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Computer Simulation of the Origin of Life
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Computer Simulation of the Origin of Life

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Origin of Life".

Deadline for manuscript submissions: closed (29 December 2023) | Viewed by 14301

Special Issue Editors

Dr. Wentao Ma

E-Mail Website
Guest Editor
Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
Interests: origin of life; chemical evolution; early Darwinian evolution; the RNA world; theoretical modeling; computer simulation; computational biology
Prof. Dr. Paul Higgs

E-Mail Website
Guest Editor
Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada
Interests: origin of life; RNA structure and evolution; RNA world; mathematical and computational models; phylogenetic methods; molecular evolution; population genetics; biophysics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

To date, we are still by and large in the dark in the field of the origin of life. However, clues have been accumulating from both experimental and theoretical studies. On the one hand, the origin of life is certainly a problem of chemistry, which involves molecular mechanisms in a prebiotic context— so-called prebiotic chemistry. Experimental work has been contributing to this aspect, and we have seen exciting discoveries. On the other hand, the origin of life is also a problem of evolution. It is believed to have been a long-lasting process, perhaps including a series of stages and transitions. In fact, even a small scene within the process may have involved some notable evolutionary mechanisms. In this aspect, experimental work is difficult, though not completely inactive. Fortunately, theoretical work, now largely based on computer simulation, may contribute by demonstrating relevant evolutionary dynamics, and has revealed many interesting mechanisms. It is expected that the combination of experimental and theoretical efforts will ultimately lead to a breakthrough (perhaps more) in this special field dealing with one of the most amazing events in nature.

This Special Issue focuses on computer simulation studies on the origin of life—mainly studies related to the evolutionary aspect, but the scope encompasses a wider range of topics, and includes any potential in silico work concerning the origin of life. Prospective authors may send a short abstract or tentative title to the Editorial Office at first. If the Editors deem the topic to be appropriate for inclusion in the Special Issue, the author will be encouraged to submit a full manuscript.

Dr. Wentao Ma
Prof. Dr. Paul Higgs
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

  • origin of life
  • chemical evolution
  • prebiotic evolution
  • early darwinian evolution
  • the RNA world
  • protocells
  • self-sustaining chemical systems
  • evolutionary dynamics
  • theoretical modeling
  • computer simulation
  • in silico studies

Published Papers (8 papers)

