Related papers: Sparse approximations of protein structure from no…
Single molecule X-ray scattering experiments using free electron lasers hold the potential to resolve both single structures and structural ensembles of biomolecules. However, molecular electron density determination has so far not been…
Inverse imaging problems that are ill-posed can be encountered across multiple domains of science and technology, ranging from medical diagnosis to astronomical studies. To reconstruct images from incomplete and distorted data, it is…
Cryo-electron microscopy (cryo-EM) is a widely used technique for recovering the 3-D structure of biological molecules from a large number of experimentally generated noisy 2-D tomographic projection images of the 3-D structure, taken from…
Proteins move and deform to ensure their biological functions. Despite significant progress in protein structure prediction, approximating conformational ensembles at physiological conditions remains a fundamental open problem. This paper…
We consider the counting rate estimation of an unknown radioactive source, which emits photons at times modeled by an homogeneous Poisson process. A spectrometer converts the energy of incoming photons into electrical pulses, whose number…
Cryo-electron microscopy (cryo-EM) has achieved near-atomic level resolution of biomolecules by reconstructing 2D micrographs. However, the resolution and accuracy of the reconstructed particles are significantly reduced due to the…
Cryo-electron microscopy (cryo-EM) is an experimental technique for protein structure determination that images an ensemble of macromolecules in near-physiological contexts. While recent advances enable the reconstruction of dynamic…
The observations in many applications consist of counts of discrete events, such as photons hitting a detector, which cannot be effectively modeled using an additive bounded or Gaussian noise model, and instead require a Poisson noise…
Predicting the structure of a protein from its sequence is a cornerstone task of molecular biology. Established methods in the field, such as homology modeling and fragment assembly, appeared to have reached their limit. However, this year…
Single-shot wide-angle diffraction imaging is a widely used method to investigate the structure of non-crystallizing objects such as nanoclusters, large proteins or even viruses. Its main advantage is that information about the…
The protein backbone is described as a smooth curved and twisted line in three-dimensional (3D) space and characterized by its curvature $\kappa(s)$ and torsion $\tau(s)$ both expressed as a function of arc length s. It is shown that the…
Single particle electron cryomicroscopy (cryo-EM) allows for structures of proteins and protein complexes to be determined from images of non-crystalline specimens. Cryo-EM data analysis requires electron microscope images of randomly…
Proteins are dynamic, adopting ensembles of conformations. The nature of this conformational heterogenity is imprinted in the raw electron density measurements obtained from X-ray crystallography experiments. Fitting an ensemble of protein…
We propose a simple scheme to estimate potential energy surface (PES) with which the accuracy can be easily controlled and improved up to the level of the density functional theory (DFT) calculations. It is based on a model selection within…
We consider the problem of recovering the three-dimensional atomic structure of a flexible macromolecule from a heterogeneous cryo-EM dataset. The dataset contains noisy tomographic projections of the electrostatic potential of the…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
Achieving a comprehensive understanding of the behaviour of proteins is greatly facilitated by the knowledge of their structures, thermodynamics and dynamics. All this information can be provided in an effective manner in terms of…
Ultrafast diffraction imaging is a powerful tool to retrieve the geometric structure of gas-phase molecules with combined picometre spatial and attosecond temporal resolution. However, structural retrieval becomes progressively difficult…
Cryo-electron tomography (Cryo-ET) is a powerful tool in structural biology for 3D visualization of cells and biological systems at resolutions sufficient to identify individual proteins in situ. The measurements are collected by tilting…
A sparsity-exploiting algorithm intended for few-view Single Photon Emission Computed Tomography (SPECT) reconstruction is proposed and characterized. The algorithm models the object as piecewise constant subject to a blurring operation. To…