Computing methods for icosahedral and symmetry-mismatch reconstruction of viruses by cryo-electron microscopy

Three-dimensional（3 D） reconstruction of icosahedral viruses has played a crucial role in the development of cryoelectron microscopy single-particle reconstruction, with many cryo-electron microscopy techniques first established for structural studies of icosahedral viruses, owing to their high symmetry and large mass. This review summarizes the computational methods for icosahedral and symmetry-mismatch reconstruction of viruses, as well as the likely challenges and bottlenecks in virus reconstruction, such as symmetry mismatch reconstruction, contrast transformation function（CTF）correction, and particle distortion.

Structural biology revolution led by technical breakthroughs in cryo-electron microscopy

Recent technical breakthroughs in cryo-electron microscopy（cryo-EM） revolutionized structural biology, which led to the 2017 Nobel Prize in chemistry being awarded to three scientists, Jacques Dubochet, Joachim Frank, and Richard Henderson, who made groundbreaking contributions to the development of cryo-EM. In this review, I will give a comprehensive review of the developmental history of cryo-EM, the technical aspects of the breakthrough in cryo-EM leading to the structural biology revolution, including electron microscopy, image recording devices and image processing algorithms,and the major scientific achievements by Chinese researchers employing cryo-EM, covering protein complexes involved in or related to gene expression and regulation, protein synthesis and degradation, membrane proteins, immunity, and viruses.Finally, I will give a perspective outlook on the development of cryo-EM in the future.

Cryo-electron microscopy structure of the intact photosynthetic light-harvesting antenna-reaction center complex from a green sulfur bacterium

The photosynthetic reaction center complex(RCC)of green sulfur bacteria(GSB)consists of the membrane-imbedded RC core and the peripheric energy transmitting proteins called Fenna–Matthews–Olson(FMO).Functionally,FMO transfers the absorbed energy from a huge peripheral light-harvesting antenna named chlorosome to the RC core where charge separation occurs.In vivo,one RC was found to bind two FMOs,however,the intact structure of RCC as well as the energy transfer mechanism within RCC remain to be clarified.Here we report a structure of intact RCC which contains a RC core and two FMO trimers from a thermophilic green sulfur bacterium Chlorobaculum tepidum at 2.9A resolution by cryo-electron microscopy.The second FMO trimer is attached at the cytoplasmic side asymmetrically relative to the first FMO trimer reported previously.We also observed two new subunits(PscE and PscF)and the N-terminal transmembrane domain of a cytochrome-containing subunit(PscC)in the structure.These two novel subunits possibly function to facilitate the binding of FMOs to RC core and to stabilize the whole complex.A new bacteriochlorophyll(numbered as 816)was identified at the interspace between PscF and PscA-1,causing an asymmetrical energy transfer from the two FMO trimers to RC core.Based on the structure,we propose an energy transfer network within this photosynthetic apparatus.

Estimation-free spatial-domain image reconstruction of structured illumination microscopy

Structured illumination microscopy(SIM)achieves super-resolution(SR)by modulating the high-frequency information of the sample into the passband of the optical system and subsequent image reconstruction.The traditional Wiener-filtering-based reconstruction algorithm operates in the Fourier domain,it requires prior knowledge of the sinusoidal illumination patterns which makes the time-consuming procedure of parameter estimation to raw datasets necessary,besides,the parameter estimation is sensitive to noise or aberration-induced pattern distortion which leads to reconstruction artifacts.Here,we propose a spatial-domain image reconstruction method that does not require parameter estimation but calculates patterns from raw datasets,and a reconstructed image can be obtained just by calculating the spatial covariance of differential calculated patterns and differential filtered datasets(the notch filtering operation is performed to the raw datasets for attenuating and compensating the optical transfer function(OTF)).Experiments on reconstructing raw datasets including nonbiological,biological,and simulated samples demonstrate that our method has SR capability,high reconstruction speed,and high robustness to aberration and noise.

