Improving Molecular Simulation through Accessibility and Capability

Master's Thesis


In recent decades, molecular simulation has become an increasing popular tool and field for study in Chemical Engineering. Simulation has made it possible to tackle problems which otherwise could not be addressed by experimentation due to barriers like a difficulty measuring specific properties, a difficulty safely experimenting, or a difficulty conducting enough experiments to fully explore a material class. However, there are a number of drawbacks which hamstring the proliferation of molecular simulation. The accessibility of molecular simulation for new users is poor, with advanced knowledge of Statistic Mechanics required for success. Logistically, popular molecular simulation codes require users to develop their own complex multi-step workflow. Additionally, the capability of molecular simulation, while ever expanding, can still be improved. Popular classical molecular simulation techniques like Metropolis Monte Carlo still struggle with common systems, such as the phase equilibria of dense fluids.

This work addresses the accessibility and capability of the open source Monte Carlo Code Cassandra. Through collaboration with the Scienomics Company, a Cassandra plugin was added to their commercial Materials and Process Simulation (MAPS) software. MAPS provides a graphical user interface platform for users to conduct their entire simulation workflow cradle-to-grave, including visual system construction, force-field selection/application, simulation code selection. job manager, and post-analysis toolset. It is hoped that this plugin will lower the high barrier to entry for Cassandra for new users, as well as expose Cassandra to existing MAPS enterprise customers. This work also demonstrates the improvement of the capability of Monte Carlo by introducing the Identity Switch move. This move is a compound molecular swap move which may ameliorate sampling issues in dense systems and is explored in detail. A derivation is provided for the acceptance criterion of this move, which is implemented in the Cassandra V1.3 release.


Attribute NameValues
Author Jacob J. Gerace
Contributor Edward Maginn, Research Director
Contributor Jonathan Whitmer, Committee Member
Contributor Alexander Dowling, Committee Member
Degree Level Master's Thesis
Degree Discipline Chemical and Biomolecular Engineering
Degree Name Master of Science in Chemical Engineering
Banner Code

Defense Date
  • 2019-03-25

Submission Date 2019-04-04
  • Metropolis Monte Carlo

  • Phase Equilibria

  • Classical Simulation

  • Molecular Simulation

  • Monte Carlo

  • Graphical User Interface

  • Markov Chain

  • English

Record Visibility Public
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