The detection of a blue macronova following the event GW170817 has emphasized the role that neutrinos play in merging neutron stars. In particular, neutrinos are able to drive mass ejection, the so-called neutrino-driven winds, and change the neutron richness of the matter by absorption. Since the amount of neutrons in the ejecta sets the r-process nucleosynthesis and the matter opacity, the macronova signal arising from the decay of unstable r-process nuclei in the wind carries the signature of weak interactions in mergers as it shines in the optical wavelength band. However, other mass ejection channels have been shown to potentially contribute to this optical counterpart of the macronova. Looking forward to future, new macronovae detections, it is therefore important to systematically explore the impact of neutrino-driven winds in shaping macronovae light curves. For this purpose, in this thesis we introduce a computationally efficient neutrino scheme, called Advanced Spectral Leakage (ASL), that, together with hydrodynamic simulations of binary neutron star mergers, will allow to characterize macronovae and link the physics of binary neutron star mergers with observations. 

In August 2017 a gravitational wave signal from a binary neutron star merger was detected for the first time, and it was followed by several electromagnetic detections that spanned the whole electromagnetic spectrum. Those observations proved the ejection of two dynamical components: mildly-relativistic neutron rich ejecta and an ultra-relativistic jet. The first one produced a rapidly evolving thermal transient powered by the radioactive decay of the freshly synthesized r-process nuclei and subsequent recombination, named "macronova" or "kilonova".  The second component powered instead a gamma-ray burst consisting of an early (and anomalous) gamma-ray signal ≈1.7 second after the merger followed by a long lasting multi-wavelength afterglow. These two dynamical components are typically observed and modelled independently, but when a jet is produced and propagates through the surrounding environment the properties of both may change significantly because of the interaction. However the observational consequences of such interaction are still unclear.

In this thesis I present a comprehensive introduction to the properties of jets and post-merger ejecta, with the aim to show how 3D hydrodynamic simulations form a key instrument in investigating their interaction. I present the results of some of the first simulations of jets propagating within a realistic post-merger wind, and how the properties of the macronova are significantly affected. As an example, this work shows how a jet can "punch-away" a fraction of high-opacity material at early times, causing the macronova becoming brighter and bluer for on-axis observers in the first few days following the merger. Moreover such interaction represents the main contribution to the final shape of the jet, that has a crucial impact in the late time emission for off-axis observers. While looking forward for future detections, this thesis aims to show how crucial is a detailed understanding of the environment surrounding the merger and how, in case of a joint observation of a macronova and a jet, should be taken into account how the interaction might have an impact on the inferred properties of the system.