Abstract

We explore the possibility for orientation recovery in single-molecule coherent diffractive imaging with diffusion map. This algorithm approximates the Laplace-Beltrami operator, which we diagonalize with a metric that corresponds to the mapping of Euler angles onto scattering images. While suitable for images of objects with specific properties we show why this approach fails for realistic molecules. We introduce a modification of the form factor in the scattering images which facilitates the orientation recovery and should be suitable for all recovery algorithms based on the distance of individual images.

© 2016 Optical Society of America

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2015 (1)

J. J. Donatelli, P. H. Zwart, and J. A. Sethian, “Iterative phasing for fluctuation X-ray scattering,” Proc. Natl. Acad. Sci. U. S. A. 112, 10286–10291 (2015).
[Crossref] [PubMed]

2014 (3)

T. R. M. Barends, L. Foucar, S. Botha, R. B. Doak, R. L. Shoeman, K. Nass, J. E. Koglin, G. J. Williams, S. Boutet, M. Messerschmidt, and I. Schlichting, “De novo protein crystal structure determination from X-ray free-electron laser data,” Nature 505, 244–247 (2014).
[Crossref]

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

C. H. Yoon, M. Barthelmess, R. J. Bean, F. Capotondi, R. A. Kirian, M. Kiskinova, E. Pedersoli, L. Raimondi, F. Stellato, F. Wang, and H. N. Chapman, “Conformation sequence recovery of a non-periodic object from a diffraction-before-destruction experiment,” Opt. Express 22, 8085–8093 (2014).
[Crossref] [PubMed]

2013 (2)

H.-C. Poon, P. Schwander, M. Uddin, and D. K. Saldin, “Fiber diffraction without fibers,” Phys. Rev. Lett. 110, 265505 (2013).
[Crossref] [PubMed]

H. Liu, B. K. Poon, D. K. Saldin, J. C. H. Spence, and P. H. Zwart, “Three-dimensional single-particle imaging using angular correlations from X-ray laser data,” Acta Cryst. A 69, 365–373 (2013).
[Crossref]

2012 (3)

2011 (4)

F. Filsinger, G. Meijer, H. Stapelfeldt, H. N. Chapman, and J. Küpper, “State- and conformer-selected beams of aligned and oriented molecules for ultrafast diffraction studies,” Phys. Checm. Chem. Phys. 13, 2076–2087 (2011).
[Crossref]

R. A. Kirian, T. A. White, J. M. Holton, H. N. Chapman, P. Fromme, A. Barty, L. Lomb, A. Aquila, F. R. N. C. Maia, A. V. Martin, R. Fromme, X. Wang, M. S. Hunter, K. E. Schmidt, and J. C. H. Spence, “Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals,” Acta Crystallogr. A 67, 131–140 (2011).
[Crossref] [PubMed]

D. K. Saldin, H. C. Poon, M. J. Bogan, S. Marchesini, D. A. Shapiro, R. A. Kirian, U. Weierstall, and J. C. H. Spence, “New light on disordered ensembles: Ab initio structure determination of one particle from scattering fluctuations of many copies,” Phys. Rev. Lett. 106, 115501 (2011).
[Crossref]

V. Elser, “Strategies for processing diffraction data from randomly oriented particles,” Ultramicroscopy 111, 788–792 (2011).
[Crossref]

2010 (2)

R. R. Coifman, Y. Shkolnisky, F. J. Sigworth, and A. Singer, “Reference free structure determination through eigenvectors of center of mass operators,” Appl. Comput. Harmon. Anal. 28, 296–312 (2010).
[Crossref] [PubMed]

S. Pabst, P. J. Ho, and R. Santra, “Computational studies of X-ray scattering from three-dimensionally-aligned asymmetric-top molecules,” Phys. Rev. A 81, 043425 (2010).
[Crossref]

2009 (3)

P. Ho, D. Starodub, D. K. Saldin, V. L. Shneerson, A. Ourmazd, and R. Santra, “Molecular structure determination from X-ray scattering patterns of laser-aligned symmetric-top molecules,” J. Chem. Phys. 131, 131101 (2009).
[Crossref] [PubMed]

N. D. Loh and V. Elser, “Reconstruction algorithm for single-particle diffraction imaging experiments,” Phys. Rev. E 80, 026705 (2009).
[Crossref]

D. K. Saldin, V. L. Shneerson, R. Fung, and A. Ourmazd, “Structure of isolated biomolecules obtained from ultrashort x-ray pulses: Exploiting the symmetry of random orientations,” J. Phys.: Condens. Matter 21, 134014 (2009).

2008 (1)

V. L. Shneerson, A. Ourmazd, and D. K. Saldin, “Crystallography without crystals. I. the common-line method for assembling a three-dimensional diffraction volume from single-particle scattering,” Acta Crystallogr. A 64, 303–315 (2008).
[Crossref] [PubMed]

2006 (1)

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

2003 (1)

M. Belkin and P. Niyogi, “Laplacian eigenmaps for dimensionality reduction and data representation,” Neural Comput. 15, 1373–1396 (2003).
[Crossref]

1982 (1)

1977 (1)

Z. Kam, “Determination of macromolecular structure in solution by spatial correlation of scattering fluctuations,” Macromolecules 10, 927–934 (1977).
[Crossref]

1973 (1)

S. Stenholm, “Quantum theory of electromagnetic fields interacting with atoms and molecules,” Phys. Rep. 6, 1–121 (1973).
[Crossref]

Adolph, M.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Aquila, A.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

R. A. Kirian, T. A. White, J. M. Holton, H. N. Chapman, P. Fromme, A. Barty, L. Lomb, A. Aquila, F. R. N. C. Maia, A. V. Martin, R. Fromme, X. Wang, M. S. Hunter, K. E. Schmidt, and J. C. H. Spence, “Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals,” Acta Crystallogr. A 67, 131–140 (2011).
[Crossref] [PubMed]

Bajt, S.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Barends, T. R. M.

