Replication of simulated prebiotic amphiphile vesicles controlled by experimental lipid physicochemical properties
Abstract
We present a new embodiment of the graded autocatalysis replication domain (GARD) for the growth, replication and evolution of lipid vesicles based on a semi-empirical foundation using experimentally measured kinetic values of selected extant lipid species. Extensive simulations using this formalism elucidated the details of the dependence of the replication and properties of the vesicles on the physicochemical properties and concentrations of the lipids, both in the environment and in the vesicle. As expected, the overall concentration and number of amphiphilic components strongly affect average replication time. Furthermore, variations in acyl chain length and unsaturation of vesicles also influence replication rate, as do the relative concentrations of individual lipid types. Understanding of the dependence of replication rates on physicochemical parameters opens a new direction in the study of prebiotic vesicles and lays the groundwork for future studies involving the competition between lipid vesicles for available amphiphilic monomers.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
R-GARD, using experimentally measured kinetic values for true phospholipids and cholesterol, fully confirmed standard GARD dynamics, including homeostatic growth and composome emergence.
“This closer-to-nature model fully confirmed the standard GARD dynamics, including homeostatic growth and composome emergence.”
From Systems protobiology: origin of life in lipid catalytic networks (2018) · cites this paper as [60]
In R-GARD simulations with a finite supply of amphiphiles, complex kinetic behaviour including inter-assembly competition was transiently observed.
“In such simulations, we were able to transiently observe complex kinetic behaviour, including inter-assembly competition.”
From Systems protobiology: origin of life in lipid catalytic networks (2018) · cites this paper as [60]
GARD is much less abstract than many other models for life's origin because it uses rigorous chemical kinetic equations, and it is the only model in its genre that uses experiment-based graded catalytic parameters and in two papers also the properties of real lipid molecules.
“This is wrong: in using rigorous chemical kinetic equations, GARD is much less abstract than many other models for life's origin. Further, it is the only model in its genre that uses experiment-based graded catalytic parameters (§4) and in two papers also the properties of real lipid molecules [60,119].”
From Systems protobiology: origin of life in lipid catalytic networks (2018) · cites this paper as [60]
Cites
The antiquity of RNA-based evolution.
Joyce, G. F. (2002) · Nature · doi:10.1038/418214a · Cited by 1,070 · see citing works
Segré, D., Ben-Eli, D., Deamer, D. W., & Lancet, D. (2001) · Origins of life and evolution of the biosphere · doi:10.1023/a:1006746807104 · Cited by 620 · see citing works
Self-citationThe Emergence of Competition Between Model Protocells
Chen, I. A., Roberts, R. W., & Szostak, J. W. (2004) · Science · doi:10.1126/science.1100757 · Cited by 435 · see citing works
Compositional genomes: Prebiotic information transfer in mutually catalytic noncovalent assemblies
Segré, D., Ben-Eli, D., & Lancet, D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.8.4112 · Cited by 398 · see citing works
Self-citationDeamer, D. W., & Pashley, R. M. (1989) · Origins of life and evolution of the biosphere · doi:10.1007/bf01808285 · Cited by 272 · see citing works
Self-assembling amphiphilic molecules: Synthesis in simulated interstellar/precometary ices
Dworkin, J. P., Deamer, D. W., Sandford, S. A., & Allamandola, L. J. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.98.3.815 · Cited by 244 · see citing works
The origin of the RNA world: Co-evolution of genes and metabolism
Copley, S. D., Smith, E., & Morowitz, H. J. (2007) · Bioorganic Chemistry · doi:10.1016/j.bioorg.2007.08.001 · Cited by 184 · see citing works
Expanding roles for diverse physical phenomena during the origin of life
Budin, I., & Szostak, J. W. (2010) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.050708.133753 · Cited by 171 · see citing works
The Molecular Roots of Compositional Inheritance
SEGRÉ, D., SHENHAV, B., KAFRI, R., & LANCET, D. (2001) · Journal of Theoretical Biology · doi:10.1006/jtbi.2001.2440 · Cited by 82 · see citing works
Self-citationCoevolution of compositional protocells and their environment
Shenhav, B., Oz, A., & Lancet, D. (2007) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2007.2073 · Cited by 40 · see citing works
Self-citationMutations and Lethality in Simulated Prebiotic Networks
Inger, A., Solomon, A., Shenhav, B., Olender, T., & Lancet, D. (2009) · Journal of Molecular Evolution · doi:10.1007/s00239-009-9281-y · Cited by 14 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Systems protobiology: origin of life in lipid catalytic networks
Lancet, D., Zidovetzki, R., & Markovitch, O. (2018) · Journal of The Royal Society Interface · doi:10.1098/rsif.2018.0159 · Cited by 182 · see citing works
Self-citationPredicting species emergence in simulated complex pre-biotic networks
Markovitch, O., & Krasnogor, N. (2018) · PLOS ONE · doi:10.1371/journal.pone.0192871 · Cited by 19 · see citing works
Self-citation
- Authors
- Armstrong, D. L., Markovitch, O., Zidovetzki, R., & Lancet, D.
- Affiliations
- University of California, Riverside (US)
- Weizmann Institute of Science (IL)
- Venue
- Physical Biology
- Publisher
- IOP Publishing
- Published
- 2011-09-26
- Volume
- 8
- Issue
- 6
- Pages
- 066001
- ISSN
- 1478-3967 (ISSN-L)
- 1478-3975
- OpenAlex
- W2065980053
- Cited by
- 9
- References
- 11
- Citations by year
- 2023: 1 · 2022: 2 · 2019: 1 · 2018: 3 · 2014: 1 · 2012: 1
- FWCI
- 0.34
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Physical Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation
- Topics
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- acyl chain length, lipid unsaturation, semi-empirical kinetic model, origin of life
- MeSH terms
- Computer Simulation, Kinetics, Lipid Bilayers, Lipids, Liposomes, Micelles, Models, Biological, Models, Chemical, Surface-Active Agents, Thermodynamics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