Probing the Nucleation and Growth Kinetics of Bismuth Nanoparticles via In-situ Transmission Electron Microscopy

The nucleation and growth mechanism of nanoparticles is an important theory,which can guide the preparation of nanomaterials.However,it is still lacking in direct observation on the details of the evolution of intermediate state structure during nucleation and growth.In this work,the evolution process of bismuth nanoparticles induced by electron beam was revealed by in-situ transmission electron microscopy(TEM)at atomic scale.The experimental results demonstrate that the size,stable surface and crystallographic defect have important influences on the growth of Bi nanoparticles.Two non-classical growth paths including single crystal growth and polycrystalline combined growth,as well as,corresponding layer-by-layer growth mechanism along{012}stable crystal plane of Bi nanoparticles with dodecahedron structure were revealed by in-situ TEM directly.These results provide important guidance and a new approach for in-depth understanding of the nucleation and growth kinetics of nanoparticles.

Ultrafast photoemission electron microscopy:A multidimensional probe of nonequilibrium physics

Exploring the realms of physics that extend beyond thermal equilibrium has emerged as a crucial branch of condensed matter physics research.It aims to unravel the intricate processes involving the excitations,interactions,and annihilations of quasi-and many-body particles,and ultimately to achieve the manipulation and engineering of exotic non-equilibrium quantum phases on the ultrasmall and ultrafast spatiotemporal scales.Given the inherent complexities arising from many-body dynamics,it therefore seeks a technique that has efficient and diverse detection degrees of freedom to study the underlying physics.By combining high-power femtosecond lasers with real-or momentum-space photoemission electron microscopy(PEEM),imaging excited state phenomena from multiple perspectives,including time,real space,energy,momentum,and spin,can be conveniently achieved,making it a unique technique in studying physics out of equilibrium.In this context,we overview the working principle and technical advances of the PEEM apparatus and the related laser systems,and survey key excited-state phenomena probed through this surface-sensitive methodology,including the ultrafast dynamics of electrons,excitons,plasmons,spins,etc.,in materials ranging from bulk and nano-structured metals and semiconductors to low-dimensional quantum materials.Through this review,one can further envision that time-resolved PEEM will open new avenues for investigating a variety of classical and quantum phenomena in a multidimensional parameter space,offering unprecedented and comprehensive insights into important questions in the field of condensed matter physics.

Recent progress about transmission electron microscopy characterizations on lithium-ion batteries

With the rapid development of portable electronics,new energy vehicles,and smart grids,ion batteries are becoming one of the most widely used energy storage devices,while the safety concern of ion batteries has always been an urgent problem to be solved.To develop a safety-guaranteed battery,the characterization of the internal structure is indispensable,where electron microscopy plays a crucial role.Based on this,this paper summarizes the application of transmission electron microscopy(TEM)in battery safety,further concludes and analyzes the aspects of dendrite growth and solid electrolyte interface(SEI)formation that affect the safety of ion batteries,and emphasizes the importance of electron microscopy in battery safety research and the potential of these techniques to promote the future development of this field.These advanced electron microscopy techniques and their prospects are also discussed.

Investigation of reflection anisotropy induced by micropipe defects on the surface of a 4H-SiC single crystal using scanning anisotropy microscopy

Optical reflection anisotropy microscopy mappings of micropipe defects on the surface of a 4H-SiC single crystal are studied by the scanning anisotropy microscopy(SAM)system.The reflection anisotropy(RA)image with a'butterfly pattern'is obtained around the micropipes by SAM.The RA image of the edge dislocations is theoretically simulated based on dislocation theory and the photoelastic principle.By comparing with the Raman spectrum,it is verified that the micropipes consist of edge dislocations.The different patterns of the RA images are due to the different orientations of the Burgers vectors.Besides,the strain distribution of the micropipes is also deduced.One can identify the dislocation type,the direction of the Burgers vector and the optical anisotropy from the RA image by using SAM.Therefore,SAM is an ideal tool to measure the optical anisotropy induced by the strain field around a defect.