T. R. M. Barends, L. Foucar, S. Botha, R. B. Doak, R. L. Shoeman, K. Nass, J. E. Koglin, G. J. Williams, S. Boutet, M. Messerschmidt, and I. Schlichting, “De novo protein crystal structure determination from X-ray free-electron laser data,” Nature 505, 244–247 (2014).
[Crossref]

Barthelmess, M.

Barty, A.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

R. A. Kirian, T. A. White, J. M. Holton, H. N. Chapman, P. Fromme, A. Barty, L. Lomb, A. Aquila, F. R. N. C. Maia, A. V. Martin, R. Fromme, X. Wang, M. S. Hunter, K. E. Schmidt, and J. C. H. Spence, “Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals,” Acta Crystallogr. A 67, 131–140 (2011).
[Crossref] [PubMed]

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Bean, R. J.

Belkin, M.

M. Belkin and P. Niyogi, “Laplacian eigenmaps for dimensionality reduction and data representation,” Neural Comput. 15, 1373–1396 (2003).
[Crossref]

Benner, W. H.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Bergh, M.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Bogan, M. J.

D. K. Saldin, H. C. Poon, M. J. Bogan, S. Marchesini, D. A. Shapiro, R. A. Kirian, U. Weierstall, and J. C. H. Spence, “New light on disordered ensembles: Ab initio structure determination of one particle from scattering fluctuations of many copies,” Phys. Rev. Lett. 106, 115501 (2011).
[Crossref]

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Bostedt, C.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Botha, S.

T. R. M. Barends, L. Foucar, S. Botha, R. B. Doak, R. L. Shoeman, K. Nass, J. E. Koglin, G. J. Williams, S. Boutet, M. Messerschmidt, and I. Schlichting, “De novo protein crystal structure determination from X-ray free-electron laser data,” Nature 505, 244–247 (2014).
[Crossref]

Boutet, S.

T. R. M. Barends, L. Foucar, S. Botha, R. B. Doak, R. L. Shoeman, K. Nass, J. E. Koglin, G. J. Williams, S. Boutet, M. Messerschmidt, and I. Schlichting, “De novo protein crystal structure determination from X-ray free-electron laser data,” Nature 505, 244–247 (2014).
[Crossref]

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Bozek, J.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Burmeister, F.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Caleman, C.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Capotondi, F.

Chapman, H. N.

C. H. Yoon, M. Barthelmess, R. J. Bean, F. Capotondi, R. A. Kirian, M. Kiskinova, E. Pedersoli, L. Raimondi, F. Stellato, F. Wang, and H. N. Chapman, “Conformation sequence recovery of a non-periodic object from a diffraction-before-destruction experiment,” Opt. Express 22, 8085–8093 (2014).
[Crossref] [PubMed]

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

J. C. H. Spence, U. Weierstall, and H. N. Chapman, “X-ray lasers for structural and dynamic biology,” Rep. Prog. Phys. 75, 102601 (2012).
[Crossref] [PubMed]

F. Filsinger, G. Meijer, H. Stapelfeldt, H. N. Chapman, and J. Küpper, “State- and conformer-selected beams of aligned and oriented molecules for ultrafast diffraction studies,” Phys. Checm. Chem. Phys. 13, 2076–2087 (2011).
[Crossref]

R. A. Kirian, T. A. White, J. M. Holton, H. N. Chapman, P. Fromme, A. Barty, L. Lomb, A. Aquila, F. R. N. C. Maia, A. V. Martin, R. Fromme, X. Wang, M. S. Hunter, K. E. Schmidt, and J. C. H. Spence, “Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals,” Acta Crystallogr. A 67, 131–140 (2011).
[Crossref] [PubMed]

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Coffee, R.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Coifman, R. R.

R. R. Coifman, Y. Shkolnisky, F. J. Sigworth, and A. Singer, “Reference free structure determination through eigenvectors of center of mass operators,” Appl. Comput. Harmon. Anal. 28, 296–312 (2010).
[Crossref] [PubMed]

Coppola, N.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

de la Porte, J.

J. de la Porte, B. M. Herbst, W. Hereman, and S. J. van der Walt, “An introduction to diffusion maps,” Tech. rep., Proceedings of the 19th Symposium of the Pattern Recognition Association of South Africa (PRASA 2008) (2008).

Delmas, T.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Devanathan, V.

V. Devanathan, Angular Momentum Techniques in Quantum Mechanics (Springer, 2002).
[Crossref]

Doak, R. B.

T. R. M. Barends, L. Foucar, S. Botha, R. B. Doak, R. L. Shoeman, K. Nass, J. E. Koglin, G. J. Williams, S. Boutet, M. Messerschmidt, and I. Schlichting, “De novo protein crystal structure determination from X-ray free-electron laser data,” Nature 505, 244–247 (2014).
[Crossref]

Donatelli, J. J.

J. J. Donatelli, P. H. Zwart, and J. A. Sethian, “Iterative phasing for fluctuation X-ray scattering,” Proc. Natl. Acad. Sci. U. S. A. 112, 10286–10291 (2015).
[Crossref] [PubMed]

Dusterer, S.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Elser, V.

V. Elser, “Strategies for processing diffraction data from randomly oriented particles,” Ultramicroscopy 111, 788–792 (2011).
[Crossref]

N. D. Loh and V. Elser, “Reconstruction algorithm for single-particle diffraction imaging experiments,” Phys. Rev. E 80, 026705 (2009).
[Crossref]

Epp, S.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Erk, B.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Fienup, J. R.

