Binaries hosting a massive star and a non-accreting pulsar are powerful non-thermal emitters due to the interaction of the pulsar and the stellar wind. The winds of massive stars are thought to be inhomogeneous, which could have an impact on the non-thermal emission. We study numerically the impact of the presence of inhomogeneities or clumps in the stellar wind on the high-energy non-thermal radiation of high-mass binaries hosting a non-accreting pulsar. We compute the trajectories and physical properties of the streamlines in the shocked pulsar wind without clumps, with a small clump, and with a large one. This information is used to compute the synchrotron and inverse Compton emission from the non-thermal populations, accounting also for the effect of gamma-ray absorption through pair creation. A specific study is done for PSR B1259-63/LS2883. When stellar wind clumps perturb the two-wind interaction region, the associated non-thermal radiation in the X-ray band,of synchrotron origin, and in the GeV-TeV band, of inverse Compton origin, is affected by several effects: (i) strong changes in the the plasma velocity direction that result in Doppler boosting factor variations, (ii) strengthening of the magnetic field that mainly enhances the synchrotron radiation, (iii) strengthening of the pulsar wind kinetic energy dissipation at the shock, potentially available for particle acceleration, and (iv) changes in the rate of adiabatic losses that affect the lower energy part of the non-thermal particle population. The radiation above 100 GeV detected, presumably, during the post-periastron crossing of the Be star disc in PSR B1259-63/LS2883, can be roughly reproduced assuming that the crossing of the disc is modeled as the encounter with a large inhomogeneity.
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