A review of understanding electrocatalytic reactions in energy conversion and energy storage systems via scanning electrochemical microscopy

To address climate change and promote environmental sustainability,electrochemical energy conversion and storage systems emerge as promising alternative to fossil fuels,catering to the escalating demand for energy.Achieving optimal energy efficiency and cost competitiveness in these systems requires the strategic design of electrocatalysts,coupled with a thorough comprehension of the underlying mechanisms and degradation behavior occurring during the electrocatalysis processes.Scanning electrochemical microscopy(SECM),an analytical technique for studying surface electrochemically,stands out as a powerful tool offering electrochemical insights.It possesses remarkable spatiotemporal resolution,enabling the visualization of the localized electrochemical activity and surface topography.This review compiles crucial research findings and recent breakthroughs in electrocatalytic processes utilizing the SECM methodology,specifically focusing on applications in electrolysis,fuel cells,and metal–oxygen batteries within the realm of energy conversion and storage systems.Commencing with an overview of each energy system,the review introduces the fundamental principles of SECM,and aiming to provide new perspectives and broadening the scope of applied research by describing the major research categories within SECM.

Characterization of local chemical ordering and deformation behavior in high entropy alloys by transmission electron microscopy

Short-range ordering(SRO)is one of the most important structural features of high entropy alloys(HEAs).However,the chemical and structural analyses of SROs are very difficult due to their small size,complexed compositions,and varied locations.Transmission electron microscopy(TEM)as well as its aberration correction techniques are powerful for characterizing SROs in these compositionally complex alloys.In this short communication,we summarized recent progresses regarding characterization of SROs using TEM in the field of HEAs.By using advanced TEM techniques,not only the existence of SROs was confirmed,but also the effect of SROs on the deformation mechanism was clarified.Moreover,the perspective related to application of TEM techniques in HEAs are also discussed.

Advancing respirable coal mine dust source apportionment:a preliminary laboratory exploration of optical microscopy as a novel monitoring tool

Exposure to respirable coal mine dust(RCMD)can cause chronic and debilitating lung diseases.Real-time monitoring capabilities are sought which can enable a better understanding of dust components and sources.In many underground mines,RCMD includes three primary components which can be loosely associated with three major dust sources:coal dust from the coal seam itself,silicates from the surrounding rock strata,and carbonates from the inert‘rock dust’products that are applied to mitigate explosion hazards.A monitor which can reliably partition RCMD between these three components could thus allow source apportionment.And tracking silicates,specifically,could be valuable since the most serious health risks are typically associated with this component-particularly if abundant in crystalline silica.Envisioning a monitoring concept based on field microscopy,and following up on prior research using polarized light,the aim of the current study was to build and test a model to classify respirable-sized particles as either coal,silicates,or carbonates.For model development,composite dust samples were generated in the laboratory by successively depositing dust from high-purity materials onto a sticky transparent substrate,and imaging after each deposition event such that the identity of each particle was known a priori.Model testing followed a similar approach,except that real geologic materials were used as the source for each dust component.Results showed that the model had an overall accuracy of 86.5%,indicating that a field-microscopy based moni-tor could support RCMD source apportionment and silicates tracking in some coal mines.

Microscopic Analysis of Cementitious Sand and Gravel Damming Materia

The mechanical properties of cementitious sand and gravel damming material have been experimentally determined by means of microscopic SEM(Scanning Electron Microscopy)image analysis.The results show that the combination of fly ash and water can fill the voids in cemented sand and gravel test blocks because of the presence of hydrated calcium silicate and other substances;thereby,the compactness and mechanical properties of these materials can be greatly improved.For every 10 kg/m^(3) increase in the amount of cementitious material,the density increases by about 2%,and the water content decreases by 0.2%.The amount of cementitious material used in the sand and gravel in these tests was 80-110 kg/m^(3),the water-binder ratio was 1-1.50.Moreover,the splitting tensile strength was 1/10 of the compressive strength,and the maximum strength was 7.42 MPa at 90 d.The optimal mix ratio has been found to be 50 kg of cement,60 kg of fly ash and 120 kg of water(C50F60W120).The related dry density was 2.6 g/cm^(3),the water content was 6%,and the water-binder ratio was 1.09.

