Synthetic Cells Engaged in Molecular Communication: An Opportunity for Modelling Shannon- and Semantic-Information in the Chemical Domain

Magarini, Maurizio; Stano, Pasquale

doi:10.3389/frcmn.2021.724597

Cited by 18 publications

(21 citation statements)

References 53 publications

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“…The ability to relay, amplify, and process information distinguishes molecular systems in a biological context from those that are purely chemical. − Information processing in biology involves intermolecular interactions, either between biological macromolecules or between a macromolecule and a small ligand, , with messages transmitted by way of conformational changes that propagate through those macromolecules. , …”

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confidence: 99%

Reversible Capture and Release of a Ligand Mediated by a Long-Range Relayed Polarity Switch in a Urea Oligomer

2022

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Ethylene-bridged oligoureas characterized by a continuous, switchable chain of hydrogen bonds and carrying a binding site (an N,N′-disubstituted urea) for a hydrogen-bond-accepting ligand (a phosphine oxide) were synthesized. These oligomers show stronger ligand binding when the binding site is located at the hydrogen-bond-donating terminus than when the same binding site is at the hydrogen-bond-accepting terminus. An acidic group at the terminus remote from the binding site allows hydrogen bond polarity, and hence ligand binding ability, to be controlled remotely by a deprotonation/reprotonation cycle. Addition of base induces a remote conformational change that is relayed through up to five urea linkages, reducing the ability of the binding site to retain an intermolecular association to its ligand, which is consequently released into solution. Reprotonation returns the polarity of the oligomer to its original directionality, restoring the function of the remote binding site, which consequently recaptures the ligand. This is the first example of a synthetic molecular structure that relays intermolecular binding information, and these “dynamic foldamer” structures are prototypes of components for chemical systems capable of controlling chemical function from a distance.

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confidence: 99%

Reversible Capture and Release of a Ligand Mediated by a Long-Range Relayed Polarity Switch in a Urea Oligomer

2022

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“…Instead of focusing solely on message transmission, the study of semantic communication introduces a new paradigm shift toward the definition of a Post-Shannon metric of information [ 41 ]. This implies a change from the conventional design to a new one that goes beyond the transmission of purely message bits and considers the meaning associated with the conveyed message.…”

Section: Four Perspectives On Biological Communicationsmentioning

confidence: 99%

Toward Interdisciplinary Synergies in Molecular Communications: Perspectives from Synthetic Biology, Nanotechnology, Communications Engineering and Philosophy of Science

Egan

Kuscu

Barros

et al. 2023

Life

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Within many chemical and biological systems, both synthetic and natural, communication via chemical messengers is widely viewed as a key feature. Often known as molecular communication, such communication has been a concern in the fields of synthetic biologists, nanotechnologists, communications engineers, and philosophers of science. However, interactions between these fields are currently limited. Nevertheless, the fact that the same basic phenomenon is studied by all of these fields raises the question of whether there are unexploited interdisciplinary synergies. In this paper, we summarize the perspectives of each field on molecular communications, highlight potential synergies, discuss ongoing challenges to exploit these synergies, and present future perspectives for interdisciplinary efforts in this area.

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“…Hence, information can be readily encoded in the chemical nature of the molecules themselves, and does not necessarily requires complex encoding processes (e.g., frequency or intensity modulation). Chemical signaling is yet usually short range (except when flows of the surrounding medium are involved), slow, and stochastic due to the possible degradation of molecules, their diffusion, and the presence of a high background molecular noise ( Okaie and Nakano, 2020 ; Magarini and Stano, 2021 ). These peculiarities may explain why, despite an in-depth phenomenological knowledge on biological chemical signaling, a rigorous information and communication theory of chemical communication is still lacking.…”

Section: Future Challengesmentioning

confidence: 99%

Chemical Communication in Artificial Cells: Basic Concepts, Design and Challenges

Karoui

Patwal

Kumar

et al. 2022

Front. Mol. Biosci.

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In the past decade, the focus of bottom-up synthetic biology has shifted from the design of complex artificial cell architectures to the design of interactions between artificial cells mediated by physical and chemical cues. Engineering communication between artificial cells is crucial for the realization of coordinated dynamic behaviours in artificial cell populations, which would have implications for biotechnology, advanced colloidal materials and regenerative medicine. In this review, we focus our discussion on molecular communication between artificial cells. We cover basic concepts such as the importance of compartmentalization, the metabolic machinery driving signaling across cell boundaries and the different modes of communication used. The various studies in artificial cell signaling have been classified based on the distance between sender and receiver cells, just like in biology into autocrine, juxtacrine, paracrine and endocrine signaling. Emerging tools available for the design of dynamic and adaptive signaling are highlighted and some recent advances of signaling-enabled collective behaviours, such as quorum sensing, travelling pulses and predator-prey behaviour, are also discussed.

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Synthetic Cells Engaged in Molecular Communication: An Opportunity for Modelling Shannon- and Semantic-Information in the Chemical Domain

Cited by 18 publications

References 53 publications

Reversible Capture and Release of a Ligand Mediated by a Long-Range Relayed Polarity Switch in a Urea Oligomer

Reversible Capture and Release of a Ligand Mediated by a Long-Range Relayed Polarity Switch in a Urea Oligomer

Toward Interdisciplinary Synergies in Molecular Communications: Perspectives from Synthetic Biology, Nanotechnology, Communications Engineering and Philosophy of Science

Chemical Communication in Artificial Cells: Basic Concepts, Design and Challenges

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