In the context of linear scaling methods for electronic structure and molec
ular dynamics calculations, SIESTA was developed as a fully first-principle
s method able to deal with systems with an unprecedented number of atoms, w
ith a modest computational workload. The method has allowed us to study a l
arge variety of problems involving nanoscale materials, such as nanocluster
s, nanotubes, biological molecules, adsorbates at surfaces, etc. Here we pr
esent a review of such applications.