Single Particle Imaging And Instruments Conceptual Design With X-ray Free-Electron Lasers

The advent of ultra-intense,ultrashort and fully coherent X-ray free-electron laser(FEL)opens great opportunities for ultra-small and ultrafast spatial&temporal structure determination.It's of great importance to physics,materials science,life science,frontier research,and several major issues in the fields of earth science and environmental science.The X-ray FEL provides unprecedented high-performance light sources and pioneering research methods,as well as a breakthrough tool for research on protein structure analysis,green energy exploration,and the ultra-fast process of chemical reactions.The X-ray FEL has made breakthrough progress in the major fields of structural biology,photosynthetic reaction process and electron movement within materials since the public operations of LCLS,SLAC on 2009.Besides,it will make a breakthrough in basic research fields such as new clean energy material exploration,membrane protein dynamic structure analysis,chemical catalysis reaction process,and light-matter interaction.Many countries and organizations around the world actions quickly in the X-ray free-electron laser facility.At present,for soft X-ray laser facilities around the world,FLASH(Germany)and FERMI(Italy)have been under operations for years.For hard X-ray laser facilities around the world,LCLS(United States),SACLA(Japan),PAL-XFEL(South Korea),and SwissFEL(Switzerland)are under operation.For high repetition rate facilities,European-XFEL opened to users last year and the LCLS-? is under construction.In China,Shanghai Soft X-ray free-electron laser(SXFEL)and high repetition rate hard X-ray free-electron laser(SHINE)are both under Construction.In addition,China Academy of Engineering Physics,Hefei Advanced Light Source Cluster,Dalian Advanced Light Source also proposed hard X-ray free-electron laser,soft X-ray/Terahertz/Infrared free-electron laser and high repetition rate soft X-ray free-electron laser facilities.Meanwhile,Beijing Huairou Comprehensive National Science Center and Wuhan Light Source have also investigated and discussed the construction of associated facilities.The emergence of a new type of light source can greatly promote the development of basic scientific research and engineering applications.The related methodological research and layout need to be pushed in advance.Single-particle Imaging with X-ray lasers,a lensless imaging method,has gained the favor of scientists and has been the main scientific case for the propose of Linac Coherent Light Source(LCLS),SLAC National Accelerator Laboratory,the United States of America.The DOE of the United States proved $379 million for the LCLS.High-resolution imaging of biological cells,bacteria.viruses,nanoparticles,aerosol particles,clusters,protein particles and biological macromolecules is the basic concept of single particle imaging with X-ray free-electron laser.The physical principle of single particle imaging is not so complex.The approximation behind the single particle imaging is Fraunhofer diffraction.Single particle imaging mainly contains five parts:The sample,sample delivery system,light source and the instruments,light-matter interaction,data acquisition,processing,and analysis.Regarding the main parts,single particle imaging technology involves multiple disciplines and is associated with many experimental methods,experimental techniques,and engineering challenges.In order to solve the technical and engineering problems during the development of single particle imaging technology,this thesis studies and discusses the principle,experimental method,technology and engineering practice of single particle imaging:(1)Sample Selection.Self-assembled nanostructures with a size of 700 nm and 400 nm by Focused Ion Beam were detected.In addition,the PR772 coliphage virus particles with a size of?68 nm,and the MS2 phage particles with a size of?30 nm were imaged by the single particle imaging with X-ray lasers.We confirmed that the large size of the nanostructure and the biological virus particles have better diffraction efficiency than that of the smaller size.If the actual application is involved,there aren't too many alternatives for the sample selection.However,the diffraction efficiency can be improved by increasing the coherent scattering cross-section.It is possible to select a large size to improve the success rate of the experiment when the resolution improvement is the target.(2)Photon Energy Selection.Combined with theoretical analysis,experiments were carried out to study the MS2 particles under 1.6 keV and 7.0 keV.What's more,the above-mentioned nanostructures were also investigated under 5 keV and 10 keV.It is confirmed that the low photon energy can obtain better diffraction efficiency,and high photon energy tends to obtain higher resolution.Therefore,the corresponding photon energy can be selected according to the requirements of the experiment.