effects of concentration and distribution.

    • Write a final report that discusses my research and the outcomes.



Sensor schematic Corrosion is measured through changes in electrical resistivity

Composite schematic Diffusion of particles through composite samples will be studied via molecular dynamics

Molecular Dynamics Simulation

  • United-atom model of polymer

  • Self-avoiding random walk construction

  • Initial tasks focused on code development

Huang and Spearot, University of Arkansas, CMMI Award #800718

Research tools
Research Tools

  • Lammps

    • Lammps is the molecular dynamics software we use to create and manipulate the experiments.

    • Using Linux computer code we create the experiment in a file which tells the computer how to run the experiment and the different properties we would like it compute during the experiment.

    • Because the amount of information being processed we have to use the supercomputer “Trillion” to run the simulations.


Research tools1
Research Tools

  • Ensight

    • Ensight is the computer program we use to visualize the simulations after the experiment has been run through “Trillion”.

    • It allows us to make observations about such things as: potential / kinetic energy, displacement, temperature, centro-symmetry, etc.

Oxygen Diffusion through Polymer

Works cited
Works cited

  • (2009, May 11). Polydimethylsiloxane. Retrieved May 26, 2009, from Wikipedia Web site:

  • (2009, April 14). Arkansas High Performance Computing Center. Retrieved May 26, 2009, Web site:

  • Kam Liu, Wing Retrieved May 26, 2009, Web site:,com_zoom/Itemid,41/PageNo,2/catid,4/hit,1/key,15/page,view/

  • Retrieved May 26, 2009, from Gallery of Polymers and Polymer Simulation Web site:

  • Dr. Douglas Spearot – Faculty Advisor, Alex Huang – Graduate Student Advisor