Related papers: Towards better structural models from cryo-electro…
Programmable self-assembly has recently enabled the creation of complex structures through precise control of the interparticle interactions and the particle geometries. Targeting ever more structurally complex, dynamic, and functional…
Cryo-electron microscopy (cryo-EM) emerges as a pivotal technology for determining the architecture of cells, viruses, and protein assemblies at near-atomic resolution. Traditional particle picking, a key step in cryo-EM, struggles with…
The description of complex physical phenomena often involves sophisticated models that rely on a large number of parameters, with many dimensions and scales. One practical way to simplify that kind of models is to discard some of the…
Single particle cryo-electron microscopy is a vital tool for 3D characterization of protein structures. A typical workflow involves acquiring projection images of a collection of randomly oriented particles, picking and classifying…
Cryo-electron microscopy is a revolutionary technique that can provide 3D density maps at near-atomic resolution. However, map validation is still an open issue in the field. Despite several efforts from the community, it is possible to…
Biomolecular force fields have been traditionally derived based on a mixture of reference quantum chemistry data and experimental information obtained on small fragments. However, the possibility to run extensive molecular dynamics…
We present for static density functional theory and time-dependent density functional theory calculations an all-electron method which employs high-order hierarchical finite element bases. Our mesh generation scheme, in which structured…
Most modern calculations of many-electron atoms use basis sets of atomic orbitals. An accurate account for the electronic correlations in heavy atoms is very difficult computational problem and optimization of the basis sets can reduce…
In situ electron microscopy is a key tool for understanding the mechanisms driving novel phenomena in 2D structures. Unfortunately, due to various practical challenges, technologically relevant 2D heterostructures prove challenging to…
Computational modeling of a complex system is limited by the parts of the system with the least information. While detailed models and high-resolution data may be available for parts of a system, abstract relationships are often necessary…
The study of plasma physics under conditions of extreme temperatures, densities and electromagnetic field strengths is significant for our understanding of astrophysics, nuclear fusion and fundamental physics. These extreme physical systems…
Electron tomography has become a commonly used tool to investigate the three-dimensional (3D) structure of nanomaterials, including colloidal nanoparticle assemblies. However, electron microscopy is typically carried out under high vacuum…
Materials science inherently spans disciplines: experimentalists use advanced microscopy to uncover micro- and nanoscale structure, while theorists and computational scientists develop models that link processing, structure, and properties.…
Many tools and techniques measure local structure in materials in contexts ranging from biology to geology. We provide a survey of those tools and metrics that are especially useful for analyzing particulate soft matter. The metrics we…
Modern TEM instrumentation can probe a wide range of structural, optical, and chemical properties with unprecedented resolution. However, each of these properties must be recorded in independent datasets using different detector modes with…
Macroscopic elastic core-shell systems can be generated as toy models to be deformed and haptically studied by hand. On the mesoscale, colloidal core-shell particles and microgels are fabricated and investigated by different types of…
In this chapter we focus first on the theoretical methods and relevant computational approaches to calculate the electronic structure of atoms, molecules, and clusters containing heavy elements for which relativistic effects become…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
The electron density of a molecule or material has recently received major attention as a target quantity of machine-learning models. A natural choice to construct a model that yields transferable and linear-scaling predictions is to…
Atomic force microscopy (AFM) is a key tool for characterising nanoscale structures, with functionalised tips now offering detailed images of the atomic structure. In parallel, AFM simulations using the particle probe model provide a…