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Modelling Life-Like Behavior in Systems Chemistry
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Modelling Life-Like Behavior in Systems Chemistry

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Synthetic Biology and Systems Biology".

Deadline for manuscript submissions: closed (31 March 2019) | Viewed by 55313

Special Issue Editors

Prof. Dr. Gonen Ashkenasy

E-Mail Website
Guest Editor
Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
Interests: systems chemistry; origin of life; biomaterial self-assembly and self-replication
Prof. Dr. David G. Lynn

E-Mail Website
Guest Editor
Emory University, Atlanta GA, USA
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 submissions that pass pre-check are 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 monthly 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 2600 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

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Published Papers (10 papers)

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Research

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11 pages, 2283 KiB  
Article
Modelling Bacteria-Inspired Dynamics with Networks of Interacting Chemicals
by Tamás Bánsági and Annette F. Taylor
Life 2019, 9(3), 63; https://doi.org/10.3390/life9030063 - 29 Jul 2019
Cited by 7 | Viewed by 3915
Abstract
One approach to understanding how life-like properties emerge involves building synthetic cellular systems that mimic certain dynamical features of living cells such as bacteria. Here, we developed a model of a reaction network in a cellular system inspired by the ability of bacteria [...] Read more.
One approach to understanding how life-like properties emerge involves building synthetic cellular systems that mimic certain dynamical features of living cells such as bacteria. Here, we developed a model of a reaction network in a cellular system inspired by the ability of bacteria to form a biofilm in response to increasing cell density. Our aim was to determine the role of chemical feedback in the dynamics. The feedback was applied through the enzymatic rate dependence on pH, as pH is an important parameter that controls the rates of processes in cells. We found that a switch in pH can be used to drive base-catalyzed gelation or precipitation of a substance in the external solution. A critical density of cells was required for gelation that was essentially independent of the pH-driven feedback. However, the cell pH reached a higher maximum as a result of the appearance of pH oscillations with feedback. Thus, we conclude that while feedback may not play a vital role in some density-dependent behavior in cellular systems, it nevertheless can be exploited to activate internally regulated cell processes at low cell densities. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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10 pages, 1324 KiB  
Article
Mathematical Analysis of a Prototypical Autocatalytic Reaction Network
by Ekaterina V. Skorb and Sergey N. Semenov
Life 2019, 9(2), 42; https://doi.org/10.3390/life9020042 - 20 May 2019
Cited by 5 | Viewed by 5459
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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14 pages, 324 KiB  
Article
Molecular Diversity Required for the Formation of Autocatalytic Sets
by Wim Hordijk, Mike Steel and Stuart A. Kauffman
Life 2019, 9(1), 23; https://doi.org/10.3390/life9010023 - 1 Mar 2019
Cited by 19 | Viewed by 5443
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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28 pages, 6302 KiB  
Review
Synthetic Approaches for Nucleic Acid Delivery: Choosing the Right Carriers
by Rong Ni, Ruilu Feng and Ying Chau
Life 2019, 9(3), 59; https://doi.org/10.3390/life9030059 - 9 Jul 2019
Cited by 57 | Viewed by 8566
Abstract
The discovery of the genetic roots of various human diseases has motivated the exploration of different exogenous nucleic acids as therapeutic agents to treat these genetic disorders (inherited or acquired). However, the physicochemical properties of nucleic acids render them liable to degradation and [...] Read more.
The discovery of the genetic roots of various human diseases has motivated the exploration of different exogenous nucleic acids as therapeutic agents to treat these genetic disorders (inherited or acquired). However, the physicochemical properties of nucleic acids render them liable to degradation and also restrict their cellular entrance and gene translation/inhibition at the correct cellular location. Therefore, gene condensation/protection and guided intracellular trafficking are necessary for exogenous nucleic acids to function inside cells. Diversified cationic formulation materials, including natural and synthetic lipids, polymers, and proteins/peptides, have been developed to facilitate the intracellular transportation of exogenous nucleic acids. The chemical properties of different formulation materials determine their special features for nucleic acid delivery, so understanding the property–function correlation of the formulation materials will inspire the development of next-generation gene delivery carriers. Therefore, in this review, we focus on the chemical properties of different types of formulation materials and discuss how these formulation materials function as protectors and cellular pathfinders for nucleic acids, bringing them to their destination by overcoming different cellular barriers. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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16 pages, 3897 KiB  
Review
Open Prebiotic Environments Drive Emergent Phenomena and Complex Behavior
by Nathaniel Wagner, David Hochberg, Enrique Peacock-Lopez, Indrajit Maity and Gonen Ashkenasy
Life 2019, 9(2), 45; https://doi.org/10.3390/life9020045 - 3 Jun 2019
Cited by 22 | Viewed by 4339
Abstract
We have been studying simple prebiotic catalytic replicating networks as prototypes for modeling replication, complexification and Systems Chemistry. While living systems are always open and function far from equilibrium, these prebiotic networks may be open or closed, dynamic or static, divergent or convergent [...] Read more.
We have been studying simple prebiotic catalytic replicating networks as prototypes for modeling replication, complexification and Systems Chemistry. While living systems are always open and function far from equilibrium, these prebiotic networks may be open or closed, dynamic or static, divergent or convergent to a steady state. In this paper we review the properties of these simple replicating networks, and show, via four working models, how even though closed systems exhibit a wide range of emergent phenomena, many of the more interesting phenomena leading to complexification and emergence indeed require open systems. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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13 pages, 567 KiB  
Review
Protobiotic Systems Chemistry Analyzed by Molecular Dynamics
by Amit Kahana and Doron Lancet
Life 2019, 9(2), 38; https://doi.org/10.3390/life9020038 - 10 May 2019
Cited by 19 | Viewed by 5905
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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Other