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Research

14 pages, 4704 KiB  
Article
Structural Phenomena in a Vesicle Membrane Obtained through an Evolution Experiment: A Study Based on MD Simulations
by María J. Dávila and Christian Mayer
Life 2023, 13(8), 1735; https://doi.org/10.3390/life13081735 - 12 Aug 2023
Viewed by 985
Abstract
The chemical evolution of biomolecules was clearly affected by the overall extreme environmental conditions found on Early Earth. Periodic temperature changes inside the Earth’s crust may have played a role in the emergence and survival of functional peptides embedded in vesicular compartments. In [...] Read more.
The chemical evolution of biomolecules was clearly affected by the overall extreme environmental conditions found on Early Earth. Periodic temperature changes inside the Earth’s crust may have played a role in the emergence and survival of functional peptides embedded in vesicular compartments. In this study, all-atom molecular dynamic (MD) simulations were used to elucidate the effect of temperature on the properties of functionalized vesicle membranes. A plausible prebiotic system was selected, constituted by a model membrane bilayer from an equimolar mixture of long-chain fatty acids and fatty amines, and an octapeptide, KSPFPFAA, previously identified as an optimized functional peptide in an evolution experiment. This peptide tends to form the largest spontaneous aggregates at higher temperatures, thereby enhancing the pore-formation process and the eventual transfer of essential molecules in a prebiotic scenario. The analyses also suggest that peptide–amphiphile interactions affect the structural properties of the membrane, with a significant increase in the degree of interdigitation at the lowest temperatures under study. Full article
(This article belongs to the Special Issue Computer Simulation of the Origin of Life)
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13 pages, 2286 KiB  
Article
Order and Complexity in the RNA World
by Christian Mayer
Life 2023, 13(3), 603; https://doi.org/10.3390/life13030603 - 21 Feb 2023
Cited by 1 | Viewed by 2205
Abstract
The basic idea of the RNA world as an early step towards life relies on a molecular evolution process based on self-replicating RNA strands. It is probably the oldest and most convincing model for efficient prebiotic evolution. Obviously, the functionality of RNA sequences [...] Read more.
The basic idea of the RNA world as an early step towards life relies on a molecular evolution process based on self-replicating RNA strands. It is probably the oldest and most convincing model for efficient prebiotic evolution. Obviously, the functionality of RNA sequences depends on order (i.e., the definition of their sequence) as well as on complexity (i.e., the length of their sequence). Order and complexity seem to be crucial parameters in the course of RNA evolution. In the following, an attempt is made to define these parameters and to identify characteristic mechanisms of their development. Using a general RNA world scenario including the free monomer units, the sequential order is defined based on statistical thermodynamics. The complexity, on the other hand, is determined by the size of a minimal algorithm fully describing the system. Under these conditions, a diagonal line in an order/complexity-diagram represents the progress of molecular evolution. Elementary steps such as repeated random polymerization and selection follow characteristic pathways and finally add up to a state of high system functionality. Furthermore, the model yields a thermodynamic perspective on molecular evolution, as the development of a defined polymer sequence has a distinct influence on the entropy of the overall system. Full article
(This article belongs to the Special Issue Computer Simulation of the Origin of Life)
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19 pages, 2431 KiB  
Article
Towards an RNA/Peptides World by the Direct RNA Template Mechanism: The Emergence of Membrane-Stabilizing Peptides in RNA-Based Protocells
by Yu Shi, Chunwu Yu and Wentao Ma
Life 2023, 13(2), 523; https://doi.org/10.3390/life13020523 - 14 Feb 2023
Cited by 1 | Viewed by 1731
Abstract
How functional peptides may have arisen is a significant problem for the scenario of the RNA world. An attractive idea, the direct RNA template (DRT) hypothesis, proposes that RNA molecules can bind amino acids specifically and promote the synthesis of corresponding peptides, thereby [...] Read more.
How functional peptides may have arisen is a significant problem for the scenario of the RNA world. An attractive idea, the direct RNA template (DRT) hypothesis, proposes that RNA molecules can bind amino acids specifically and promote the synthesis of corresponding peptides, thereby starting the RNA/peptides world. To investigate the plausibility of this idea, we modeled the emergence of a “membrane-stabilizing peptide” in RNA-based protocells—such a peptide was suggested to have appeared early in the RNA world based on experimental evidence. The computer simulation demonstrated that the protocells containing the “RNA gene” encoding this peptide may spread in the system owing to the peptide’s function. The RNA gene may either originate de novo in protocells or emerge in protocells already containing ribozymes—here we adopt a nucleotide synthetase ribozyme as an example. Furthermore, interestingly, we show that a “nucleotide synthetase peptide” encoded by RNA (also via the DRT mechanism) may substitute the nucleotide synthetase ribozyme in evolution, which may represent how “functional-takeover” in the RNA world could have occurred. Overall, we conclude that the transition from the RNA world towards an RNA/peptides world may well have been mediated by the DRT mechanism. Remarkably, the successful modeling on the emergence of membrane-stabilizing peptide in RNA-based protocells is per se significant, which may imply a “promising” way for peptides to enter the RNA world, especially considering the weak interaction between RNA and the membrane in chemistry. Full article
