Muhamed Amin

Research associate

Center for Free-Electron Laser Science (CFEL)
Deutsches Elektronen-Synchrotron DESY
Notkestrasse 85 (building 99, room O3.016)
22607 Hamburg
Germany

COMOTION

muhamed.amin@cfel.de

Research

My research is focused on modeling the sample delivery process starting from the injector till the imaging XFEL beam. I use Navier–Stokes equations and Lattice Boltzmann method combined with optical forces to model the optical trapping of nanoparticles to get highly focused particles beam. In addition, I study the electromagnetic interactions between the aligning laser and the nanoparticles.

Curriculum Vitae

2017–	Research associate, Center for Free Electron Laser Science, DESY, Hamburg
2014–2016	Postdoctoral researcher at the Lawrence Berkeley National Lab, CA, USA
2008–2013	PhD Student at the City University of New York, NY, USA
2006–2008	MA at the City College of New York, NY, USA
2000–2005	BEE at the Cairo University, Egypt

Publications

Journal Article Peravali, S. K. (Corresponding author)CFEL*Extern* ; Samanta, A. K.CFEL*XFEL.EU*DESY* ; Amin, M.CFEL*Extern* ; Neumann, P.Extern*DESY* ; Küpper, J.CFEL*XFEL.EU*DESY* ; Breuer, M. (Corresponding author)CFEL*
An improved numerical simulation methodology for nanoparticle injection through aerodynamic lens systems
Physics of fluids 37, 033380 (2025) [10.1063/5.0260295]2025 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Preprint Peravali, S. K.CFEL*Extern*DESY* ; Jafari, V. ; Samanta, A. K.CFEL*XFEL.EU*DESY* ; Küpper, J.CFEL*XFEL.EU*DESY* ; Amin, M.CFEL*Extern*DESY* ; Neumann, P.Extern*DESY* ; Breuer, M. (Corresponding author)CFEL*
Accuracy and Performance Evaluation of Low Density Internal and External Flow Predictions using CFD and DSMC
[10.3204/PUBDB-2024-04925] OpenAccess Files Fulltext by arXiv.org BibTeX | EndNote: XML, Text | RIS

Journal Article Peravali, S. K.CFEL*Extern*DESY* ; Samanta, A. K.CFEL*XFEL.EU*DESY* ; Küpper, J.CFEL*XFEL.EU*DESY* ; Amin, M.CFEL*Extern*DESY* ; Neumann, P. ; Breuer, M. (Corresponding author)
Accuracy and Performance Evaluation of Low Density Internal and External Flow Predictions using CFD and DSMC
Computers & fluids 279, 106346 (2024) [10.1016/j.compfluid.2024.106346]2024 OpenAccess Files Fulltext Fulltext by arXiv.org BibTeX | EndNote: XML, Text | RIS

Preprint Amin, M.CFEL*Extern*DESY* ; Hartmann, J.-M. ; Samanta, A. K.CFEL*XFEL.EU*DESY* ; Küpper, J. (Corresponding author)CFEL*XFEL.EU*DESY*
Laser-induced alignment of nanoparticles and macromolecules for single-particle-imaging applications
[10.3204/PUBDB-2024-01943] OpenAccess Files Fulltext by arXiv.org BibTeX | EndNote: XML, Text | RIS

Journal Article Amin, M. (Corresponding author)CFEL*DESY*
Predicting the oxidation states of Mn ions in the oxygen-evolving complex of photosystem II using supervised and unsupervised machine learning
Photosynthesis research 156(1), 89 - 100 (2023) [10.1007/s11120-022-00941-8]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Gisriel, C. J. (Corresponding author)Extern*XFEL.EU* ; Shen, G. ; Flesher, D. A.Extern*XFEL.EU* ; Kurashov, V. ; Golbeck, J. H. ; Brudvig, G. W. ; Amin, M.CFEL*Extern*DESY* ; Bryant, D. A. (Corresponding author)
Structure of a dimeric photosystem II complex from a cyanobacterium acclimated to far-red light
The journal of biological chemistry 299(1), 102815 (2023) [10.1016/j.jbc.2022.102815]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Preprint Welker, S.CFEL* ; Amin, M.CFEL* ; Küpper, J. (Corresponding author)CFEL*XFEL.EU*DESY*
CMInject: Python framework for the numerical simulation of nanoparticle injection pipelines
arXiv Files Fulltext by arXiv.org BibTeX | EndNote: XML, Text | RIS

Journal Article Welker, S.CFEL* ; Amin, M.CFEL* ; Küpper, J. (Corresponding author)CFEL*XFEL.EU*DESY*
CMInject: Python framework for the numerical simulation of nanoparticle injection pipelines
Computer physics communications 270, 108138 (2022) [10.1016/j.cpc.2021.108138]2022 Embargoed OpenAccess Files Fulltext by arXiv.org BibTeX | EndNote: XML, Text | RIS

Preprint Amin, M. (Corresponding author)CFEL*Extern* ; Küpper, J. (Corresponding author)CFEL*XFEL.EU*DESY*
Variations in Proteins Dielectric Constants
arXiv Files Fulltext by arXiv.org BibTeX | EndNote: XML, Text | RIS

