DOI: 10.5061/dryad.866t1g1qs
title: Evolution towards increasing complexity through functional diversification in a protocell model of the RNA world

description: The encapsulation of genetic material inside compartments together with
 the creation and sustenance of functionally diverse internal components
 are likely to have been key steps in the formation of ’live’, replicating
 protocells in an RNA world. Several experiments have shown that RNA
 encapsulated inside lipid vesicles can lead to vesicular growth and
 division through physical processes alone. Replication of RNA inside such
 vesicles can produce a large number of RNA strands. Yet, the impact of
 such replication processes on the emergence of the first ribozymes inside
 such protocells and on the subsequent evolution of the protocell
 population remains an open question. In this paper, we present a model for
 the evolution of protocells with functionally diverse ribozymes. Distinct
 ribozymes can be created with small probabilities during the error-prone
 RNA replication process via the rolling circle mechanism. We identify the
 conditions that can synergistically enhance the number of different
 ribozymes inside a protocell and allow functionally diverse protocells
 containing multiple ribozymes to dominate the population. Our work
 demonstrates the existence of an effective pathway towards increasing
 complexity of protocells that might have eventually led to the origin of
 life in an RNA world.
description: The data was collected through computer simulations using Python.
 The detailed algorithm is given in  the electronic supplementary material
 (ESM) file associated with the paper titled
 "Roy-Sengupta_figures_tables_ESM". All the parameter values used
 for generating the specific figures given in the main text as well as in
 the ESM are specified in the respective figure captions.
description: Python codes and data files used for generating results given in
 the main text: Main_code: Can be used to generate the
 data files for Fig-2, 3, 4, S6, S7, S8 and S9 by properly modifying the
 code. The current<br> Code will generate the data files for
 Fig-4 data_Fig_2A : Actually the data file for Fig.2C;
 Column-1 corresponds to time, Column-2, 6, 7, 9 gives the abundance of RC,
 R, C and null protocells data_Fig_2B : Data file for
 Fig.2B. Column-1 corresponds to time, Column-2, 6, 7, 9 gives the
 abundance of RC, R, C and null protocells data_Fig_2C :
 Data file for Fig.2A. Column-1 corresponds to time, Column-2, 6, 7, 9
 gives the abundance of RC, R, C and null protocells
 heatmap-data_Fig_2D : Data file for Fig.2D
 data_Fig_3A : Data file for Fig.3A. Column-1 stands for time, 
 Column-2, 3, 4, 5, 6, 7, 8, 9 for abundance of RC, CN, RN, RCN, R, C, N
 and null protocells data_Fig_3B : Data file for
 Fig.3B.  Column-1 stands for time,  Column-2, 3, 4, 5, 6, 7, 8, 9 for
 abundance of RC, CN, RN, RCN, R, C, N and null protocells
 data_Fig_3C : Data file for Fig.3C. Column-1 stands for time, 
 Column-2, 3, 4, 5, 6, 7, 8, 9 for abundance of RC, CN, RN, RCN, R, C, N
 and null protocells data_Fig_3D : Data file for Fig.3D.
 Column-1 stands for time,  Column-2, 3, 4, 5, 6, 7, 8, 9 for abundance of
 RC, CN, RN, RCN, R, C, N and null protocells
 data_Fig_4A : Data file for Fig.4A with k=30. Column-1, 4 stands
 for time and average volume respectively data_Fig_4B :
 Data file for Fig.4B. Column-1, 2, 3 stands for time, abundance of RCNP
 and null protocells respectively. data_Fig_4C_4A : Data
 file for Fig.4C and also for Fig. 4A with k=20. Column-1, 2, 3, 4 stands
 for time, abundance of RCNP and null protocells and average volume
 respectively.
 =========================================
 Python codes and data files used for generating results given in
 the Supplementary material Python
 Codes Code_for_data_Fig_S1.py : Code used to
 generate data for Fig.S1 Code_for_data_Fig_S2.py : Code
 used to generate data for Fig.S2 Code_Fig_S4.py : Code
 to generate Fig.S4 Code_Fig_S5.py : Code to generate
 Fig.S5 Data Files
 data_Fig_S1.txt data file for Fig-S1. Column-1, 2 stands for temperature and probability of exponential growth respectively data_Fig_S2A_t_27.txt data file for Fig-S2A for temp=27 C. Column-1, 2 stands for time and number of strands respectively data_Fig_S2A_t_37.txt data file for Fig-S2A for temp=37 C. Column-1, 2stands for time and number of strands respectively data_Fig_S2A_t_45.txt data file for Fig-S2A for temp=45 C. Column-1, 2 stands for time and number of strands respectively data_Fig_S2A_t_50.txt data file for Fig-S2A for temp=50 C. Column-1, 2 stands for time and number of strands respectively data_Fig_S2A_t_55.txt data file for Fig-S2A for temp=55 C. Column-1, 2 stands for time and number of strands respectively data_Fig_S2B_t_27.txt data file for Fig-S2B for temp=27 C. Column-1, 2 stands for time and number of strands respectively data_Fig_S2B_t_37.txt data file for Fig-S2B for temp=37 C. Column-1, 2 stands for time and number of strands respectively data_Fig_S2B_t_45.txt data file for Fig-S2B for temp=45 C. Column-1, 2 stands for time and number of strands respectively data_Fig_S2B_t_50.txt data file for Fig-S2B for temp=50 C. Column-1, 2 stands for time and number of strands respectively data_Fig_S2B_t_55.txt data file for Fig-S2B for temp=55 C. Column-1, 2 for time and number of strands respectively data_Fig_S6A.txt data file for Fig-S6A. Column-1, 2, 3 for time,<br> Abundance of RCN and null protocells respectively data_Fig_S6B.txt data file for Fig-S6B. Column-1, 2, 3 for time,<br> Abundance of RCN and null protocells respectively data_Fig_S6C.txt data file for Fig-S6. Column-1, 2, 3 for time,<br> Abundance of RCN and null protocells respectively data_Fig_S7_S8_dividing_cells.txt data file for Fig-S7,S8 in case of dividing cells. Column-1, 2, 3, 4, 5, 6 stands for number of replicase, cyclase, nucleotide synthase, peptidyl transferase, all ribozymes and non-catalytic open-ended strands inside a dividing cell respectively data_Fig_S7_S8_dying_cells.txt data file for Fig-S7,S8 in case of dying cells. Column-1, 2, 3, 4, 5, 6 for number of replicase, cyclase, nucleotide synthase, peptidyl transferase, all ribozymes and non-catalytic Open-ended strands inside a dividing cell respectively data_Fig_S9A.txt data file for Fig-S9A. Column-1, 2, 3 stands for time,<br> Abundance of RCNP and null protocells respectively data_Fig_S9B.txt data file for Fig-S9B. Column-1, 2, 3 stands for time,<br> Abundance of RCNP and null protocells respectively rate0.txt Template-directed primer extension rates after a match<br> For different templating bases and incoming monomers rate1.txt Template-directed primer extension rates after a mis-match for different templating bases and incoming monomers