Capturing the non-equilibrium state in light–matter–free-electron interactions through ultrafast transmission electron microscopy

Ultrafast transmission electron microscope(UTEM) with the multimodality of time-resolved diffraction, imaging,and spectroscopy provides a unique platform to reveal the fundamental features associated with the interaction between free electrons and matter. In this review, we summarize the principles, instrumentation, and recent developments of the UTEM and its applications in capturing dynamic processes and non-equilibrium transient states. The combination of the transmission electron microscope with a femtosecond laser via the pump–probe method guarantees the high spatiotemporal resolution, allowing the investigation of the transient process in real, reciprocal and energy spaces. Ultrafast structural dynamics can be studied by diffraction and imaging methods, revealing the coherent acoustic phonon generation and photoinduced phase transition process. In the energy dimension, time-resolved electron energy-loss spectroscopy enables the examination of the intrinsic electronic dynamics of materials, while the photon-induced near-field electron microscopy extends the application of the UTEM to the imaging of optical near fields with high real-space resolution. It is noted that light–free-electron interactions have the ability to shape electron wave packets in both longitudinal and transverse directions, showing the potential application in the generation of attosecond electron pulses and vortex electron beams.

Correlation of work function and stacking fault energy through Kelvin probe force microscopy and nanohardness in diluteα-magnesium

Electronic interactions of the Group 2A elements with magnesium have been studied through the dilute solid solutions in binary Mg-Ca,Mg-Sr and Mg-Ba systems.This investigation incorporated the difference in the‘Work Function'(ΔWF)measured via Kelvin Probe Force Microscopy(KPFM),as a property directly affected by interatomic bond types,i.e.the electronic structure,nanoindentation measurements,and Stacking Fault Energy values reported in the literature.It was shown that the nano-hardness of the solid-solutionα-Mg phase changed in the order of Mg-Ca>Mg-Sr>Mg-Ba.Thus,it was shown,by also considering the nano-hardness levels,that SFE of a solid-solution is closely correlated with its‘Work Function'level.Nano-hardness measurements on the eutectics andΔWF difference between eutectic phases enabled an assessment of the relative bond strength and the pertinent electronic structures of the eutectics in the three alloys.Correlation withΔWF and at least qualitative verification of those computed SFE values with some experimental measurement techniques were considered important as those computational methods are based on zero Kelvin degree,relatively simple atomic models and a number of assumptions.As asserted by this investigation,if the results of measurement techniques can be qualitatively correlated with those of the computational methods,it can be possible to evaluate the electronic structures in alloys,starting from binary systems,going to ternary and then multi-elemental systems.Our investigation has shown that such a qualitative correlation is possible.After all,the SFE values are not treated as absolute values but rather become essential in comparative investigations when assessing the influences of alloying elements at a fundamental level,that is,free electron density distributions.Our study indicated that the principles of‘electronic metallurgy'in developing multi-elemental alloy systems can be followed via practical experimental methods,i.e.ΔWF measurements using KPFM and nanoindentation.

Microscopic growth mechanism and edge states of monolayer 1T'-MoTe_(2)

Transition metal ditellurides(TMTDs)have versatile physical properties,including non-trivial topology,Weyl semimetal states and unique spin texture.Controlled growth of high-quality and large-scale monolayer TMTDs with preferred crystal phases is crucial for their applications.Here,we demonstrate the epitaxial growth of 1T'-MoTe_(2) on Au(111)and graphitized silicon carbide(Gr/SiC)by molecular beam epitaxy(MBE).We investigate the morphology of the grown1T'-MoTe_(2) at the atomic level by scanning tunnelling microscopy(STM)and reveal the corresponding microscopic growth mechanism.It is found that the unique ordered Te structures preferentially deposited on Au(111)regulate the growth of monolayer single crystal 1T'-MoTe_(2),while the Mo clusters were preferentially deposited on the Gr/SiC substrate,which impedes the ordered growth of monolayer MoTe_(2).We confirm that the size of single crystal 1T'-MoTe_(2) grown on Au(111)is nearly two orders of magnitude larger than that on Gr/SiC.By scanning tunnelling spectroscopy(STS),we observe that the STS spectrum of the monolayer 1T'-MoTe_(2) nano-island at the edge is different from that at the interior,which exhibits enhanced conductivity.

