Related papers: Simulated single molecule microscopy with SMeagol
The stochastic simulation of large-scale biochemical reaction networks is of great importance for systems biology since it enables the study of inherently stochastic biological mechanisms at the whole cell scale. Stochastic Simulation…
The MAterials Simulation Toolkit (MAST) is a workflow manager and post-processing tool for ab initio defect and diffusion workflows. MAST codifies research knowledge and best practices for such workflows, and allows for the generation and…
The human neuromuscular system consisting of skeletal muscles and neural circuits is a complex system that is not yet fully understood. Surface electromyography (EMG) can be used to study muscle behavior from the outside. Computer…
We present MXtalTools, a flexible Python package for the data-driven modelling of molecular crystals, facilitating machine learning studies of the molecular solid state. MXtalTools comprises several classes of utilities: (1) synthesis,…
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…
Scanning probe microscopy (SPM) investigations of on-surface chemistry on passivated silicon have only shown in-plane chemical reactions, and studies on bare silicon are limited in facilitating additional reactions…
We propose a new microscopy simulation system that can depict atomistic models in a micrograph visual style, similar to results of physical electron microscopy imaging. This system is scalable, able to represent simulation of electron…
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…
Super-resolution ultrasound via microbubble (MB) localisation and tracking, also known as ultrasound localisation microscopy (ULM), can resolve microvasculature beyond the acoustic diffraction limit. However, significant challenges remain…
ESPResSo 4.0 is an extensible simulation package for research on soft matter. This versatile molecular dynamics program was originally developed for coarse-grained simulations of charged systems Limbach et al., Comput. Phys. Commun. 174,…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
Training sophisticated machine learning (ML) models requires large datasets that are difficult or expensive to collect for many applications. If prior knowledge about system dynamics is available, mechanistic representations can be used to…
MLE-Toolbox is a comprehensive open-source MATLAB toolbox for end-to-end analysis of magnetoencephalography (MEG) and electroencephalography (EEG) data. Inspired by widely used neuroimaging platforms such as Brainstorm and FieldTrip, it…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…
SparseChem provides fast and accurate machine learning models for biochemical applications. Especially, the package supports very high-dimensional sparse inputs, e.g., millions of features and millions of compounds. It is possible to train…
Nuclear and particle physics are the core components of most undergraduate and postgraduate physics courses worldwide. While few fundamental concepts like particle counting and detector characterisation are taught in tandem with laboratory…
Regular, automated testing is a foundational principle of modern software development. Numerous widely-used continuous integration systems exist, but they are often not suitable for the unique needs of scientific simulation software. Here…
Motivation: Building and iterating machine learning models is often a resource-intensive process. In biomedical research, scientific codebases can lack scalability and are not easily transferable to work beyond what they were intended.…
Using optical speckle scanning microscopy [1], we demonstrate that clear images of multiple cells can be obtained through biological scattering tissue, with subcellular resolution and good image quality, as long as the size of the imaging…
The process of setting up and successfully running Molecular Dynamics Simulations (MDS) is outlined to be incredibly labour and computationally expensive with a very high barrier to entry for newcomers wishing to utilise the benefits and…