Electron Tomography （ET） is an important method for studying cell ultrastructure in three-dimensional （3D） space. By combining cryo-electron tomography of frozen-hydrated samples （cryo-ET） and a sub-tomogram ave...Electron Tomography （ET） is an important method for studying cell ultrastructure in three-dimensional （3D） space. By combining cryo-electron tomography of frozen-hydrated samples （cryo-ET） and a sub-tomogram averaging approach, ET has recently reached sub-nanometer resolution, thereby realizing the capability for gaining direct insights into function and mechanism. To obtain a high-resolution 3D ET reconstruction, alignment and geometry determination of the ET tilt series are necessary. However, typical methods for determining geometry require human intervention, which is not only subjective and easily introduces errors, but is also labor intensive for high-throughput tomographic reconstructions. To overcome these problems, we have developed an automatic geometry-determination method, called AutoGDeterm. By taking advantage of the high-contrast re-projections of the Iterative Compressed-sensing Optimized Non-Uniform Fast Fourier Transform （NUFFT） reconstruction （ICON） and a series of numerical analysis methods, AutoGDeterm achieves high-precision fully automated geometry determination. Experimental results on simulated and resin-embedded datasets show that the accuracy of AutoGDeterm is high and comparable to that of the typical ＂manual positioning＂ method. We have made AutoGDeterm available as software, which can be freely downloaded from our website http：//ear.ict.ac.cn.展开更多
We provide a way to precisely control the geometry of a SiNx nanopore by adjusting the applied electric pulse. The pore is generated by applying the current pulse across a SiNx membrane, which is immersed in potassium...We provide a way to precisely control the geometry of a SiNx nanopore by adjusting the applied electric pulse. The pore is generated by applying the current pulse across a SiNx membrane, which is immersed in potassium chloride solution. We can generate single conical and cylindrical pores with different electric pulses. A theoretical model based on the Poisson and Nernst-Planck equations is employed to simulate the ion transport properties in the channel. In turn, we can analyze pore geometries by fitting the experimental current-voltage （I-V） curves. for the conical pores with a pore size of 0.5-2nm in diameter, the slope angles are around -2.5% to -10%. Moreover, the pore orifice can be enlarged slightly by additional repeating pulses. The conic pore lumen becomes close to a cylindrical channel, resulting in a symmetry I-V transport under positive and negative biases. A qualitative understanding of these effects will help us to prepare useful solid-nanopores as demanded.展开更多
基金supported by the National Natural Science Foundation of China (Nos. U1611263, U1611261, 61232001, 61472397, 61502455, and 61672493)the Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (the second phase)+1 种基金the Strategic Priority Research Program of Chinese Academy of Sciences (No. XDB08030202)the National Key Research and Development Program of China (No. 2017YFA0504702)
文摘Electron Tomography （ET） is an important method for studying cell ultrastructure in three-dimensional （3D） space. By combining cryo-electron tomography of frozen-hydrated samples （cryo-ET） and a sub-tomogram averaging approach, ET has recently reached sub-nanometer resolution, thereby realizing the capability for gaining direct insights into function and mechanism. To obtain a high-resolution 3D ET reconstruction, alignment and geometry determination of the ET tilt series are necessary. However, typical methods for determining geometry require human intervention, which is not only subjective and easily introduces errors, but is also labor intensive for high-throughput tomographic reconstructions. To overcome these problems, we have developed an automatic geometry-determination method, called AutoGDeterm. By taking advantage of the high-contrast re-projections of the Iterative Compressed-sensing Optimized Non-Uniform Fast Fourier Transform （NUFFT） reconstruction （ICON） and a series of numerical analysis methods, AutoGDeterm achieves high-precision fully automated geometry determination. Experimental results on simulated and resin-embedded datasets show that the accuracy of AutoGDeterm is high and comparable to that of the typical ＂manual positioning＂ method. We have made AutoGDeterm available as software, which can be freely downloaded from our website http：//ear.ict.ac.cn.
基金Supported by the National Natural Science Foundation of China under Grant Nos 61471336,51503207 and 61504146the Joint-Scholar of West Light Foundation of Chinese Academy of Sciences
文摘We provide a way to precisely control the geometry of a SiNx nanopore by adjusting the applied electric pulse. The pore is generated by applying the current pulse across a SiNx membrane, which is immersed in potassium chloride solution. We can generate single conical and cylindrical pores with different electric pulses. A theoretical model based on the Poisson and Nernst-Planck equations is employed to simulate the ion transport properties in the channel. In turn, we can analyze pore geometries by fitting the experimental current-voltage （I-V） curves. for the conical pores with a pore size of 0.5-2nm in diameter, the slope angles are around -2.5% to -10%. Moreover, the pore orifice can be enlarged slightly by additional repeating pulses. The conic pore lumen becomes close to a cylindrical channel, resulting in a symmetry I-V transport under positive and negative biases. A qualitative understanding of these effects will help us to prepare useful solid-nanopores as demanded.