Filsinger, F.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

F. Filsinger, G. Meijer, H. Stapelfeldt, H. N. Chapman, and J. Küpper, “State- and conformer-selected beams of aligned and oriented molecules for ultrafast diffraction studies,” Phys. Checm. Chem. Phys. 13, 2076–2087 (2011).
[Crossref]

Foucar, L.

T. R. M. Barends, L. Foucar, S. Botha, R. B. Doak, R. L. Shoeman, K. Nass, J. E. Koglin, G. J. Williams, S. Boutet, M. Messerschmidt, and I. Schlichting, “De novo protein crystal structure determination from X-ray free-electron laser data,” Nature 505, 244–247 (2014).
[Crossref]

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Frank, M.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Fromme, P.

R. A. Kirian, T. A. White, J. M. Holton, H. N. Chapman, P. Fromme, A. Barty, L. Lomb, A. Aquila, F. R. N. C. Maia, A. V. Martin, R. Fromme, X. Wang, M. S. Hunter, K. E. Schmidt, and J. C. H. Spence, “Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals,” Acta Crystallogr. A 67, 131–140 (2011).
[Crossref] [PubMed]

Fromme, R.

R. A. Kirian, T. A. White, J. M. Holton, H. N. Chapman, P. Fromme, A. Barty, L. Lomb, A. Aquila, F. R. N. C. Maia, A. V. Martin, R. Fromme, X. Wang, M. S. Hunter, K. E. Schmidt, and J. C. H. Spence, “Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals,” Acta Crystallogr. A 67, 131–140 (2011).
[Crossref] [PubMed]

Fung, R.

D. K. Saldin, V. L. Shneerson, R. Fung, and A. Ourmazd, “Structure of isolated biomolecules obtained from ultrashort x-ray pulses: Exploiting the symmetry of random orientations,” J. Phys.: Condens. Matter 21, 134014 (2009).

Giannakis, D.

Gorkhover, T.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Gumprecht, L.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Hajdu, J.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Ham, J.

J. Ham, D. D. Lee, S. Mika, and B. Schölkopf, “A kernel view of the dimensionality reduction of manifolds,” in “Proceedings of the twenty-first international conference on machine learning,” (ACM, 2004), pp. 47.

Hartmann, A.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
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Hartmann, R.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Hau-Riege, S. P.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Hauser, G.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
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Herbst, B. M.

J. de la Porte, B. M. Herbst, W. Hereman, and S. J. van der Walt, “An introduction to diffusion maps,” Tech. rep., Proceedings of the 19th Symposium of the Pattern Recognition Association of South Africa (PRASA 2008) (2008).

Hereman, W.

J. de la Porte, B. M. Herbst, W. Hereman, and S. J. van der Walt, “An introduction to diffusion maps,” Tech. rep., Proceedings of the 19th Symposium of the Pattern Recognition Association of South Africa (PRASA 2008) (2008).

Ho, P.

P. Ho, D. Starodub, D. K. Saldin, V. L. Shneerson, A. Ourmazd, and R. Santra, “Molecular structure determination from X-ray scattering patterns of laser-aligned symmetric-top molecules,” J. Chem. Phys. 131, 131101 (2009).
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Ho, P. J.

S. Pabst, P. J. Ho, and R. Santra, “Computational studies of X-ray scattering from three-dimensionally-aligned asymmetric-top molecules,” Phys. Rev. A 81, 043425 (2010).
[Crossref]

Hodgson, K. O.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Hoener, M.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Holl, P.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Holmegaard, L.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Holton, J. M.

R. A. Kirian, T. A. White, J. M. Holton, H. N. Chapman, P. Fromme, A. Barty, L. Lomb, A. Aquila, F. R. N. C. Maia, A. V. Martin, R. Fromme, X. Wang, M. S. Hunter, K. E. Schmidt, and J. C. H. Spence, “Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals,” Acta Crystallogr. A 67, 131–140 (2011).
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Hömke, A.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
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Huldt, G.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Hunter, M. S.

R. A. Kirian, T. A. White, J. M. Holton, H. N. Chapman, P. Fromme, A. Barty, L. Lomb, A. Aquila, F. R. N. C. Maia, A. V. Martin, R. Fromme, X. Wang, M. S. Hunter, K. E. Schmidt, and J. C. H. Spence, “Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals,” Acta Crystallogr. A 67, 131–140 (2011).
[Crossref] [PubMed]

Johnsson, P.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
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Jost, J.

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Kam, Z.

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Kimmel, N.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
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Kirian, R. A.

C. H. Yoon, M. Barthelmess, R. J. Bean, F. Capotondi, R. A. Kirian, M. Kiskinova, E. Pedersoli, L. Raimondi, F. Stellato, F. Wang, and H. N. Chapman, “Conformation sequence recovery of a non-periodic object from a diffraction-before-destruction experiment,” Opt. Express 22, 8085–8093 (2014).
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D. K. Saldin, H. C. Poon, M. J. Bogan, S. Marchesini, D. A. Shapiro, R. A. Kirian, U. Weierstall, and J. C. H. Spence, “New light on disordered ensembles: Ab initio structure determination of one particle from scattering fluctuations of many copies,” Phys. Rev. Lett. 106, 115501 (2011).
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R. A. Kirian, T. A. White, J. M. Holton, H. N. Chapman, P. Fromme, A. Barty, L. Lomb, A. Aquila, F. R. N. C. Maia, A. V. Martin, R. Fromme, X. Wang, M. S. Hunter, K. E. Schmidt, and J. C. H. Spence, “Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals,” Acta Crystallogr. A 67, 131–140 (2011).
[Crossref] [PubMed]

Kiskinova, M.

