Related papers: Determining the accuracy of spatial gradient sensi…

Cells sense and predict their environment via energy-dissipating pathways. However, it is unclear whether dissipation helps or harms prediction. Here we study dissipation and prediction for a minimal sensory module of receptors that…

Bacterial chemotaxis is controlled by the signalling of a cluster of receptors. A cooperative model is presented, in which coupling between neighbouring receptor dimers enhances the sensitivity with which stimuli can be detected, without…

The analysis of spatial data from biological imaging technology, such as imaging mass spectrometry (IMS) or imaging mass cytometry (IMC), is challenging because of a competitive sampling process which convolves signals from molecules in a…

Finding reduced models of spatially-distributed chemical reaction networks requires an estimation of which effective dynamics are relevant. We propose a machine learning approach to this coarse graining problem, where a maximum entropy…

In nature, microorganisms must often cope with hostile environmental conditions. To do so they have developed sophisticated cooperative behavior and intricate communication capabilities, such as: direct cell-cell physical interactions via…

Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…

We introduce a graphical method originating from the computer graphics domain that is used for the arbitrary and intuitive placement of cells over a two-dimensional manifold. Using a bitmap image as input, where the color indicates the…

We present a variation of two-dimensional electronic spectroscopy that is capable of mapping spatially-varying differences in electronic couplings using a correlated map of excitation and detection frequencies, with sensitivity orders of…

In digital pathology, both detection and classification of cells are important for automatic diagnostic and prognostic tasks. Classifying cells into subtypes, such as tumor cells, lymphocytes or stromal cells is particularly challenging.…

We study a chemotaxis-consumption mechanism, in which some chemical signal and cells density interact each other. In order to control the concentration of such a population, sources involving gradient nonlinearities, which introduce a…

For a long time, many methods are developed to make temporal signal analyses based on time series. However, for geographical systems, spatial signal analyses are as important as temporal signal analyses. Nonstationary spatial and temporal…

We consider four main goals when fitting spatial linear models: 1) estimating covariance parameters, 2) estimating fixed effects, 3) kriging (making point predictions), and 4) block-kriging (predicting the average value over a region). Each…

Unmeasured, spatially-structured factors can confound associations between spatial environmental exposures and health outcomes. Adding flexible splines to a regression model is a simple approach for spatial confounding adjustment, but the…

A living cell senses its environment and responds to external signals. In this work, we study theoretically, the precision at which cells can determine the position of a spatially localized transient extracellular signal. To this end, we…

We consider the influence of a power-law deviation from the critical coupling such that the system is critical at its surface. We develop a scaling theory showing that such a perturbation introduces a new length scale which governs the…

Biological cells sense external chemical stimuli in their environment using cell-surface receptors. To increase the sensitivity of sensing, receptors often cluster, most noticeably in bacterial chemotaxis, a paradigm for signaling and…

The movement of intracellular cargo transported by molecular motors is commonly marked by switches between directed motion and stationary pauses. The predominant measure for assessing movement is effective diffusivity, which predicts the…

The early fly embryo offers a relatively pure version of the problem of spatial scaling in biological pattern formation. Within three hours, a "blueprint" for the final segmented body plan of the animal is visible in striped patterns of…

Inputs to signaling pathways can have complex statistics that depend on the environment and on the behavioral response to previous stimuli. Such behavioral feedback is particularly important in navigation. Successful navigation relies on…

Spectro-microscopy is an experimental technique which can be used to observe spatial variations in chemical state and changes in chemical state over time or under experimental conditions. As a result it has broad applications across areas…