Related papers: Improving the resolution of Cryo-EM single particl…
Cryo-electron microscopy (cryo-EM) is an imaging modality that provides unique insights into the dynamics of proteins and other building blocks of life. The algorithmic challenge of jointly estimating the poses, 3D structure, and…
In this paper we study the formal algebraic structure underlying the intrinsic classification algorithm, recently introduced by Hadani, Shkolnisky, Singer and Zhao, for classifying noisy projection images of similar viewing directions in…
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…
We present a finite element analysis of electrical impedance tomography for reconstructing the conductivity distribution from electrode voltage measurements by means of Tikhonov regularization. Two popular choices of the penalty term, i.e.,…
Single particle reconstruction has recently emerged in 3D fluorescence microscopy as a powerful technique to improve the axial resolution and the degree of fluorescent labeling. It is based on the reconstruction of an average volume of a…
Cryo-EM reconstruction algorithms seek to determine a molecule's 3D density map from a series of noisy, unlabeled 2D projection images captured with an electron microscope. Although reconstruction algorithms typically model the 3D volume as…
Cryogenic electron microscopy (Cryo-EM) has become an essential tool for capturing high-resolution biological structures. Despite its advantage in visualizations, the large storage size of Cryo-EM data file poses significant challenges for…
The cryo-electron microscope (cryo-EM) is increasingly popular these years. It helps to uncover the biological structures and functions of macromolecules. In this paper, we address image denoising problem in cryo-EM. Denoising the cryo-EM…
Motivated by problems where the response is needed at select localized regions in a large computational domain, we devise a novel finite element discretization that results in exponential convergence at pre-selected points. The two key…
Cellular Electron Cryo-Tomography (CECT) is a powerful imaging technique for the 3D visualization of cellular structure and organization at submolecular resolution. It enables analyzing the native structures of macromolecular complexes and…
Cryo-EM is a vital technique for determining 3D structure of biological molecules such as proteins and viruses. The cryo-EM reconstruction problem is challenging due to the high noise levels, the missing poses of particles, and the…
Density matrix embedding theory (DMET) is a powerful quantum embedding method for solving strongly correlated quantum systems. Theoretically, the performance of a quantum embedding method should be limited by the computational cost of the…
An exact arithmetic, memory efficient direct solution method for finite element method (FEM) computations is outlined. Unlike conventional black-box or low-rank direct solvers that are opaque to the underlying physical problem, the proposed…
In this paper, we demonstrate a computationally efficient new approach based on deep learning (DL) techniques for analysis, design, and optimization of electromagnetic (EM) nanostructures. We use the strong correlation among features of a…
This paper introduces an accurate edge-based smoothed finite element method (ES-FEM) for electromagnetic analysis for both two dimensional cylindrical and three dimensional cartesian systems, which shows much better performance in terms of…
Proteins typically undergo conformational dynamics on the microsecond to millisecond timescale as they perform their function, which is much faster than the time-resolution of cryo-electron microscopy and has thus prevented real-time…
This work presents a practical finite element modeling strategy, the Crack Element Method (CEM), for simulating the dynamic crack propagation in two-dimensional structures. The method employs an element-splitting algorithm based on the…
A major challenge in single particle reconstruction methods using cryo-electron microscopy is to attain a resolution sufficient to interpret fine details in three-dimensional (3D) macromolecular structures. Obtaining high resolution 3D…
To solve boundary integral equations for potential problems using collocation Boundary Element Method (BEM) on smooth curved 3D geometries, an analytical singularity extraction technique is employed. By adopting the isoparametric approach,…
This paper presents a novel method for fully automatic and convenient extrinsic calibration of a 3D LiDAR and a panoramic camera with a normally printed chessboard. The proposed method is based on the 3D corner estimation of the chessboard…