MiS Preprint Repository

We have decided to discontinue the publication of preprints on our preprint server as of 1 March 2024. The publication culture within mathematics has changed so much due to the rise of repositories such as ArXiV ( that we are encouraging all institute members to make their preprints available there. An institute's repository in its previous form is, therefore, unnecessary. The preprints published to date will remain available here, but we will not add any new preprints here.

MiS Preprint

Objective molecular dynamics

Traian Dumitrică and Richard D. James


We introduce a generalization of periodic molecular dynamics that we term objective molecular dynamics. It is a method of doing classical molecular dynamics for a restricted set of atoms, nonperiodically mapping the time-dependent displacements of this small set of atoms onto the full, typically infinite structure, such that the full structure satisfies exactly the full, unconstrained set of equations of molecular dynamics subject to certain group-invariant initial conditions. The method is applicable to a wide variety of interesting molecular structures including the tails, capsids and other parts of many viruses, carbon nanotubes, many of the common proteins, C60 and many other nanostructures now being synthesized, especially via the process of self-assembly. The method is illustrated by simulations of carbon nanotubes.

Atomistic structures, numerical algorithms

Related publications

2007 Repository Open Access
Richard D. James and Traian Dumitrica

Objective molecular dynamics

In: Journal of the mechanics and physics of solids, 55 (2007) 10, pp. 2206-2236