Related papers: Design Patterns of Biological Cells
To address the issues of reusability and evolvability in designing self- describing systems, this paper proposes a pattern-based, object-oriented, description-driven system architecture. The proposed architecture embodies four pillars -…
This paper describes an approach for reusing specification patterns. Specification patterns are design patterns that are expressed in a formal specification language. Reusing a specification pattern means instantiating it or composing it…
Living systems, particularly multicellular systems, often seem hopelessly complex. But recent studies have suggested that beneath this complexity, there may be unifying quantitative principles that we are only now starting to unravel. All…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
These patterns describe the strategies I use to find novel or unorthodox insights in the area of software design and research. The patterns are driven by inconsistencies between what we say and what we do, and they provide techniques for…
The spatially distributed reaction networks are indispensable for the understanding of many important phenomena concerning the development of organisms, coordinated cell behavior, and pattern formation. The purpose of this brief discussion…
The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
A dynamic model for cell differentiation is studied, where cells with internal chemical reaction dynamics interact with each other and replicate. It leads to spontaneous differentiation of cells and determination, as is discussed in the…
We present a general computational theory of stem cell networks and their developmental dynamics. Stem cell networks are special cases of developmental control networks. Our theory generates a natural classification of all possible stem…
A common trait of complex systems is that they can be represented by means of a network of interacting parts. It is, in fact, the network organisation (more than the parts) what largely conditions most higher-level properties, which are not…
This paper introduces a continuous model for Multi-cellular Developmental Design. The cells are fixed on a 2D grid and exchange "chemicals" with their neighbors during the growth process. The quantity of chemicals that a cell produces, as…
Patterns are fundamental to human cognition, enabling the recognition of structure and regularity across diverse domains. In this work, we focus on structural repeats, patterns that arise from the repetition of hierarchical relations within…
Context: Software architecture is a knowledge-intensive field. One mechanism for storing architecture knowledge is the recognition and description of architectural patterns. Selecting architectural patterns is a challenging task for…
This paper proposes new languages for basic skills in the Creative Society, where people create their own goods, tools, concepts, knowledge, and mechanisms with their own hands: the skills of learning, presentation, and collaboration. These…
Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown.…
A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as…
The Turing patterning mechanism is believed to underly the formation of repetitive structures in development, such as zebrafish stripes and mammalian digits, but it has proved difficult to isolate the specific biochemical species…
Biological and technological networks contain patterns, termed network motifs, which occur far more often than in randomized networks. Network motifs were suggested to be elementary building blocks that carry out key functions in the…
Biological organisms are simple at heart: cells, their basic units, perform a variety of behaviors by expressing proteins from DNA-encoded genes. Gene expression though depends on sets of often-convoluted regulatory interactions known as…