We performed GRMHD and RMHD simulations of weakly and highly magnetized gamma-ray burst (GRB) jets propagating in binary neutron star (BNS) merger ejecta. Using the simulations, we first find that mixing between the jet and cocoon, which is present in all types of jets, inhibits the formation of subphotospheric collisionless shocks. However, we show that a mild magnetization may lead to the formation of collisionless subshocks which allow efficient proton acceleration. We consider shear acceleration and diffusive shock acceleration at collimation shocks, internal shocks, shock breakout, and external shocks, to provide the first estimate for neutrino and cosmic-ray (CR) signals from self-consistent simulations of GRBs in BNS mergers. We find that short GRBs do not produce detectable neutrino signals with current-day facilities. Shock breakout yields ~10 PeV neutrinos at viewing angles of 20 degrees, independent of the jet magnetization. However, a neutrino signal from shock breakout is well below detection limits of current detectors. Such a signal would allow a coincident neutrino-γ−ray detection, providing a testable prediction for shock breakout as a neutrino production site. Using the numerical modeling that fits GW170817 afterglow emission, we find that blast waves in BNS mergers can account for 5%-10% of the Galactic CR luminosity in the PeV-EeV energy range. Based on these estimates, the observed level of CR anisotropy places a constraint on the distance of the latest Galactic binary neutron star merger to <3 kiloparsecs.

Mounting evidence suggests that the launching of collapsar jets is magnetically driven. Recent general relativistic magnetohydrodynamic simulations of collapsars reveal that the jet is continuously loaded with baryons, owing to strong mixing with the cocoon. This results in a high photosphere at >1e12 cm . Consequently, collisionless internal shocks below the photosphere are disfavored, and neutrino production in the deepest jet regions is prevented, in contrast to what has been assumed in the literature. We find that subphotospheric neutrino production could take place in the presence of collisionless subshocks or magnetic reconnection. Efficient particle acceleration is not possible in the cocoon, at the cocoon-countercocoon shock interface, or at the shock driven by the cocoon in the event of a jet halted in an extended envelope. These subphotospheric neutrinos have energy E<1e5 GeV for initial jet magnetizations 15-2000. More than one neutrino event is expected to be observed in Hyper-Kamiokande and IceCube DeepCore for bursts occurring at z < O(0.1). Because of their energy, these neutrinos cannot contribute to the diffuse flux detected by the IceCube Neutrino Observatory. Our findings have implications on neutrino searches ranging from gamma-ray bursts to luminous fast blue optical transients.