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(Preprint) Direct observation of the exciton polaron by serial femtosecond crystallography on single CsPbBr3 quantum dots

Z Shen, M Samoli, O Erdem, J Bielecki, AK Samanta, J E, A Estillore, C Kim, Y Kim, J Koliyadu, R Letrun, F Locardi, J Lübke, A Mall, D Melo, G Mills, S Rafie-Zinedine, A Round, T Sato, R de Wijn, T Wollweber, L Worbs, Y Zhuang, AP Mancuso, R Bean, HN Chapman, J Küpper, I Infante, H Lange, Z Hens, K Ayyer
arXiv:2502.02343 (2025)

(Preprint) SPRING: an effective and reliable approach for image reconstruction in single-shot Coherent Diffraction Imaging

A Colombo, M Sauppe, A Al Haddad, K Ayyer, M Babayan, R Boll, R Dagar, S Dold, T Fennel, L Hecht, G Knopp, K Kolatzki, B Langbehn, F Maia, A Mall, P Mazumder, T Mazza, Y Ovcharenko, IC Polat, JC Schäfer-Zimmermann, K Schnorr, ML Schubert, A Sehati, JA Sellberg, B Senfftleben, Z Shen, Z Sun, P Svensson, P Tümmler, S Usenko, CF Ussling, O Veteläinen, S Wächter, N Walsh, AV Weitnauer, T You, M Zuod, M Meyer, C Bostedt, DE Galli, M Patanen, D Rupp
arXiv:2409.07413 (2024)

(Preprint) Observation of Aerosolization-induced Morphological Changes in Viral Capsids

A Mall, A Munke, Z Shen, P Mazumder, J Bielecki, A Estillore, C Kim, R Letrun, J Lübke, S Rafie-Zinedine, A Round, E Round, M Rütten, AK Samanta, A Sarma, T Sato, F Schulz, C Seuring, T Wollweber, L Worbs, P Vagovic, R Bean, AP Mancuso, NTD Loh, T Beck, J Küpper, FRNC Maia, HN Chapman, K Ayyer
arXiv:2407.11687 (2024)

(Preprint) Understanding conformational dynamics from macromolecular crystal diffuse scattering

P Mazumder, K Ayyer
bioRxiv 2021.02.11.429988 (2021)

Resolving Nonequilibrium Shape Variations among Millions of Gold Nanoparticles

Z Shen, PL Xavier, R Bean, J Bielecki, M Bergemann, BJ Daurer, T Ekeberg, AD Estillore, H Fangohr, K Giewekemeyer, M Karnevskiy, RA Kirian, H Kirkwood, Y Kim, JCP Koliyadu, H Lange, R Letrun, J Lübke, A Mall, T Michelat, AJ Morgan, N Roth, AK Samanta, T Sato, M Sikorski, F Schulz, P Vagovic, T Wollweber, L Worbs, FRNC Maia, DA Horke, J Küpper, AP Mancuso, HN Chapman, K Ayyer, ND Loh
ACS Nano 18, 24, 15576-15589 (2024)  

Nanoscale X-ray imaging with high spectral sensitivity using fluorescence intensity correlations

T Wollweber, K Ayyer
Structural Dynamics 11, 024307 (2024)  

Observation of a single protein by ultrafast X-ray diffraction

T Ekeberg, D Assalauova, J Bielecki, R Boll, BJ Daurer, LA Eichacker, LE Franken, DE Galli, L Gelisio, L Gumprecht, LH Gunn, J Hajdu, R Hartmann, D Hasse, A Ignatenko, J Koliyadu, O Kulyk, R Kurta, M Kuster, W Lugmayr, J Lübke, AP Mancuso, T Mazza, C Nettelblad, Y Ovcharenko, DE Rivas, M Rose, AK Samanta, P Schmidt, E Sobolev, N Timneanu, S Usenko, D Westphal, T Wollweber, L Worbs, PL Xavier, H Yousef, K Ayyer, HN Chapman, JA Sellberg, C Seuring, IA Vartanyants, J Küpper, M Meyer, FRNC Maia
Light Sci Appl 13, 15 (2024)  

