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

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Breakthrough in laser-alignment for macromolecular single-particle imaging

10 April 2025

Single-particle diffractive imaging (SPI) using X-ray free-electron lasers allows researchers to reconstruct the structure of nanoparticles and biomolecules. However, the technique often requires imaging up to several billion nanoparticles to produce the image and imposes limitations on its clarity and sharpness. Researchers at the Center for Free-Electron Laser Science at DESY, together with international colleagues, recently demonstrated that laser-induced alignment can indeed be achieved to significantly improve molecular imaging techniques. This geometric confinement of the molecules in the x-ray-imaging experiment will greatly facilitate the recovery of the molecular orientation and, therefore, the structure retrieval. It thus overcomes a significant challenge in single-particle diffractive imaging. This novel development further paves the way for solving the three-dimensional structures of proteins and other macromolecules using SPI.

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