Would it be possible to effectively prevent Eminent Domain from being used on intellectual property?
There are none
Eminent domain is the doctrine that government can seize a person's property and convert it to public use. IP is just property and it can be acquired by government on the same basis that any other property can be.
The 5th amendment requires that this requires payment of just compensation and that the appropriation is for public use (which is pretty broadly defined). The power can be exercised by the Federal Government or the states and, through proper delegation of power to local government. In Florida Prepaid Postsecondary Education Expense Board v. College Savings Bank, the U.S. Supreme Court held that states are generally immune from patent infringement if due process via just compensation is afforded to the patent owner.
Eminent domain is not a concern for you, under the normal understanding of what it refers to. The government might take your house for a public purpose, and given the nature of land, you wouldn't have that land anymore. The government would not have the power to compel production of your research results through ordinary land-grab means. That does not mean that Congress could not pass a law enabling "seizure" of property for a public good, but such a law would have to pass some substantial tests, to be constitutional. Your property right to this research product is a fundamental constitutionally-protected right, and such a law would be subject to strict scrutiny when its constitutionality is challenged. I don't see how the narrow-tailoring and least-restrictive requirements could be satisfied, and the compelling government interest is questionable.
There are two property-rights issues that are typically typically interconnected in the case of physical property: the power of the government to use the property as it sees fit, and the right of the property owner to exploit their property. If the government plans to build a factory or park where your house is, by the nature of such a use, you have to entirely lose your rights to the property. With intellectual property, there are more possibilities since you can make copies of IP. "Condemnation" in this case would not only translate into the government overriding your copyright / patent rights (requiring an act of Congress) so that your permission is not required to copy (and use), it would even mean that you are deprived of your normal right to also exploit the property. The legal stones that would have to be rolled uphill are quite massive (I cannot conceive of such laws passing strict scrutiny upon appeal).