Related papers: Initiating Heavy-atom Based Phasing by Multi-Dimen…

Non--Contact Atomic Force Microscopy with CO--functionalized metal tips (referred to as HR-AFM) provides access to the internal structure of individual molecules adsorbed on a surface with totally unprecedented resolution. Previous works…

Atomic force microscopy (AFM) with molecule-functionalized tips has emerged as the primary experimental technique for probing the atomic structure of organic molecules on surfaces. Most experiments have been limited to nearly planar…

Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule's reactivity to different probes is quantified at single-nucleotide resolution and used to constrain structural modeling. This…

The paper investigates the problem of fitting protein complexes into electron density maps. They are represented by high-resolution cryoEM density maps converted into overlapping matrices and partly show a structure of a complex. The…

Successful scientific applications of large-scale molecular dynamics often rely on automated methods for identifying the local crystalline structure of condensed phases. Many existing methods for structural identification, such as Common…

One of the great challenges of modern science is to faithfully model, and understand, matter at a wide range of scales. Starting with atoms, the vastness of the space of possible configurations poses a formidable challenge to any simulation…

Protein structure determination has long been one of the primary challenges of structural biology, to which deep machine learning (ML)-based approaches have increasingly been applied. However, these ML models generally do not incorporate…

Multi-technique high resolution X-ray mapping enhanced by the recent advent of 4th generation synchrotron facilities can produce colossal datasets, challenging traditional analysis methods. Such difficulty is clearly materialized when…

We present a novel, physically-based morphing technique for elastic shapes, leveraging the differentiable material point method (MPM) with space-time control through per-particle deformation gradients to accommodate complex topology…

The limits of molecular dynamics (MD) simulations of macromolecules are steadily pushed forward by the relentless developments of computer architectures and algorithms. This explosion in the number and extent (in size and time) of MD…

Building on top of our recent work [arXiv:2502.08511], we introduce a new strategy to solve the problem of detecting atoms in high-resolution images of microtrap arrays. By alternating estimation and detection steps, we get rid of the need…

Utilizing the Pauli equation based multislice method, introduced in Phys. Rev. Lett. 116, 127203 (2016), we study the atomic resolution differential phase contrast (DPC) imaging on an example of a hard magnet FePt with in-plane…

Nuclear magnetic resonance (NMR) spectroscopy is one of the leading techniques for protein studies. The method features a number of properties, allowing to explain macromolecular interactions mechanistically and resolve structures with…

Iterative phase retrieval algorithms typically employ projections onto constraint subspaces to recover the unknown phases in the Fourier transform of an image, or, in the case of x-ray crystallography, the electron density of a molecule.…

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…

We propose differential phase contrast (DPC) imaging using energy-filtered electrons to image the magnetic properties of materials at the atomic scale. Compared to DPC measurements with elastic electrons, our simulations predict about two…

A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central alpha-carbon coordinates. We employ advances in virtual reality to address the problem. The…

Searches for new physics typically rely on proton-proton collisions, where isolated mass bumps are the primary signatures. However, when a new particle is nearly degenerate in mass with a known Standard Model resonance, it can be partially…

The prediction of energetically stable crystal structures formed by a given chemical composition is a central problem in solid-state physics. In principle, the crystalline state of assembled atoms can be determined by optimizing the energy…

High harmonic generation in the interaction of femtosecond lasers with atoms and molecules opens the path to molecular orbital tomography and to probe the electronic dynamics with attosecond-{\AA}ngstr\"{o}m resolutions. Molecular orbital…