Related papers: Modeling Microenvironment Trajectories on Spatial …
Many biological systems evolve through continuous local dynamics while switching between latent regimes defined by learning, stimulus context, internal state, or developmental stage. These processes are often observed only as unpaired…
Many living and physical systems such as cell aggregates, tissues or bacterial colonies behave as unconventional systems of particles that are strongly constrained by volume exclusion and shape interactions. Understanding how these…
The cell cycle duration is a variable cellular phenotype that underlies long-term population growth and age structures. By analyzing the stationary solutions of a branching process with heritable cell division times, we demonstrate…
The hippocampus supports spatial navigation by encoding cognitive maps through collective place cell activity. We model the place cell population as non-negative spatial embeddings derived from the spectral decomposition of multi-step…
Existing studies comparing individual-based models of growing cell populations and their continuum counterparts have mainly focused on homogeneous populations, in which all cells have the same phenotypic characteristics. However,…
We propose a multi-scale lung model to investigate spatio-temporal distributions of ventilation variables. Lung envelope and large airway geometries are derived from CT scans; smaller airways are generated using a physiologically consistent…
Diffusion models have transformed image synthesis through iterative denoising, by defining trajectories from noise to coherent data. While their capabilities are widely celebrated, a critical challenge remains unaddressed: ensuring…
The day we understand the time evolution of subcellular elements at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our…
A distinguishing feature of a multicellular living system is that it operates at various scales, from the intracellular to organismal. Very little is known at present on how tissue level properties are related to cell and subcellular…
Stochastic agent-based models can account for millions of cells with spatiotemporal movement that can be a function of different factors. However, these simulations can be computationally expensive. In this work, we develop a novel…
Single-cell RNA sequencing (scRNA-seq) technologies have enabled the profiling of gene expression for a collection of cells across time during a dynamic biological process. Given that each time point provides only a static snapshot,…
In this paper, we derive an effective macroscale description suitable to describe the growth of biological tissue within a porous tissue-engineering scaffold. As in our recent work (Holden \textit{et al.} "A multiphase multiscale model for…
The Dynamic Template model of biological cell membranes and the cytoplasm as spatially organised fluid layers is extended to plant cells, and is shown to offer a feasible shear driven mechanism for the co-alignment of internal and external…
Spatio-temporal processes often exhibit highly heterogeneous and non-intuitive responses to localized disruptions, limiting the effectiveness of conventional message passing approaches in modeling local heterogeneity. We reformulate…
Existing deep learning-based surrogate models facilitate efficient data generation, but fall short in uncertainty quantification, efficient parameter space exploration, and reverse prediction. In our work, we introduce SurroFlow, a novel…
For tracing the spatiotemporal evolution of electronic systems, we suggest and analyze theoretically a setup that exploits the excellent spatial resolution based on scanning tunneling microscopy techniques combined with the temporal…
In this work, we introduce a spatial branching process to model the growth of the mycelial network of a filamentous fungus. In this model, each filament is described by the position of its tip, the trajectory of which is solution to a…
This paper proposes a two-stage framework named ST-PAD for spatio-temporal fluid dynamics modeling in the field of earth sciences, aiming to achieve high-precision simulation and prediction of fluid dynamics through spatio-temporal physics…
Multiphase systems are ubiquitous in engineering, biology, and materials science, where understanding their complex interactions and rheological behavior is crucial for advancing applications ranging from emulsion stability to cellular…
We develop a simple computational model for cell boundary evolution in plastic deformation. We study the cell boundary size distribution and cell boundary misorientation distribution that experimentally have been found to have scaling forms…