This thesis work focuses on technical developments in the field of plasmonic nanomaterials and its related areas of synthesis and optical characterization. Metal nanopart [...]

A concise overview of the weighted ensemble path sampling method for rare events is given, aimed at beginners.

The "Hill relation" is a key result for anyone interested in calculating rates from trajectories of any kind, whether molecular simulations or otherwise. I am not aware o [...]

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 [...]

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 [...]

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 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 [...]

Basic concepts and limitations of path sampling are described.

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

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 [...]