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This article presents a novel computational model to study the selective filtering of biological hydrogels due to the surface charge and size of diffusing particles. It is the first model that includes the random 3D fiber orientation and…
We present a unifying empirical description of the structural and kinematic properties of all spheroids embedded in dark matter halos. We find that the stellar spheroidal components of galaxy clusters, which we call cluster spheroids…
One of the key characteristics of cancer cells is an increased phenotypic plasticity, driven by underlying genetic and epigenetic perturbations. However, at a systems-level it is unclear how these perturbations give rise to the observed…
This paper describes an embedded boundary (EB) approach for simulating three-dimensional fluid flow on a staggered mesh where the velocity components are defined on cell faces and the thermodynamic state is defined on cell centers. Most EB…
We investigate the folding and forced-unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe biologically relevant phenomena that include adhesive interactions between proteins…
In recent work we revisited the phase diagram of hard ellipsoids of revolution (spheroids) by means of replica exchange Monte Carlo simulations. This was done by setting random initial configurations, and allows to confirm the formation of…
Background: The Epithelial-Mesenchymal Transition (EMT) endows epithelial-looking cells with enhanced migratory ability during embryonic development and tissue repair. EMT can also be co-opted by cancer cells to acquire metastatic potential…
Nanogranular material systems are promising for a variety of applications in research and development. Their physical properties are often determined by grain sizes, shapes, mutual distances and by the chemistry of the embedding matrix With…
Understanding and manipulating the interactions between foreign bodies and cell membranes during endo- and phagocytosis is of paramount importance, not only for the fate of living cells but also for numerous biomedical applications. This…
The shear-induced deformation of a capsule with a stiff nucleus, a model of eukaryotic cells, is studied numerically. The membrane of the cell and of its nucleus are modelled as a thin and impermeable elastic material obeying a Neo-Hookean…
A theoretical model based on the molecular interactions between a growing tumor and a dynamically evolving blood vessel network describes the transformation of the regular vasculature in normal tissues into a highly inhomogeneous tumor…
The transition from the epithelial to mesenchymal phenotype and its reverse (from mesenchymal to epithelial) are crucial processes necessary for the progression and spread of cancer. In this paper, we investigate how phenotypic switching at…
The field of biomedical imaging has undergone a rapid growth in recent years, mostly due to the implementation of ad-hoc designed experimental setups, theoretical support methods and numerical reconstructions. Especially for biological…
In this paper we study the growth of a tumor colony of multilayer type and focus on how the tumor grows from a near flat (when compared to the length of the tumor as, for instance, in the case of a bone tumor in a femur) initial colony. In…
After injury, if regeneration can be observed in hydra, planaria and some vertebrates, regeneration is rare in mammals and particularly in humans. In this paper, we investigate the mechanisms by which biological tissues recover after…
We study a phenomenological model in which the simulated packing of hard, attractive spheres on a prolate spheroid surface with convexity constraints produces structures identical to those of prolate virus capsid structures. Our simulation…
Filter-exchange imaging (FEXI) has already been utilized in several biomedical studies for evaluating the permeability of cell membranes. The method relies on suppressing the extracellular signal using strong diffusion weighting (the…
Most cancers in humans are large, measuring centimeters in diameter, composed of many billions of cells. An equivalent mass of normal cells would be highly heterogeneous as a result of the mutations that occur during each cell division.…
We study equilibrium shapes and shape transformations of a confined semiflexible chain inside a soft lipid tubule using simulations and continuum theories. The deformed tubular shapes and chain conformations depend on the relative magnitude…
In this review, we discuss recent advances on the plasticity of cancer stem cells and highlight their relevance to understand the metastatic process and to guide therapeutic interventions. Recent results suggest that the strict hierarchical…