Special Issue "Modelling Life-Like Behavior in Systems Chemistry"

A special issue of Life (ISSN 2075-1729).

Deadline for manuscript submissions: closed (31 March 2019)

Special Issue Editors

Guest Editor
Prof. Dr. Gonen Ashkenasy

Ben-Gurion University of the Negev, Beer Sheva, Israel
Website | E-Mail
Phone: 972-8-6461637
Interests: systems chemistry; origin of life; biomaterial self-assembly and self-replication
Guest Editor
Prof. Dr. David G. Lynn

Emory University, Atlanta GA, USA
Website | E-Mail
Interests: systems chemistry; dynamic chemical networks; supramolecular assemblies; alternative chemistries of life

Special Issue Information

Dear Colleagues,

The main difference between man-made processes and products, and those found in the living world, is that the former are typically passive and static while the latter are active and dynamic. Life is the product of complex systems of molecular reactions; connections and interactions giving rise to a highly dynamic and functional whole. It is now possible that the ability to control dynamic chemical systems may pave the way to understanding the emergence of function in early evolution, and consequently, for the design and preparation of functional biomimetic systems as complex as artificial cells and tissues. Furthermore, it is anticipated that developing such systems can deliver, in the short and long term, radically different approaches in areas ranging from materials science to evolvable biologics for medicine. The design and study of complex systems, i.e., of dynamic, self-organized, multi-component chemical networks, has been integrated under the umbrella of the recently inaugurated discipline of Systems Chemistry.

The first Gordon Research Conference offered an international venue for presenting and discussing breakthrough results in systems chemistry, for sharing new emerging methodology, and for refinement of the ideas coherently across these rapidly emerging new research directions. This Special Issue of Life will continue these discussions through the publication of a collection of philosophy, theory, simulation and modelling studies related to “Systems Chemistry and the Origin of Life”.

The Gordon Research Conference “Systems Chemistry from Concepts to Conception” organized by David Lynn and Gonen Ashkenasy was held at Newry, Maine, USA on July 29–August 3, 2018. Speakers and poster presenters in the conference are cordially invited to contribute original research papers or reviews to this Special Issue of Life.

Prof. Dr. Gonen Ashkenasy
Prof. Dr. David Lynn
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 650 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • systems chemistry
  • chemical evolution
  • chemical networks
  • self-replication and replication networks
  • dynamic simulations
  • reaction networks
  • far-from-equilibrium systems

Published Papers (3 papers)

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Research

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Open AccessArticle
Mathematical Analysis of a Prototypical Autocatalytic Reaction Network
Received: 15 April 2019 / Revised: 15 May 2019 / Accepted: 18 May 2019 / Published: 20 May 2019
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Abstract
Network autocatalysis, which is autocatalysis whereby a catalyst is not directly produced in a catalytic cycle, is likely to be more common in chemistry than direct autocatalysis is. Nevertheless, the kinetics of autocatalytic networks often does not exactly follow simple quadratic or cubic [...] Read more.
Network autocatalysis, which is autocatalysis whereby a catalyst is not directly produced in a catalytic cycle, is likely to be more common in chemistry than direct autocatalysis is. Nevertheless, the kinetics of autocatalytic networks often does not exactly follow simple quadratic or cubic rate laws and largely depends on the structure of the network. In this article, we analyzed one of the simplest and most chemically plausible autocatalytic networks where a catalytic cycle is coupled to an ancillary reaction that produces the catalyst. We analytically analyzed deviations in the kinetics of this network from its exponential growth and numerically studied the competition between two networks for common substrates. Our results showed that when quasi-steady-state approximation is applicable for at least one of the components, the deviation from the exponential growth is small. Numerical simulations showed that competition between networks results in the mutual exclusion of autocatalysts; however, the presence of a substantial noncatalytic conversion of substrates will create broad regions where autocatalysts can coexist. Thus, we should avoid the accumulation of intermediates and the noncatalytic conversion of the substrate when designing experimental systems that need autocatalysis as a source of positive feedback or as a source of evolutionary pressure. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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Open AccessArticle
Molecular Diversity Required for the Formation of Autocatalytic Sets
Received: 11 February 2019 / Revised: 21 February 2019 / Accepted: 26 February 2019 / Published: 1 March 2019
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Abstract
Systems chemistry deals with the design and study of complex chemical systems. However, such systems are often difficult to investigate experimentally. We provide an example of how theoretical and simulation-based studies can provide useful insights into the properties and dynamics of complex chemical [...] Read more.
Systems chemistry deals with the design and study of complex chemical systems. However, such systems are often difficult to investigate experimentally. We provide an example of how theoretical and simulation-based studies can provide useful insights into the properties and dynamics of complex chemical systems, in particular of autocatalytic sets. We investigate the issue of the required molecular diversity for autocatalytic sets to exist in random polymer libraries. Given a fixed probability that an arbitrary polymer catalyzes the formation of other polymers, we calculate this required molecular diversity theoretically for two particular models of chemical reaction systems, and then verify these calculations by computer simulations. We also argue that these results could be relevant to an origin of life scenario proposed recently by Damer and Deamer. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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Review

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Open AccessReview
Protobiotic Systems Chemistry Analyzed by Molecular Dynamics
Received: 16 April 2019 / Revised: 6 May 2019 / Accepted: 8 May 2019 / Published: 10 May 2019
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Abstract
Systems chemistry has been a key component of origin of life research, invoking models of life’s inception based on evolving molecular networks. One such model is the graded autocatalysis replication domain (GARD) formalism embodied in a lipid world scenario, which offers rigorous computer [...] Read more.
Systems chemistry has been a key component of origin of life research, invoking models of life’s inception based on evolving molecular networks. One such model is the graded autocatalysis replication domain (GARD) formalism embodied in a lipid world scenario, which offers rigorous computer simulation based on defined chemical kinetics equations. GARD suggests that the first pre-RNA life-like entities could have been homeostatically-growing assemblies of amphiphiles, undergoing compositional replication and mutations, as well as rudimentary selection and evolution. Recent progress in molecular dynamics has provided an experimental tool to study complex biological phenomena such as protein folding, ligand-receptor interactions, and micellar formation, growth, and fission. The detailed molecular definition of GARD and its inter-molecular catalytic interactions make it highly compatible with molecular dynamics analyses. We present a roadmap for simulating GARD’s kinetic and thermodynamic behavior using various molecular dynamics methodologies. We review different approaches for testing the validity of the GARD model by following micellar accretion and fission events and examining compositional changes over time. Near-future computational advances could provide empirical delineation for further system complexification, from simple compositional non-covalent assemblies towards more life-like protocellular entities with covalent chemistry that underlies metabolism and genetic encoding. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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