Publications
2025
62. Z. Lentz, R. Tang-Kong, M. Rakitin, T. Morris, S. Miskovich. "ML-assisted beamline optimization at LCLS." Proc. 20th Int. Conf. Accel. Large Exp. Phys. Control Syst. (ICALEPCS'25), 1873-1877 (2025). DOI: 10.18429/JACoW-ICALEPCS2025-FRAG001
61. D. Gavrilov, T. Caswell, A. Sligar, M. Rakitin. "Bluesky Queue Server for beamline control at NSLS-II." Proc. 20th Int. Conf. Accel. Large Exp. Phys. Control Syst. (ICALEPCS'25), 1706-1710 (2025). DOI: 10.18429/JACoW-ICALEPCS2025-THPD053
60. Y. Hidaka, D. Allan, M. Rakitin. "A new Python middle layer framework: Particle Accelerator MIddle LAyer (PAMILA)." Proc. 6th North American Particle Accel. Conf. (NAPAC2025), 48-51 (2025). DOI: 10.18429/JACoW-NAPAC2025-MOP005
2024
59. H. Wijesinghe, A. Barbour, L. Wiegart, E. Carlin, J. Einstein-Curtis, P. Moeller, R. Nagler, R. O'Rourke, N. Cook, M. Rakitin. "Bluesky and Raydata: An Integrated Platform for Adaptive Experiment Orchestration." SC24-W: Workshops of the International Conference for High Performance Computing, Networking, Storage and Analysis, 2162-2167 (2024). DOI: 10.1109/SCW63240.2024.00271
58. A. Tayal, D. S. Coburn, D. Abel, M. Rakitin, O. Ivashkevych, J. Wlodek, D. Wierzbicki, W. Xu, E. Nazaretski, E. Stavitski, D. Leshchev. "Five-analyzer Johann spectrometer for hard X-ray photon-in/photon-out spectroscopy at the Inner Shell Spectroscopy beamline at NSLS-II: design, alignment and data acquisition." Journal of Synchrotron Radiation, 1609–1621 (2024). DOI: 10.1107/S1600577524009342
57. T. W. Morris, M. Rakitin, Y. Du, M. Fedurin, A. C. Giles, D. Leshchev, W. H. Li, B. Romasky, E. Stavitski, A. L. Walter, P. Moeller, B. Nash, A. Islegen-Wojdyla. "A general Bayesian algorithm for the autonomous alignment of beamlines." Journal of Synchrotron Radiation, 1446–1456 (2024). DOI: 10.1107/S1600577524008993
56. H. Goel, O. Chubar, R. Li, L. Wiegart, M. Rakitin, A. Fluerasu. "Efficient end-to-end simulation of time-dependent coherent X-ray scattering experiments." Journal of Synchrotron Radiation, 517–526 (2024). DOI: 10.1107/S1600577524001267
55. N. M. Cook, A. M. Barbour, E. G. Carlin, J. A. Einstein-Curtis, R. Nagler, R. O'Rourke, M. Rakitin, L. Wiegart, H. Wijesinghe. "Integrating Online Analysis with Experiments to Improve X-Ray Light Source Operations." Proc. 19th Int. Conf. Accel. Large Exp. Phys. Control Syst. (ICALEPCS'23), 921–924 (2024). DOI: 10.18429/JACoW-ICALEPCS2023-TUSDSC02
54. J. A. Einstein-Curtis, D. T. Abell, Y. Du, A. Giles, M. V. Keilman, J. Lynch, P. Moeller, T. Morris, B. Nash, I. V. Pogorelov, M. Rakitin, A. L. Walter. "Online Models for X-ray Beamlines Using Sirepo-Bluesky." Proc. 19th Int. Conf. Accel. Large Exp. Phys. Control Syst. (ICALEPCS'23), 165–170 (2024). DOI: 10.18429/JACoW-ICALEPCS2023-MO3BCO05
2023
53. P. M. Maffettone, D. B. Allan, A. Barbour, T. A. Caswell, D. Gavrilov, M. D. Handwell, T. Morris, D. Olds, M. Rakitin, S. I. Campbell, B. Ravel. "Book “Methods and Applications of Autonomous Experimentation”. Chapter 8: “Artificial Intelligence Driven Experiments at User Facilities”." (2023). DOI: 10.1201/9781003359593
52. M. Rakitin, R. Bode, T. W. Morris, A. C. Giles, A. L. Walter, J. K. Lynch, J. Maldonado, Y. Du, B. Romasky, M. Fedurin, P. Moeller, B. Nash. "Recent updates of the Sirepo-Bluesky library for virtual beamline representation." Advances in Computational Methods for X-Ray Optics VI, 126970D (2023). DOI: 10.1117/12.2678030