New aerodynamic lens injector for single particle diffractive imaging

N Roth, DA Horke, J Lübke, AK Samanta, AD Estillore, L Worbs, N Pohlman, K Ayyer, A Morgan, H Fleckenstein, M Domaracky, B Erk, C Passow, J Correa, O Yefanov, A Barty, S Bajt, RA Kirian, HN Chapman, J Küpper
Nucl. Instrum. Methods Phys. Res. A 1058, 168820 (2024)  

Form factor determination of biological molecules with X-ray free electron laser small-angle scattering (XFEL-SAS)

CE Blanchet, A Round, HDT Mertens, K Ayyer, M Graewert, S Awel, D Franke, K Dörner, S Bajt, R Bean, TF Custódio, R de Wijn, E Juncheng, A Henkel, A Gruzinov, CM Jeffries, Y Kim, H Kirkwood, M Kloos, J Knoška, J Koliyadu, R Letrun, C Löw, J Makroczyova, A Mall, R Meijers, GE Pena Murillo, D Oberthür, E Round, C Seuring, M Sikorski, P Vagovic, J Valerio, T Wollweber, Y Zhuang, J Schulz, H Haas, HN Chapman, AP Mancuso, D Svergun
Commun. Biol. 6, 1057 (2023)  

Ab initio spatial phase retrieval via intensity triple correlations

N Peard, K Ayyer, HN Chapman
Optics Express 31(15) 25082-25092 (2023)  

Time-resolved single-particle x-ray scattering reveals electron-density as coherent plasmonic-nanoparticle-oscillation source

D Hoeing, R Salzwedel, L Worbs, Y Zhuang, AK Samanta, J Lübke, A Estillore, K Dlugolecki, C Passow, B Erk, N Ekanayaje, D Ramm, J Correa, CC Papadooulou, AT Noor, F Schulz, M Selig, A Knorr, K Ayyer, J Küpper, H Lange
Nano Letters 23, 13, 5943–5950 (2023)  

Holographic single particle imaging for weakly scattering, heterogeneous nanoscale objects

A Mall, K Ayyer
Phys. Rev. Applied 19, 054027 (2023)  

Imaging via Correlation of X-Ray Fluorescence Photons

F Trost, K Ayyer, M Prasciolu, H Fleckenstein, M Barthelmess, O Yefanov, JL Dresselhaus, C Li, S Bajt, J Carnis, T Wollweber, A Mall, Z Shen, Y Zhuang, S Richter, S Karl, S Cardoch, KK Patra, J Möller, A Zozulya, R Shayduk, W Lu, F Brauße, B Friedrich, U Boesenberg, I Petrov, S Tomin, M Guetg, A Madsen, N Timneanu, C Caleman, R Röhlsberger, J von Zanthier, and HN Chapman
Phys. Rev. Lett. 130, 173201 (2023)  
Commentary: "Bringing Interferometric Imaging into the X-Ray Regime", P Ho, Physics 16, 66 (2023)

Inter-Bragg crystallographic phase retrieval from shape transforms, stacking faults and substitutional disorder

JPJ Chen, K Pande, JJ Donatelli, AV Martin, K Ayyer, HN Chapman, R Bean, KE Schmidt, RA Kirian
Ultramicroscopy 249, 113728 (2023)  

Speckle contrast of interfering fluorescence X-rays

F Trost, K Ayyer, D Oberthuer, O Yefanov, S Bajt, C Caleman, A Weimer, A Feld, H Weller, S Boutet, J Koglin, N Timneanu, J von Zanthier, R Röhlsberger and HN Chapman
J. Synch. Rad. 30(1) (2023)  

Unsupervised learning approaches to characterize heterogeneous samples using X-ray single particle imaging

Y Zhuang, S Awel, A Barty, R Bean, J Bielecki, M Bergemann, BJ Daurer, T Ekeberg, AD Estillore, H Fangohr, K Giewekemeyer, MS Hunter, M Karnevskiy, RA Kirian, H Kirkwood, Y Kim, J Koliyadu, H Lange, R Letrun, J Lübke, A Mall, T Michelat, AJ Morgan, N Roth, AK Samanta, T Sato, Z Shen, M Sikorski, F Schulz, JCH Spence, P Vagovic, T Wollweber, L Worbs, PL Xavier, O Yefanov, FRNC Maia, DA Horke, J Küpper, ND Loh, AP Mancuso, HN Chapman, K Ayyer
IUCrJ 9(2) (2022)  

