Introduction to Computational Molecular Bioengineering


protein This class is designed to introduce students to the principles, methods and software used for simulation and modeling of macromolecules of biological interest. Along with experiment and theory, computational modeling provides new tools for analysis, explanation and prediction.

The course is useful for students who plan to use experimental techniques as their primary approach but who will employ computational modeling as a tool to obtain integrative understanding of complex systems. The course should also be valuable as an introductory overview for students planning to conduct their thesis research in computational modeling of biological systems.

  Class topics:

  • Basic statistical thermodynamics
  • Force fields
  • Molecular dynamics/ monte carlo methods
  • Advanced simulation methods
  • Conformational analysis
  • Fluctuations & transport properties
  • Free-energy calculations
  • Coarse-graining approaches
  • Multiscale modeling

  • Molecular modeling to discover and design new molecules
  • Drug design, protein dynamics, molecular complexation (protein-ligand, protein-DNA)  and membrane-protein interactions

BIOE120, BIOE121, BIOE241, MATH246, PHYS260/261, BIOE 232, BIOE371

The course has lectures and a computational laboratory. The calculations for the course will be performed using the computing resources of the University of Maryland High Performance Computing Cluster.


  • Characterize the role of biomolecular modeling in current bioengineering research
  • Describe functionality, advantages and limitations of standard computing strategies for simulation of biomolecules
  • Acquire a working knowledge of freely available software to carry out independent research projects in biomolecular modeling

  Class meetings:

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