Context. Recent observations of the X-ray emission from T Tauri stars in the Orion nebula have shown that they undergo frequent outbursts in their X-ray luminosity. These X-ray flares are characterised by increases in luminosity by two orders of magnitude, a typical duration of less than one day, and a significant hardening of the X-ray spectrum. Aims. It is unknown what effect these X-ray flares will have on the ionisation fraction and dead-zone structure in protoplanetary disks. We present the results of calculations designed to address this question. Methods. We have performed calculations of the ionisation fraction in a standard $\alpha$-disk model using two different chemical reaction networks. We include in our models ionisation due to X-rays from the central star, and calculate the time-dependent ionisation fraction and dead--zone structure for the inner 10 AU of a protoplanetary disk model. Results. We find that the disk response to X-ray flares depends on whether the plasma temperature increases during flares and/or whether heavy metals (such as magnesium) are present in the gas phase. Under favourable conditions the outer disk dead--zone can disappear altogether,and the dead-zone located between 0.5 < R < 2 AU can disappear and reappear in phase with the X-ray luminosity. Conclusions. X-ray flares can have a significant effect on the dead-zone structure in protoplanetary disks. Caution is required in interpreting this result as the duration of X-ray bursts is considerably shorter than the growth time of MHD turbulence due to the magnetorotational instability.

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