51. T. W. Morris, Y. Du, M. Fedurin, A. C. Giles, P. Moeller, B. Nash, M. Rakitin, B. Romasky, A. L. Walter, N. Wilson, A. Wojdyla. "Latent Bayesian optimization for the autonomous alignment of synchrotron beamlines." Advances in Computational Methods for X-Ray Optics VI, 126970B (2023). DOI: 10.1117/12.2677895
50. B. Nash, M. S. Rakitin, D. T. Abell, M. Keilman, P. Moeller, I. Pogorelov, Y. Du, A. Giles, J. Lynch, T. W. Morris, A. L. Walter, N. Goldring. "Reduced model representations of synchrotron radiation and a software framework for beamline control." Advances in Computational Methods for X-Ray Optics VI, PC1269703 (2023). DOI: 10.1117/12.2676921
49. L. Huang, T. Wang, O. Chubar, G. Dovillaire, A. He, M. Rakitin, Y. Yang, A. M. Kiss, M. Idir. "Investigation of x-ray Hartmann wavefront sensing: from simulation to the initial experiment test." Advances in Computational Methods for X-Ray Optics VI, PC1269705 (2023). DOI: 10.1117/12.2675754
48. H. Goel, O. Chubar, L. Wiegart, A. Fluerasu, R. Li, A. He, M. Rakitin, M. Lin, P. Moeller, R. Nagler. "GPU accelerated simulations of time-dependent coherent x-ray scattering experiments." Advances in Computational Methods for X-Ray Optics VI, 1269709 (2023). DOI: 10.1117/12.2677888
47. N. Cook, E. Carlin, R. Nagler, R. O'Rourke, A. Barbour, M. Rakitin, L. Wiegart. "An online analysis platform for improving X-ray light source operations." Proc. IPAC'23, 4266-4268 (2023). DOI: 10.18429/JACoW-IPAC2023-THPA128
2022
46. M. Rakitin, S. Campbell, D. Allan, T. Caswell, D. Gavrilov, M. Hanwell, S. Wilkins. "Next generation experimental data access at NSLS-II." Journal of Physics: Conference Series, 012100 (2022). DOI: 10.1088/1742-6596/2380/1/012100
45. B. Nash, D. Abell, R. Nagler, P. Moeller, M. Keilman, I. Pogorelov, N. Goldring, M. Rakitin, J. Lynch, A. Giles, A. Walter, J. Maldonado, T. Morris, S. Bak, Y. Du. "Combining diagnostics, modeling, and control systems for automated alignment of the TES beamline." Journal of Physics: Conference Series, 012103 (2022). DOI: 10.1088/1742-6596/2380/1/012103
44. H. Goel, O. Chubar, L. Wiegart, A. Fluerasu, R. Li, A. He, M. Rakitin, P. Moeller, R. Nagler. "Developments in SRW Code and Sirepo Framework Supporting Simulation of Time-Dependent Coherent X-ray Scattering Experiments." Journal of Physics: Conference Series, 012126 (2022). DOI: 10.1088/1742-6596/2380/1/012126
43. T. W. Morris, M. Rakitin, A. Giles, J. Lynch, A. L. Walter, B. Nash, D. Abell, P. Moeller, I. Pogorelov, N. Goldring. "On-the-fly optimization of synchrotron beamlines using machine learning." Optical System Alignment, Tolerancing, and Verification XIV, 122220M (2022). DOI: 10.1117/12.2644996
42. L. Huang, T. Wang, O. Chubar, G. Dovillaire, A. He, M. Rakitin, M. Idir. "Simulation of X-ray Hartmann wavefront sensing with the Synchrotron Radiation Workshop." Opt. Express (2022). DOI: 10.1364/oe.470197
41. T. Konstantinova, L. Wiegart, M. Rakitin, A. M. DeGennaro, A. M. Barbour. "Machine Learning for analysis of speckle dynamics: quantification and outlier detection." Phys. Rev. Research, 033228 (2022). DOI: 10.1103/PhysRevResearch.4.033228
40. D. Leshchev, M. Rakitin, B. Luvizotto, R. Kadyrov, B. Ravel, K. Attenkofer, E. Stavitski. "The Inner Shell Spectroscopy beamline at NSLS-II: a facility for in situ and operando X-ray absorption spectroscopy for materials research." Journal of Synchrotron Radiation (2022). DOI: 10.1107/S160057752200460X