Koglin, J. E.

T. R. M. Barends, L. Foucar, S. Botha, R. B. Doak, R. L. Shoeman, K. Nass, J. E. Koglin, G. J. Williams, S. Boutet, M. Messerschmidt, and I. Schlichting, “De novo protein crystal structure determination from X-ray free-electron laser data,” Nature 505, 244–247 (2014).
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Krasniqi, F.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Kuhlmann, M.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Kühnel, K.-U.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
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Küpper, J.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

F. Filsinger, G. Meijer, H. Stapelfeldt, H. N. Chapman, and J. Küpper, “State- and conformer-selected beams of aligned and oriented molecules for ultrafast diffraction studies,” Phys. Checm. Chem. Phys. 13, 2076–2087 (2011).
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Lee, D. D.

J. Ham, D. D. Lee, S. Mika, and B. Schölkopf, “A kernel view of the dimensionality reduction of manifolds,” in “Proceedings of the twenty-first international conference on machine learning,” (ACM, 2004), pp. 47.

Lee, R. W.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
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Liu, H.

H. Liu, B. K. Poon, D. K. Saldin, J. C. H. Spence, and P. H. Zwart, “Three-dimensional single-particle imaging using angular correlations from X-ray laser data,” Acta Cryst. A 69, 365–373 (2013).
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Loh, N. D.

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[Crossref]

Lomb, L.

R. A. Kirian, T. A. White, J. M. Holton, H. N. Chapman, P. Fromme, A. Barty, L. Lomb, A. Aquila, F. R. N. C. Maia, A. V. Martin, R. Fromme, X. Wang, M. S. Hunter, K. E. Schmidt, and J. C. H. Spence, “Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals,” Acta Crystallogr. A 67, 131–140 (2011).
[Crossref] [PubMed]

London, R. A.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Maia, F. R. N. C.

R. A. Kirian, T. A. White, J. M. Holton, H. N. Chapman, P. Fromme, A. Barty, L. Lomb, A. Aquila, F. R. N. C. Maia, A. V. Martin, R. Fromme, X. Wang, M. S. Hunter, K. E. Schmidt, and J. C. H. Spence, “Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals,” Acta Crystallogr. A 67, 131–140 (2011).
[Crossref] [PubMed]

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Marchesini, S.

D. K. Saldin, H. C. Poon, M. J. Bogan, S. Marchesini, D. A. Shapiro, R. A. Kirian, U. Weierstall, and J. C. H. Spence, “New light on disordered ensembles: Ab initio structure determination of one particle from scattering fluctuations of many copies,” Phys. Rev. Lett. 106, 115501 (2011).
[Crossref]

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Martin, A. V.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

R. A. Kirian, T. A. White, J. M. Holton, H. N. Chapman, P. Fromme, A. Barty, L. Lomb, A. Aquila, F. R. N. C. Maia, A. V. Martin, R. Fromme, X. Wang, M. S. Hunter, K. E. Schmidt, and J. C. H. Spence, “Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals,” Acta Crystallogr. A 67, 131–140 (2011).
[Crossref] [PubMed]

Maurer, J.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Meijer, G.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

F. Filsinger, G. Meijer, H. Stapelfeldt, H. N. Chapman, and J. Küpper, “State- and conformer-selected beams of aligned and oriented molecules for ultrafast diffraction studies,” Phys. Checm. Chem. Phys. 13, 2076–2087 (2011).
[Crossref]

Messerschmidt, M.

T. R. M. Barends, L. Foucar, S. Botha, R. B. Doak, R. L. Shoeman, K. Nass, J. E. Koglin, G. J. Williams, S. Boutet, M. Messerschmidt, and I. Schlichting, “De novo protein crystal structure determination from X-ray free-electron laser data,” Nature 505, 244–247 (2014).
[Crossref]

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Mika, S.

J. Ham, D. D. Lee, S. Mika, and B. Schölkopf, “A kernel view of the dimensionality reduction of manifolds,” in “Proceedings of the twenty-first international conference on machine learning,” (ACM, 2004), pp. 47.

Möller, T.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Moshammer, R.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Nass, K.

T. R. M. Barends, L. Foucar, S. Botha, R. B. Doak, R. L. Shoeman, K. Nass, J. E. Koglin, G. J. Williams, S. Boutet, M. Messerschmidt, and I. Schlichting, “De novo protein crystal structure determination from X-ray free-electron laser data,” Nature 505, 244–247 (2014).
[Crossref]

Niyogi, P.

M. Belkin and P. Niyogi, “Laplacian eigenmaps for dimensionality reduction and data representation,” Neural Comput. 15, 1373–1396 (2003).
[Crossref]

Ourmazd, A.

D. Giannakis, P. Schwander, and A. Ourmazd, “The symmetries of image formation by scattering. I. Theoretical framework,” Opt. Express 20, 12799–12826 (2012).
[Crossref] [PubMed]

P. Schwander, D. Giannakis, C. H. Yoon, and A. Ourmazd, “The symmetries of image formation by scattering. II. Applications,” Opt. Express 20, 12827–12849 (2012).
[Crossref] [PubMed]

D. K. Saldin, V. L. Shneerson, R. Fung, and A. Ourmazd, “Structure of isolated biomolecules obtained from ultrashort x-ray pulses: Exploiting the symmetry of random orientations,” J. Phys.: Condens. Matter 21, 134014 (2009).