(This article belongs to the Special Issue Computer Simulation of the Origin of Life)
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10 pages, 2475 KiB  
Article
Effect of the Addition of the Fifth Amino Acid to [GADV]-Protein on the Three-Dimensional Structure
by Koichi Kato, Tomoki Nakayoshi, Ryota Oyaizu, Natsuko Noda, Eiji Kurimoto and Akifumi Oda
Life 2023, 13(1), 246; https://doi.org/10.3390/life13010246 - 16 Jan 2023
Cited by 1 | Viewed by 1538
Abstract
The [GADV]-protein, consisting only of glycine (G), alanine (A), aspartic acid (D), and valine (V), is frequently studied as a candidate for a primitive protein that existed at the beginning of life on Earth. The number of proteogenic amino acids increased during evolution, [...] Read more.
The [GADV]-protein, consisting only of glycine (G), alanine (A), aspartic acid (D), and valine (V), is frequently studied as a candidate for a primitive protein that existed at the beginning of life on Earth. The number of proteogenic amino acids increased during evolution, and glutamic acid may have been added as the fifth amino acid. In this study, we used molecular dynamics simulations to estimate the conformation of random peptides when glutamate is added to G, A, D, and V ([GADVE]), when leucine is added ([GADVL]), and when the frequency of alanine is doubled ([GADVA]). The results showed that the secondary structure contents of the [GADVE]-peptide and [GADVL]-peptide were higher than that of the [GADVA]-peptide. Although the [GADVL]-peptide had a higher secondary structure formation ability than the [GADVE]-peptide, it was less water soluble, suggesting that it may not be a primitive protein. The [GA(D/E)V]-peptide with G:A:D:V:E = 2:2:1:2:1 according to the occurrence ratio in the codon table also increased the secondary structure contents compared to the [GADV]-peptide, indicating that the addition of glutamic acid increased the structure formation ability of the primitive protein candidates. Full article
(This article belongs to the Special Issue Computer Simulation of the Origin of Life)
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18 pages, 2431 KiB  
Article
Preliminary Free Energy Map of Prebiotic Compounds Formed from CO2, H2 and H2S
by Jeremy Kua and Nicole A. Miller
Life 2022, 12(11), 1763; https://doi.org/10.3390/life12111763 - 02 Nov 2022
Cited by 1 | Viewed by 1640
Abstract
What kinds of CHOS compounds might be formed in a prebiotic milieu by reducing CO2 in the presence of H2 and H2S? How might the presence of sulfur influence the chemical composition of the mixture? We explore these questions [...] Read more.
What kinds of CHOS compounds might be formed in a prebiotic milieu by reducing CO2 in the presence of H2 and H2S? How might the presence of sulfur influence the chemical composition of the mixture? We explore these questions by using first-principles quantum chemistry to calculate the free energies of CHOS compounds in aqueous solution, by first generating a thermodynamic map of one- and two-carbon species. We find that while thiols are thermodynamically favored, thioesters, thioacids, and thiones are less favorable than their non-sulfur counterparts. We then focus on the key role played by mercaptoacetaldehyde in sulfur analogs of the autocatalytic formose reaction, whereby the thiol group introduces asymmetry and potential thermodynamic selectivity of some compounds over others. Full article
(This article belongs to the Special Issue Computer Simulation of the Origin of Life)
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10 pages, 312 KiB  
Article
Autocatalytic Sets Arising in a Combinatorial Model of Chemical Evolution
by Wim Hordijk, Mike Steel and Stuart Kauffman
Life 2022, 12(11), 1703; https://doi.org/10.3390/life12111703 - 26 Oct 2022
Cited by 6 | Viewed by 1595
Abstract
The idea that chemical evolution led to the origin of life is not new, but still leaves open the question of how exactly it could have led to a coherent and self-reproducing collective of molecules. One possible answer to this question was proposed [...] Read more.
The idea that chemical evolution led to the origin of life is not new, but still leaves open the question of how exactly it could have led to a coherent and self-reproducing collective of molecules. One possible answer to this question was proposed in the form of the emergence of an autocatalytic set: a collection of molecules that mutually catalyze each other’s formation and that is self-sustaining given some basic “food” source. Building on previous work, here we investigate in more detail when and how autocatalytic sets can arise in a simple model of chemical evolution based on the idea of combinatorial innovation with random catalysis assignments. We derive theoretical results, and compare them with computer simulations. These results could suggest a possible step towards the (or an) origin of life. Full article
(This article belongs to the Special Issue Computer Simulation of the Origin of Life)
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Graphical abstract

