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Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their…
Important recent advances in transmission electron microscopy instrumentation and capabilities have made it indispensable for atomic-scale materials characterization. At the same time, the availability of two-dimensional materials has…
Molecular-level understanding of the interactions between the constituents of an atomic structure is essential for designing novel materials in various applications. This need goes beyond the basic knowledge of the number and types of…
Investigating nanoplasmonics using time-dependent approaches permits shedding light on the dynamic optical properties of plasmonic structures, which are intrinsically connected with their potential applications in photochemistry and…
Atomic resolution imaging in transmission electron microscopy (TEM) and scanning TEM (STEM) of light elements in electron-transparent materials has long been a challenge. Biomolecular materials, for example, are rapidly altered when…
Three-dimensional electron diffraction (3D ED) has emerged as a powerful method for solving the structures of sub-micron-sized particles down to nanoparticles. However, it faces technical challenges when applied to beam-sensitive samples or…
In this paper, we address the challenge of obtaining a comprehensive and symmetric representation of point particle groups, such as atoms in a molecule, which is crucial in physics and theoretical chemistry. The problem has become even more…
Cryo-electron tomography (cryo-ET) enables in situ visualization of macromolecular structures, where subtomogram analysis tasks such as classification, alignment, and averaging are critical for structural determination. However, effective…
Atom probe tomography (APT) fills a crucial need in the characterization workflow of materials by its ability to inform the 3D chemical microstructure at the nanoscale. As with any characterization techniques, APT has strengths and…
The optical cross sections of plasmonic nanoparticles are intricately linked to the morphology of the particle. If this connection can be made accurately enough, it would become possible to determine a particles shape solely from its…
Doping impurity atoms is a strategy commonly used to tune the functionality of materials including catalysts, semiconductors, and quantum emitters. The location of dopants and their interaction with surrounding atoms could significantly…
We report on a new algorithm for detection of crystallographic information in 3D, as retained in Atom Probe Tomography (APT), with improved robustness and signal detection performance. The algorithm is underpinned by 1D distribution…
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…
We present a novel approach for extracting 3D atomic-level information from transmission electron microscopy (TEM) images affected by significant noise. The approach is based on formulating depth estimation as a semantic segmentation…
Photoemission orbital tomography provides direct access from laboratory measurements to the real-space molecular orbitals of well-ordered organic semiconductor layers. Specifically, the application of phase retrieval algorithms to…
Data-driven machine learning methods have the potential to dramatically accelerate the rate of materials design over conventional human-guided approaches. These methods would help identify or, in the case of generative models, even create…
Scanning transmission electron microscopy (STEM) has advanced rapidly in the last decade thanks to the ability to correct the major aberrations of the probe forming lens. Now atomic-sized beams are routine, even at accelerating voltages as…
Computed tomography is a method for synthesizing volumetric or cross-sectional images of an object from a collection of projections. Popular reconstruction methods for computed tomography are based on idealized models and assumptions that…
A direct three dimensional EIT reconstruction algorithm based on complex geometrical optics solutions and a nonlinear scattering transform is presented and implemented for spherically symmetric conductivity distributions. The scattering…
The shape of a molecule determines its physicochemical and biological properties. However, it is often underrepresented in standard molecular representation learning approaches. Here, we propose using the Euler Characteristic Transform…