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Energy functions for pure and heterogenous systems are one of the backbones for molecular simulation of condensed phase systems. With the advent of machine learned potential energy surfaces (ML-PESs) a new era has started. Statistical…
The extracellular matrix (ECM) is a highly complex structure through which biochemical and mechanical signals are transmitted. In processes of cell migration, the ECM also acts as a scaffold, providing structural support to cells as well as…
This paper concerns multiphase models of tumor growth in interaction with a surrounding tissue, taking into account also the interplay with diffusible nutrients feeding the cells. Models specialize in nonlinear systems of possibly…
Complexes of cationic and neutral lipids and DNA (lipoplexes) are emerging as promising vectors for gene therapy applications. Their appeal stems from their non pathogenic nature and the fact that they self-assemble under conditions of…
Cancer development is a multistep process often starting with a single cell in which a number of epigenetic and genetic alterations have accumulated thus transforming it into a tumor cell. The progeny of such a single benign tumor cell…
Neovascularisation is essential for tissue development and regeneration, in addition to playing a key role in pathological settings such as ischemia and tumour development. Experimental findings in the past two decades have led to the…
In this paper, we are concerned with the simulation of blood flow in microvascular networks and the surrounding tissue. To reduce the computational complexity of this issue, the network structures are modeled by a one-dimensional graph,…
Tumor-immune interactions are central to cancer progression and treatment outcomes. In this study, we present a stochastic agent-based model that integrates cellular heterogeneity, spatial cell-cell interactions, and drug resistance…
We present an approach for flux analysis in process algebra models of biological systems. We perceive flux as the flow of resources in stochastic simulations. We resort to an established correspondence between event structures, a broadly…
Phase-field models of tumour growth have proved useful as theoretical tools to investigate cancer invasion. A key implicit assumption underlying mathematical models of this type which have so far been proposed, though, is that cells in the…
In this paper we consider chemotherapy in a spatial model of tumor growth. The model, which is of reaction-diffusion type, takes into account the complex interactions between the tumor and surrounding stromal cells by including densities of…
Intra-tumor heterogeneity driving disease progression is characterized by distinct growth and spatial proliferation patterns of cells and their nuclei within tumor and non-tumor tissues. A widely accepted hypothesis is that these spatial…
Robust and generalizable segmentation of brain tumors on multi-parametric magnetic resonance imaging (MRI) remains difficult because tumor types differ widely. The BraTS 2025 Lighthouse Challenge benchmarks segmentation methods on diverse…
Tumor segmentation in PET-CT images is challenging due to the dual nature of the acquired information: low metabolic information in CT and low spatial resolution in PET. U-Net architecture is the most common and widely recognized approach…
We present a new method for the geometric reconstruction of elastic surfaces simulated by the immersed boundary method with the goal of simulating the motion and interactions of cells in whole blood. Our method uses parameter-free radial…
A contemporary procedure to grow artificial tissue is to seed cells onto a porous biomaterial scaffold and culture it within a perfusion bioreactor to facilitate the transport of nutrients to growing cells. Typical models of cell growth for…
Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. The Waddington landscape posits that gene circuits in a cell form a potential landscape of different cell types, wherein cells follow attractors of…
Cancer stem cells have been shown to be critical to the development of a variety of solid cancers. The precise interplay mechanisms between cancer stem cells and the rest of a tissue are still not elucidated. To shed light on the…
Positron Emission Tomography (PET) and Computed Tomography (CT) are essential for diagnosing, staging, and monitoring various diseases, particularly cancer. Despite their importance, the use of PET/CT systems is limited by the necessity for…
International initiatives such as METABRIC (Molecular Taxonomy of Breast Cancer International Consortium) have collected several multigenomic and clinical data sets to identify the undergoing molecular processes taking place throughout the…