Related papers: In silico transitions to multicellularity
Living organisms rely on endogenous feedback mechanisms to maintain homeostasis in the presence of uncertainty and environmental fluctuations. An emerging challenge at the interface of control systems engineering and synthetic biology is…
Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase…
The physics of the glass transition and amorphous materials continues to attract the attention of a wide research community after decades of effort. Supercooled liquids and glasses have been studied numerically since the advent of molecular…
Modeling and simulation (M&S) has revolutionized the way modern engineered products are designed, tested and evaluated. Yet modeling and simulation is much less frequently applied in the study of natural biological and active matter…
Computational simulations are a popular method for testing hypotheses about the emergence of communication. This kind of research is performed in a variety of traditions including language evolution, developmental psychology, cognitive…
The building of minimal self-reproducing systems with a physical embodiment (generically called protocells) is a great challenge, with implications for both theory and applied sciences. Although the classical view of a living protocell…
Simulation especially real-time simulation have been widely used for the design and testing of real-time systems. The advancement of simulation tools has largely attributed to the evolution of computing technologies. With the reduced cost…
The in silico simulations are widely used in contemporary systems biology including the analysis of nerve pulse propagation. As known from numerous experiments, the propagation of an action potential is accompanied by mechanical and thermal…
Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of…
In this review we introduce the framework of reality-assisted evolution to summarize a growing trend towards combining model-based and model-free approaches to improve the design of physically embodied soft robots. In silico, data-driven…
Multiphase systems are ubiquitous in engineering, biology, and materials science, where understanding their complex interactions and rheological behavior is crucial for advancing applications ranging from emulsion stability to cellular…
We present and analyse a model for cell signalling processes in biological tissues. The model includes diffusion and nonlinear reactions on the cell surfaces, and both inter- and intracellular signalling. Using techniques from the theory of…
We consider a continuum mechanical model for the migration of multiple cell populations through parts of tissue separated by thin membranes. In this model, cells belonging to different populations may be characterised by different…
Detailed models of galactic disk formation and evolution require knowledge about the initial conditions under which disk galaxies form, the boundary conditions that affect their secular evolution and the micro-physical processes that drive…
Multiscale modeling of material properties has emerged as one of the grand challenges in material science and engineering. We provide a comprehensive, though not exhaustive, overview of the current status of multiscale simulations of…
The structure of surfaces and interfaces of silica (SiO2) is investigated by large scale molecular dynamics computer simulations. In the case of a free silica surface, the results of a classical molecular dynamics simulation are compared to…
An astonishingly diverse biomolecular circuitry orchestrates the functioning machinery underlying every living cell. These biomolecules and their circuits have been engineered not only for various industrial applications but also to perform…
Excellent computer simulations are done for a purpose. The most valid purposes are to explore uncharted territory, to resolve a well-posed scientific or technical question, or to make a design choice. Stand-alone modeling can serve the…
Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript…
Computational multiscale modeling encompasses a wide range of end-products and a great number of technological applications. This paper provides an overview of the computational multiscale modeling approach based on the utilization of MBN…