Related papers: Kam method for Cryo-EM particle reconstruction
Calculations of the photonic band structure, transmission coefficients, and quality factors of various two-dimensional, periodic and aperiodic, dielectric photonic crystals by using the finite element method (FEM) are reported. The…
A method is proposed for high-resolution, three-dimensional reconstruction of internal structure of objects from planar transmission images. The described approach can be used with any form of radiation or matter waves, in principle,…
The interaction of a protein with its environment can be understood and controlled via its 3D structure. Experimental methods for protein structure determination, such as X-ray crystallography or cryogenic electron microscopy, shed light on…
Structural dynamics of macromolecules is critical to their structural-function relationship. Cryogenic electron microscopy (CryoEM) provides snapshots of vitrified protein at different compositional and conformational states, and the…
Fourier ptychographic microscopy (FPM) is a pivotal computational imaging technique that achieves phase and amplitude reconstruction with high resolution and wide field of view, using low numerical aperture objectives and LED array…
Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. CryoEM provides direct visualization of individual macromolecules sampling different conformational and compositional states.…
Single-particle cryo-electron microscopy (cryo-EM) has recently joined X-ray crystallography and NMR spectroscopy as a high-resolution structural method for biological macromolecules. Cryo-EM was selected by Nature Methods as Method of the…
Modern tomography involves gathering projection data from multiple directions and feeding them into a software algorithm for tomographic reconstruction. We focus our study on image reconstruction from Radon data in the setting of…
The problem of image restoration in cryo-EM entails correcting for the effects of the Contrast Transfer Function (CTF) and noise. Popular methods for image restoration include `phase flipping', which corrects only for the Fourier phases but…
Single-particle cryo-EM has transformed structural biology but still faces challenges in resolving conformational heterogeneity at atomic resolution. Existing cryo-EM heterogeneity analysis methods either lack atomic details or tend to…
Macromolecules change their shape (conformation) in the process of carrying out their functions. The imaging by cryo-electron microscopy of rapidly-frozen, individual copies of macromolecules (single particles) is a powerful and general…
Here we apply hyperspectral bright field imaging to collect computed tomographic images with excellent energy resolution (800 eV), applying it for the first time to map the distribution of stain in a fixed biological sample through its…
Background and Objective: The contrast of cryo-EM images varies from one to another, primarily due to the uneven thickness of the ice layer. This contrast variation can affect the quality of 2-D class averaging, 3-D ab-initio modeling, and…
With the development of low order scaling methods for performing Kohn-Sham Density Functional Theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an…
Structured illumination microscopy (SIM) is a very important super-resolution microscopy technique, which provides high speed super-resolution with about two-fold spatial resolution enhancement. Several attempts aimed at improving the…
Electrical impedance tomography is an imaging modality for extracting information on the conductivity distribution inside a physical body from boundary measurements of current and voltage. In many practical applications, it is a priori…
Modern technology for producing extremely bright and coherent X-ray laser pulses provides the possibility to acquire a large number of diffraction patterns from individual biological nanoparticles, including proteins, viruses, and DNA.…
We consider the imaging problem of the reconstruction of a three-dimensional object via optical diffraction tomography under the assumptions of the Born approximation. Our focus lies in the situation that a rigid object performs an…
High-resolution structure determination by cryo-electron microscopy (cryo-EM) requires the accurate fitting of an atomic model into an experimental density map. Traditional refinement pipelines such as Phenix.real_space_refine and Rosetta…
We present an end-to-end reconstruction algorithm to build particle candidates from detector hits in next-generation granular calorimeters similar to that foreseen for the high-luminosity upgrade of the CMS detector. The algorithm exploits…