A synthetic Escherichia coli predator–prey ecosystem

We have constructed a synthetic ecosystem consisting of two Escherichia coli populations, which communicate bi-directionally through quorum sensing and regulate each other's gene expression and survival via engineered gene circuits. Our synthetic ecosystem resembles canonical predator–prey systems in terms of logic and dynamics. The predator cells kill the prey by inducing expression of a killer protein in the prey, while the prey rescue the predators by eliciting expression of an antidote protein in the predator. Extinction, coexistence and oscillatory dynamics of the predator and prey populations are possible depending on the operating conditions as experimentally validated by long-term culturing of the system in microchemostats. A simple mathematical model is developed to capture these system dynamics. Coherent interplay between experiments and mathematical analysis enables exploration of the dynamics of interacting populations in a predictable manner

Designer Gene Networks: Towards Fundamental Cellular Control

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 formulation leads to computational and analytical approaches relevant to nonlinear dynamics and statistical physics.Comment: 35 pages, 8 figure

Programming an Amorphous Computational Medium

Amorphous computing considers the problem of controllingmillions of spatially distributed unreliable devices which communicateonly with nearby neighbors. To program such a system, we need a highleveldescription language for desired global behaviors, and a system tocompile such descriptions into locally executing code which robustly createsand maintains the desired global behavior. I survey existing amorphouscomputing primitives and give desiderata for a language describingcomputation on an amorphous computer. I then bring these together inAmorphous Medium Language, which computes on an amorphous computeras though it were a space-filling computational medium

Design and Simulation of Self-Organizing Microbial Cellular Automata

This paper discusses the design and implementation of cellular automata based on the alteration of genetic sequences in bacteria. The work is composed of five chapters covering the problem, the system’s design, the software simulation of the system and future issues on the problem. The section covering the problem explores the reasons for this work as well as issues that this work solves. The section covering system design details the modified genetic sequences and the algorithm that these sequences implement. The simulation section describes the layout of an experiment along with the test cases experimented on. Finally, the future work section points out lacking information from the work or possible difficulties this solution reveals

Amorphous Computing

The goal of amorphous computing is to identify organizationalprinciples and create programming technologies for obtainingintentional, pre-specified behavior from the cooperation of myriadunreliable parts that are arranged in unknown, irregular, andtime-varying ways. The heightened relevance of amorphous computingtoday stems from the emergence of new technologies that could serve assubstrates for information processing systems of immense power atunprecedentedly low cost, if only we could master the challenge ofprogramming them. This document is a review of amorphous computing

Synthetic biology: new engineering rules for an emerging discipline

Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development