On the use of multilayer Laue lenses with X-ray free electron lasers

M Prasciolu, KT Murray, N Ivanov, H Fleckenstein, M Domaracký, L Gelisio, F Trost, K Ayyer, D Krebs, S Aplin, S Awel, U Boesenberg, G Belšak, A Barty, AD Estillore, M Fuchs, Y Gevorkov, J Hallmann, C Kim, J Knoška, J Küpper, C Li, W Lu, V Mariani, AJ Morgan, J Möller, A Madsen, D Oberthür, GE Peña Murillo, DA Reis, M Scholz, B Šarler, P Villanueva-Perez, O Yefanov, KA Zielinski, A Zozulya, HN Chapman, S Bajt
Intl. Conf. on X-ray Lasers 11886, 118860 (2021)  

An encryption-decryption framework for validating single-particle imaging

Z Shen, CZW Teo, K Ayyer, ND Loh
Scientific reports 11, 1 (2021)  

3D diffractive imaging of nanoparticle ensembles using an X-ray laser

K Ayyer, PL Xavier, J Bielecki, Z Shen, BJ Daurer, AK Samanta, S Awel, R Bean, A Barty, T Ekeberg, AD Estillore, K Giewekemeyer, MS Hunter, RA Kirian, H Kirkwood, Y Kim, J Koliyadu, H Lange, R Letruin, J Lübke, AJ Morgan, N Roth, T Sato, M Sikorski, F Schulz, JCH Spence, P Vagovic, T Wollweber, L Worbs, O Yefanov, Y Zhuang, FRNC Maia, DA Horke, J Küpper, ND Loh, AP Mancuso, HN Chapman
Optica 8(1), 15-23 (2021)  

Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source

H Li, R Nazari, B Abbey, R Alvarez, A Aquila, K Ayyer, A Barty, P Berntsen, J Bielecki, A Pietrini, M Bucher, G Carini, HN Chapman, A Contreras, BJ Daurer, H DeMirci, L Flűckiger, M Frank, J Hajdu, MF Hantke, BG Hogue, A Hosseinizadeh, MS Hunter, H Jönsson, RA Kirian, RP Kurta, D Loh, FRNC Maia, AP Mancuso, AJ Morgan, M McFadden, K Muehlig, A Munke, HKN Reddy, C Nettelblad, A Ourmazd, M Rose, P Schwander, M Seibert, JA Sellberg, RG Sierra, Z Sun, M Svenda, IA Vartanyants, P Walter, D Westphal, G Williams, PL Xavier, CH Yoon, S Zaare
Scientific Data 7, 404 (2020)  

Segmented flow generator for serial crystallography at the European X-ray free electron laser

A Echelmeier, JC Villarreal, M Messerschmidt, D Kim, JD Coe, D Thifault, S Botha, A Egatz-Gomez, S Gandhi, G Brehm, CE Conrad, DT Hansen, C Madsen, S Bajt, JD Meza-Aguilar, D Oberthür, MO Wiedorn, H Fleckenstein, D Mendez, J Knoška, JM Martin-Garcia, H Hu, S Lisova, A Allahgholi, Y Gevorkov, K Ayyer, S Aplin, HM Ginn, H Graafsma, AJ Morgan, D Greiffenberg, A Klujev, T Laurus, J Poehlsen, U Trunk, D Mezza, B Schmidt, M Kuhn, R Fromme, J Sztuk-Dambietz, N Raab, S Hauf, A Silenzi, T Michelat, C Xu, C Danilevski, A Parenti, L Mekinda, B Weinhausen, G Mills, P Vagovic, Y Kim, H Kirkwood, R Bean, J Bielecki, S Stern, K Giewekemeyer, AR Round, J Schulz, K Dörner, TD Grant, V Mariani, A Barty, AP Mancuso, U Weierstall, JCH Spence, HN Chapman, N Zatsepin, P Fromme, RA Kirian, A Ros
Nature Communications 11, 4511 (2020)  