39. D. Hidas, A. M. Kiss, M. Rakitin, J. Sinsheimer, T. Tanabe, M. Musardo. "High precision real-time insertion device and monochromator synchronization at NSLS-II." Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 166505 (2022). DOI: 10.1016/j.nima.2022.166505
2021
38. B. Nash, D. T. Abell, D. L. Bruhwiler, E. G. Carlin, Y. Du, J. P. Edelen, A. Giles, M. V. Keilman, J. Lynch, J. Maldonado, P. Moeller, R. Nagler, I. V. Pogorelov, M. S. Rakitin, A. Walter, S. D. Webb. "X-Ray Beamline Control with Machine Learning and an Online Model." Proc. ICALEPCS'21, 695–699 (2021). DOI: 10.18429/JACoW-ICALEPCS2021-WEPV024
37. N. M. Cook, A. M. Barbour, E. G. Carlin, P. Moeller, R. Nagler, B. Nash, M. S. Rakitin, L. Wiegart. "An Integrated Data Processing and Management Platform for X-Ray Light Source Operations." Proc. ICALEPCS'21, 1059–1063 (2021). DOI: 10.18429/JACoW-ICALEPCS2021-FRBR02
36. R. Jain, D. Abel, M. Rakitin, M. Sullivan, D. T. Lodowski, M. R. Chance, E. R. Farquhar. "New high-throughput endstation to accelerate the experimental optimization pipeline for synchrotron X-ray footprinting." Journal of Synchrotron Radiation, 1321–1332 (2021). DOI: 10.1107/S1600577521005026
35. L. Yang, E. Lazo, J. Byrnes, S. Chodankar, S. Antonelli, M. Rakitin. "Tools for supporting solution scattering during the COVID-19 pandemic." Journal of Synchrotron Radiation, 1237–1244 (2021). DOI: 10.1107/S160057752100521X
34. M. S. Rakitin, A. A. Mirzoev. "Ab initio Simulation of Dissolution Energy and Bond Energy of Hydrogen with 3sp, 3d, and 4d Impurities in bcc Iron." Phys. Solid State, 1065–1068 (2021). DOI: 10.1134/s1063783421070180
33. T. Konstantinova, L. Wiegart, M. Rakitin, A. M. DeGennaro, A. M. Barbour. "Noise reduction in X-ray photon correlation spectroscopy with convolutional neural networks encodermodels." Sci Rep (2021). DOI: 10.1038/s41598-021-93747-y
32. S. I. Campbell, D. B. Allan, A. M. Barbour, D. Olds, M. S. Rakitin, R. Smith, S. B. Wilkins. "Outlook for artificial intelligence and machine learning at the NSLS-II." Machine Learning: Science and Technology, 013001 (2021). DOI: 10.1088/2632-2153/abbd4e
2020
31. O. Chubar, L. Wiegart, S. Antipov, R. Celestre, R. Coles, A. Fluerasu, M. Rakitin. "Analysis of hard x-ray focusing by 2D diamond CRL." Advances in Computational Methods for X-Ray Optics V, 119–127 (2020). DOI: 10.1117/12.2568980
30. O. Chubar, R. A. Coles, L. Wiegart, A. Fluerasu, M. Rakitin, J. Condie, P. Moeller, R. Nagler. "Simulations of coherent scattering experiments at storage ring synchrotron radiation sources in the hard x-ray range." Advances in Computational Methods for X-Ray Optics V, 201–208 (2020). DOI: 10.1117/12.2568833
29. A. He, O. Chubar, M. Rakitin, L. Samoylova, C. Fortmann-Grote, S. Yakubov, A. Buzmakov. "Parallel performance of “Synchrotron Radiation Workshop” code: partially coherent calculations for storage rings and time-dependent calculations for XFELs." Advances in Computational Methods for X-Ray Optics V, 78–87 (2020). DOI: 10.1117/12.2567448
28. M. S. Rakitin, A. Giles, K. Swartz, J. Lynch, P. Moeller, R. Nagler, D. B. Allan, T. A. Caswell, L. Wiegart, O. Chubar, Y. Du. "Introduction of the Sirepo-Bluesky interface and its application to the optimization problems." Advances in Computational Methods for X-Ray Optics V, 209–226 (2020). DOI: 10.1117/12.2569000
2019
27. B. Nash, O. Chubar, D. Bruhwiler, M. Rakitin, P. Moeller, R. Nagler, N. Goldring. "Undulator radiation brightness calculations in the Sirepo GUI for SRW." Advances in Laboratory-based X-Ray Sources, Optics, and Applications VII, 79–92 (2019). DOI: 10.1117/12.2530663