Preprint Roth, N. (First author)CFEL*XFEL.EU*DESY* ; Amin, M.CFEL*DESY* ; Samanta, A. K.CFEL*DESY* ; Küpper, J. (Corresponding author)CFEL*DESY*
Microscopic force for aerosol transport
[10.3204/PUBDB-2020-02411] OpenAccess Files Fulltext by arXiv.org BibTeX | EndNote: XML, Text | RIS

Journal Article Amin, M. (Corresponding author)CFEL*DESY* ; Küpper, J. (Corresponding author)CFEL*DESY*
Variations in Proteins Dielectric Constants
ChemistryOpen 9(6), 691 - 694 (2020) [10.1002/open.202000108]2020 OpenAccess Files Fulltext by arXiv.org BibTeX | EndNote: XML, Text | RIS

Journal Article Amin, M. (Corresponding author)CFEL*DESY* ; Sorour, M. K. ; Kasry, A.
Comparing the Binding Interactions in the Receptor Binding Domains of SARS-CoV-2 and SARS-CoV
The journal of physical chemistry letters 11, 4897−4900 (2020) [10.1021/acs.jpclett.0c01064]2020 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Samanta, A. K. (First author)CFEL*DESY* ; Amin, M.CFEL*DESY* ; Estillore, A.CFEL*DESY* ; Roth, N.CFEL*XFEL.EU*DESY* ; Worbs, L.CFEL*DESY* ; Horke, D.CFEL*XFEL.EU*DESY* ; Küpper, J. (Corresponding author)CFEL*DESY*
Controlled beams of shock-frozen, isolated, biological and artificial nanoparticles
Structural dynamics 7(2), 024304 - (2020) [10.1063/4.0000004]2020 OpenAccess Files Fulltext by arXiv.org BibTeX | EndNote: XML, Text | RIS

Preprint Samanta, A. K. (First author)CFEL*DESY* ; Amin, M.CFEL*DESY* ; Estillore, A. D.CFEL*DESY* ; Roth, N.CFEL*Extern*XFEL.EU* ; Worbs, L.CFEL*DESY* ; Horke, D. A.CFEL*XFEL.EU*DESY* ; Küpper, J. (Corresponding author)CFEL*DESY*
Controlled beams of shockfrozen, isolated, biological and artificial nanoparticles
arXiv Files Fulltext by arXiv.org BibTeX | EndNote: XML, Text | RIS

Bachelor Thesis Welker, S. (Corresponding author)CFEL* ; Küpper, J. (Thesis advisor)CFEL*DESY* ; Amin, M. (Thesis advisor)CFEL*DESY*
Simulation of artificial and biological nanoparticles’ trajectories in hybrid force-fields
Hamburg 79 pp. (2019) [10.3204/PUBDB-2019-03623]2019 = Bachelorarbeit, Universität Hamburg, 2019 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Amin, M. (Corresponding author)CFEL*DESY* ; Matta, D. ; Yang, K. ; Wang, J. ; Mohamed, Z. ; Brudvig, G. ; Gunner, M. ; Batista, V. S.
Thermodynamics of the S2-to-S3 State Transition of the Oxygen-Evolving Complex of Photosystem II
Physical chemistry, chemical physics 21(37), 20840 - 20848 (2019) [10.1039/C9CP02308A]2019 Embargoed OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Amin, M.CFEL*DESY* ; Samy, H. ; Küpper, J. (Corresponding author)CFEL*DESY*
Robust and Accurate Computational Estimation of the Polarizability Tensors of Macromolecules
The journal of physical chemistry letters 10, 2938 - 2943 (2019) [10.1021/acs.jpclett.9b00963]2019 Embargoed OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Etman, N. ; Said, A. M. A. ; Atia, K. S. R. ; Sultan, R. ; Hameed, M. F. O. ; Amin, M. (Corresponding author)CFEL*DESY* ; Obayya, S. S. A.
Quantum Effects In Imaging Nano-Structures Using Photon-Induced Near-Field Electron Microscopy
Scientific reports 9(1), 6139 (2019) [10.1038/s41598-019-42624-w]2019 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Mandal, M. ; Askerka, M. ; Banerjee, G. ; Amin, M.CFEL*DESY* ; Brudvig, G. ; Batista, V. S. ; Gunner, M. (Corresponding author)
Characterization of Ammonia Binding to the Second Coordination Shell of the Oxygen-Evolving Complex of Photosystem II
Dalton transactions 46, 16089 - 16095 (2017) [10.1039/C7DT03901H]2017 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Amin, M. (Corresponding author)CFEL*DESY* ; Askerka, M. ; Batista, V. S. ; Brudvig, G. W. ; Gunner, M. R.
X-ray Free Electron Laser Radiation Damage through the S-State Cycle of the Oxygen-Evolving Complex of Photosystem II
The journal of physical chemistry <Washington, DC> / B 121(40), 9382-9388 (2017) [10.1021/acs.jpcb.7b08371]2017 Files BibTeX | EndNote: XML, Text | RIS

