Related papers: Towards better structural models from cryo-electro…

Cryo-electron microscopy (cryo-EM) has become a tool of fundamental importance in structural biology, helping us understand the basic building blocks of life. The algorithmic challenge of cryo-EM is to jointly estimate the unknown 3D poses…

Linear-scaling electronic structure methods based on the calculation of moments of the underlying electronic Hamiltonian offer a computationally efficient and numerically robust scheme to drive large-scale atomistic simulations, in which…

EBSD has evolved into an effective tool for microstructure investigations in the scanning electron microscope. The purpose of this contribution is to give an overview of various simulation approaches for EBSD Kikuchi patterns and to discuss…

We propose a new microscopy simulation system that can depict atomistic models in a micrograph visual style, similar to results of physical electron microscopy imaging. This system is scalable, able to represent simulation of electron…

Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…

We implement and benchmark the frozen core approximation, a technique commonly adopted in electronic structure theory to reduce the computational cost by means of mathematically fixing the chemically inactive core electron states. The…

Exploration of structure-property relationships as a function of dopant concentration is commonly based on mean field theories for solid solutions. However, such theories that work well for semiconductors tend to fail in materials with…

Three-dimensional reconstruction of atomic structure, known as atomic electron tomography (AET), has found increasing applications in materials science. The AET has been limited to very small nanoparticles due to the challenges of obtaining…

An overview of quantum-mechanical methods to generate cross-section data for electron collisions with atoms and molecules is presented. Particular emphasis is placed on the time-independent close-coupling approach, since it is particularly…

Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…

We present a (proto) Foundation Model for Nuclear Physics, capable of operating on low-level detector inputs from Imaging Cherenkov Detectors at the future Electron Ion Collider. Building upon established next-token prediction approaches,…

Solid state theory, density functional theory and its generalizations for correlated systems together with numerical simulations on supercomputers allow nowadays to model magnetic systems realistically and in detail and can be even used to…

In recent years impressive progress has been made in the development of highly accurate energy density functionals, which allow to treat medium-heavy nuclei. In this approach one tries to describe not only the ground state but also the…

Cryo-electron microscopy (cryo-EM) has recently emerged as a powerful tool for obtaining three-dimensional (3D) structures of biological macromolecules in native states. A minimum cryo-EM image data set for deriving a meaningful…

Understanding protein flexibility and its dynamic interactions with other molecules is essential for studying protein function. Although cryogenic electron microscopy(cryo-EM) provides an opportunity to observe macromolecular dynamics…

A large collaboration carefully benchmarks 20 first principles many-body electronic structure methods on a test set of 7 transition metal atoms, and their ions and monoxides. Good agreement is attained between the 3 systematically converged…

Molecular structure is often considered as emerging from the decoherence effect of the environment. Electrons are part of the environment of the nuclei in a molecule. In this work, their contribution to the classical-like geometrical…

When the dynamics of a quantum system of interest is known, an informationally-complete set of observables is not needed for state reconstruction via tomographic techniques: letting the system evolve before performing the measurement allows…

Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based x-ray crystallography and…

In cryo-electron microscopy (EM), molecular structures are determined from large numbers of projection images of individual particles. To harness the full power of this single-molecule information, we use the Bayesian inference of EM…