Related papers: Design Patterns of Biological Cells
Patterns embody repeating phenomena, and, as such, they are partly but not fully detachable from their context. 'Design patterns' and 'pattern languages' are established methods for working with patterns. They have been applied in…
Reaction systems are discrete dynamical systems inspired by bio-chemical processes, whose dynamical behaviour is expressed by set-theoretic operations on finite sets. Reaction systems thus provide a description of bio-chemical phenomena…
The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they…
With the growing scale and complexity of high-performance computing (HPC) systems, resilience solutions that ensure continuity of service despite frequent errors and component failures must be methodically designed to balance the…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
Reliability is a serious concern for future extreme-scale high-performance computing (HPC) systems. While the HPC community has developed various resilience solutions, the solution space remains fragmented. There are no formal methods and…
Designing new chemical compounds with desired pharmaceutical properties is a challenging task and takes years of development and testing. Still, a majority of new drugs fail to prove efficient. Recent success of deep generative modeling…
We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…
This paper examines the four main types of Evolutionary Design by computers: Evolutionary Design Optimisation, Evolutionary Art, Evolutionary Artificial Life Forms and Creative Evolutionary Design. Definitions for all four areas are…
Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative…
Complexity in biology is often described using a multi-map architecture, where the genotype, representing the encoded information, is mapped to the functional level, known as the phenotype, which is then connected to a latent phenotype we…
The quality of software is enhanced by using the design patterns. The design patterns are the reusable component used in the development of the software, which delivers improved quality software to the end users. The researchers have…
In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…
During development, spatio-temporal patterns ranging from checkerboard to engulfing occur with precise proportions of the respective cell fates. Key developmental regulators are intracellular transcriptional interactions and intercellular…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
Development combines three basic processes asymmetric --- cell division, signaling and gene regulation --- in a multitude of ways to create an overwhelming diversity of multicellular life-forms. Here, we attempt to chart this diversity…
Patterns describe proven solutions for recurring problems. Typically, patterns in a particular domain are interrelated and organized in pattern languages. As real-world problems often require patterns of multiple domains, different pattern…
Design patterns are elegant and well-tested solutions to recurrent software development problems. They are the result of software developers dealing with problems that frequently occur, solving them in the same or a slightly adapted way. A…