Simulations of radiation damage in biomolecular nanocrystals induced by femtosecond X-ray pulses

Carl Caleman, Magnus Bergh, Howard A. Scott, John Spence, Henry N. Chapman, Nicuşor Timneanu

Research output: Contribution to journalArticlepeer-review

45 Scopus citations


The Linac Coherent Light Source (LCLS) is the first X-ray free electron laser to achieve lasing at subnanometer wavelengths (6 ). LCLS is poised to reach even shorter wavelengths (1.5 ) and thus holds the promise of single molecular imaging at atomic resolution. The initial operation at a photon energy of 2 keV provides the possibility to perform the first experiments on damage to biological particles, and to assess the limitations to coherent imaging of biological samples, which are directly relevant at atomic resolution. In this paper we theoretically investigate the damage formation and detection possibilities for a biological crystal, by employing and comparing two different damage models with complementary strengths. Molecular dynamics provides a discrete approach which investigates structural details at the atomic level by tracking all atoms in the real space. Our continuum model is based on a non-local thermodynamics equilibrium code with atomic kinetics and radiation transfer and can treat hydrodynamic expansion of the entire system. The latter approach captures the essential features of atomic displacements, without taking into account structural information and intrinsic atomic movements. This proves to be a powerful computational tool for many samples, including biological crystals, which will be studied with X-ray free electron lasers.

Original languageEnglish (US)
Pages (from-to)1486-1497
Number of pages12
JournalJournal of Modern Optics
Issue number16
StatePublished - Sep 20 2011


  • X-ray free electron laser
  • molecular dynamics
  • non-LTE
  • radiation damage

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics


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