Related papers: InferenceMAP: Mapping of Single-Molecule Dynamics …
Abridged abstract: Inert interactions between randomly moving entities and spatial disorder play a crucial role in quantifying the diffusive properties of a system. These interactions affect only the movement of the entities, and examples…
Adaptive Informative Path Planning with Multimodal Sensing (AIPPMS) considers the problem of an agent equipped with multiple sensors, each with different sensing accuracy and energy costs. The agent's goal is to explore the environment and…
Aggregation and fragmentation of single molecules in the cell environment lead to a spectrum of diffusivities and to statistical laws of movement very different from typical Brownian motion. Current models of intracellular transport do not…
While pathology foundation models have transformed cancer image analysis, they often lack integration with molecular data at single-cell resolution, limiting their utility for precision oncology. Here, we present PAST, a pan-cancer…
Cell segmentation and tracking allow us to extract a plethora of cell attributes from bacterial time-lapse cell movies, thus promoting computational modeling and simulation of biological processes down to the single-cell level. However, to…
Of later years, numerous bottom-up attention models have been proposed on different assumptions. However, the produced saliency maps may be different from each other even from the same input image. We also observe that human fixation map…
Molecular dynamics is a valuable tool to probe biological processes at the atomistic level - a resolution often elusive to experiments. However, the credibility of molecular models is limited by the accuracy of the underlying force field,…
Diatoms are characterised by silica cell walls (frustules), which have highly ordered micro-/nano-structures. As the synthesis of such structures remains challenging, diatom frustules offer a promissing alternative to conventional porous…
We developed a 6D multi-particle tracking program CETASim in C++ programming language to simulate intensity-dependent effects in electron storage rings. The program can simulate the beam collective effects due to short-range/long-range…
Tracking single fluorescent molecules has offered resolution into dynamic molecular processes at the single-molecule level. This perspective traces the evolution of single-molecule tracking, highlighting key developments across various…
Tracking single molecules is instrumental for quantifying the transport of molecules and nanoparticles in biological samples, e.g., in brain drug delivery studies. Existing intensity-based localisation methods are not developed for imaging…
Spatial transcriptomics (ST) enables the visualization of gene expression within the context of tissue morphology. This emerging discipline has the potential to serve as a foundation for developing tools to design precision medicines.…
Motivation: Sparse autoencoders (SAEs) decompose foundation model activations into interpretable features, but causal feature-to-feature interactions across network depth remain unknown for biological foundation models. Results: We…
Podocytes, specialized epithelial cells that envelop the glomerular capillaries, play a pivotal role in maintaining renal health. The current description and quantification of features on pathology slides are limited, prompting the need for…
Cell tracking enables data extraction from time-lapse "cell movies" and promotes modeling biological processes at the single-cell level. We introduce a new fully automated computational strategy to track accurately cells across frames in…
For organic molecules adsorbed as well-oriented ultra-thin films on metallic surfaces, angle-resolved photoemission spectroscopy has evolved into a technique called photoemission tomography (PT). By approximating the final state of the…
Trajectory inference is used to order single-cell omics data along a path that reflects a continuous transition between cells. This approach is useful for studying processes like cell differentiation, where a stem cell matures into a…
PolyMAPS is an open-source library that helps researchers to initialize LAMMPS molecular dynamics simulations. It introduces an integrated workflow by combining preparation, launching, visualization, and analysis into a single Jupyter…
Interferometric scattering microscopy (iSCAT) can image the dynamics of nanometer-scale systems. The typical approach to analyzing interferometric images involves intensive processing, which discards data and limits the precision of…
In order to understand the complexities of cellular biology, researchers are interested in two important metrics: the genetic expression information of cells and their spatial coordinates within a tissue sample. However, state-of-the art…