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Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…
The goal of cryo-electron microscopy (EM) is to reconstruct the 3-dimensional structure of a molecule from a collection of its 2-dimensional projected images. In this article, we show that the basic premise of cryo-EM --- patching together…
Single-particle cryo-Electron Microscopy (EM) has become a popular technique for determining the structure of challenging biomolecules that are inaccessible to other technologies. Recent advances in automation, both in data collection and…
Computational modelling offers a cost-effective and time-efficient alternative to experimental studies in biomedical engineering. In cardiac electro-mechanics, finite element method (FEM)-based simulations provide valuable insights into…
For structural health monitoring, continuous and automatic crack detection has been a challenging problem. This study is conducted to propose a framework of automatic crack segmentation from high-resolution images containing crack…
Cryogenic electron microscopy (cryo-EM) is an invaluable technique for determining high-resolution three-dimensional structures of biological macromolecules using transmission particle images. The inherent symmetry in these macromolecules…
Coupling between electrical and mechanical phenomena is a near-universal characteristic of inorganic and biological systems alike, with examples ranging from ferroelectric perovskites to electromotor proteins in cellular membranes.…
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…
Motivation: Structural heterogeneity in single-particle cryo-electron microscopy (cryo-EM) data represents a major challenge for high-resolution structure determination. Unsupervised classification may serve as the first step in the…
Cryogenic electron microscopy is widely used in structural biology, but its resolution is often limited by the dynamics of the macromolecule. Here, we developed a refinement protocol based on Gaussian mixture models that integrates particle…
The accurate and efficient prediction of crack propagation in dielectric materials is a critical challenge in structural health monitoring and the design of smart systems. This work presents a hybrid modeling framework that combines an…
Structural biology relies on accurate three-dimensional biomolecular structures to advance our understanding of biological functions, disease mechanisms, and therapeutics. While recent advances in deep learning have enabled the development…
Due to the extremely low signal-to-noise ratio (SNR) and unknown poses (projection angles and image shifts) in cryo-electron microscopy (cryo-EM) experiments, reconstructing 3D volumes from 2D images is very challenging. In addition to…
Structure-based protein design has attracted increasing interest, with numerous methods being introduced in recent years. However, a universally accepted method for evaluation has not been established, since the wet-lab validation can be…
Cryo-electron tomography (cryoET) is a technique that captures images of biological samples at different tilts, preserving their native state as much as possible. Along with the partial tilt series and noise, one of the major challenges in…
The implementation of natural and artificial proteins with designer properties and functionalities offers unparalleled opportunity for functional nanoarchitectures formed through self-assembly. However, to exploit the opportunities offered…
Structure determination is key to understanding protein function at a molecular level. Whilst significant advances have been made in predicting structure and function from amino acid sequence, researchers must still rely on expensive,…
Phase reconstruction is important in transmission electron microscopy for structural studies. We describe electron Fourier ptychography and its application to phase reconstruction of both radiation-resistant and beam-sensitive materials. We…
We propose a framework to jointly determine the deformation parameters and reconstruct the unknown volume in electron cryotomography (CryoET). CryoET aims to reconstruct three-dimensional biological samples from two-dimensional projections.…
Foundation models in computer vision have demonstrated exceptional performance in zero-shot and few-shot tasks by extracting multi-purpose features from large-scale datasets through self-supervised pre-training methods. However, these…