Introduction to Amorphous Computing

Coore, Daniel

doi:10.1007/11527800_8

Cited by 16 publications

(13 citation statements)

References 8 publications

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“…Drawing inspiration from biology, AC-based systems are comprised of identical but autonomous agents that make use of local information to differentiate and act across space and time. The resulting space-time programming frameworks enable both the analysis and forward engineering of complex systems capable of programmed pattern formation and restoration (i.e., “healing”) in the presence of noise or damage [3-5]. However, much improved cell-cell communication platforms are needed for scientists and engineers to practically benefit from and advance such research.…”

Section: Introductionmentioning

confidence: 99%

Engineered cell-cell communication via DNA messaging

Ortiz

Endy

2012

J Biol Eng

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BackgroundEvolution has selected for organisms that benefit from genetically encoded cell-cell communication. Engineers have begun to repurpose elements of natural communication systems to realize programmed pattern formation and coordinate other population-level behaviors. However, existing engineered systems rely on system-specific small molecules to send molecular messages among cells. Thus, the information transmission capacity of current engineered biological communication systems is physically limited by specific biomolecules that are capable of sending only a single message, typically “regulate transcription.”ResultsWe have engineered a cell-cell communication platform using bacteriophage M13 gene products to autonomously package and deliver heterologous DNA messages of varying lengths and encoded functions. We demonstrate the decoupling of messages from a common communication channel via the autonomous transmission of various arbitrary genetic messages. Further, we increase the range of engineered DNA messaging across semisolid media by linking message transmission or receipt to active cellular chemotaxis.ConclusionsWe demonstrate decoupling of a communication channel from message transmission within engineered biological systems via the autonomous targeted transduction of user-specified heterologous DNA messages. We also demonstrate that bacteriophage M13 particle production and message transduction occurs among chemotactic bacteria. We use chemotaxis to improve the range of DNA messaging, increasing both transmission distance and communication bit rates relative to existing small molecule-based communication systems. We postulate that integration of different engineered cell-cell communication platforms will allow for more complex spatial programming of dynamic cellular consortia.

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Section: Introductionmentioning

confidence: 99%

Engineered cell-cell communication via DNA messaging

Ortiz

Endy

2012

J Biol Eng

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“…The evo-devo works of [25], [26], or with lesser morphogenetic abilities [27], [4], are among these few notable achievements. Other interesting studies have explored pairs of mechanisms: SA and PF, no GR-selfassembly based on cell adhesion and signaling pattern formation, but using only predefined cell types without internal genetic variables, e.g., [28]; PF and GR, no SA-non-trivial pattern formation from instruction-driven intercellular signaling, but on a fixed lattice without self-assembling motion, e.g., [29], [3]; SA and GR, no PF-heterogeneous swarms of genetically programmed, self-assembling particles, but in empty space without mutual differentiation signals, e.g., [30].…”

Section: Discussionmentioning

confidence: 99%

“…For example, the field of amorphous computing has set the stage for a myriad of micro-processors containing the same instructions to self-organize without exact blueprint map or functional reliability, unlike traditional VLSI, e.g., [3], [4]. Such self-assembling components can also represent mobile sensors and actuators in complex self-managing networks [5].…”

Section: A Rethinking Computing Systems As Complex Systemsmentioning

confidence: 99%

Spatial Self-Organization of Heterogeneous, Modular Architectures

Doursat

2008

2008 Second IEEE International Conference on Self-Adaptive and Self-Organizing Systems Workshops

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Abstract-On the one hand, natural phenomena of spontaneous pattern formation are generally random and repetitive, whereas, on the other hand, complicated heterogeneous architectures are the product of human design. The only examples of selforganized and structured systems are biological organisms produced by development. Can we export their precise self-formation capabilities to computing systems? This work proposes an "embryomorphic engineering" approach inspired by evo-devo to solve the paradoxical challenge of planning autonomous systems. Its goal is to artificially reconstruct complex morphogenesis by integrating three fundamental ingredients: self-assembly and pattern formation under genetic regulation. It presents a spatial computational agent-based model that can be equivalently construed as (a) moving cellular automata, in which cell rearrangement is influenced by the pattern they form, or (b) heterogeneous swarm motion, in which agents differentiate into patterns according to their location. It offers a new abstract framework to explore the causal and programmable link from genotype to phenotype that is needed in many emerging computational domains, such as amorphous computing or artificial embryogeny.

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“…Other major approaches include viral code systems, (e.g. TOTA co-fields [9], paintable computing [10]) Regiment [11], which gathers streaming data from spatial regions, Kairos [12], which operates on abstract graphs, pattern languages like Origami Shape Language [13] and Growing Point Language [14], and modular robotics systems (e.g. [15]).…”

Section: B the Proto Languagementioning

confidence: 99%

Cells Are Plausible Targets for High-Level Spatial Languages

Beal

Bachrach

2008

2008 Second IEEE International Conference on Self-Adaptive and Self-Organizing Systems Workshops

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Abstract-High level languages greatly increase the power of a programmer at the cost of programs that consume more resources than those written at a lower level of abstraction. This inefficiency is a major concern for the programming of biological systems: although advances in synthetic biology are beginning to allow bacteria to be programmed at an "assembly language" level, metabolic and chemical constraints currently place tight limits on the computational resources available. We find, however, that the semantics of the Proto spatial computing language appear to be a good match for engineered genetic regulatory networks, and particularly for describing the spatial differentiation necessary to construct tissues or organs. In this paper, we propose a mapping between Proto programs and standardized biological parts. We then demonstrate the plausibility of this mapping by applying it to a band detection program, finding that standard code optimization techniques can transform the inefficient program produced by the initial mapping into an efficient design equivalent to the Weiss laboratory's handdesigned band detector [1].

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Introduction to Amorphous Computing

Cited by 16 publications

References 8 publications

Engineered cell-cell communication via DNA messaging

Engineered cell-cell communication via DNA messaging

Spatial Self-Organization of Heterogeneous, Modular Architectures

Cells Are Plausible Targets for High-Level Spatial Languages

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