Related papers: InferenceMAP: Mapping of Single-Molecule Dynamics …
We focus on the biological problem of tracking organelles as they move through cells. In the past, most intracellular movements were recorded manually, however, the results are too incomplete to capture the full complexity of organelle…
Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…
The study of biomolecular folding has been greatly advanced by single-molecule force spectroscopy (SMFS), which enables the observation of the dynamics of individual molecules. However, extracting quantitative models of fundamental…
Pathology foundation models learn morphological representations through self-supervised pretraining on large-scale whole-slide images, yet they do not explicitly capture the underlying molecular state of the tissue. Spatial transcriptomics…
Cells use signalling pathways as windows into the environment to gather information, transduce it into their interior, and use it to drive behaviours. MAPK (ERK) is a highly conserved signalling pathway in eukaryotes, directing multiple…
Like natural complex systems such as the Earth's climate or a living cell, semiconductor lithography systems are characterized by nonlinear dynamics across more than a dozen orders of magnitude in space and time. Thousands of sensors…
Spatial transcriptomics methods capture cellular measurements such as gene expression and cell types at specific locations in a cell, helping provide a localized picture of tissue health. Traditional visualization techniques superimpose the…
Introduction: molecular geometry, the three-dimensional arrangement of atoms within a molecule, is fundamental to understanding chemical reactivity, physical properties, and biological activity. The prevailing models used to describe…
Understanding the dynamics of an environment, such as the movement of humans and vehicles, is crucial for agents to achieve long-term autonomy in urban environments. This requires the development of methods to capture the multi-modal and…
Simulators driven by deep learning are gaining popularity as a tool for efficiently emulating accurate but expensive numerical simulators. Successful applications of such neural simulators can be found in the domains of physics, chemistry,…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Arrhythmias are potentially fatal disruptions to the normal heart rhythm, but their underlying dynamics is still poorly understood. Theoretical modeling is an important tool to fill this gap. Typical studies often employ detailed…
The analysis of single particle trajectories plays an important role in elucidating dynamics within complex environments such as those found in living cells. However, the characterization of intracellular particle motion is often confounded…
In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which is crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics…
Many collective systems exist in nature far from equilibrium, ranging from cellular sheets up to flocks of birds. These systems reflect a form of active matter, whereby individual material components have internal energy. Under specific…
Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the…
Tracking of objects in cellular environments has become a vital tool in molecular cell biology. A particularly important example is single molecule tracking which enables the study of the motion of a molecule in cellular environments and…
Molecular systems can exhibit a complex, chemically tailorable inner structure which allows for targeting of specific mechanical, electronic and optical properties. At the single-molecule level, two major complementary ways to explore these…
The accurate tracking of live cells using video microscopy recordings remains a challenging task for popular state-of-the-art image processing based object tracking methods. In recent years, several existing and new applications have…
Spatial connectivity is an important consideration when modelling infectious disease data across a geographical region. Connectivity can arise for many reasons, including shared characteristics between regions, and human or vector movement.…