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Open AccessArticle

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 5919

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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Open AccessArticle

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 25 | Viewed by 7907

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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Open AccessArticle

Complexity through Recombination: From Chemistry to Biology

by

,

,

and

Entropy 2011, 13(1), 17-37; https://doi.org/10.3390/e13010017 - 24 Dec 2010

Cited by 8 | Viewed by 8115

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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Open AccessReview

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 8 | Viewed by 8414

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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Open AccessReview

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 14 | Viewed by 8717

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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Open AccessReview

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 3 | Viewed by 6186

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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Open AccessReview

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 10 | Viewed by 8263

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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Open AccessReview

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 102 | Viewed by 12750

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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