Photon statistics and signal to noise ratio for incoherent diffractive imaging

F Trost, K Ayyer, HN Chapman
New Journal of Physics 22, 083070 (2020)  

Megahertz single-particle imaging at the European XFEL

E Sobolev, S Zolotarev, K Giewekemeyer, J Bielecki, K Okamoto, HKN Reddy, J Andreasson, K Ayyer, I Barak, S Bari, A Barty, R Bean, S Bobkov, HN Chapman, G Chojnowski, BJ Daurer, K Dörner, T Ekeberg, L Flückiger, O Galzitskaya, L Gelisio, S Hauf, BG Hogue, DA Horke, A Hosseinizadeh, V Ilyin, C Jung, C Kim, Y Kim, RA Kirian, H Kirkwood, O Kulyk, R Letrun, D Loh, M Messerschmidt, K Mühlig, A Ourmazd, N Raab, AV Rode, M Rose, A Round, T Sato, R Schubert, P Schwander, JA Sellberg, M Sikorski, A Silenzi, C Song, JCH Spence, S Stern, J Sztuk-Dambietz, A Teslyuk, N Timneanu, M Trebbin, C Uetrecht, B Weinhausen, GJ Williams, P Lourdu Xavier, C Xu, I Vartanyants, V Lamzin, A Mancuso, FRNC Maia
Communications Physics (2020)  

Reference-enhanced x-ray single particle imaging

K Ayyer
Optica 7(6), 593-601 (2020)  

Low-signal limit of X-ray single particle diffractive imaging

K Ayyer, AJ Morgan, A Aquila, H DeMirci, BG Hogue, RA Kirian, PL Xavier, CH Yoon, HN Chapman, A Barty
Optics Express 27(26), 37816-37833 (2019)  

Ab initio phasing of the diffraction of crystals with translational disorder

AJ Morgan, K Ayyer, A Barty, JPJ Chen, T Ekeberg, D Oberthuer, TA White, OM Yefanov, HN Chapman
Acta Crytallographica A 75(1), 24-40 (2019)  
Journal Cover: Link

Structure Determination by Continuous Diffraction from Imperfect Crystals

K Ayyer, OM Yefanov, HN Chapman
In: X-ray Free Electron Lasers. Springer, Cham (2018)  

Single-particle imaging without symmetry constraints at an X-ray free-electron laser

M Rose, S Bobkov, K Ayyer, RP Kurta, D Dzhigaev, YY Kim, AJ Morgan, CH Yoon, D Westphal, J Bielecki, JA Sellberg, G Williams, FRNC Maia, OM Yefanov, V Ilyin, AP Mancuso, HN Chapman, BG Hogue, A Aquila, A Barty, IA Vartanyants
IUCrJ 5(6) (2018)  

Megahertz serial crystallography

MO Wiedorn, D Oberthür, R Bean, R Schubert, N Werner, B Abbey, M Aepfelbacher, L Adriano, A Allahgholi, N Al-Qudami, J Andreasson, S Aplin, S Awel, K Ayyer, S Bajt, I Barák, S Bari, J Bielecki, S Botha, D Boukhelef, W Brehm, S Brockhauser, I Cheviakov, MA Coleman, F Cruz-Mazo, C Danilevski, C Darmanin, RB Doak, M Domaracky, K Dörner, Y Du, H Fangohr, H Fleckenstein, M Frank, P Fromme, AM Gañán-Calvo, Y Gevorkov, K Giewekemeyer, HM Ginn, H Graafsma, R Graceffa, D Greiffenberg, L Gumprecht, P Göttlicher, J Hajdu, S Hauf, M Heymann, S Holmes, DA Horke, MS Hunter, S Imlau, A Kaukher, Y Kim, A Klyuev, J Knoška, B Kobe, M Kuhn, C Kupitz, J Küpper, JM Lahey-Rudolph, T Laurus, K Le Cong, R Letrun, PL Xavier, L Maia, FRNC Maia, V Mariani, M Messerschmidt, M Metz, D Mezza, T Michelat, G Mills, DCF Monteiro, A Morgan, K Mühlig, A Munke, A Münnich, J Nette, KA Nugent, T Nuguid, AM Orville, S Pandey, G Pena, P Villanueva-Perez, J Poehlsen, G Previtali, L Redecke, WM Riekehr, H Rohde, A Round, T Safenreiter, I Sarrou, T Sato, M Schmidt, B Schmitt, R Schönherr, J Schulz, JA Sellberg, MM Seibert, C Seuring, ML Shelby, RL Shoeman, M Sikorski, A Silenzi, CA Stan, X Shi, S Stern, J Sztuk-Dambietz, J Szuba, A Tolstikova, M Trebbin, U Trunk, P Vagovic, T Ve, B Weinhausen, TA White, K Wrona, C Xu, O Yefanov, N Zatsepin, J Zhang, M Perbandt, AP Mancuso, C Betzel, H Chapman, A Barty
Nature Communications 9(1) (2018)  
Highlight: "The fast and the luminous", JP Kraack, Nature Physics 14, 1071 (2018)

