// get the name of the assembly
string exeAssembly = Assembly.GetEntryAssembly().FullName;
// setup - there you put the path to the config file
AppDomainSetup setup = new AppDomainSetup();
setup.ApplicationBase = System.Environment.CurrentDirectory;
setup.ConfigurationFile = "<path to your config file>";
// create the app domain
AppDomain appDomain = AppDomain.CreateDomain("My AppDomain", null, setup);
// create proxy used to call the startup method
YourStartupClass proxy = (YourStartupClass)appDomain.CreateInstanceAndUnwrap(
exeAssembly, typeof(YourStartupClass).FullName);
// call the startup method - something like alternative main()
proxy.StartupMethod();
// in the end, unload the domain
AppDomain.Unload(appDomain);