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16 pages, 4741 KiB  
Essay
The Informational Substrate of Chemical Evolution: Implications for Abiogenesis
by Andrés de la Escosura
Life 2019, 9(3), 66; https://doi.org/10.3390/life9030066 - 8 Aug 2019
Cited by 6 | Viewed by 5958
Abstract
A key aspect of biological evolution is the capacity of living systems to process information, coded in deoxyribonucleic acid (DNA), and used to direct how the cell works. The overall picture that emerges today from fields such as developmental, synthetic, and systems biology [...] Read more.
A key aspect of biological evolution is the capacity of living systems to process information, coded in deoxyribonucleic acid (DNA), and used to direct how the cell works. The overall picture that emerges today from fields such as developmental, synthetic, and systems biology indicates that information processing in cells occurs through a hierarchy of genes regulating the activity of other genes through complex metabolic networks. There is an implicit semiotic character in this way of dealing with information, based on functional molecules that act as signs to achieve self-regulation of the whole network. In contrast to cells, chemical systems are not thought of being able to process information, yet they must have preceded biological organisms, and evolved into them. Hence, there must have been prebiotic molecular assemblies that could somehow process information, in order to regulate their own constituent reactions and supramolecular organization processes. The purpose of this essay is then to reflect about the distinctive features of information in living and non-living matter, and on how the capacity of biological organisms for information processing was possibly rooted in a particular type of chemical systems (here referred to as autonomous chemical systems), which could self-sustain and reproduce through organizational closure of their molecular building blocks. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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9 pages, 7349 KiB  
Essay
The Essence of Systems Chemistry
by Peter Strazewski
Life 2019, 9(3), 60; https://doi.org/10.3390/life9030060 - 11 Jul 2019
Cited by 9 | Viewed by 4435
Abstract
Systems Chemistry investigates the upkeep of specific interactions of an exceptionally broad choice of objects over longer periods of time than the average time of existence of the objects themselves. This maintenance of a dynamic state focuses on conditions where the objects are [...] Read more.
Systems Chemistry investigates the upkeep of specific interactions of an exceptionally broad choice of objects over longer periods of time than the average time of existence of the objects themselves. This maintenance of a dynamic state focuses on conditions where the objects are thermodynamically not very stable and should be rare or virtually inexistent. It does not matter whether they are homochirally enriched populations of chiral molecules, a specific composition of some sort of aggregate, supramolecules, or even a set of chemically relatively unstable molecules that constantly transform one into another. What does matter is that these specific interactions prevail in complex mixtures and eventually grow in numbers and frequency through the enhancing action of autocatalysis, which makes such systems ultimately resemble living cells and interacting living populations. Such chemical systems need to be correctly understood, but also intuitively described. They may be so complex that metaphors become practically more important, as a means of communication, than the precise and correct technical description of chemical models and complex molecular or supramolecular relations. This puts systems chemists on a tightrope walk of science communication, between the complex reality and an imaginative model world. This essay addresses, both, scientists who would like to read “A Brief History of Systems Chemistry”, that is, about its “essence”, and systems chemists who work with and communicate complex life-like chemical systems. I illustrate for the external reader a light mantra, that I call “to make more of it”, and I charily draw systems chemists to reflect upon the fact that chemists are not always good at drawing a clear line between a model and “the reality”: The real thing. We are in a constant danger of taking metaphors for real. Yet in real life, we do know very well that we cannot smoke with Magritte’s pipe, don’t we? Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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9 pages, 2206 KiB  
