logical topology?

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logical topology?

I am planning to set up two segments on my network. I would like to ask which logical topology would be best to use and would meet the following criteria:

1. at normal instances, segment A and B would be connected using 1 physical router. The router should detect them as 2 separate network segments.

2. at special instances, segment A and B can also be connected together making them 1 big network.

3. I also want security on the two segments. For instance, how can I prevent malware in segment A from infecting segment b?

another question, do i need to use a network OS (for example windows server) to accomplish this? by the way i am using a linksys router and the computers' OS varies from XP, vista and 7.