Related papers: PalaCell2D: A framework for detailed tissue morpho…
Modern biology and biomedicine are undergoing a big-data explosion needing advanced computational algorithms to extract mechanistic insights on the physiological state of living cells. We present the motivation for the Cell Physiome: a…
Effective wound repair treatments rely on a clear picture of how cell proliferation and migration are coordinated during tissue restoration. Fibroblasts are key contributors to tissue restoration in the dermis, and modern imaging tools…
T cells undergo large shape changes (morphodynamics) when migrating. While progress has been made elucidating the molecular basis of cell migration, statistical characterization of morphodynamics and migration has been limited, particularly…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
The growth of plants is a hydromechanical phenomenon in which cells enlarge by absorbing water, while their walls expand and remodel under turgor-induced tension. In multicellular tissues, where cells are mechanically interconnected,…
The formation of biomolecular materials via dynamical interfacial processes such as self-assembly and fusion, for diverse compositions and external conditions, can be efficiently probed using ensemble Molecular Dynamics. However, this…
Based on a recently proposed non-equilibrium mechanism for spatial pattern formation [cond-mat/0312366] we study how morphogenesis can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
We investigate morphologies of proliferating cellular tissues using a newly developed numerical simulation model for mechanical cell division and migration in 2D. The model is applied to a bimodal mixture consisting of stiff cells with a…
Organogenesis is a tightly regulated process that has been studied experimentally for decades. We are developing mechanistic models for the morphogenesis of limbs, lungs, and kidneys with a view to integrate available knowledge and to…
We take up the challenge of designing realistic computational models of large interacting cell populations. The goal is essentially to bring Gillespie's celebrated stochastic methodology to the level of an interacting population of cells.…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
Cell-based, mathematical modeling of collective cell behavior has become a prominent tool in developmental biology. Cell-based models represent individual cells as single particles or as sets of interconnected particles, and predict the…
Statistical and mathematical modeling are crucial to describe, interpret, compare and predict the behavior of complex biological systems including the organization of hematopoietic stem and progenitor cells in the bone marrow environment.…
Simulating in silico cellular responses to interventions is a promising direction to accelerate high-content image-based assays, critical for advancing drug discovery and gene editing. To support this, we introduce MorphGen, a…
Most biological tissues grow by the synthesis of new material close to the tissue's interface, where spatial interactions can exert strong geometric influences on the local rate of growth. These geometric influences may be mechanistic, or…
It is widely recognized that reciprocal interactions between cells and their microenvironment, via mechanical forces and biochemical signaling pathways, regulate cell behaviors during normal development, homeostasis and disease progression…
Computational models have become an essential part of exploratory protocols in cell biology, as a complement to in vivo or in vitro experiments. These virtual models have the twofold advantage of enabling access to new types of data and…
Eukaryotic cells intrinsically change their shape, by changing the composition of their membrane and by restructuring their underlying cytoskeleton. We present here further studies and extensions of a minimal physical model, describing a…