Related papers: Design Patterns of Biological Cells
Cell differentiation in multicellular organisms is a complex process whose mechanism can be understood by a reductionist approach, in which the individual processes that control the generation of different cell types are identified.…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
An observational study was conducted on a professional designer working on a design project in aerospace industry. The protocol data were analyzed in order to gain insight into the actions the designer used for the development of a solution…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
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…
The unification of statistical (data-driven) and symbolic (knowledge-driven) methods is widely recognised as one of the key challenges of modern AI. Recent years have seen large number of publications on such hybrid neuro-symbolic AI…
Process model quality has been an area of considerable research efforts. In this context, the correctness-by-construction principle of change patterns provides promising perspectives. However, using change patterns for model creation…
Biomolecular interactions underpin almost all biological processes, and their rational design is central to programming new biological functions. Generative AI models have emerged as powerful tools for molecular design, yet most remain…
Within the diverse interdisciplinary life sciences domains, semantic, workflow, and methodological ambiguities can prevent the appreciation of explanations of phenomena, handicap the use of computational models, and hamper communication…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
In this paper I present some of the most representative biological models applied to robotics. In particular, this work represents a survey of some models inspired, or making use of concepts, by gene regulatory networks (GRNs): these…
Deceptive and coercive design practices are increasingly used by companies to extract profit, harvest data, and limit consumer choice. Dark patterns represent the most common contemporary amalgamation of these problematic practices,…
Ordered item response models that are in common use can be divided into three groups, cumulative, sequential and adjacent categories model. The derivation and motivation of the models is typically based on the assumed presence of latent…
We consider a reaction-diffusion system with discontinuous reaction terms modeled by non-ideal relays. The system is motivated by an epigenetic population model of evolution of two-phenotype bacteria which switch phenotype in response to…
First we shortly review the different kinds of network modelling methods for systems biology with an emphasis on the different subtypes of logical models, which we review in more detail. Then we show the advantages of Boolean networks…