CFEL Home

Next seminars

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Position in scientific management

03 January 2025

Timepix3: single-pixel multi-hit energy-measurement behaviour

13 November 2024

The event-driven hybrid-pixel detector readout chip, Timepix3, has the ability to simultaneously measure the time of an event on the nanosecond timescale and the energy deposited in the sensor. However, the behaviour of the system when two events are recorded in quick succession of each other on the same pixel was not studied in detail previously. We present experimental measurements, circuit simulations, and an empirical model for the impact of a preceding event on this energy measurements, which can result in a loss as high as 70%. Accounting for this effect enables more precise compensation, particularly for phenomena like timewalk. This results in significant improvements in time resolution — in the best case, multiple tens of nanoseconds — when two events happen in rapid succession.

Recent Publications

Journal Article Ekeberg, T.CFEL*Extern*XFEL.EU* ; Assalauova, D.Extern*XFEL.EU*DESY* ; Bielecki, J.XFEL.EU* ; Boll, R.XFEL.EU* ; Daurer, B. J.Extern* ; Eichacker, L. A.Extern*XFEL.EU* ; Franken, L. E.CSSB* ; Galli, D. E.XFEL.EU* ; Gelisio, L.CFEL*XFEL.EU*DESY* ; Gumprecht, L.CFEL*XFEL.EU*DESY* ; Gunn, L. H.Extern*XFEL.EU* ; Hajdu, J.Extern* ; Hartmann, R.Extern* ; Hasse, D. ; Ignatenko, A.CFEL*XFEL.EU*DESY* ; Koliyadu, J.XFEL.EU*DESY* ; Kulyk, O.Extern* ; Kurta, R.XFEL.EU* ; Kuster, M.XFEL.EU* ; Lugmayr, W.CSSB* ; Lübke, J.CFEL*Extern*XFEL.EU* ; Mancuso, A. P.Extern*XFEL.EU* ; Mazza, T.XFEL.EU* ; Nettelblad, C.Extern*XFEL.EU* ; Ovcharenko, Y.XFEL.EU* ; Rivas, D. E.XFEL.EU* ; Rose, M.Extern*XFEL.EU* ; Samanta, A. K.CFEL*XFEL.EU*DESY* ; Schmidt, P.XFEL.EU* ; Sobolev, E.XFEL.EU*EMBL* ; Timneanu, N.Extern* ; Usenko, S.XFEL.EU* ; Westphal, D.Extern* ; Wollweber, T.Extern* ; Worbs, L.CFEL*XFEL.EU*DESY* ; Xavier, P. L. ; Yousef, H.XFEL.EU* ; Ayyer, K.CFEL*MPG*XFEL.EU* ; Chapman, H. N.CFEL*XFEL.EU*DESY* ; Sellberg, J. A.Extern*XFEL.EU* ; Seuring, C.CFEL*CSSB*XFEL.EU* ; Vartanyants, I. A.XFEL.EU*DESY* ; Küpper, J.CFEL*XFEL.EU*DESY* ; Meyer, M. ; Maia, F. R. N. C. (Corresponding author)Extern*XFEL.EU*
Observation of a single protein by ultrafast X-ray diffraction
Light 13(1), 15 (2024) [10.1038/s41377-023-01352-7]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article He, L.CFEL*Extern*XFEL.EU* ; Johny, M.CFEL*Extern*XFEL.EU* ; Kierspel, T.CSSB*DESY* ; Dlugolecki, K.CFEL*XFEL.EU*DESY* ; Bari, S.DESY* ; Boll, R.XFEL.EU* ; Bromberger, H.CFEL*XFEL.EU*DESY* ; coreno, m.Extern*XFEL.EU* ; De Fanis, A.XFEL.EU* ; Di Fraia, M.Extern* ; Erk, B.XFEL.EU*DESY* ; Gisselbrecht, M.Extern* ; Grychtol, P.XFEL.EU* ; Eng-Johnsson, P.Extern*XFEL.EU* ; Mazza, T.XFEL.EU* ; Onvlee, J.CFEL*Extern*XFEL.EU* ; Ovcharenko, Y.XFEL.EU* ; Petrovic, J.Extern*XFEL.EU*DESY* ; Rennhack, N.XFEL.EU* ; Rivas, D.XFEL.EU* ; Rudenko, A.Extern* ; Ruehl, E.Extern* ; Schwob, L.XFEL.EU*DESY* ; Simon, M.Extern* ; Trinter, F.Extern*XFEL.EU* ; Usenko, S.XFEL.EU* ; Wiese, J.CFEL*Extern*XFEL.EU* ; Meyer, M.XFEL.EU* ; Trippel, S. (Corresponding author)CFEL*XFEL.EU*DESY* ; Küpper, J. (Corresponding author)CFEL*XFEL.EU*DESY*
Controlled molecule injector for cold, dense, and pure molecular beams at the European x-ray free-electron laser
Review of scientific instruments 95(11), 113301 (2024) [10.1063/5.0219086]2024 OpenAccess Files Fulltext BibTeX | EndNote: XML, Text | RIS