P. Ho, D. Starodub, D. K. Saldin, V. L. Shneerson, A. Ourmazd, and R. Santra, “Molecular structure determination from X-ray scattering patterns of laser-aligned symmetric-top molecules,” J. Chem. Phys. 131, 131101 (2009).
[Crossref] [PubMed]

V. L. Shneerson, A. Ourmazd, and D. K. Saldin, “Crystallography without crystals. I. the common-line method for assembling a three-dimensional diffraction volume from single-particle scattering,” Acta Crystallogr. A 64, 303–315 (2008).
[Crossref] [PubMed]

Pabst, S.

S. Pabst, P. J. Ho, and R. Santra, “Computational studies of X-ray scattering from three-dimensionally-aligned asymmetric-top molecules,” Phys. Rev. A 81, 043425 (2010).
[Crossref]

Pedersoli, E.

Plönjes, E.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Poon, B. K.

H. Liu, B. K. Poon, D. K. Saldin, J. C. H. Spence, and P. H. Zwart, “Three-dimensional single-particle imaging using angular correlations from X-ray laser data,” Acta Cryst. A 69, 365–373 (2013).
[Crossref]

Poon, H. C.

D. K. Saldin, H. C. Poon, M. J. Bogan, S. Marchesini, D. A. Shapiro, R. A. Kirian, U. Weierstall, and J. C. H. Spence, “New light on disordered ensembles: Ab initio structure determination of one particle from scattering fluctuations of many copies,” Phys. Rev. Lett. 106, 115501 (2011).
[Crossref]

Poon, H.-C.

H.-C. Poon, P. Schwander, M. Uddin, and D. K. Saldin, “Fiber diffraction without fibers,” Phys. Rev. Lett. 110, 265505 (2013).
[Crossref] [PubMed]

Raimondi, L.

Reich, C.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Rolles, D.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Rouzée, A.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Rudek, B.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Rudenko, A.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Saldin, D. K.

H. Liu, B. K. Poon, D. K. Saldin, J. C. H. Spence, and P. H. Zwart, “Three-dimensional single-particle imaging using angular correlations from X-ray laser data,” Acta Cryst. A 69, 365–373 (2013).
[Crossref]

H.-C. Poon, P. Schwander, M. Uddin, and D. K. Saldin, “Fiber diffraction without fibers,” Phys. Rev. Lett. 110, 265505 (2013).
[Crossref] [PubMed]

D. K. Saldin, H. C. Poon, M. J. Bogan, S. Marchesini, D. A. Shapiro, R. A. Kirian, U. Weierstall, and J. C. H. Spence, “New light on disordered ensembles: Ab initio structure determination of one particle from scattering fluctuations of many copies,” Phys. Rev. Lett. 106, 115501 (2011).
[Crossref]

P. Ho, D. Starodub, D. K. Saldin, V. L. Shneerson, A. Ourmazd, and R. Santra, “Molecular structure determination from X-ray scattering patterns of laser-aligned symmetric-top molecules,” J. Chem. Phys. 131, 131101 (2009).
[Crossref] [PubMed]

D. K. Saldin, V. L. Shneerson, R. Fung, and A. Ourmazd, “Structure of isolated biomolecules obtained from ultrashort x-ray pulses: Exploiting the symmetry of random orientations,” J. Phys.: Condens. Matter 21, 134014 (2009).

V. L. Shneerson, A. Ourmazd, and D. K. Saldin, “Crystallography without crystals. I. the common-line method for assembling a three-dimensional diffraction volume from single-particle scattering,” Acta Crystallogr. A 64, 303–315 (2008).
[Crossref] [PubMed]

Santra, R.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

S. Pabst, P. J. Ho, and R. Santra, “Computational studies of X-ray scattering from three-dimensionally-aligned asymmetric-top molecules,” Phys. Rev. A 81, 043425 (2010).
[Crossref]

P. Ho, D. Starodub, D. K. Saldin, V. L. Shneerson, A. Ourmazd, and R. Santra, “Molecular structure determination from X-ray scattering patterns of laser-aligned symmetric-top molecules,” J. Chem. Phys. 131, 131101 (2009).
[Crossref] [PubMed]

Schlichting, I.

T. R. M. Barends, L. Foucar, S. Botha, R. B. Doak, R. L. Shoeman, K. Nass, J. E. Koglin, G. J. Williams, S. Boutet, M. Messerschmidt, and I. Schlichting, “De novo protein crystal structure determination from X-ray free-electron laser data,” Nature 505, 244–247 (2014).
[Crossref]

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Schmidt, C.

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Schmidt, K. E.

R. A. Kirian, T. A. White, J. M. Holton, H. N. Chapman, P. Fromme, A. Barty, L. Lomb, A. Aquila, F. R. N. C. Maia, A. V. Martin, R. Fromme, X. Wang, M. S. Hunter, K. E. Schmidt, and J. C. H. Spence, “Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals,” Acta Crystallogr. A 67, 131–140 (2011).
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J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
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Seibert, M. M.

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H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
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Shkolnisky, Y.

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Shneerson, V. L.

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P. Ho, D. Starodub, D. K. Saldin, V. L. Shneerson, A. Ourmazd, and R. Santra, “Molecular structure determination from X-ray scattering patterns of laser-aligned symmetric-top molecules,” J. Chem. Phys. 131, 131101 (2009).
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V. L. Shneerson, A. Ourmazd, and D. K. Saldin, “Crystallography without crystals. I. the common-line method for assembling a three-dimensional diffraction volume from single-particle scattering,” Acta Crystallogr. A 64, 303–315 (2008).
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Shoeman, R. L.

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Sigworth, F. J.

R. R. Coifman, Y. Shkolnisky, F. J. Sigworth, and A. Singer, “Reference free structure determination through eigenvectors of center of mass operators,” Appl. Comput. Harmon. Anal. 28, 296–312 (2010).
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Singer, A.

