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Entropy
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Emergence in Chemical Systems
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Emergence in Chemical Systems

A special issue of Entropy (ISSN 1099-4300).

Deadline for manuscript submissions: closed (31 January 2011) | Viewed by 81123

Special Issue Editor

Dr. Pierre-Alain Monnard

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Guest Editor
FLinT center, Institute for Physics and Chemistry, University of Southern Denmark, Campusvej, 55, 5230 Odense M, Denmark
Interests: self-replicating chemical systems and protocells; interface catalysis and membrane chemistry; microcompartmentalization; non-enzymatic polymerization; RNA world

Special Issue Information

Dear Colleagues,

The concept of emergence in chemical systems is challenging to define. In general, the term refers to phenomena in which the structures and behavior of multicomponent systems exceed those predicted from knowledge of the individual components. Entropy is at the core of emergent properties, driving essential processes such as self-assembly of lipid bilayers and folding of macromolecules, as well as molecular recognition.

The first appearance of living systems on the early Earth can be understood as an emergent phenomenon, because the simpler progenitors of living cells referred to as protocells were composed of a self-assembled collection of molecules that by themselves were non-living, yet together exhibited properties of self-maintenance, self-reproduction and evolution.

Because such system-level processes also occur in simpler chemical assemblies, emergence can be studied in model systems that display functions similar to those of living systems. Examples of such systems include dissipative structures like those generated by the Belousov-Zhabotinsky reaction, and molecular networks that consume energy and resources to achieve cooperative growth and self-replication, as well as to react to external constraints.

Studies of such systems conducted both in laboratory settings and in silico are leading to a deeper understanding of the complexity underlying emergent properties. This special issue of Entropy provides a repository for information, research and insight regarding emergent phenomena in chemical systems.

Pierre-Alain Monnard
Guest Editor

Keywords

  • emergent properties
  • chemical systems
  • self-assembly
  • self-replication
  • self-maintenance
  • metabolism
  • molecular networks
  • dissipative structures
  • protocells
  • minimal cell
  • logic gates
  • motility
  • evolution
  • adaptation
  • energetics

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Published Papers (8 papers)

