Related papers: Improving the resolution of Cryo-EM single particl…
Cryo-electron tomography (cryo-ET) has emerged as a powerful technique for imaging macromolecular complexes in their near-native states. However, the localization of 3D particles in cellular environments still presents a significant…
Recent interest in structure solution and refinement using electron diffraction (ED) has been fuelled by its inherent advantages when applied to crystals of sub-micron size, as well as a better sensitivity to light elements. Currently, data…
The number of noisy images required for molecular reconstruction in single-particle cryo-electron microscopy (cryo-EM) is governed by the autocorrelations of the observed, randomly-oriented, noisy projection images. In this work, we…
Cryogenic Electron Tomography (CryoET) combined with sub-volume averaging (SVA) is the only imaging modality capable of resolving protein structures inside cells at molecular resolution. Particle picking, the task of localizing and…
Cryo-electron tomography (cryo-ET) is an imaging technique that allows three-dimensional visualization of macro-molecular assemblies under near-native conditions. Cryo-ET comes with a number of challenges, mainly low signal-to-noise and…
We implement and benchmark the frozen core approximation, a technique commonly adopted in electronic structure theory to reduce the computational cost by means of mathematically fixing the chemically inactive core electron states. The…
The determination of molecular orientations is crucial for the three-dimensional reconstruction of Cryo-EM images. Traditionally addressed using the common-line method, this challenge is reformulated as a self-consistency error minimization…
Cryo-electron microscopy (cryo-EM) has revolutionized experimental protein structure determination. Despite advances in high resolution reconstruction, a majority of cryo-EM experiments provide either a single state of the studied…
We present a new sink particle algorithm developed for the Adaptive Mesh Refinement code RAMSES. Our main addition is the use of a clump finder to identify density peaks and their associated regions (the peak patches). This allows us to…
The vitrification of aqueous solutions through rapid cooling is a remarkable achievement that launched the field of cryo-electron microscopy (cryo-EM) and has enabled the cryopreservation of biological specimens. For judging the feasibility…
In the present work we introduce a novel refinement algorithm for two-dimensional elliptic partial differential equations discretized with Virtual Element Method (VEM). The algorithm improves the numerical solution accuracy and the mesh…
The scanning electron microscope (SEM) produces an image of a sample by scanning it with a focused beam of electrons. The electrons interact with the atoms in the sample, which emit secondary electrons that contain information about the…
Constructing atomic models from cryo-electron microscopy (cryo-EM) maps is a crucial yet intricate task in structural biology. While advancements in deep learning, such as convolutional neural networks (CNNs) and graph neural networks…
In this work, we present a study combining two approaches in the context of solving PDEs: the continuous finite element method (FEM) and more recent techniques based on neural networks. In recent years, physics-informed neural networks…
This paper presents novel methods for estimating certified radii in randomized smoothing, a technique crucial for certifying the robustness of neural networks against adversarial perturbations. Our proposed techniques significantly improve…
The maximum entropy method (MEM) is a well known deconvolution technique in radio-interferometry. This method solves a non-linear optimization problem with an entropy regularization term. Other heuristics such as CLEAN are faster but highly…
A simple method for improving cache efficiency of serial and parallel explicit finite procedure with application to casting solidification simulation over three-dimensional complex geometries is presented. The method is based on division of…
We introduce adaptive particle refinement for compressible smoothed particle hydrodynamics (SPH). SPH calculations have the natural advantage that resolution follows mass, but this is not always optimal. Our implementation allows the user…
We develop an iterative refinement method that improves the accuracy of a user-chosen subset of $k$ eigenvectors ($k\ll n$) of an $n\times n$ real symmetric matrix. Using an orthogonal matrix represented in compact WY form, the method…
We present a finite element method (FEM) solver for computation of optical resonance modes in VCSELs. We perform a convergence study and demonstrate that high accuracies for 3D setups can be attained on standard computers. We also…