Modules

From Wiketomica

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.

Piston-Cylinder		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		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		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.
Osmosis		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.
Lennard-Jones Molecular Dynamics		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.
Polymerization		Model of two fundamental polymerization reaction types: stepwise growth and chain addition. The difference between the reaction mechanisms can be visualized, the resulting products of each can be observed, and calculations of molecular weights, molecular weight distributions, and kinetics can be conducted.
Virial-VLE		A molecular model is fit to experimental data for the 2nd virial coefficient, and the vapor-liquid equilibrium (VLE) behavior of the fitted model is examined by Gibbs-ensemble molecular simulation. Resulting data can be compared to experimental VLE data for the system used to fit the model.
Discontinuous Molecular Dynamics		An integrated tutorial on pressure, temperature, density, and model equations through the piston/cylinder module combined with 2D and 3D simulations using periodic boundary conditions. The simulations are based on the square well potential, which characterizes the fundamental repulsions and attractions in a discontinuous but simple manner.
Monolayer		Demonstration of mechanical properties of tethered monolayers. The module can be used as a supplement in materials science and engineering courses to illustrate the molecular basis of stress and strain.
Interfacial tension		Model of an explicit vapor-liquid interface, permitting computation of the surface tension and other thermodynamic and structural properties at various conditions.
Dual Control Volume Grand Canonical Molecular Dynamics		Dual Control Volume Grand-Canonical Molecular Dynamics (DCVGCMD) 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.
DCVGCMD with Nanotube		An extension of the previous DCVGCMD module. The atoms must diffuse through a tube composed of hexagonally arranged atoms.
Material Fracture		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.
Multiharmonic		A toy model that is used to demonstrate bias in the calculation of free energies by molecular simulation. [documentation incomplete]
1D Normal Modes		Demonstrates the independent collective motions that can be used to described the dynamics of a system of one-dimensional coupled harmonic oscillators.