Related papers: Mapping the conformations of biological assemblies
Single-particle electron cryomicroscopy (cryo-EM) is an increasingly popular technique for elucidating the three-dimensional structure of proteins and other biologically significant complexes at near-atomic resolution. It is an imaging…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Super-resolution microscopy, or nanoscopy, enables the use of fluorescent-based molecular localization tools to study molecular structure at the nanoscale level in the intact cell, bridging the mesoscale gap to classical structural biology…
Computer models are commonly used to represent a wide range of real systems, but they often involve some unknown parameters. Estimating the parameters by collecting physical data becomes essential in many scientific fields, ranging from…
Imaging individual conformational instances of generic, inhomogeneous, transient or intrinsically disordered protein systems at the single molecule level in situ is one of the notable challenges in structural biology. Present techniques…
Numerical investigation of the interaction of electromagnetic fields with eukaryotic cells requires specifically adapted computer models. Virtual microdosimetry, used to investigate exposure, requires volumetric cell models, which are…
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…
Whole-cell computational models aim to predict cellular phenotypes from genotype by representing the entire genome, the structure and concentration of each molecular species, each molecular interaction, and the extracellular environment.…
Experiments have reached a monumental capacity for designing and synthesizing microscopic particles for self-assembly, making it possible to precisely control particle concentrations, shapes, and interactions. However, more physical insight…
Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph…
Recent advances in propagation-based phase-contrast imaging, such as hierarchical imaging, have enabled the visualization of internal structures in large biological specimens and material samples. However, modulation-based techniques, which…
Single fluorescent molecules, behaving as ideal electric dipole emitters, are powerful nanoscopic probes of complex optical fields. Here, this property is exploited to precisely map the polarization and vectorial structure of tightly…
Many living and non-living complex systems can be modeled and understood as collective systems made of heterogeneous components that self-organize and generate nontrivial morphological structures and behaviors. This chapter presents a brief…
Given the crucial role of microtubules for cell survival, many researchers have found success using microtubule-targeting agents in the search for effective cancer therapeutics. Understanding microtubule responses to targeted interventions…
Assessing the convergence of a biomolecular simulation is an essential part of any computational investigation. This is because many important quantities (e.g., free energy differences) depend on the relative populations of different…
Nowadays, the amount of heterogeneous biomedical data is increasing more and more thanks to novel sensing techniques and high-throughput technologies. In reference to biomedical image analysis, the advances in image acquisition modalities…
Characterization of microstructures in live tissues is one of the keys to diagnosing early stages of pathology and understanding disease mechanisms. However, the extraction of reliable information on biomarkers based on microstructure…
The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, where a whole macromolecule is represented by a small number of particles, can be of…
Single particle cryo-electron microscopy has become a critical tool in structural biology over the last decade, able to achieve atomic scale resolution in three dimensional models from hundreds of thousands of (noisy) two-dimensional…