14 papers · ranked by Valyu relevance
Anna M. Langmüller, Courtney C. Murdock, Philipp W. Messer
Ordinary differential equation models such as the classical SIR model are widely used in epidemiology to study and predict infectious disease dynamics. However, these models typically assume that populations are homogeneously mixed, disregarding possible variations in disease prevalence due to spatial heterogeneity. To…
Siyu He, Yuefei Zhu, Daniel Naveed Tavakol, Haotian Ye + 10 more
Single-cell sequencing has revolutionized our understanding of cellular heterogeneity and responses to environmental stimuli. However, mapping transcriptomic changes across diverse cell types in response to various stimuli and elucidating underlying disease mechanisms remains challenging. Studies involving physical…
Robin Vloeberghs, Francis Tuerlinckx, Anne E. Urai, Kobe Desender
A widely used framework for studying the computational mechanisms of decision making is the Drift Diffusion Model (DDM). To account for the presence of both fast and slow errors in empirical data, the DDM incorporates across-trial variability in parameters such as the drift rate and the starting point. Although these…
Iman Aganj, Thorsten Feiweier, John E. Kirsch, Bruce R. Fischl + 1 more
In the course of diffusion, water molecules experience varying values for the relaxation-time properties of the underlying tissue. This factor, which has rarely been accounted for in diffusion MRI (dMRI) modeling, is modeled in this work, allowing for the estimation of the gradient of the relaxation-time properties…
Iman Aganj, Thorsten Feiweier, John E. Kirsch, Bruce R. Fischl + 1 more
In the course of diffusion, water molecules experience varying values for the relaxation-time properties of the underlying tissue. This factor, which has rarely been accounted for in diffusion MRI (dMRI), is modeled in this work, allowing for the estimation of the gradient of the relaxation-time properties from the…
François Simon, Guillaume Ramadier, Inès Fonquernie, Janka Zsok + 5 more
Single-particle tracking is a powerful tool for understanding protein dynamics and characterizing microenvironments. As the motion of unconstrained nanoscale particles is governed by Brownian diffusion, deviations from this behavior are biophysically insightful. However, the stochastic nature of particle movement and…
Yin Hoon Chew, Fabian Spill
Metabolites have to diffuse within the sub-cellular compartments they occupy to specific locations where enzymes are, so reactions could occur. Conventional flux balance analysis (FBA), a method based on linear programming that is commonly used to model metabolism, implicitly assumes that all enzymatic reactions are…
Thomas Williams, James McCaw, James Osborne
There has been an increasing recognition of the utility of models of the spatial dynamics of viral spread within tissues. Multicellular models, where cells are represented as discrete regions of space coupled to a virus density surface, are a popular approach to capture these dynamics. Conventionally, such models are…
Andrew J. Loza, Marc S. Sherman
Biological systems frequently contain biochemical species present as small numbers of slowly diffusing molecules, leading to fluctuations that invalidate deterministic analyses of system dynamics. The development of mathematical tools that account for the spatial distribution and discrete number of reacting molecules…
Johannes G. Borgqvist, Philip Gerlee, Carl Lundholm
The formation of buds on the cell membrane of budding yeast cells is thought to be driven by reactions and diffusion involving the protein Cdc42. These processes can be described by a coupled system of partial differential equations known as the Schnakenberg system. The Schnakenberg system is known to exhibit…
Aishani Ghosal, Yu-Huan Wang, Nguyen Nguyen, Laura Troyer + 1 more
Advances in fluorescence microscopy have enabled high-resolution tracking of individual biomolecules in living cells. However, accurate estimation of diffusion parameters from single-particle trajectories remains challenging due to static and dynamic localization errors inherent in these measurements. While previous…
Ramona Cirstian, Natalie J. Forde, Jesper L.R. Andersson, Stamatios N. Sotiropoulos + 2 more
Diffusion MRI is a neuroimaging modality used to evaluate brain structure at a microscopic level and can be exploited to map white matter fibre bundles and microstructure in the brain. One common issue is the presence of artefacts, such as acquisition artefacts, physiological artefacts, distortions or image…
Jurgen Riedel, Chris P. Barnes
In this study we examine the emergence of complex biological patterns through the lens of reaction-diffusion systems. We introduce two novel complexity metrics, Diversity of Number of States (DNOS) and Diversity of Pattern Complexity (DPC), which aim to quantify structural intricacies in pattern formation, enhancing…
Bastiaan J R Cockx, Tim Foster, Robert J Clegg, Kieran Alden + 4 more
Microbial communities are found in all habitable environments and often occur in assemblages with self-organized spatial structures developing over time. This complexity can only be understood, predicted, and managed by combining experiments with mathematical modeling. Individual-based models are particularly suited if…