Related papers: Towards better structural models from cryo-electro…
Cryo-electron microscopy (cryo-EM) enables single-particle analysis of biological macromolecules under strict low-dose imaging conditions, but the resulting micrographs often exhibit extremely low signal-to-noise ratios and weak particle…
A single-particle cryo-electron microscopy (cryo-EM) measurement, called a micrograph, consists of multiple two-dimensional tomographic projections of a three-dimensional (3-D) molecular structure at unknown locations, taken under unknown…
Electronic structure methods offer in principle accurate predictions of molecular properties, however, their applicability is limited by computational costs. Empirical methods are cheaper, but come with inherent approximations and are…
We have applied the Finite Element Method to the self-consistent electronic structure calculations of molecules and solids for the first time. In this approach all the calculations are performed in "real space" and the use of non-uniform…
The goal of cryo-electron microscopy (EM) is to reconstruct the 3-dimensional structure of a molecule from a collection of its 2-dimensional projected images. In this article, we show that the basic premise of cryo-EM --- patching together…
New techniques for imaging electromagnetic near-fields in nanostructures drive advancements in nanotechnology, optoelectronics, materials science, and biochemistry. Most existing techniques probe near-fields along surfaces, lacking the…
Cryo-electron tomography (cryoET) is a technique that captures images of biological samples at different tilts, preserving their native state as much as possible. Along with the partial tilt series and noise, one of the major challenges in…
Image acquisition techniques such as micro-computed tomography are nowadays widely available. Quantitative analysis of the resulting 3D image data enables geometric characterization of the micro-structure of materials. Stochastic geometry…
Modeling of physical systems includes extensive use of software packages that implement the accurate finite element method for solving differential equations considered along with the appropriate initial and boundary conditions. When the…
Determining the three-dimensional structure of proteins and protein complexes at atomic resolution is a fundamental task in structural biology. Over the last decade, remarkable progress has been made using "single particle" cryo-electron…
It is important to accurately model materials' properties at lower length scales (micro-level) while translating the effects to the components and/or system level (macro-level) can significantly reduce the amount of experimentation required…
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…
The theorems of density functional theory (DFT) and reduced density matrix functional theory (RDMFT) establish a bijective map between the external potential of a many-body system and its electron density or one-particle reduced density…
We consider the problem of recovering the three-dimensional atomic structure of a flexible macromolecule from a heterogeneous cryo-EM dataset. The dataset contains noisy tomographic projections of the electrostatic potential of the…
Recent advances in Foundation Models for Materials Science are poised to revolutionize the discovery, manufacture, and design of novel materials with tailored properties and responses. Although great strides have been made, successes have…
Accurate determination of three-dimensional (3D) atomic structures is crucial for understanding and controlling the properties of nanomaterials. Atomic electron tomography (AET) offers non-destructive atomic imaging with picometer-level…
This review article provides an overview of structurally oriented experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature…
The first step in the construction of a regression model or a data-driven analysis, aiming to predict or elucidate the relationship between the atomic scale structure of matter and its properties, involves transforming the Cartesian…
While offering unprecedented resolution of atomic and electronic structure, Scanning Probe Microscopy techniques have found greater challenges in providing reliable electrostatic characterization at the same scale. In this work, we…
Nowadays, most structural integrity concepts rely on simplified isotropic ma-terial data that are used within continuum mechanics modeling approaches. In contrast, modern casting and forming processes yield complex microstruc-tures coming…