Related papers: Atomic Force Microscopy Simulations for CO-functio…
The rapid advancement of deep learning has facilitated the automated processing of electron microscopy (EM) big data stacks. However, designing a framework that eliminates manual labeling and adapts to domain gaps remains challenging.…
Training robust deep learning (DL) systems for medical image classification or segmentation is challenging due to limited images covering different disease types and severity. We propose an active learning (AL) framework to select most…
Atomic force microscope (AFM) generally works on the basis of manipulating absolute magnitude of van der Waals (vdW) force between the tip and specimen. The force is, however, less sensitive to alternation of atom species than to tip-sample…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
AI-based in silico methods have improved protein structure prediction but often struggle with large protein complexes (PCs) involving multiple interacting proteins due to missing 3D spatial cues. Experimental techniques like Cryo-EM are…
Simulations at the atomic scale provide a direct and effective way to understand the mechanical properties of materials. In the regime of classical mechanics, simulations for the thermodynamic properties of metals and alloys can be done by…
Atomistic modeling of thin-film processes provides an avenue not only for discovering key chemical mechanisms of the processes but also to extract quantitative metrics on the events and reactions taking place at the gas-surface interface.…
A numerical analysis of the origin of the atomic-scale contrast in Kelvin probe force microscopy (KPFM) is presented. Atomistic simulations of the tip-sample interaction force field have been combined with a non-contact Atomic Force…
We present imaging and force spectroscopy measurements of DNA molecules adsorbed on functionalized mica. By means of Non-Contact mode AFM (NC-AFM) in Ultra High Vacuum (UHV), the frequency shift (\Delta f) versus separation (z) curves were…
Coarse-grained (CG) molecular simulations have become a standard tool to study molecular processes on time- and length-scales inaccessible to all-atom simulations. Parameterizing CG force fields to match all-atom simulations has mainly…
Electromagnetic (EM) metasurfaces can present a versatile platform for realization of multiple diverse EM functionalities with incident wave frequency, polarization, propagation direction, or power intensity through appropriate choice of…
Molecular dynamics (MD) simulates the time evolution of atomic systems governed by interatomic forces, and the fidelity of these simulations depends critically on the underlying force model. Classical force fields (CFFs) rely on fixed…
We propose a non-collinear spin-constrained method that generates training data for deep-learning-based magnetic model, which provides a powerful tool for studying complex magnetic phenomena that requires large-scale simulations at the…
Milli-Kelvin atomic force microscopy (mK-AFM) presents an ongoing experimental challenge due to the intense vibrations in a cryogen-free dilution refrigerator and the low cooling power available at mK temperatures. A viable approach is to…
Scattering scanning near-field optical microscopy (s-SNOM) is a promising technique for overcoming Abbe diffraction limit and substantially enhancing the spatial resolution in spectroscopic imaging. The s-SNOM works by exposing an atomic…
We present the design and experimental results of a near-field scanning microwave microscope (NSMM) working at a frequency of 1GHz. Our microscope is unique in that the sensing probe is separated from the excitation electrode to…
Atomic Force Microscopy (AFM) enables high-resolution surface imaging at the nanoscale, yet the output is often degraded by artifacts introduced by environmental noise, scanning imperfections, and tip-sample interactions. To address this…
In this article, we present a deflection measurement setup for Atomic Force Microscopy (AFM). It is based on a quadrature phase differential interferometer: we measure the optical path difference between a laser beam reflecting above the…
Molecular dynamics (MD) simulations are essential for studying complex molecular systems, but their high computational cost limits scalability. Coarse-grained (CG) models reduce this cost by simplifying the system, yet traditional…