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Research

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22 pages, 581 KiB  
Article
On the Growth Rate of Non-Enzymatic Molecular Replicators
by Harold Fellermann and Steen Rasmussen
Entropy 2011, 13(10), 1882-1903; https://doi.org/10.3390/e13101882 - 21 Oct 2011
Cited by 6 | Viewed by 6945
Abstract
It is well known that non-enzymatic template directed molecular replicators X + nO -> 2X exhibit parabolic growth d[X]/dt -> k[X]1/2. Here, we analyze the dependence of the effective replication rate constant k on [...] Read more.
It is well known that non-enzymatic template directed molecular replicators X + nO -> 2X exhibit parabolic growth d[X]/dt -> k[X]1/2. Here, we analyze the dependence of the effective replication rate constant k on hybridization energies, temperature, strand length, and sequence composition. First we derive analytical criteria for the replication rate k based on simple thermodynamic arguments. Second we present a Brownian dynamics model for oligonucleotides that allows us to simulate their diffusion and hybridization behavior. The simulation is used to generate and analyze the effect of strand length, temperature, and to some extent sequence composition, on the hybridization rates and the resulting optimal overall rate constant k. Combining the two approaches allows us to semi-analytically depict a replication rate landscape for template directed replicators. The results indicate a clear replication advantage for longer strands at lower temperatures in the regime where the ligation rate is rate limiting. Further the results indicate the existence of an optimal replication rate at the boundary between the two regimes where the ligation rate and the dehybridization rates are rate limiting. Full article
(This article belongs to the Special Issue Emergence in Chemical Systems)
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11 pages, 1691 KiB  
Article
Mode Switching and Collective Behavior in Chemical Oil Droplets
by Naoto Horibe, Martin M. Hanczyc and Takashi Ikegami
Entropy 2011, 13(3), 709-719; https://doi.org/10.3390/e13030709 - 18 Mar 2011
Cited by 28 | Viewed by 8929
Abstract
We have characterized several dynamic aspects of a simple chemical system capable of self-movement: An oil droplet in water system. We focused on spontaneous mode switching and collective behavior of droplets as emergent properties of the system. Droplets demonstrated spontaneous mode switching by [...] Read more.
We have characterized several dynamic aspects of a simple chemical system capable of self-movement: An oil droplet in water system. We focused on spontaneous mode switching and collective behavior of droplets as emergent properties of the system. Droplets demonstrated spontaneous mode switching by changing speed, direction and acceleration over time, and collective behaviors of droplets resulted from such autonomous characteristics. In this paper, we quantitatively measured those characteristics to show that droplets did not act completely independently in the same system, but tend to be attracted to one another and interact with each other by adjusting their motion. Full article
(This article belongs to the Special Issue Emergence in Chemical Systems)
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21 pages, 302 KiB  
Article
Complexity through Recombination: From Chemistry to Biology
by Niles Lehman, Carolina Díaz Arenas, Wesley A. White and Francis J. Schmidt
Entropy 2011, 13(1), 17-37; https://doi.org/10.3390/e13010017 - 24 Dec 2010
Cited by 9 | Viewed by 9831
Abstract
Recombination is a common event in nature, with examples in physics, chemistry, and biology. This process is characterized by the spontaneous reorganization of structural units to form new entities. Upon reorganization, the complexity of the overall system can change. In particular the components [...] Read more.
Recombination is a common event in nature, with examples in physics, chemistry, and biology. This process is characterized by the spontaneous reorganization of structural units to form new entities. Upon reorganization, the complexity of the overall system can change. In particular the components of the system can now experience a new response to externally applied selection criteria, such that the evolutionary trajectory of the system is altered. In this work we explore the link between chemical and biological forms of recombination. We estimate how the net system complexity changes, through analysis of RNA-RNA recombination and by mathematical modeling. Our results underscore the importance of recombination in the origins of life on the Earth and its subsequent evolutionary divergence. Full article
(This article belongs to the Special Issue Emergence in Chemical Systems)
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Review

