Related papers: Ensemble reweighting using Cryo-EM particles

The sparse interferometric coverage of the Event Horizon Telescope (EHT) poses a significant challenge for both reconstruction and model fitting of black-hole images. PRIMO is a new principal components analysis-based algorithm for image…

In this thesis, a computational framework for microstructural modelling of transverse behaviour of heterogeneous materials is presented. The context of this research is part of the broad and active field of Computational Micromechanics,…

Multi-reference alignment (MRA) is the problem of recovering a signal from its multiple noisy copies, each acted upon by a random group element. MRA is mainly motivated by single-particle cryo-electron microscopy (cryo-EM) that has recently…

We give a mathematical framework for weighted ensemble (WE) sampling, a binning and resampling technique for efficiently computing probabilities in molecular dynamics. We prove that WE sampling is unbiased in a very general setting that…

Simulation-based inference provides a powerful framework for cryo-electron microscopy, employing neural networks in methods like CryoSBI to infer biomolecular conformations via learned latent representations. This latent space represents a…

Finite mixture models have been widely used for the modelling and analysis of data from heterogeneous populations. Maximum likelihood estimation of the parameters is typically carried out via the Expectation-Maximization (EM) algorithm. The…

Disordered proteins play essential roles in myriad cellular processes, yet their structural characterization remains a major challenge due to their dynamic and heterogeneous nature. We here present a community-driven initiative to address…

There is a growing interest in reconstructing the density matrix of photoelectron wavepackets, in particular in complex systems where decoherence can be introduced either by a partial measurement of the system or through coupling with a…

Electron cryo-tomography (cryo-ET) enables 3D imaging of complex, radiation-sensitive structures with molecular detail. However, image contrast from the interference of scattered electrons is nonlinear with atomic density and multiple…

In a mixture of linear regression model, the regression coefficients are treated as random vectors that may follow either a continuous or discrete distribution. We propose two Expectation-Maximization (EM) algorithms to estimate this prior…

Single particle reconstruction (SPR) from cryo-electron microscopy (EM) is a technique in which the 3D structure of a molecule needs to be determined from its contrast transfer function (CTF) affected, noisy 2D projection images taken at…

In this report, we applied expectation and maximization (EM) method described by Philips et al [1] to recover two-dimensional (2D) structure from multiple sparse signal images in random orientation. The detailed derivation of EM algorithm…

The single-particle cryo-EM field faces the persistent challenge of preferred orientation, lacking general computational solutions. We introduce cryoPROS, an AI-based approach designed to address the above issue. By generating the auxiliary…

Throughout the history of electron microscopy, ribosomes have served as an ideal subject for imaging and technological development, which in turn has driven our understanding of ribosomal biology. Here, we provide a historical perspective…

Accurate exploration of protein conformational ensembles is essential for uncovering function but remains hard because molecular-dynamics (MD) simulations suffer from high computational costs and energy-barrier trapping. This paper presents…

In the paper [Angelini M C, Parisi G, and Ricci-Tersenghi F, Ensemble renormalization group for disordered systems, Phys. Rev. B 87 134201 (2013)] we introduced a real-space renormalization group called Ensemble Renormalization Group (ERG)…

Electron microscopy has enabled many scientific breakthroughs across multiple fields. A key challenge is the tuning of microscope parameters based on images to overcome optical aberrations that deteriorate image quality. This calibration…

Electrocardiogram (ECG) analysis plays a vital role in the early detection, monitoring, and management of various cardiovascular conditions. While existing models have achieved notable success in ECG interpretation, they fail to leverage…

Conventional simulations of complex systems in the canonical ensemble suffer from the quasi-ergodicity problem. A simulation in generalized ensemble overcomes this difficulty by performing a random walk in potential energy space and other…

We present initial results on the use of Mixture Models for density estimation in large astronomical databases. We provide herein both the theoretical and experimental background for using a mixture model of Gaussians based on the…