(3)Noise Assessment of Sample Delivery Equipment.The background noise of the gas dynamic virtual nozzle(GDVN)and electro spray was evaluated by the single particle imaging experimental data.And then compared with the beamline noise and detector dark noise.For the first time,the electrospray,commonly used in serial femtosecond crystallography,is applied to single particle imaging,resulting in higher levels of background noise due to the diffraction of driving gases such as CO2,N2,etc.,which is very detrimental to the imaging of biological samples such as small size MS2 virus particles.In the design of the subsequent sample delivery device,it is necessary to take into account the problem of hit efficiency and background noise.(4)The Classification of Single Particle Imaging Data Based on Diffusion Maps.With the 120 Hz operating frequency of LCLS and 1 MHz of LCLS-?,an efficient,unsupervised machine learning method is essential for automatic classification of large quantities of diffraction data(measured in tens of millions of and billions).In this paper,a non-linear diffusion maps method is applied to classify 14,441 single-particle diffraction patterns after the manual screening,which can be found to be significantly improved.Through two-dimensional/three-dimensional and custom polygon visualization selection,the diffraction data can be efficiently and conveniently classified and can be applied to the data screening and classification of high-frequency facilities such as LCLS-? and SHINE.(5)The Application of Single Particle Imaging in DNA-based Nanostructure.There is still a little case for the application of single particle imaging.The main research direction is the improvement of resolution.Based on this,we select the important self-assembly DNA nanostructures and carried out the imaging experiment at SACLA,Japan.Quantitative analysis of the causes of failures was performed.In addition,the numerical simulation of DNA self-assembly nanostructure under 1.6 keV?7.0 keV,with the pulse energy of 0.1,0.8,2.0,4.0 mJ were complemented.The results show that in the case of 7.0 keV with a pulse energy greater than 2.0 mJ,10 nm could be achieved.For 1 nm,it depends on the sample,phase retrieval algorithms,deep learning classification methods,and detector systems.(6)The Commissioning of Macromolecular Femtosecond Crystallography Instrument(MFX)at LCLS.It is important to study the beamline and endstations after the sample selection,sample delivery device,the data classification,and the application exploration.The transfocator commissioning of MFX at LCLS is carried out.And the characteristics of the focusing optical system and the properties of focusing spot are analyzed under the common photon energy 7.5 and 9.5 keV.respectively,which can be used for reference in the subsequent single particle imaging instruments and experiments.(7)Conceptual Design of Single Particle Imaging Instruments.After the completion of the experimental method and the accumulation of experimental technology,gradually converted to engineering practice.In view of the domestic flourishing X-ray free-electron laser facilities,the conceptual design of a single particle imaging instrument was started.The dual sample chamber and the multi-optical focusing system can be applied to make use of various forward scattering methods and to ensure the ability to upgrade at any Time.It can be applied to the high repetition frequency hard X-ray free electron laser(SHINE),and also can be used for reference to the similar instruments of domestic-related facilities.In conclusions,this paper talks about the single particle imaging with X-ray free electron laser.It includes the research background,scientific significance/driven force,and physical principle.In order to solve the technical and engineering challenges,photon energy,experimental samples,the sample delivery system,massive data screening and classification,and the application exploration in the self-assembly DNA nanostructures were discussed.Through the optical commissioning of MFX instrument of LCLS,the characteristics of forward scattering experimental endstation are obtained.The conceptual design of a single particle imaging instrument is carried out based on the main photon parameters of SHINE(A high-repetition-rate hard X-ray free electron laser facility in Shanghai).Single particle imaging with near-atomic resolution and single-molecule imaging is our final research goal.It involves the principles of physics,the development of experimental methods,the innovation of experimental technology and the overcoming of engineering difficulties.Although full of challenges,we believe that with the continuous efforts and progress,we will gradually get closer to the goal finally.