Related papers: In silico transitions to multicellularity
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
We study open-ended evolution by focusing on computational and information-processing dynamics underlying major evolutionary transitions. In doing so, we consider biological organisms as hierarchical dynamical systems that generate…
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…
Multilevel modeling is increasingly relevant in the context of modelling and simulation since it leads to several potential benefits, such as software reuse and integration, the split of semantically separated levels into sub-models, the…
While experiments and computer simulations to study biological phenomena are usually performed in diluted in vitro conditions, such phenomena happen inside the cell, an environment densely packed with diverse macromolecules. Here, we revise…
The minimal requirements for life are autopoiesis and cognition. We propose autopoietic models with cognition and perform three classes of evolutionary simulation. In our models the plasticity of the metabolic cycle and the regulation…
Computer-based modelling and simulation have become useful tools to facilitate humans to understand systems in different domains, such as physics, astrophysics, chemistry, biology, economics, engineering and social science. A complex system…
Computer simulations of coarse-grained molecular models for amphiphilic systems can provide insight into the the structure of amphiphiles at interfaces. They can help to identify the factors that determine the phase behavior, and they can…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
Many biological and physical systems exhibit behaviour at multiple spatial, temporal or population scales. Multiscale processes provide challenges when they are to be simulated using numerical techniques. While coarser methods such as…
A model for artificial evolution in native x86 Windows systems has been developed at the end of 2010. In this text, further improvements and additional analogies to natural microbiologic processes are presented. Several experiments indicate…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
Despite substantial potential to transform bioscience, medicine, and bioengineering, whole-cell models remain elusive. One of the biggest challenges to whole-cell models is assembling the large and diverse array of data needed to model an…
Collective cell migration is a key driver of embryonic development, wound healing, and some types of cancer invasion. Here we provide a physical perspective of the mechanisms underlying collective cell migration. We begin with a catalogue…
This chapter reviews the purpose and use of models from the field of complex systems and, in particular, the implications of trying to use models to understand or make decisions within complex situations, such as policy makers usually face.…
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…
Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations…
In a previous paper we have introduced a phenomenological model of cell metabolism and of the cell cycle to simulate the behavior of large tumor cell populations (Chignola R and Milotti E, Phys. Biol. 2 (2005) 8-22). Here we describe a…
Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems…
How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes…