Related papers: Modeling mammalian gastrulation with embryonic ste…
Multitype branching processes (MTBP) model branching structures, where the nodes of the resulting tree are objects of different types. One field of application of such models in biology is in studies of cell proliferation. A sampling scheme…
Cell biomechanics involve a great number of complex phenomena that are fundamental to the evolution of life itself and other associated processes, ranging from the very early stages of embryo-genesis to the maintenance of damaged structures…
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…
A key process in the life of any multicellular organism is its development from a single egg into a full grown adult. The first step in this process often consists of forming a tissue layer out of randomly placed cells on the surface of the…
Spermatogenesis is sustained by the proliferation and differentiation of spermatogonial stem cells (SSCs). SSCs are derived from primordial germ cells (PGCs) during embryonic development. The signal from the mammalian embryonic tissue is…
"Self-organization" has become a watchword in developmental biology, characterizing observations in which embryonic or induced stem cells of animals replicate morphological steps and outcomes seen in intact embryos. While the term was…
The self-organization of cells into complex tissues relies on a tight coordination of cell behavior. Identifying the cellular processes driving tissue growth is key to understanding the emergence of tissue forms and devising targeted…
A new model for evolving Evolutionary Algorithms (EAs) is proposed in this paper. The model is based on the Multi Expression Programming (MEP) technique. Each MEP chromosome encodes an evolutionary pattern that is repeatedly used for…
To study how a zygote develops into an embryo with different tissues, large-scale 4D confocal movies of C. elegans embryos have been produced recently by experimental biologists. However, the lack of principled statistical methods for the…
Computational models provide crucial insights into complex biological processes such as cancer evolution, but their mechanistic nature often makes them nonlinear and parameter-rich, complicating calibration. We systematically evaluate…
In this work, we review previously developed coarse-grained (CG) particle models for biological membrane and red blood cells (RBCs) and discuss the advantages of the CG particle method over the continuum and atomic simulations on modeling…
This review article discusses some common enhanced sampling methods in relation to the process of self-assembly of biomolecules. An introduction to self-assembly and its challenges is covered followed by a brief overview of the methods and…
We propose a two-scale model to resolve essential features of developmental tissue deformations. The model couples individual cellular behavior to the mechanics at tissue scale. This is realized by a multiphase-field model addressing the…
100 years after Smoluchowski introduces his approach to stochastic processes, they are now at the basis of mathematical and physical modeling in cellular biology: they are used for example to analyse and to extract features from large…
Based on recent experiments with time-lapse fluorescent imaging, we propose a cellular automaton model for the dynamics of vascular endothelial cells (ECs) in angiogenic morphogenesis. The model successfully reproduces cell mixing behavior,…
Motivation: Despite being often perceived as the main contributors to cell fate and physiology, genes alone cannot predict cellular phenotype. During the process of gene expression, 95% of human genes can code for multiple proteins due to…
Modeling galaxy formation in a cosmological context presents one of the greatest challenges in astrophysics today, due to the vast range of scales and numerous physical processes involved. Here we review the current status of models that…
During embryogenesis tissue layers continuously rearrange and fold into specific shapes. Developmental biology identified patterns of gene expression and cytoskeletal regulation underlying local tissue dynamics, but how actions of multiple…
The deformation of cellular membranes regulates trafficking processes, such as exocytosis and endocytosis. Classically, the Helfrich continuum model is used to characterize the forces and mechanical parameters that cells tune to accomplish…
Cells exhibit a wide variety of different shapes. This diversity poses a challenge for computational approaches that attempt to shed light on the role cell geometry plays in regulating cell physiology and behavior. The simulation platform…