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When filming a movie, capturing the essence of a story goes beyond still shots of key scenes. Imagine trying to understand the plot of a movie by only looking at a single [...]

LC8 is a key molecular hub protein involved in a wide array of cellular processes (e.g., apoptosis, viral interactions, signal transduction). LC8 interacts with over 100 [...]

Most behavior, observed via a subset of coordinates or discretized states, should not be Markovian even though the underlying dynamics generally will be.

The basics of trajectories and the different types of trajectory ensembles are explained.

Molecular dynamics simulations often fail to reach timescales characteristic of equilibrium sampling, so great care must be taken in computing and reporting statistical u [...]

The trajectory ensemble is fundamental in statistical physics and relatively easy to understand. It is also information-rich, as both equilibrium and non-equilibrium obse [...]

Basic concepts and limitations of path sampling are described.

The potential of mean force (PMF) is one of the most widely used characterizations of a biomolecular system computed from simulation, but calculating and interpreting a P [...]