Related papers: Simulated single molecule microscopy with SMeagol
We developed a Bessel-beam photoacoustic microscopical simulation platform by using the k-Wave: MATLAB toolbox. The simulation platform uses the ring slit method to generate Bessel beam. By controlling the inner and outer radius of the ring…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
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…
We introduce software for reading, writing and processing fluorescence single-molecule and image spectroscopy data and developing analysis pipelines that unifies various spectroscopic analysis tools. Our software can be used for processing…
Slime mould \emph{Physarum polycephalum} is a large single cell capable for distributed sensing, concurrent information processing, parallel computation and decentralised actuation. The ease of culturing and experimenting with Physarum…
Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges,…
{\it Ab initio} computational methods for electronic transport in nanoscaled systems are an invaluable tool for the design of quantum devices. We have developed a flexible and efficient algorithm for evaluating $I$-$V$ characteristics of…
Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example…
Summary: Advances in 3D live cell microscopy are enabling high-resolution capture of previously unobserved processes. Unleashing the power of modern machine learning methods to fully benefit from these technologies is, however, frustrated…
We developed Macular, a simulation platform with a graphical interface, designed to produce in silico experiment scenarios for the retina and the primary visual system. A scenario consists of generating a three-dimensional structure with…
Advanced microscopy techniques are essential in biomedical research for visualising and tracking biomolecules within living cells and their compartments. Conventional fluorescence microscopy methods, however, often struggle with accurately…
SMILEI is a collaborative, open-source, object-oriented (C++) particle-in-cell code. To benefit from the latest advances in high-performance computing (HPC), SMILEI is co-developed by both physicists and HPC experts. The code's structures,…
In-situ small- and wide-angle scattering experiments at synchrotrons often result in massive amounts of data within seconds only. Especially during such beamtimes, processing of the acquired data online, so without mentionable delay, is key…
We present Full SMS, a multipurpose graphical user interface (GUI)-based software package for analysing single-molecule spectroscopy (SMS) data. SMS typically delivers multiparameter data -- such as fluorescence brightness, lifetime, and…
Understanding the spatio-temporal evolution of radiolytic species created by high-energy electrons in water underpins key applications from radiotherapy and nuclear safety to environmental processing and electron microscopy. Here, using the…
Summary: Biospectrogam is an open-source software for the spectral analysis of DNA and protein sequences. The software can fetch (from NCBI server), import and manage biological data. One can analyze the data using Digital Signal Processing…
Single-particle tracking (SPT) grants unprecedented insight into cellular function at the molecular scale [1]. Throughout the cell, the movement of single-molecules is generally heterogeneous and complex. Hence, there is an imperative to…
Summary: More sophisticated models are needed to address problems in bioscience, synthetic biology, and precision medicine. To help facilitate the collaboration needed for such models, the community developed the Simulation Experiment…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Unambiguously identifying molecules in spectra is of fundamental importance for a variety of scientific and industrial uses. Interpreting atmospheric spectra for the remote detection of volatile compounds requires information about the…