Our **latest work** on *conformational heterogeneity of chromosomes* is on Nature Communication now!

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This is part III of a series of three posts about optimizing python code. The particular example given is the computation of pair-wise distances under periodic boundary condition which is an essential part of molecular dynamics simulations. In this post, I show how to use Numpy to do the computation.

This is part II of a series of three posts about optimizing python code. The particular example given is the computation of pair-wise distances under periodic boundary condition which is an essential part of molecular dynamics simulations. In this post, I show how to use Numpy to do the computation.

In this series of posts, using calculation of pair-wise distances under periodic boundary condition as an example, I show several different methods to optimize Python codes. The performances from different methods are benchmarked for comparison.