26. B. Nash, N. Goldring, D. L. Bruhwiler, O. Tchoubar, A. He, M. Rakitin, R. Nagler, P. Moeller. "Phase IIA Final Technical Report for "Development of software framework for x-Ray optics simulation and modeling"." (2019). Link
25. D. Allan, T. Caswell, S. Campbell, M. Rakitin. "Bluesky's Ahead: A Multi-Facility Collaboration for an a la Carte Software Project for Data Acquisition and Management." Synchrotron Radiation News, 19–22 (2019). DOI: 10.1080/08940886.2019.1608121
24. L. Wiegart, M. Rakitin, Y. Zhang, A. Fluerasu, O. Chubar. "Towards the simulation of partially coherent x-ray scattering experiments." AIP Conference Proceedings, 060079 (2019). DOI: 10.1063/1.5084710
23. B. Nash, O. Chubar, N. Goldring, D. L. Bruhwiler, P. Moeller, R. Nagler, M. Rakitin. "Detailed x-ray brightness calculations in the sirepo GUI for SRW." AIP Conference Proceedings, 060080 (2019). DOI: 10.1063/1.5084711
2018
22. M. S. Rakitin, P. Moeller, R. Nagler, B. Nash, D. L. Bruhwiler, D. Smalyuk, M. Zhernenkov, O. Chubar. ": an open-source cloud-based software interface for X-ray source and optics simulations." Journal of Synchrotron Radiation, 1877–1892 (2018). DOI: 10.1107/S1600577518010986
21. A. Blednykh, B. Bacha, G. Bassi, W. Cheng, O. Chubar, A. Derbenev, R. Lindberg, M. Rakitin, V. Smaluk, M. Zhernenkov, Y. K. Chen-Wiegart, L. Wiegart. "New aspects of longitudinal instabilities in electron storage rings (DOE Science Highlight)." Scientific Reports, 11918 (2018). DOI: 10.1038/s41598-018-30306-y
20. O. Chubar, C. Kitegi, Y. K. Chen-Wiegart, D. Hidas, Y. Hidaka, T. Tanabe, G. Williams, J. Thieme, T. Caswell, M. Rakitin, L. Wiegart, A. Fluerasu, L. Yang, S. Chodankar, M. Zhernenkov. "Spectrum-Based Alignment of In-Vacuum Undulators in a Low-Emittance Storage Ring." Synchrotron Radiation News, 4–8 (2018). DOI: 10.1080/08940886.2018.1460173
19. M. Rakitin, A. A. Mirzoev, D. A. Mirzaev. "First-Principles and Thermodynamic Simulation of Elastic Stress Effect on Energy of Hydrogen Dissolution in Alpha Iron." Russian Physics Journal, 2136–2143 (2018). DOI: 10.1007/s11182-018-1337-2
2017
18. M. S. Rakitin, O. Chubar, P. Moeller, R. Nagler, D. L. Bruhwiler. "Sirepo: a web-based interface for physical optics simulations - its deployment and use at NSLS-II (invited paper)." Proc. SPIE, Advances in Computational Methods for X-Ray Optics IV (23 August 2017), 103880R (2017). DOI: 10.1117/12.2274031
17. O. Chubar, M. Rakitin, Y. Chen-Wiegart, A. Fluerasu, L. Wiegart. "Simulation of experiments with partially coherent x-rays using Synchrotron Radiation Workshop." Proc. SPIE, Advances in Computational Methods for X-Ray Optics IV (23 August 2017), 1038811 (2017). DOI: 10.1117/12.2274481
16. O. Chubar, M. Rakitin, Y. Chen-Wiegart, Y. S. Chu, A. Fluerasu, D. Hidas, L. Wiegart. "Main functions, recent updates, and applications of Synchrotron Radiation Workshop code (invited paper)." Proc. SPIE, Advances in Computational Methods for X-Ray Optics IV (23 August 2017), 1038805 (2017). DOI: 10.1117/12.2274285
15. L. Wiegart, M. Rakitin, A. Fluerasu, O. Chubar. "X-ray optical simulations supporting advanced commissioning of the coherent hard x-ray beamline at NSLS-II." Proc. SPIE, Advances in Computational Methods for X-Ray Optics IV (23 August 2017), 103880N (2017). DOI: 10.1117/12.2274403
