Proceedings ArticleDOI
Swarms and Genes: Exploring λ - Switch Gene Regulation through Swarm Intelligence
C. Jacob,A. Barbasiewicz,G. Tsui +2 more
- pp 2535-2542
TLDR
A 3-dimensional, agent-based model of the lambda-switch gene regulatory system is demonstrated, which displays the regulatory lambda switch behavior observed in E. coli, where proteins regulate their own production.Abstract:
We demonstrate a 3-dimensional, agent-based model of the lambda-switch gene regulatory system, which simulates the interactions of proteins, promoters and operators during the phases of lysogenic and lytic growth in the phage lambda infected bacterium Escherichia coli. Following a decentralized approach, all regulatory mechanisms result from local interactions of the biomolecular agents within a simulated 3D cytoplasm. We show that our model displays the regulatory lambda switch behavior observed in E. coli, where proteins regulate their own production. Our lambda switch simulations provide a versatile testbed for studying gene regulation in silico, complementing in vitro experiments.read more
Citations
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Journal ArticleDOI
The evolution of swarm grammars- growing trees, crafting art, and bottom-up design
S. von Mammen,Christian Jacob +1 more
TL;DR: In this article, the authors presented swarm grammars as an extension of Lindenmayer systems and used a swarm of agents which navigate in 3D space and place structural building blocks into their environment.
Proceedings ArticleDOI
Genetic swarm grammar programming: Ecological breeding like a gardener
S. von Mammen,Christian Jacob +1 more
TL;DR: This work explores new ways of designing ecologies of swarm agents by immersing the breeder into the growth and evolution processes, and takes on the role of a 'tinkerer' or 'gardener', who is equipped with tools to influence and shape the on-going growth, evolutionary, and other dynamic processes within the swarm grammar ecology.
Book ChapterDOI
The swarming body: simulating the decentralized defenses of immunity
TL;DR: The IMMS:VIGO::3D simulation environment as discussed by the authors uses swarm intelligence techniques to simulate human immune system cells and related entities inside 3D, decentralized and compartmentalized environments that represent primary and secondary lymphoid organs.
Journal ArticleDOI
PROKARYO: an illustrative and interactive computational model of the lactose operon in the bacterium Escherichia coli.
TL;DR: A 3-dimensional, interactive computer model of an Escherichia coli bacterium and its associated biomolecular processes is built and the classic gene regulatory mechanism of the lactose operon is used to demonstrate the model’s resolution, visual presentation, and real-time interactivity.
Book ChapterDOI
Evolutionary and Swarm Design in Science, Art, and Music
Christian Jacob,Gerald Hushlak +1 more
TL;DR: This chapter describes how different evolutionary techniques can be applied to a wide variety of nature-inspired designs and shows how techniques of interactive evolutionary breeding can facilitate the creative processes of design.
References
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BookDOI
Swarm intelligence: from natural to artificial systems
TL;DR: This chapter discusses Ant Foraging Behavior, Combinatorial Optimization, and Routing in Communications Networks, and its application to Data Analysis and Graph Partitioning.
BookDOI
Self-Organization in Biological Systems
TL;DR: This book is a self-contained introduction to self-organization and complexity in biology - a field of study at the forefront of life sciences research.
Book
Emergence: The Connected Lives of Ants, Brains, Cities, and Software
TL;DR: Emergence is what happens when an interconnected system of relatively simple elements self-organizes to form more intelligent, more adaptive higher-level behavior as discussed by the authors, i.e., when agents residing on one scale start producing behavior that lies a scale above them.
Journal ArticleDOI
Computational studies of gene regulatory networks: in numero molecular biology
TL;DR: The implications of the underlying logic of genetic networks are difficult to deduce through experimental techniques alone, and successful approaches will probably involve the union of new experiments and computational modelling techniques.
Journal ArticleDOI
Quantitative model for gene regulation by lambda phage repressor
TL;DR: The model predicts repression curves at the divergent promoters PR and PRM that control transcription of genes coding for the regulatory proteins cro and repressor, respectively, and demonstrates the importance of cooperative interactions between repressor dimers bound to the adjacent operator sites OR1 and OR2 in maintaining a stable lysogenic state.