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Soltau, H.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
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J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
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D. K. Saldin, H. C. Poon, M. J. Bogan, S. Marchesini, D. A. Shapiro, R. A. Kirian, U. Weierstall, and J. C. H. Spence, “New light on disordered ensembles: Ab initio structure determination of one particle from scattering fluctuations of many copies,” Phys. Rev. Lett. 106, 115501 (2011).
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Spiller, E.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
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Stapelfeldt, H.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
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F. Filsinger, G. Meijer, H. Stapelfeldt, H. N. Chapman, and J. Küpper, “State- and conformer-selected beams of aligned and oriented molecules for ultrafast diffraction studies,” Phys. Checm. Chem. Phys. 13, 2076–2087 (2011).
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Starodub, D.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

P. Ho, D. Starodub, D. K. Saldin, V. L. Shneerson, A. Ourmazd, and R. Santra, “Molecular structure determination from X-ray scattering patterns of laser-aligned symmetric-top molecules,” J. Chem. Phys. 131, 131101 (2009).
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J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
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Strüder, L.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
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Szöke, A.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
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Thøgersen, J.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
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Tîmneanu, N.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
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Treusch, R.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
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Tschentscher, T.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
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Uddin, M.

H.-C. Poon, P. Schwander, M. Uddin, and D. K. Saldin, “Fiber diffraction without fibers,” Phys. Rev. Lett. 110, 265505 (2013).
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Ullrich, J.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
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van der Spoel, D.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

van der Walt, S. J.

J. de la Porte, B. M. Herbst, W. Hereman, and S. J. van der Walt, “An introduction to diffusion maps,” Tech. rep., Proceedings of the 19th Symposium of the Pattern Recognition Association of South Africa (PRASA 2008) (2008).

Vrakking, M. J.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Walczak, M.

M. Walczak, “Bayesian orientation estimate from single molecule X-ray scattering data,” Master’s thesis, Georg-August-Universität Göttingen (2010).

Wang, F.

Wang, X.

R. A. Kirian, T. A. White, J. M. Holton, H. N. Chapman, P. Fromme, A. Barty, L. Lomb, A. Aquila, F. R. N. C. Maia, A. V. Martin, R. Fromme, X. Wang, M. S. Hunter, K. E. Schmidt, and J. C. H. Spence, “Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals,” Acta Crystallogr. A 67, 131–140 (2011).
[Crossref] [PubMed]

Weidenspointner, G.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Weierstall, U.

J. C. H. Spence, U. Weierstall, and H. N. Chapman, “X-ray lasers for structural and dynamic biology,” Rep. Prog. Phys. 75, 102601 (2012).
[Crossref] [PubMed]

D. K. Saldin, H. C. Poon, M. J. Bogan, S. Marchesini, D. A. Shapiro, R. A. Kirian, U. Weierstall, and J. C. H. Spence, “New light on disordered ensembles: Ab initio structure determination of one particle from scattering fluctuations of many copies,” Phys. Rev. Lett. 106, 115501 (2011).
[Crossref]

White, T. A.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

R. A. Kirian, T. A. White, J. M. Holton, H. N. Chapman, P. Fromme, A. Barty, L. Lomb, A. Aquila, F. R. N. C. Maia, A. V. Martin, R. Fromme, X. Wang, M. S. Hunter, K. E. Schmidt, and J. C. H. Spence, “Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals,” Acta Crystallogr. A 67, 131–140 (2011).
[Crossref] [PubMed]

Williams, G. J.

T. R. M. Barends, L. Foucar, S. Botha, R. B. Doak, R. L. Shoeman, K. Nass, J. E. Koglin, G. J. Williams, S. Boutet, M. Messerschmidt, and I. Schlichting, “De novo protein crystal structure determination from X-ray free-electron laser data,” Nature 505, 244–247 (2014).
[Crossref]

Woods, B. W.

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Wunderer, C.

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

Yoon, C. H.

Zwart, P. H.

J. J. Donatelli, P. H. Zwart, and J. A. Sethian, “Iterative phasing for fluctuation X-ray scattering,” Proc. Natl. Acad. Sci. U. S. A. 112, 10286–10291 (2015).
[Crossref] [PubMed]

H. Liu, B. K. Poon, D. K. Saldin, J. C. H. Spence, and P. H. Zwart, “Three-dimensional single-particle imaging using angular correlations from X-ray laser data,” Acta Cryst. A 69, 365–373 (2013).
[Crossref]

Acta Cryst. A (1)

H. Liu, B. K. Poon, D. K. Saldin, J. C. H. Spence, and P. H. Zwart, “Three-dimensional single-particle imaging using angular correlations from X-ray laser data,” Acta Cryst. A 69, 365–373 (2013).
[Crossref]

Acta Crystallogr. A (2)

V. L. Shneerson, A. Ourmazd, and D. K. Saldin, “Crystallography without crystals. I. the common-line method for assembling a three-dimensional diffraction volume from single-particle scattering,” Acta Crystallogr. A 64, 303–315 (2008).
[Crossref] [PubMed]

R. A. Kirian, T. A. White, J. M. Holton, H. N. Chapman, P. Fromme, A. Barty, L. Lomb, A. Aquila, F. R. N. C. Maia, A. V. Martin, R. Fromme, X. Wang, M. S. Hunter, K. E. Schmidt, and J. C. H. Spence, “Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals,” Acta Crystallogr. A 67, 131–140 (2011).
[Crossref] [PubMed]

Appl. Comput. Harmon. Anal. (1)

R. R. Coifman, Y. Shkolnisky, F. J. Sigworth, and A. Singer, “Reference free structure determination through eigenvectors of center of mass operators,” Appl. Comput. Harmon. Anal. 28, 296–312 (2010).
[Crossref] [PubMed]

Appl. Opt. (1)

J. Chem. Phys. (1)

P. Ho, D. Starodub, D. K. Saldin, V. L. Shneerson, A. Ourmazd, and R. Santra, “Molecular structure determination from X-ray scattering patterns of laser-aligned symmetric-top molecules,” J. Chem. Phys. 131, 131101 (2009).
[Crossref] [PubMed]

J. Phys.: Condens. Matter (1)

D. K. Saldin, V. L. Shneerson, R. Fung, and A. Ourmazd, “Structure of isolated biomolecules obtained from ultrashort x-ray pulses: Exploiting the symmetry of random orientations,” J. Phys.: Condens. Matter 21, 134014 (2009).