14. M. Idir, M. Rakitin, B. Gao, J. Xue, L. Huang, O. Chubar. "Alignment of KB mirrors with at-wavelength metrology tool simulated using SRW." Proc. SPIE, Advances in Computational Methods for X-Ray Optics IV (23 August 2017), 103880Z (2017). DOI: 10.1117/12.2274264
13. M. M. Davari Esfahani, Q. Zhu, H. Dong, A. R. Oganov, S. Wang, M. S. Rakitin, X. Zhou. "Novel magnesium borides and their superconductivity." Phys. Chem. Chem. Phys., 14486–14494 (2017). DOI: 10.1039/C7CP00840F
12. O. V. Chubar, T. A. Caswell, Y. Chen-Wiegart, A. Fluerasu, Y. Hidaka, D. A. Hidas, C. A. Kitegi, M. S. Rakitin, T. Tanabe, J. Thieme, L. Wiegart, G. Williams. "Analysis and Correction of in-Vacuum Undulator Misalignment Effects in a Storage Ring Synchrotron Radiation Source." Proc. of International Particle Accelerator Conference (IPAC'17), Copenhagen, Denmark, 14–19 May, 2017, 1663–1665 (2017). DOI: https://doi.org/10.18429/JACoW-IPAC2017-TUPAB140
11. A. Blednykh, B. Bacha, G. Bassi, O. V. Chubar, M. S. Rakitin, V. V. Smaluk, M. Zhernenkov. "A Comprehensive Study of the Microwave Instability." Proc. of International Particle Accelerator Conference (IPAC'17), Copenhagen, Denmark, 14–19 May, 2017, 3224–3226 (2017). DOI: https://doi.org/10.18429/JACoW-IPAC2017-WEPIK117
2016
10. D. A. Mirzaev, A. A. Mirzoev, M. S. Rakitin. "Alloying Effects on Thermodynamic Characteristics of Hydrogen in BCC Iron." Bulletin of the South Ural State University, Ser. Metallurgy, 40–53 (2016). DOI: 10.14529/met160405
9. Y. H. R. Chang, T. L. Yoon, T. L. Lim, M. Rakitin. "Thorough investigations of the structural and electronic properties of AlxIn1-xN ternary compound via initio computations." Journal of Alloys and Compounds, 338–344 (2016). DOI: 10.1016/j.jallcom.2016.04.281
8. M. M. Davari Esfahani, Z. Wang, A. R. Oganov, H. Dong, Q. Zhu, S. Wang, M. S. Rakitin, X. Zhou. "Superconductivity of novel tin hydrides (SnnHm) under pressure." Scientific Reports, 22873 (2016). DOI: 10.1038/srep22873
2015
7. M. S. Rakitin, A. R. Oganov, H. Niu, M. M. Davari Esfahani, X. Zhou, G. Qian, V. L. Solozhenko. "A novel phase of beryllium fluoride at high pressure." Phys. Chem. Chem. Phys., 26283–26288 (2015). DOI: 10.1039/C5CP04010H
2013–2015
6. A. R. Oganov, C. W. Glass, A. O. Lyakhov, Q. Zhu, G. Qian, H. T. Stokes, M. S. Rakitin, M. Davari, P. Bushlanov, Z. Allahyari, S. Lepeshkin. "USPEX manual: Universal Structure Predictor: Evolutionary Xtallography." (2013–2015). Link
2012
5. D. A. Mirzaev, A. A. Mirzoev, K. Y. Okishev, M. S. Rakitin. "Theory of hydrogen solubility in binary iron alloys based on initio calculation results." Molecular Physics, 1299–1304 (2012). DOI: 10.1080/00268976.2011.645895
2011
4. A. V. Ursaeva, M. S. Rakitin, G. E. Ruzanova, A. A. Mirzoev. "initio study of hydrogen interaction with point defects in bcc iron." Bulletin of the South Ural State University: Math., Mech. and Phys., 114–119 (2011). Link
3. A. A. Mirzoev, D. A. Mirzaev, M. S. Rakitin. "Impurities influence on dissolution of hydrogen in bcc iron." Bulletin of the South Ural State University: Math., Mech. and Phys., 77–83 (2011). Link
2010
2. M. S. Rakitin, A. A. Mirzoev, D. A. Mirzaev. "Change of electronic structure in iron containing interstitial atoms of hydrogen." Bulletin of the South Ural State University: Metallurgy, 67–71 (2010). Link
2005
1. A. A. Mirzoev, M. M. Yalalov, M. S. Rakitin. "Dependence of TB-LMTO calculations accuracy on k-points number: effect of iterations mixing parameter using Broyden scheme." Bulletin of the South Ural State University: Math., Phys. and Chem., 103–105 (2005). Link