We study the local distortion of the atomic structure in small biological
samples illuminated by x-ray free electron laser (XFEL) pulses. We concentrate
on the effect of inhomogenities: heavy atoms in a light matrix and
non-homogeneous spatial distribution of atoms. In biological systems we find
both. Using molecular-dynamics type modeling it is shown that the local
distortions about heavy atoms are larger than the average distortion in the
light matrix. Further it is also shown that the large spatial density
fluctuations also significantly alter the time evolution of atomic
displacements as compared to samples with uniform density. This fact has
serious consequences on single particle imaging. This is discussed and the
possibility of a correction is envisaged.Comment: Movies: http://www.szfki.hu/~jurek/art2009_1/index.htm