Cryo-electron microscopy reconstructions of two types of wild rabbit hemorrhagic disease viruses characterized the structural features of Lagovirus

Rabbit hemorrhagic disease was described in China in 1984 and can cause hemorrhagic necrosis of the liver within two or three days after infection.The etiological agent,rabbit hemorrhagic disease virus(RHDV),belongs to the Lagovirus genus in the Caliciviridae family.Compared to other calicivirus,such as rNV and SMSV,the structure of Lagovirus members is not well characterized.In this report,structures of two types of wild RHDV particles,the intact virion and the core-like particle(CLP),were reconstructed by cryo-electron microscopy at 11Åand 17Å,respectively.This is the first time the 3D structure of wild caliciviruses CLP has been provided,and the 3D structure of intact RHDV virion is the highest resolution structure in Lagovirus.Comparison of the intact virion and CLP structures clearly indicated that CLP was produced from the intact virion with the protrusion dissociated.In contrast with the crystal structures of recombinant Norovirus and San Miguel sea lion virus,the capsomers of RHDV virion exhibited unique structural features and assembly modes.Both P1 and P2 subdomains have interactions inside the AB capsomer,while only P2 subdomains have interaction inside CC capsomer.The pseudo atomic models of RHDV capsomers were constructed by homology modeling and density map fitting,and the rotation of RHDV VP60 P domain with respect to its S domain,compared with SMSV,was observed.Collectively,our cryo-electron microscopic studies of RHDV provide close insight into the structure of Lagovirus,which is important for functional analysis and better vaccine development in the future.

Cryo-electron microscopy finds place in materials science

The fast development of electron microscopy has enabled unprecedented achievements in the field of life science and materials science[1–6].In particular,the 2017 Nobel Prize of chemistry was awarded to three scientists who contributed significantly to developing cryo-electron microscopy(Cryo-EM)[7].This technique,involving fast freezing the biological samples using liquid nitrogen,was originally designed to keep"live cells"intact from water evaporation and crystallization and immune to

Assembly mechanism and energy transfer pathways of plant photosystem II-LHCII supercomplexes discovered through cryo-electron microscopy

Funded by the National Natural Science Foundation of China,Chinese Ministry of Science and Technology,and Chinese Academy of Sciences,ajoint team of three laboratories from the Institute of Biophysics of Chinese Academy of Sciences,namely Liu Zhenfeng’s(柳振峰),Zhang

Structural variation of molecular chaperone group Ⅱ by crystallography and cryo-electron microscopy

Chaperonins, a class of molecular chaperones, are oligomeric complexes acting as a protein-folding chamber in an ATP-dependent manner. Chaperonins have been classifed

The three-dimensional structure of Infectious flacherie virus capsid determined by cryo-electron microscopy

Cryo-electron microscopy and image reconstruction were used to determine the three-dimensional structure of Infectious flacherie virus (IFV). 5047 particles were selected for the final reconstruction. The FSC curve showed that the resolution of this capsid structure was 18 ·. The structure is a psuedo T=3 (P=3) icosahedral capsid with a diameter of 302.4 · and a single shell thickness of 15 ·. The density map showed that IFV has a smooth surface without any prominent protrude or depression. Comparison of the IFV structure with those of the insect picorna-like virus-Cricket paralysis virus (CrPV)and human picornavirus-Human rhinovirus 14 (HRV 14) revealed that the IFV structure resembles the CrPV structure. The "Rossmann canyon" is absent in both IFV and CrPV particles. The polypeptide topology of IFV VP2, IFV VP3 was predicted and the subunit location at the capsid surface was further analyzed.