19 pages, 3029 KiB  
Article
Rolling Circles as a Means of Encoding Genes in the RNA World
by Felipe Rivera-Madrinan, Katherine Di Iorio and Paul G. Higgs
Life 2022, 12(9), 1373; https://doi.org/10.3390/life12091373 - 02 Sep 2022
Cited by 2 | Viewed by 1745
Abstract
The rolling circle mechanism found in viroids and some RNA viruses is a likely way that replication could have begun in the RNA World. Here, we consider simulations of populations of protocells, each containing multiple copies of rolling circle RNAs that can replicate [...] Read more.
The rolling circle mechanism found in viroids and some RNA viruses is a likely way that replication could have begun in the RNA World. Here, we consider simulations of populations of protocells, each containing multiple copies of rolling circle RNAs that can replicate non-enzymatically. The mechanism requires the presence of short self-cleaving ribozymes such as hammerheads, which can cleave and re-circularize RNA strands. A rolling circle must encode a hammerhead and the complement of a hammerhead, so that both plus and minus strands can cleave. Thus, the minimal functional length is twice the length of the hammerhead sequence. Selection for speed of replication will tend to reduce circles to this minimum length. However, if sequence errors occur when copying the hammerhead sequence, this prevents cleavage at one point, but still allows cleavage on the next passage around the rolling circle. Thus, there is a natural doubling mechanism that creates strands that are multiple times the length of the minimal sequence. This can provide space for the origin of new genes with beneficial functions. We show that if a beneficial gene appears in this new space, the longer sequence with the beneficial function can be selected, even though it replicates more slowly. This provides a route for the evolution of longer circles encoding multiple genes. Full article
(This article belongs to the Special Issue Computer Simulation of the Origin of Life)
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17 pages, 732 KiB  
Article
The Effect of Environment on the Evolution and Proliferation of Protocells of Increasing Complexity
by Suvam Roy and Supratim Sengupta
Life 2022, 12(8), 1227; https://doi.org/10.3390/life12081227 - 13 Aug 2022
Viewed by 1435
Abstract
The formation, growth, division and proliferation of protocells containing RNA strands is an important step in ensuring the viability of a mixed RNA–lipid world. Experiments and computer simulations indicate that RNA encapsulated inside protocells can favor the protocell, promoting its growth while protecting [...] Read more.
The formation, growth, division and proliferation of protocells containing RNA strands is an important step in ensuring the viability of a mixed RNA–lipid world. Experiments and computer simulations indicate that RNA encapsulated inside protocells can favor the protocell, promoting its growth while protecting the system from being over-run by selfish RNA sequences. Recent work has also shown that the rolling-circle replication mechanism can be harnessed to ensure the rapid growth of RNA strands and the probabilistic emergence and proliferation of protocells with functionally diverse ribozymes. Despite these advances in our understanding of a primordial RNA–lipid world, key questions remain about the ideal environment for the formation of protocells and its role in regulating the proliferation of functionally complex protocells. The hot spring hypothesis suggests that mineral-rich regions near hot springs, subject to dry–wet cycles, provide an ideal environment for the origin of primitive protocells. We develop a computational model to study protocellular evolution in such environments that are distinguished by the occurrence of three distinct phases, a wet phase, followed by a gel phase, and subsequently by a dry phase. We determine the conditions under which protocells containing multiple types of ribozymes can evolve and proliferate in such regions. We find that diffusion in the gel phase can inhibit the proliferation of complex protocells with the extent of inhibition being most significant when a small fraction of protocells is eliminated during environmental cycling. Our work clarifies how the environment can shape the evolution and proliferation of complex protocells. Full article
(This article belongs to the Special Issue Computer Simulation of the Origin of Life)
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