Related papers: PySTACHIO: Python Single-molecule TrAcking stoiCHi…
Flaky tests obstruct software development, and studying and proposing mitigations against them has therefore become an important focus of software engineering research. To conduct sound investigations on test flakiness, it is crucial to…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
Molecular-scale computation is crucial for smart materials and nanoscale devices, yet creating single-molecule systems capable of complex computations remains challenging. We present a theoretical framework for a single-molecule computer…
The performance of biomolecular molecular dynamics simulations has steadily increased on modern high performance computing resources but acceleration of the analysis of the output trajectories has lagged behind so that analyzing simulations…
Scanning tunnelling microscopy (STM) is a powerful technique for imaging surfaces with atomic resolution, providing insight into physical and chemical processes at the level of single atoms and molecules. A regular task of STM image…
We present a versatile and fast MATLAB program (UmUTracker) that automatically detects and tracks particles by analyzing video sequences acquired by either light microscopy or digital in-line holographic microscopy. Our program detects the…
We have built an open-source software system for the modeling of biomolecular reaction networks, SloppyCell, which is written in Python and makes substantial use of third-party libraries for numerics, visualization, and parallel…
Summary: The DynaSig-ML (Dynamical Signatures - Machine Learning) Python package allows the efficient, user-friendly exploration of 3D dynamics-function relationships in biomolecules, using datasets of experimental measures from large…
Advances in intensity-based microscopy techniques have improved our ability to quantify particle motion at microscopic scales, enabling insight into diffusion and collective dynamics. Building on this foundation, we introduce a novel…
Many new material systems are being explored to enable smaller, more capable and energy efficient devices. These bottom up approaches for atomic and molecular electronics, quantum computation, and data storage all rely on a well-developed…
Single Molecule Localization Microscopy (SMLM) enables the acquisition of high-resolution images by alternating between activation of a sparse subset of fluorescent molecules present in a sample and localization. In this work, the…
Scattering-based single-particle tracking (S-SPT) has opened new avenues for highly sensitive label-free detection and characterization of nanoscopic objects, making it particularly attractive for various analytical applications. However, a…
While program comprehension tools often use static program analysis techniques to obtain useful information, they usually work only with sufficiently scalable techniques with limited precision. A possible improvement of this approach is to…
In modern-day astronomy, near-infrared, optical, and ultraviolet spectroscopy are indispensable for studying a wide range of phenomena, from measuring black hole masses to analyzing chemical abundances in stellar atmospheres. However,…
We introduce pymovements: a Python package for analyzing eye-tracking data that follows best practices in software development, including rigorous testing and adherence to coding standards. The package provides functionality for key…
A reformulated implementation of single-sideband ptychography enables analysis and display of live detector data streams in 4D scanning transmission electron microscopy (STEM) using the LiberTEM open-source platform. This is combined with…
STACIE (STable AutoCorrelation Integral Estimator) is a novel algorithm and Python package that delivers robust, uncertainty-aware estimates of autocorrelation integrals from time-correlated data. While its primary application is deriving…
With the advance of fluorescence imaging technologies, recently cell biologists are able to record the movement of protein vesicles within a living cell. Automatic tracking of the movements of these vesicles become key for qualitative…
Background: The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required…
Despite more than 100 years of study, it is unclear if the movement of proteins inside the cell is best described as a mosh pit or an exquisitely choreographed dance. Recent studies suggest the latter. Local interactions induce molecular…