Simulating the formation of biofilms in an undergraduate modeling course

Abstract

Meaningful applications that illustrate fundamental concepts and techniques are crucial in computational science education. In this paper, we discuss development of a simulation on the structural growth of a biofilm that is appropriate for modeling, simulation, or high performance computing courses. Consideration of cellular automaton simulations, boundary conditions, and diffusion in this context can empower students to develop similar simulations for other applications. Moreover, extensions of the basic model can illustrate and motivate the need for high performance computing in computational science. The module, "Biofilms: United They Stand, Divided They Colonize," used for instruction and developed by the authors as an Undergraduate Petascale Education Program (UPEP) Curriculum Module is available at http://computationalscience.org/upep/curriculum.

Testing the Waters with Undergraduates (If you lead students to HPC, they will drink)

“…In an effort to extend the educational benefits of the module, the authors wrote and presented a paper, "Simulating the Formation of Biofilms in an Undergraduate Modeling Course" for the Workshop on Teaching Computational Science at the International Conference on Computational Science (ICCS) in Amsterdam [10].…”

Integrating supercomputing clusters into education: a case study in biotechnology

“…-Supercomputing training helps in the use of mathematical models [9,42,50] which allows describing a problem in a specific research field, for extracting conclusions and evaluating performance on the proposed problems. -Simulations and data design in a Supercomputer prepare students for the role of leaders in research [50] by the use of very large database systems [1], covering, at the same time, a great variety of applications [39]. -Supercomputing contributes to inventing new tools and new philosophies of work, which enhance the learning about computing [20,29].…”