Issue
EPL
Volume 86, Number 6, June 2009
Article Number 68003
Number of page(s) 6
Section Interdisciplinary Physics and Related Areas of Science and Technology
DOI http://dx.doi.org/10.1209/0295-5075/86/68003
Published online 13 July 2009
EPL, 86 (2009) 68003
DOI: 10.1209/0295-5075/86/68003

The effect of inhomogenities on single-molecule imaging by hard XFEL pulses

Z. Jurek and G. Faigel

Research Institute for Solid State Physics and Optics - H-1525 Budapest, POB 49, Hungary, EU

jurek-z@szfki.hu

received 5 March 2009; accepted in final form 9 June 2009; published June 2009
published online 13 July 2009

Abstract
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$\hbox{--} $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.

PACS
87.15.ap - Molecular dynamics simulation.
87.15.B- - Structure of biomolecules.
87.53.-j - Effects of ionizing radiation on biological systems.

© EPLA 2009