2. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 „Virtuelle Strahlen-Biophysik: Einflüsse der Zellkernarchitektur„ Monte Carlo modeling of the genome structure of the cell nucleus Virtual radiation biophysics Comparison with experimental data

3. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Fixed cells Chromosome Painting experiments I. Solovei, F. Habermann, M. Cremer, T. Cremer (Institute of Anthropology and Human Genetics University of München) Living cells H. Bornfleth, D. Zink, T. Cremer

4. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Spherical 1-Mbp Chromatin Domain (SCD) model

5. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 „Importance Sampling“ Monte Carlo method normalized Boltzmann factor Simple Sampling Monte Carlo method : choose randomly N states x 1, x 2,...., x N from phase space Importance Sampling Monte Carlo method: choose states x 1, x 2,...., x N with a probability P(x i ) from phase space with P(x i )~exp(-H(x i )/k B T) Expectation value of a canonic ensemble idea of Metropolis: consecutive states are generated by a transition probability (Markov process). The choice of the transition probability has to be made in such a way that the probability function P(x i ) of the states convergence against the equilibrium distribution

6. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 „Metropolis algorithm“ 1. Choose randomly a state from phase space. 2. An accessible state from phase space is chosen. 4. The energy difference  H between the new and the old state is computed. 4. If  H<0 the new state will be accepted. 5. If  H>0 the new state is accepted with the probability exp(-  H/kT). That means, when a random number from [0;1] < exp(-  H/kT) than the new state is accepted. 6. Go back to 2.

7. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Monte Carlo Relaxation (no real time dependency) 0 MC 1000 MC 20  m

8. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Additional constraints of the higher order nuclear architecture: distribution of chromosome territories in the nuclear volume the morphology of the active and inactive X-chromosome

9. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Positioning of chromosomes in lymphocyte cell nuclei

10. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Positioning of chromatin homologous to human CTs #18(red, gene poor) and #19(green, gene rich) in lymphocyte nuclei of higher primates (Tanabe et al. 2002) Human Chimpanzee Gorilla Marmoset Orangutan Tamarin

11. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 3D mapping algorithm

12. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Mapping of CTs: comparison (#18) and (#19) HumanChimpanzee GorillaOrang Utan

13. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Summary of primate #18 and #19 sequencies distribution in lymphocyte nuclei Mean of mean: 75,7 +- 3,2 | 53,3 +-4,3, : mean value of radial distributions of #18, 19 sd : standard deviation

14. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Virtual Microscopy

15. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 simulated gene density correlated distribution Virtual microscopy reconstructions of simulated CTs #18(red) and #19 (green)

16. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Radial distribution of chromosome territories Simulation (statistical distribution)Experiment (lymphocyte cell nuclei)

17. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Radial distribution of chromosome territories Simulation (gene density correlated distribution)Experiment (lymphocyte cell nuclei)

18. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Morphology of X-chromosomes Visualization: C. Dartu, W. Jäger ( IWR, University of Heidelberg)

19. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Simulation of the Xa and Xi chromosome Xa Convolution with the measured PSF Segmentation, Visualization Convolution with the measured PSF

20. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Interchange frequencies: comparison of Observation and Simulation

21. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Virtual radiation algorithm Random distribution of DSBs within DNA number of DSBs increases linearly with dose and is proportional to the DNA content probability p n of an individual modeled 1Mbp domain containing n DSBs: D - dose of radiation in (Gy) q - size of a domain (=1000000bp)  - yield of DSBs (=8.07 ·10 -9 Gy -1 bp -1 ) interchange is counted when the distance d of two DSBs in two directly neighbored domains followed: 1Mbp domain d DSB Intra-change Inter-change Chromosome territory i Chromosome territory j

22. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Influence of chromosome distribution on interchange frequencies absolute interchange frequencies in %, examples: (4;18)(4;19)(19;18) Exp. (1600 cells):0.3%0.3%0.1% statis. Simul. (50000cells):0.6%0.7%0.3% gendens. corr. Simul. (50000cells):0.6%0.2%0.1%

23. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Influence of chromosome distribution on interchange frequencies Relative one-chromosome yield (normalized to 1000) Error bars: E ± (E) 1/2 E

24. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Influence of chromosome distribution on interchange frequencies* Relative one-chromosome yield (normed to one) *1,600 cells (50simulated nuclei were virtually iradiated 32 times) scattered (experimental) scattered (simulated) Regression: t-rate~(DNA content) 2/3

25. Kirchhoff-Institute for Physics, University of Heidelberg G. Kreth, SKIP, Heidelberg, 05.08.2004 Heinz Eipel Claudia Batram Johann von Hase Hans Mathée Constance Grossmann Christian Carl Nick Kepper Werner Stadter Senthilkumar Pazahanisamy Andreas Schweitzer Margund Bach Stefan Stein Udo Spöri David Baddeley Gregor Kreth Jutta Finsterle Christian Wagner Helmut Schneider Susanne Fenz Jürgen Reymann