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10 pages, 134 KiB  
Review
The Nature of Stability in Replicating Systems
by Nathaniel Wagner and Addy Pross
Entropy 2011, 13(2), 518-527; https://doi.org/10.3390/e13020518 - 15 Feb 2011
Cited by 11 | Viewed by 10605
Abstract
We review the concept of dynamic kinetic stability, a type of stability associated specifically with replicating entities, and show how it differs from the well-known and established (static) kinetic and thermodynamic stabilities associated with regular chemical systems. In the process we demonstrate how [...] Read more.
We review the concept of dynamic kinetic stability, a type of stability associated specifically with replicating entities, and show how it differs from the well-known and established (static) kinetic and thermodynamic stabilities associated with regular chemical systems. In the process we demonstrate how the concept can help bridge the conceptual chasm that continues to separate the physical and biological sciences by relating the nature of stability in the animate and inanimate worlds, and by providing additional insights into the physicochemical nature of abiogenesis. Full article
(This article belongs to the Special Issue Emergence in Chemical Systems)
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19 pages, 352 KiB  
Review
Primitive Membrane Formation, Characteristics and Roles in the Emergent Properties of a Protocell
by Sarah Elizabeth Maurer and Pierre-Alain Monnard
Entropy 2011, 13(2), 466-484; https://doi.org/10.3390/e13020466 - 10 Feb 2011
Cited by 19 | Viewed by 10719
Abstract
All contemporary living cells are composed of a collection of self-assembled molecular elements that by themselves are non-living but through the creation of a network exhibit the emergent properties of self-maintenance, self-reproduction, and evolution. This short review deals with the on-going research that [...] Read more.
All contemporary living cells are composed of a collection of self-assembled molecular elements that by themselves are non-living but through the creation of a network exhibit the emergent properties of self-maintenance, self-reproduction, and evolution. This short review deals with the on-going research that aims at either understanding how life emerged on the early Earth or creating artificial cells assembled from a collection of small chemicals. In particular, this article focuses on the work carried out to investigate how self-assembled compartments, such as amphiphile and lipid vesicles, contribute to the emergent properties as part of a greater system. Full article
(This article belongs to the Special Issue Emergence in Chemical Systems)
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20 pages, 1467 KiB  
Review
Using Entropy Leads to a Better Understanding of Biological Systems
by Chih-Yuan Tseng and Jack A. Tuszynski
Entropy 2010, 12(12), 2450-2469; https://doi.org/10.3390/e12122450 - 17 Dec 2010
Cited by 5 | Viewed by 7187
Abstract
In studying biological systems, conventional approaches based on the laws of physics almost always require introducing appropriate approximations. We argue that a comprehensive approach that integrates the laws of physics and principles of inference provides a better conceptual framework than these approaches to [...] Read more.
In studying biological systems, conventional approaches based on the laws of physics almost always require introducing appropriate approximations. We argue that a comprehensive approach that integrates the laws of physics and principles of inference provides a better conceptual framework than these approaches to reveal emergence in such systems. The crux of this comprehensive approach hinges on entropy. Entropy is not merely a physical quantity. It is also a reasoning tool to process information with the least bias. By reviewing three distinctive examples from protein folding dynamics to drug design, we demonstrate the developments and applications of this comprehensive approach in the area of biological systems. Full article
(This article belongs to the Special Issue Emergence in Chemical Systems)
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25 pages, 591 KiB  
Review
Autonomously Moving Colloidal Objects that Resemble Living Matter
by Akihisa Shioi, Takahiko Ban and Youichi Morimune
Entropy 2010, 12(11), 2308-2332; https://doi.org/10.3390/e12112308 - 16 Nov 2010
Cited by 14 | Viewed by 9419
Abstract
The design of autonomously moving objects that resemble living matter is an excellent research topic that may develop into various applications of functional motion. Autonomous motion can demonstrate numerous significant characteristics such as transduction of chemical potential into work without heat, chemosensitive motion, [...] Read more.
The design of autonomously moving objects that resemble living matter is an excellent research topic that may develop into various applications of functional motion. Autonomous motion can demonstrate numerous significant characteristics such as transduction of chemical potential into work without heat, chemosensitive motion, chemotactic and phototactic motions, and pulse-like motion with periodicities responding to the chemical environment. Sustainable motion can be realized with an open system that exchanges heat and matter across its interface. Hence the autonomously moving object has a colloidal scale with a large specific area. This article reviews several examples of systems with such characteristics that have been studied, focusing on chemical systems containing amphiphilic molecules. Full article
(This article belongs to the Special Issue Emergence in Chemical Systems)
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10 pages, 177 KiB  
Review
Autocatalytic Sets and the Origin of Life
by Wim Hordijk, Jotun Hein and Mike Steel
Entropy 2010, 12(7), 1733-1742; https://doi.org/10.3390/e12071733 - 30 Jun 2010
Cited by 128 | Viewed by 16201
Abstract
The origin of life is one of the most fundamental, but also one of the most difficult problems in science. Despite differences between various proposed scenarios, one common element seems to be the emergence of an autocatalytic set or cycle at some stage. [...] Read more.
The origin of life is one of the most fundamental, but also one of the most difficult problems in science. Despite differences between various proposed scenarios, one common element seems to be the emergence of an autocatalytic set or cycle at some stage. However, there is still disagreement as to how likely it is that such self-sustaining sets could arise “spontaneously”. This disagreement is largely caused by the lack of formal models. Here, we briefly review some of the criticism against and evidence in favor of autocatalytic sets, and then make a case for their plausibility based on a formal framework that was introduced and studied in our previous work. Full article
(This article belongs to the Special Issue Emergence in Chemical Systems)
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