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Tools

Tools

Research tools:

We use multiple biophysical tools to facilitate our research. These include

  • Adaptation and application of theories from polymer physics, statistical physics, and the physics of phase transitions
  • Molecular and mesoscopic simulations based on custom homegrown software and novel Monte Carlo algorithms as well as traditional molecular dynamics methods
  • Small and large ensemble fluorescence spectroscopies and scattering methods
  • Collaborations with experimentalists within and beyond Washington University

The Pappu Lab combines both computational and experimental work, in an effort to provide molecular level understanding of complex, multi component problems. As well as applying tried and tested tools to these problems, the lab has a strong emphasis on the development of novel techniques, approaches and algorithms to tackle these issues as they arise.

Software and hardware:

The lab uses a range of different software and languages. Data analysis and presentation is carried out primarily in MATLAB, Python, R, and Perl. High performance tools are developed in C, C++, and Fortran, with version control through through CVS and git. Monte Carlo simulations are done using the CAMPARI package, while molecular dynamics simulations are done primarily in GROMACS. The web server uses Apache, and the website was built using Bootstrap. The lab maintains an active internal blog to document progress and address literature, which uses WordPress.

The lab has exclusive access to a ~600 CPU cluster and 90+ TBs of storage space, both of which are managed in house. This allows for significant flexibility for developing, testing and running both standard and bespoke applications. The lab also makes extensive use of the Washington University Center for High Performance Computing cluster.