etomica

This page provides access to a suite of instructional modules based in molecular simulation. Their purpose is to introduce molecular simulation into the standard chemical engineering curriculum with the intent of addressing two issues:
  • Fostering molecular understanding of phenomena and processes commonly taught in standard chemical engineering courses
  • Improving abilities of chemical engineering students and faculty members to use and interpret molecular simulations

Both objectives are designed to help prepare students to meet the demands of emerging technologies that are dependent upon molecular processes without introducing new courses into an already full curriculum.

Although this project was initiated with chemical engineering undergraduates as its target audience, there is little in them that is specific to this group. Undergraduates in other science and engineering disciplines should find these modules useful to their studies. Many lessons can be applied beneficially even at the high-school level. Other modules have been formulated at a higher level, and are most suitable for senior undergraduates or graduate students.

Provided with each module are:

  • Background materials on the concepts taught by the module
  • A molecular simulation that permits the user to explore the concepts taught
  • Tutorial material that illustrates the use of the simulation applet
  • Additional problems for use as homework problems

Many of the modules are still in the process of being written, debugged, and formatted for posting on the web site; we have placeholders here for some that are pretty far along. This is an ongoing process, and we expect more to be added on a regular basis.



Piston-Cylinder
Andrew Schultz and Ken Benjamin [University at Buffalo]
date posted: 07/2007
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The piston-cylinder appratus is a standard tool used to conceptualize and illustrate thermodynamic concepts involving heat, work, and internal energy. This module simulates a collection of atoms in a chamber with a movable wall under external pressure. 2-D simulation.


Crystal Viewer
David Kofke [University at Buffalo]
date posted: 12/23/02
Permits viewing of static 3-dimensional lattices and the planes they define. Various elementary lattices can be selected, and any plane or surface can be viewed by specifying it via its Miller indices. Image can be rotated to permit viewing from any angle.


Reaction Equilibrium
David Kofke [University at Buffalo], Chris Iacovella [University at Buffalo / U.Mich]
date posted: 12/23/02
Shows a simple reaction equlibrium involving two atomic species and the three dimeric molecules they can form. Atoms move about via 2-D molecular dynamics, and can "react" to form dimers. Dynamic equilibria is demonstrated through constant recombining of atoms, and equilibria can be quantified and analyzed with thermodynamic reaction equilibria models.


Joule Thomson Experiment
Ed Maginn [University of Notre Dame], David Kofke [University at Buffalo]
date posted: 02/22/03
Permits study of a system undergoing isothermal or isenthalpic expansion and compression. Isenthalpic expansion is known as  Joule-Thomson process, and is the basis of many common refrigeration processes.


Osmosis
Jhumpa Adhikari [University at Buffalo]
date posted: 01/16/02
Simulation of a system of two species and a semipermeable membrane. Allows measurement of the osmotic pressure (the difference in pressure between the phases on each side of the membrane) as a function of density and mixture mole fraction.


Material Fracture
Sang-kyu Kwak, Jim DiNunzio [University at Buffalo]
date posted:
2-D simulation of a monatomic species in the solid phase. Stress is applied and the resulting strain may be observed to and beyond the point of fracture. Vacancy defects may be introduced to examine their effect on the material's strength.


1D Normal Modes
David Kofke [University at Buffalo]
date posted: 03/09
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To be completed...


Lennard-Jones Molecular Dynamics
Andrew Schultz [University at Buffalo]
date posted: 03/06
Molecular dynamics of a 2-dimensional mono-atomic Lennard-Jones system. The Lennard-Jones model is a simple but widely-used approximation for the way atoms interact. Elementary molecular features of this model's dynamical and structural behavior are calculated in this simulation. More appropriate for a graduate-level student.


Dual Control-volume GCMD
Eric Cichowski, Todd Schmidt [University at Buffalo]
date posted: 11/04
Dual Control Volume Grand-Canonical Molecular Dynamics simulation, in which a long simulation volume is subject to grand-canonical Monte Carlo at opposite ends, with molecular dynamics in between. The MC simulations establish a chemical-potential gradient, and the resulting diffusion process can be used to measure the diffusion coefficient. Module completed as a project in CE 412 - Molecular Modeling.


Dual Control-volume GCMD with nanotube
Mike Sellers and Nate [University at Buffalo]
date posted: 03/06
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This is an extension of the previous DCVGCMD module. The atoms must diffuse through a tube composed of hexagonally arranged atoms. Module completed as a project in CE 412 - Molecular Modeling.


"Undocumented" modules
These modules are based on updated Etomica code, but lack the background information and tutorials available in the modules listed above. Some are updated or extended versions of the previous modules.


Chain Reaction Equilibrium
Matt Moynihan and William Scharmach [University at Buffalo]
date posted: 03/06
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This is an extension of the previous Reaction Equilibrium module. Each atom can bond with multiple atoms, such that chains can be formed. The resulting distribution of chain lengths is measured.


Multiharmonic
David Kofke [University at Buffalo]
date posted: 03/06
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Etomica module funding provided by :

Funded by the National Science Foundation under grant DUE-9752243 Sponsored by CACHE Developed by the MMTF (Molecular Modeling Task Force) of CACHE


Etomica is dedicated to the memory of Bryan Mihalick.

Department of Chemical Engineering | Center for Computational Research | University of Buffalo |
School of Engineering and Applied Sciences | Contact Etomica Support
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This material is based on work supported by the National Science Foundation and performed in the Chemical Engineering Department at the University of Buffalo.