Related papers: Mapping the conformations of biological assemblies
It is well-known that the architecture of macromolecules plays an important role in the hydrodynamics and viscosity of its semi-diluted solutions. However, the systematic study of the rheology of macromolecules with complex topology, such…
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…
Accurate physical modeling with 3D-printing techniques could lead to new approaches to study structure and dynamics of biological systems complementing computational methods. Computational biology has become an important part of research…
Classifying structural variability in noisy projections of biological macromolecules is a central problem in Cryo-EM. In this work, we build on a previous method for estimating the covariance matrix of the three-dimensional structure…
A combinatorial model of molecular conformational space that was previously developped (J. Gabarro-Arpa, Comp. Biol. and Chem. 27, (2003) 153-159), had the drawback that structures could not be properly embedded beacause it lacked explicit…
Examining individual components of cellular systems has been successful in uncovering molecular reactions and interactions. However, the challenge lies in integrating these components into a comprehensive system-scale map. This difficulty…
Knowing a biomolecule's structure is inherently linked to and a prerequisite for any detailed understanding of its function. Significant effort has gone into developing technologies for structural characterization. These technologies do not…
Molecular assembly offers a promising path to detect life beyond Earth, while minimizing assumptions based on terrestrial life. As mass spectrometers will be central to upcoming Solar System missions, predicting molecular assembly from…
The exploration of planetary bodies in our Solar system and beyond relies on the processing and interpretation of large, spatio-temporally inconsistent, and heterogeneous datasets. Recent advances in machine learning (ML) provide…
Finite elements of higher continuity, say conforming in $H^2$ instead of $H^1$, require a mapping from reference cells to mesh cells which is continuously differentiable across cell interfaces. In this article, we propose an algorithm to…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…
X-ray microtomography at synchrotron sources is fundamentally limited by the high radiation dose applied to the samples, which restricts investigations to non-native tissue states and thereby compromises the biological relevance of the…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
At present it is still quite difficult to match the vast knowledge on the behavior of individual tumor cells with macroscopic measurements on clinical tumors. On the modeling side, we already know how to deal with many molecular pathways…
Cells segmentation shows rapid growth in biology. Indeed, using the classical segmentation methods only is not enough to segment this type of images. In this manuscript, we will present a new method of ribosomes segmentation. A…
Electromagnetic fields with complex spatial variation routinely arise in Nature. We study the response of a small molecule to monochromatic fields of arbitrary three-dimensional geometry. First, we consider the allowed configurations of the…
The classical method of determining the atomic structure of complex molecules by analyzing diffraction patterns is currently undergoing drastic developments. Modern techniques for producing extremely bright and coherent X-ray lasers allow a…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
Tracking of plant cells in images obtained by microscope is a challenging problem due to biological phenomena such as large number of cells, non-uniform growth of different layers of the tightly packed plant cells and cell division.…