Rapid sample delivery for megahertz serial crystallography at X-ray FELs

MO Wiedorn, S Awel, AJ Morgan, K Ayyer, Y Gevorkov, H Fleckenstein, N Roth, L Adriano, R Bean, KR Beyerlein, J Chen, J Coe, F Cruz-Mazo, T Ekeberg, R Graceffa, M Heymann, DA Horke, J Knoška, V Mariani, R Nazari, D Oberthür, AK Samanta, RG Sierra, CA Stan, O Yefanov, D Rompotis, J Correa, B Erk, R Treusch, J Schulz, BG Hogue, AM Gañán-Calvo, P Fromme, J Küpper, AV Rode, S Bajt, RA Kirian, HN Chapman
IUCrJ 5(5) (2018)  

Femtosecond X-ray coherent diffraction of aligned amyloid fibrils on low background graphene

C Seuring, K Ayyer, E Filippaki, M Barthelmess, J-N Longchamp, P Ringler, T Pardini, DH Wojtas, MA Coleman, K Dörner, S Fuglerud, G Hammarin, B Habenstein, AE Langkilde, A Loquet, A Meents, R Riek, H Stahlberg, S Boutet, MS Hunter, J Koglin, M Liang, HM Ginn, RP Millane, M Frank, A Barty, HN Chapman
Nature Communications 9(1) (2018)  

Orientation and analysis of XFEL serial diffraction patterns from fibrous molecular assemblies

DH Wojtas, K Ayyer, M Liang, E Mossou, C Seuring, VT Forsyth, HN Chapman, RP Millane
Image and Vision Computing New Zealand (IVCNZ), 1-6 (2017)  

Analysis of XFEL serial diffraction data from individual crystalline fibrils

DH Wojtas, K Ayyer, M Liang, E Mossou, F Romoli, C Seuring, KR Beyerlein, RJ Bean, AJ Morgan, D Oberthür, H Fleckenstein, M Heymann, C Gati, O Yefanov, M Barthelmess, E Ornithopoulou, L Galli, PL Xavier, WL Ling, M Frank, CH Yoon, TA White, S Bajt, A Mitraki, S Boutet, A Aquila, A Barty, VT Forsyth, HN Chapman and RP Millane
IUCrJ 4(6) (2017)  

Continuous diffraction of molecules and disordered molecular crystals

HN Chapman, OM Yefanov, K Ayyer, TA White, A Barty, A Morgan, V Mariani, D Oberthür, K Pande
Journal of Applied Crystallography 50(4), 1084-1103 (2017)  
Commentary: "Structures from poorly diffracting crystals: a new start for macromolecular crystallography?", J Hajdu, J. Appl. Cryst. 50, 982-984 (2017)

Incoherent Diffractive Imaging via Intensity Correlations of hard X-rays

A Classen, K Ayyer, HN Chapman, R Röhlsberger, J von Zanthier
Physical Review Letters 119 (5), 053401 (2017)  

Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source

HKN Reddy, CH Yoon, A Aquila, S Awel, K Ayyer, A Barty, P Berntsen, J Bielecki, S Bobkov, M Bucher, GA Carini, S Carron, H Chapman, B Daurer, H Demirci, T Ekeberg, P Fromme, J Hajdu, MF Hanke, P Hart, BG Hogue, A Hosseinizadeh, Y Kim, RA Kirian, RP Kurta, DSD Larsson, ND Loh, FRNC Maia, AP Mancuso, K Mühlig, A Munke, D Nam, C Nettelblad, A Ourmazd, M Rose, P Schwander, M Seibert, JA Sellberg, C Song, JCH Spence, M Svenda, GVD Schot, IA Vartanyants, GJ Williams, PL Xavier
Scientific Data 4, 170079 (2017)  

Identifying well-oriented diffraction patterns in XFEL datasets

D Wojtas, C Seuring, K Ayyer, H Chapman, R Millane
Image and Vision Computing New Zealand (IVCNZ), 1-6 (2016)  

Coherent diffraction of single Rice Dwarf Virus particles using hard X-rays at the Linac Coherent Light Source

A Munke, J Andreasson, A Aquila, S Awel, K Ayyer, A Barty, RJ Bean, P Berntsen, J Bielecki, S Boutet, M Bucher, HN Chapman, BJ Daurer, H DeMirci, V Elser, P Fromme, J Hajdu, MF Hantke, A Higashiura, BG Hogue, A Hosseinizadeh, Y Kim, RA Kirian, HKN Reddy, T-Y Lan, DSD Larsson, H Liu, ND Loh, FRNC Maia, AP Mancuso, K Mühlig, A Nakagawa, D Nam, G Nelson, C Nettelblad, K Okamoto, A Ourmazd, M Rose, GVD Schot, P Schwander, MM Seibert, JA Sellberg, RG Sierra, C Song, M Svenda, N Timneanu, IA Vartanyants, D Westphal, MO Wiedorn, GJ Williams, PL Xavier, CH Yoon, J Zook
Scientific data 3, 160064 (2016)  

Dragonfly: an implementation of the expand-maximize-compress algorithm for single-particle imaging

K Ayyer, TY Lan, V Elser, ND Loh
Journal of Applied Crystallography 49 (4), 1320-1335 (2016)  

Macromolecular diffractive imaging using imperfect crystals

K Ayyer, OM Yefanov, D Oberthür, S Roy-Chowdhury, L Galli, V Mariani, S Basu, J Coe, CE Conrad, R Fromme, A Schaffer, K Dörner, D James, C Kupitz, M Metz, G Nelson, PL Xavier, KR Beyerlein, M Schmidt, I Sarrou, JCH Spence, U Weierstall, TA White, J-H Yang, Y Zhao, M Liang, A Aquila, MS Hunter, JS Robinson, JE Koglin, S Boutet, P Fromme, A Barty, HN Chapman
Nature 530 (7589), 202-206 (2016)  
News & Views: "Resolution beyond the diffraction limit", J-R Shen, Nature 530, 168-169 (2016)

Perspectives for imaging single protein molecules with the present design of the European XFEL

K Ayyer, G Geloni, V Kocharyan, E Saldin, S Serkez, O Yefanov, I Zagorodnov
Structural Dynamics 2 (4), 041702 (2015)  

Determination of crystallographic intensities from sparse data

K Ayyer, HT Philipp, MW Tate, JL Wierman, V Elser, SM Gruner
IUCrJ 2 (1), 29-34 (2015)  
Commentary: "Serial Crystallography for the masses?", JP Wright, IUCrJ 2(3) (2015)

Real-Space x-ray tomographic reconstruction of randomly oriented objects with sparse data frames

K Ayyer, HT Philipp, MW Tate, V Elser, SM Gruner
Optics Express 22 (3), 2403-2413 (2014)  

Recovering structure from many low-information 2-D images of randomly-oriented samples

HT Philipp, K Ayyer, MW Tate, V Elser, SM Gruner
Journal of Physics: Conference Series 425 (19), 192016 (2014)  

Solving structure with sparse, randomly-oriented x-ray data

HT Philipp, K Ayyer, MW Tate, V Elser, SM Gruner
Optics Express 20 (12), 13129-13137 (2012)