Macromolecules (1)

Z. Kam, “Determination of macromolecular structure in solution by spatial correlation of scattering fluctuations,” Macromolecules 10, 927–934 (1977).
[Crossref]

Nat. Phys. (1)

H. N. Chapman, A. Barty, M. J. Bogan, S. Boutet, M. Frank, S. P. Hau-Riege, S. Marchesini, B. W. Woods, S. Bajt, W. H. Benner, R. A. London, E. Plönjes, M. Kuhlmann, R. Treusch, S. Dusterer, T. Tschentscher, J. R. Schneider, E. Spiller, T. Möller, C. Bostedt, M. Hoener, D. A. Shapiro, K. O. Hodgson, D. van der Spoel, F. Burmeister, M. Bergh, C. Caleman, G. Huldt, M. M. Seibert, F. R. N. C. Maia, R. W. Lee, A. Szöke, N. Tîmneanu, and J. Hajdu, “Femtosecond diffractive imaging with a soft X-ray free-electron laser,” Nat. Phys. 2, 839–843 (2006).
[Crossref]

Nature (1)

T. R. M. Barends, L. Foucar, S. Botha, R. B. Doak, R. L. Shoeman, K. Nass, J. E. Koglin, G. J. Williams, S. Boutet, M. Messerschmidt, and I. Schlichting, “De novo protein crystal structure determination from X-ray free-electron laser data,” Nature 505, 244–247 (2014).
[Crossref]

Neural Comput. (1)

M. Belkin and P. Niyogi, “Laplacian eigenmaps for dimensionality reduction and data representation,” Neural Comput. 15, 1373–1396 (2003).
[Crossref]

Opt. Express (3)

Phys. Checm. Chem. Phys. (1)

F. Filsinger, G. Meijer, H. Stapelfeldt, H. N. Chapman, and J. Küpper, “State- and conformer-selected beams of aligned and oriented molecules for ultrafast diffraction studies,” Phys. Checm. Chem. Phys. 13, 2076–2087 (2011).
[Crossref]

Phys. Rep. (1)

S. Stenholm, “Quantum theory of electromagnetic fields interacting with atoms and molecules,” Phys. Rep. 6, 1–121 (1973).
[Crossref]

Phys. Rev. A (1)

S. Pabst, P. J. Ho, and R. Santra, “Computational studies of X-ray scattering from three-dimensionally-aligned asymmetric-top molecules,” Phys. Rev. A 81, 043425 (2010).
[Crossref]

Phys. Rev. E (1)

N. D. Loh and V. Elser, “Reconstruction algorithm for single-particle diffraction imaging experiments,” Phys. Rev. E 80, 026705 (2009).
[Crossref]

Phys. Rev. Lett. (3)

J. Küpper, S. Stern, L. Holmegaard, F. Filsinger, A. Rouzée, A. Rudenko, P. Johnsson, A. V. Martin, M. Adolph, A. Aquila, S. Bajt, A. Barty, C. Bostedt, J. Bozek, C. Caleman, R. Coffee, N. Coppola, T. Delmas, S. Epp, B. Erk, L. Foucar, T. Gorkhover, L. Gumprecht, A. Hartmann, R. Hartmann, G. Hauser, P. Holl, A. Hömke, N. Kimmel, F. Krasniqi, K.-U. Kühnel, J. Maurer, M. Messerschmidt, R. Moshammer, C. Reich, B. Rudek, R. Santra, I. Schlichting, C. Schmidt, S. Schorb, J. Schulz, H. Soltau, J. C. Spence, D. Starodub, L. Strüder, J. Thøgersen, M. J. Vrakking, G. Weidenspointner, T. A. White, C. Wunderer, G. Meijer, J. Ullrich, H. Stapelfeldt, D. Rolles, and H. N. Chapman, “X-ray diffraction from isolated and strongly aligned gas-phase molecules with a free-electron laser,” Phys. Rev. Lett. 112, 083002 (2014).
[Crossref]

D. K. Saldin, H. C. Poon, M. J. Bogan, S. Marchesini, D. A. Shapiro, R. A. Kirian, U. Weierstall, and J. C. H. Spence, “New light on disordered ensembles: Ab initio structure determination of one particle from scattering fluctuations of many copies,” Phys. Rev. Lett. 106, 115501 (2011).
[Crossref]

H.-C. Poon, P. Schwander, M. Uddin, and D. K. Saldin, “Fiber diffraction without fibers,” Phys. Rev. Lett. 110, 265505 (2013).
[Crossref] [PubMed]

Proc. Natl. Acad. Sci. U. S. A. (1)

J. J. Donatelli, P. H. Zwart, and J. A. Sethian, “Iterative phasing for fluctuation X-ray scattering,” Proc. Natl. Acad. Sci. U. S. A. 112, 10286–10291 (2015).
[Crossref] [PubMed]

Rep. Prog. Phys. (1)

J. C. H. Spence, U. Weierstall, and H. N. Chapman, “X-ray lasers for structural and dynamic biology,” Rep. Prog. Phys. 75, 102601 (2012).
[Crossref] [PubMed]

Ultramicroscopy (1)

V. Elser, “Strategies for processing diffraction data from randomly oriented particles,” Ultramicroscopy 111, 788–792 (2011).
[Crossref]

Other (5)

M. Walczak, “Bayesian orientation estimate from single molecule X-ray scattering data,” Master’s thesis, Georg-August-Universität Göttingen (2010).

