Related papers: Advancing Scanning Probe Microscopy Simulations: A…
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…
Universal machine-learned interatomic potentials (U-MLIPs) have demonstrated broad applicability across diverse atomistic systems but often require fine-tuning to achieve task-specific accuracy. While the number of available U-MLIPs and…
Near-field scanning optical microscopy has been an indispensable tool for designing, characterizing and understanding the functionalities of diverse nanoscale photonic devices. As the advances in fabrication technology have driven the…
We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with…
Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in…
Sub-nm resolution images can be achieved by Atomic Force Microscopy (AFM) on samples that are deposited on hard substrates. However, it is still extremely challenging to image soft interfaces, such as biological membranes, due to the…
Atomic Force Microscopy (AFM) allows to reconstruct the topography of surface with a resolution in the nanometer range. The exceptional resolution attainable with the AFM makes this instrument a key tool in nanoscience and technology. The…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
Scanning Kelvin probe microscopy (SKPM) is a powerful technique for investigating the electrostatic properties of material surfaces, enabling the imaging of variations in work function, topology, surface charge density, or combinations…
This book chapter reviews progress in crystallographic image processing (CIP) for scanning probe microscopy (SPM) that has occurred since our description of the technique was first put into open access in this book series in the year 2010.…
Progress in the atomic-scale modelling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic…
The simulation of high-energy physics collision events is a key element for data analysis at present and future particle accelerators. The comparison of simulation predictions to data allows looking for rare deviations that can be due to…
Ever increasing hardware capabilities and computation powers have made acquisition and analysis of big scientific data at the nanoscale routine, though much of the data acquired often turns out to be redundant, noisy, and/or irrelevant to…
We investigate nano scanning in tapping mode atomic force microscopy (AFM) under quality (Q) control via numerical simulations performed in SIMULINK. We focus on the simulation of whole scan process rather than the simulation of cantilever…
We report our design, development, installation and troubleshooting of an open source Gnome X Scanning Microscopy (GXSM) software package for controlling and processing of modern Scanning Probe Microscopy (SPM) system as a development tool…
Large scale atomistic simulations with suitable interatomic potentials are widely employed by scientists or engineers of different areas. Quick generation of high-quality interatomic potentials is of urgent need under present circumstances,…
Scanning probe microscopy (SPM) is a powerful technique for mapping nanoscale surface properties through tip-sample interactions. Thermal scanning-probe lithography (tSPL) is an advanced SPM variant that uses a silicon tip on a heated…
Automating experimental protocol design and execution remains as a fundamental bottleneck in realizing self-driving laboratories. We introduce PRISM (Protocol Refinement through Intelligent Simulation Modeling), a framework that automates…
Recent advances in random-walk particle-tracking have enabled direct simulation of mixing and reactions on particles by allowing the particles to interact with each other using a multi-point mass transfer scheme. The mass transfer scheme…
Data driven approaches have the potential to make modeling complex, nonlinear physical phenomena significantly more computationally tractable. For example, computational modeling of fracture is a core challenge where machine learning…