The Netherlands has a different Ph.D. system than some other countries (like the U.S.). Ph.D. candidates typically are not students, but are employed and paid by the university to do research and some amount of teaching. Only a limited number of positions (vacancies) is available, often depending on external grants that have been awarded to staff members. Also, only a full professor can be the formal promotor for a Ph.D.
If you are interested in a Ph.D. position, check the vacancies at http://www.vu.nl/nl/werken-bij-de-vu/vacatures/index.asp?Category=Faculteit+der+Exacte+Wetenschappen
or check with a small number of professors, such as the heads of the groups in the area of your primary interest. If you have a grant of your own that covers all your costs, you can likewise check if a certain professor is willing to supervise you, although capacity for externally-funded Ph.D. candidates also is limited. Either way, do not send applications to large numbers of staff members, as this is deemed inappropriate.