Related papers: Multiscale Modelling: A Mobile Membrane Approach
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…
A trend across most areas where simulation-driven development is used is the ever increasing size and complexity of the systems under consideration, pushing established methods of modeling and simulation towards their limits. This paper…
The shape of a cell influences and it is influenced by interactions with its neighbouring partners. Here, we introduce a coarse-grained model of non-reciprocal interactions between single-cell organisms to study emergent morphologies during…
Memories are stored, retained, and recollected through complex, coupled processes operating on multiple timescales. To understand the computational principles behind these intricate networks of interactions we construct a broad class of…
Recent advances in microscopy and 3D reconstruction methods have allowed for characterization of cellular morphology in unprecedented detail, including the irregular geometries of intracellular subcompartments such as membrane-bound…
Many real-world systems studied are governed by complex, nonlinear dynamics. By modeling these dynamics, we can gain insight into how these systems work, make predictions about how they will behave, and develop strategies for controlling…
Skin contraction is an important biophysical process that takes place during and after the recovery of deep tissue injury. This process is mainly caused by fibroblasts (skin cells) and myofibroblasts (differentiated fibroblasts) that exert…
The classical Mat\'ern model has been a staple in spatial statistics. Novel data-rich applications in environmental and physical sciences, however, call for new, flexible vector-valued spatial and space-time models. Therefore, the extension…
We present a bigraphical framework suited for modeling biological systems both at protein level and at membrane level. We characterize formally bigraphs corresponding to biologically meaningful systems, and bigraphic rewriting rules…
Recent developments in spatial omics technologies have enabled the generation of high dimensional molecular data, such as transcriptomes, proteomes, and epigenomes, within their spatial tissue context, either through coprofiling on the same…
The spatial distribution of population and activities within urban areas, or urban form at the mesoscopic scale, is the outcome of multiple antagonist processes. We propose in this paper to benchmark different models of urban morphogenesis,…
Diffusion models have emerged as powerful generative models in the text-to-image domain. This paper studies their application as observation-to-action models for imitating human behaviour in sequential environments. Human behaviour is…
Macromolecular complexation leading to coupling of two or more cellular membranes is a crucial step in a number of biological functions of the cell. While other mechanisms may also play a role, adhesion always involves the fluctuations of…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
Understanding processes in porous media is fundamental to a broad spectrum of environmental, energy, and geoscience applications. These processes include multiphase fluid transport, interfacial dynamics, reactive transformations, and…
Collective cell migration is a key driver of embryonic development, wound healing, and some types of cancer invasion. Here we provide a physical perspective of the mechanisms underlying collective cell migration. We begin with a catalogue…
Time-evolving perforated domains arise in many engineering and geoscientific applications, including reactive transport, particle deposition, and structural degradation in porous media. Accurately capturing the macroscopic behavior of such…
The complexity of condensed matter arises from emergent behaviors that cannot be understood by analyzing individual constituents in isolation. While traditional condensed-matter approaches-developed primarily for ideal crystalline…
There is today a growing need to accurately model the angular scattering response of metasurfaces for optical analog processing applications. However, the current metasurface modeling techniques are not well suited for such a task since…
In this paper we sum up our works on multiscale programs, mainly simulations. We first start with describing what multiscaling is about, how it helps perceiving signal from a background noise in a ?ow of data for example, for a direct…