Complexity of an optimisation problem in 3D I have a collection $P \subseteq \mathbb{R}^3$ of $N$ particles and there is a function $f : P^2 \to \mathbb{R}$. I want to find which configuration of the system minimizes the value of $f$. 

Can this problem (or similar ones) be reduced to TSP? Could you point me to literature on the topic?

In my application, $f$ is the atomic van der waals force, which for each pair of particles of atoms is attractive or repulsive depending on some predefined thresholds.

In addition, it would be great to have a list of concrete examples of problems that can be reduced to TSP.
Since TSP is NP-complete, most problems you'll encounter in practice can be.  (NP is a pretty general class.)  A classic paper of Karp gives a large number of other NP-complete problems that, by definition, can be reduced to TSP.