Related papers: Tracing and segmentation of molecular patterns in …
The phase behavior of charged rods in the presence of inter-rod linkers is studied theoretically as a model for the equilibrium behavior underlying the organization of actin filaments by linker proteins in the cytoskeleton. The presence of…
Thread-like structures are pervasive across scales, from polymeric proteins to root systems to galaxy filaments, and their characteristics can be readily investigated in the network formalism. Yet, network links usually represent only parts…
Cryo-electron microscopy (cryo-EM), the subject of the 2017 Nobel Prize in Chemistry, is a technology for determining the 3-D structure of macromolecules from many noisy 2-D projections of instances of these macromolecules, whose…
Cellular Electron Cryotomography (CryoET) offers the ability to look inside cells and observe macromolecules frozen in action. A primary challenge for this technique is identifying and extracting the molecular components within the crowded…
In recent years, an abundance of new molecular structures have been elucidated using cryo-electron microscopy (cryo-EM), largely due to advances in hardware technology and data processing techniques. Owing to these new exciting…
Computed tomography (CT) can capture volumes large enough to measure a statistically meaningful number of micron-sized particles with a sufficiently good resolution to allow for the analysis of individual particles. However, the development…
We develop a formalism to describe the equilibrium distributions for segments of confined branched networks consisting of stiff filaments. This is applicable to certain situations of cytoskeleton in cells, such as for example actin…
The current neuron reconstruction pipeline for electron microscopy (EM) data usually includes automatic image segmentation followed by extensive human expert proofreading. In this work, we aim to reduce human workload by predicting…
Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles. Remarkably, analogous high-dimensional, highly-interconnected computational architectures also…
Cryo-electron microscopy (cryo-EM) has become a major experimental technique to determine the structures of large protein complexes and molecular assemblies, as evidenced by the 2017 Nobel Prize. Although cryo-EM has been drastically…
Transmission electron microscopy (TEM) is a potent technique for the determination of three-dimensional atomic scale structure of samples in structural biology and materials science. In structural biology, three-dimensional structures of…
Cell adhesion, a fundamental process of cell biology is involved in the embryo development and in numerous pathologies especially those related to cancers. We constrained cells to adhere on extracellular matrix proteins patterned in a micro…
Cryogenic electron microscopy (cryo-EM) has transformed structural biology by allowing to reconstruct 3D biomolecular structures up to near-atomic resolution. However, the 3D reconstruction process remains challenging, as the 3D structures…
Understanding the three-dimensional (3D) structure of the genome is essential for elucidating vital biological processes and their links to human disease. To determine how the genome folds within the nucleus, chromosome conformation capture…
A reliable extraction of filament data from microscopic images is of high interest in the analysis of acto-myosin structures as early morphological markers in mechanically guided differentiation of human mesenchymal stem cells and the…
We propose a 3D convolutional neural network to simultaneously segment and detect cell nuclei in confocal microscopy images. Mirroring the co-dependency of these tasks, our proposed model consists of two serial components: the first part…
The actin cytoskeleton is remarkably adaptable and multifunctional. It often organizes into nematic bundles such as contractile rings or stress fibers. However, how a uniform and isotropic actin gel self-organizes into dense nematic bundles…
Mechanochemical simulations of actomyosin networks are traditionally based on one-dimensional models of actin filaments having zero width. Here, and in the follow up paper, approaches are presented for more efficient modelling which…
The adatom arrays on surfaces offer an ideal playground to explore the mechanisms of chemical bonding via changes in the local electronic tunneling spectra. While this information is readily available in hyperspectral scanning tunneling…
A systematic analysis of the cell behavior requires automated approaches for cell segmentation and tracking. While deep learning has been successfully applied for the task of cell segmentation, there are few approaches for simultaneous cell…