Computational Modeling of Protocell Competition: Insights into Prebiotic Evolution and Viral Membrane Origins(Estimated Calculation Simulation)
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2025
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| _version_ | 1866902164157235200 |
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| author | Reza Hashemi |
| author_facet | Reza Hashemi |
| contents | <p>The divergence of cellular and viral lineages from primitive protocells remains a pivotal question in evolutionary biology. This study employs multi-scale computational modeling to explore how resource competition among protocells under prebiotic conditions drove the emergence of prokaryotic and viral-like systems. Two protocell models were simulated: a viral-like protocell with a gp10 protein-based envelope, inspired by bacteriophage T4, and a prokaryotic-like protocell composed of prebiotically plausible phospholipid vesicles. Using quantum mechanics/molecular mechanics (QM/MM), reactive force fields (ReaxFF), constant-pH molecular dynamics (CpHMD), graph neural networks (GNNs), and 3D stochastic modeling, we demonstrate that competition for limited resources (nucleotides and pyrophosphate) under prebiotic conditions (pH 5.5–8.5, 40–70°C, 5–15% oxidative stress) prompted viral-like protocells to parasitize lipid-based protocells. This process likely contributed to the origin of host-dependent viral membranes, supporting the Matter World Hypothesis (MWH). While consistent with prior computational studies and international benchmarks, the findings are simulation-based and require experimental validation to confirm their biological relevance.All findings in this study are derived from advanced simulations and thus require empirical validation before drawing definitive conclusions.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_15281977 |
| institution | Zenodo |
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| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Computational Modeling of Protocell Competition: Insights into Prebiotic Evolution and Viral Membrane Origins(Estimated Calculation Simulation) Reza Hashemi Protocell, prebiotic competition, viral evolution, prokaryotic lineage, gp10 envelope, phospholipid vesicles, Matter World Hypothesis, computational modeling <p>The divergence of cellular and viral lineages from primitive protocells remains a pivotal question in evolutionary biology. This study employs multi-scale computational modeling to explore how resource competition among protocells under prebiotic conditions drove the emergence of prokaryotic and viral-like systems. Two protocell models were simulated: a viral-like protocell with a gp10 protein-based envelope, inspired by bacteriophage T4, and a prokaryotic-like protocell composed of prebiotically plausible phospholipid vesicles. Using quantum mechanics/molecular mechanics (QM/MM), reactive force fields (ReaxFF), constant-pH molecular dynamics (CpHMD), graph neural networks (GNNs), and 3D stochastic modeling, we demonstrate that competition for limited resources (nucleotides and pyrophosphate) under prebiotic conditions (pH 5.5–8.5, 40–70°C, 5–15% oxidative stress) prompted viral-like protocells to parasitize lipid-based protocells. This process likely contributed to the origin of host-dependent viral membranes, supporting the Matter World Hypothesis (MWH). While consistent with prior computational studies and international benchmarks, the findings are simulation-based and require experimental validation to confirm their biological relevance.All findings in this study are derived from advanced simulations and thus require empirical validation before drawing definitive conclusions.</p> |
| title | Computational Modeling of Protocell Competition: Insights into Prebiotic Evolution and Viral Membrane Origins(Estimated Calculation Simulation) |
| topic | Protocell, prebiotic competition, viral evolution, prokaryotic lineage, gp10 envelope, phospholipid vesicles, Matter World Hypothesis, computational modeling |
| url | https://doi.org/10.5281/zenodo.15281977 |