J. Ham, D. D. Lee, S. Mika, and B. Schölkopf, “A kernel view of the dimensionality reduction of manifolds,” in “Proceedings of the twenty-first international conference on machine learning,” (ACM, 2004), pp. 47.

J. de la Porte, B. M. Herbst, W. Hereman, and S. J. van der Walt, “An introduction to diffusion maps,” Tech. rep., Proceedings of the 19th Symposium of the Pattern Recognition Association of South Africa (PRASA 2008) (2008).

J. Jost, Riemannian Geometry and Geometric Analysis (Springer, 2011).
[Crossref]

V. Devanathan, Angular Momentum Techniques in Quantum Mechanics (Springer, 2002).
[Crossref]

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Figures (4)

Fig. 1
Fig. 1 Sketches of a diatomic molecule consisting of two atoms with a form factor fκ(k) = exp(−k2/[4κ]2) and an inter-atomic distance d at different orientations given by θ, the angle between intra-molecular axis and normal of the detector plane. For each orientation a cross section of the corresponding scattering image Sκd(k) = fκ2(k)[1 + cos(kd sinθ)] for weak (a–c) and strong (d) localizations is shown.
Fig. 2
Fig. 2 Metric gκ(θ) of the diatomic molecule (blue-solid line) as given in Eq. (11) for three ratios of κ/d in comparison with the reference metric gref (gray-dashed) from Eq. (12).
Fig. 3
Fig. 3 Angles (colorcoded) between the subspaces spanned by the Wigner D-matrices and the eigenfunctions of the Laplace-Beltrami operator of Chignolin as function of maximal tranfer momentum kmax and the parameter K in the image-modification factor CK(k) given in Eq. (13).
Fig. 4
Fig. 4 Equipotential surfaces of the reconstructed electron density (note that the density around the hydrogen atoms does not show since it is smaller than the chosen equipotential value) and ball-and-stick-model of Chignolin.

Equations (24)

Equations on this page are rendered with MathJax. Learn more.

P i j = e D i j 2 / D 2 with D i j | X i X j | ,
L ^ ( γ ) = 1 J ( γ ) μ , ν = 1 3 μ J ( γ ) [ g μ ν ( γ ) ] 1 ν with J ( γ ) det | g μ ν ( γ ) |
S γ ( k ) = j l N f j l ( k ) e i k R _ γ r j l ,
f j l ( k ) = f j ( k ) f l ( k ) , r j l = r j r l .
D i j 2 = Ω d 2 k [ S γ i ( k ) S γ j ( k ) ] 2 ,
g μ ν ( γ ) = 1 2 d 2 k [ μ S γ ( k ) ] [ ν S γ ( k ) ] .
R _ γ = R _ ξ ( z ) R _ θ ( y ) R _ φ ( z )
R _ α ( z ) = ( cos α sin α 0 sin α cos α 0 0 0 1 ) , R _ α ( y ) = ( cos α 0 sin α 0 1 0 sin α 0 cos α )
g μ ν [ R ] = ( 1 0 cos θ 0 1 0 cos θ 0 1 ) .
g μ ν [ P ] = ( 1 4 [ 3 + cos ( 2 θ ) ] 0 cos θ 0 1 2 0 cos θ 0 1 ) .
g μ ν ~ j l m n N e κ j l m n 2 ( r ˜ j l r ˜ m n ) 2 [ r j l A _ μ ν r m n + P μ ν ( r j l r m n ) ] ,
lim κ g μ ν ( γ ) ~ j l r j l A _ μ ν ( γ ) r j l .
g κ ( θ ) = cos 2 θ ( ( 8 [ κ d ] 2 sin 2 θ 1 ) e 4 [ κ d ] 2 sin 2 θ + 1 ) .
g [ R ] ( θ ) = cos 2 θ ,
C K ( k ) = e k 2 / [ 4 K ] 2
ρ j ( r ) = [ n j / σ j 3 ] e 4 ln 2 r 2 / σ j 2
g μ ν ( γ ) = 8 π j l , m n N n j l m n κ j l m n 4 e κ j l m n 2 [ ( d 1 , j l m n ) 2 + ( d 2 , j l m n ) 2 ] × [ [ r j l A _ μ ν r m n ] 2 κ j l m n 2 s , t = 1 2 d s , j l m n d t , j l m n [ r j l A _ s μ ν r m n ] ] ,
n j l m n n j n l n m n n
κ j l m n 2 4 ln 2 / ( σ j 2 + σ l 2 + σ m 2 + σ n 2 )
d s , j l m n e s R _ γ [ r j l r m n ]
A _ s t μ ν [ μ R _ γ ] e s e t [ ν R _ γ ]
A _ μ ν [ μ R _ γ ] P _ [ ν R _ γ ]
d j i = 1 | K j | K j R _ γ i 1 e z .
S ( K j ) = { S γ j 1 ( k j 1 ) + [ S γ j 2 ( k j 2 ) S γ j 1 ( k j 1 ) ] | k j 1 K j | | k j 1 K j | + | k j 2 K j | , if ( k j 1 K j ) ( k j 2 K j ) 0 S γ j 1 ( k j 1 ) ± [ S γ j 2 ( k j 2 ) S γ j 1 ( k j 1 ) ] | k j 1 K j | | k j 1 k j 2 | , otherwise .

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