Concept Paper
The Role of Orthogonality in Genetic Code Expansion
by Pol Arranz-Gibert, Jaymin R. Patel and Farren J. Isaacs
Life 2019, 9(3), 58; https://doi.org/10.3390/life9030058 - 5 Jul 2019
Cited by 21 | Viewed by 6546
Abstract
The genetic code defines how information in the genome is translated into protein. Aside from a handful of isolated exceptions, this code is universal. Researchers have developed techniques to artificially expand the genetic code, repurposing codons and translational machinery to incorporate nonstandard amino [...] Read more.
The genetic code defines how information in the genome is translated into protein. Aside from a handful of isolated exceptions, this code is universal. Researchers have developed techniques to artificially expand the genetic code, repurposing codons and translational machinery to incorporate nonstandard amino acids (nsAAs) into proteins. A key challenge for robust genetic code expansion is orthogonality; the engineered machinery used to introduce nsAAs into proteins must co-exist with native translation and gene expression without cross-reactivity or pleiotropy. The issue of orthogonality manifests at several levels, including those of codons, ribosomes, aminoacyl-tRNA synthetases, tRNAs, and elongation factors. In this concept paper, we describe advances in genome recoding, translational engineering and associated challenges rooted in establishing orthogonality needed to expand the genetic code. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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11 pages, 1132 KiB  
Perspective
Systems Analysis for Peptide Systems Chemistry
by Martha A. Grover, Ming-Chien Hsieh and David G. Lynn
Life 2019, 9(3), 55; https://doi.org/10.3390/life9030055 - 1 Jul 2019
Cited by 2 | Viewed by 3646
Abstract
Living systems employ both covalent chemistry and physical assembly to achieve complex behaviors. The emerging field of systems chemistry, inspired by these biological systems, attempts to construct and analyze systems that are simpler than biology, while still embodying biological design principles. Due to [...] Read more.
Living systems employ both covalent chemistry and physical assembly to achieve complex behaviors. The emerging field of systems chemistry, inspired by these biological systems, attempts to construct and analyze systems that are simpler than biology, while still embodying biological design principles. Due to the multiple phenomena at play, it can be difficult to predict which phenomena will dominate and when. Conversely, there may be no single rate-limiting step, but rather a reaction network that is difficult to intuit from a purely experimental approach. Mathematical modeling can help to sort out these issues, although it can be challenging to build such models, especially for assembly kinetics. Numerical and statistical methods can play an important role to facilitate the synergistic and iterative use of modeling and experiment, and should be part of a systems chemistry curriculum. Three case studies are presented here, from our work in peptide-based systems, to illustrate some of the tools available for model construction, model simulation, and experimental design. Examples are provided in which these tools help to evaluate hypotheses, uncover design principles, and design new experiments. Full article
(This article belongs to the Special Issue Modelling Life-Like Behavior in Systems Chemistry)
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