Which scientist was the first to conclude through experimentation that atoms have positive charges in their nuclei?

Ernest Rutherford was a British physicist and chemist of New Zealand origin, who conducted a series of experiments together with Hans Geiger and Ernest Marsden; where the result led him to propose a new atomic model.

It should be noted that at that time, the "accepted" atomic model was Thomson's raisin pudding atomic model (electrons with negative charge immersed an the atom of positive charge that counteracted the negative charge of the electrons, like raisings embedded in a pudding), who discovered the electron and formerly was a professor of Rutherford.  

Now, the experiment conducted under the direction of Ruherford at the laboratories of the University of Manchester during the year 1911; was for the purpose of corroborating Thomson's atomic model. To achieve this, a thin metal sheet was bombarded with alpha particles (nuclei of helium gas).

The idea was that these alpha particles, having positive electric charge, were attracted by the atom's negative charges and repelled by the positive charges, and it was expected that they would pass through the thin sheet without hardly deviating. Then, to observe the crash site of the particle, a phosphorescent screen was placed behind and on the sides of the metal sheet.

For according to Thomson's atomic model the positive and negative charges were evenly distributed, the sphere (the atom) had to be electrically neutral, and the alpha particles would pass through the sheet without deviating.

However, the results were surprising:

As expected, most of the particles went through the sheet without deviating.

That is:

These facts could not be explained by Thomson's atomic model, so Rutherford developed another, suggesting that:

This new model could explain the proven fact in his experiments that some particles bounced in the direction opposite to the incident particles, because the electrical charge of this nucleus was positive, equal to the electrical charge of the alpha particles.

This is how Rutherford proposed a new atomic model and discovered the existence of the nucleus. However, this was not the definitive model, because on 1913 it was replaced by Bohr's.

thermal energy is the answer