Data from: Reciprocating thermochemical mediator of pre-biotic polymer decomposition on mineral surfaces
Data files
Nov 26, 2024 version files 6.97 KB
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README.md
2.18 KB
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reciprocator.ode
2.15 KB
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reciprocator.ode.set
2.64 KB
Abstract
A continuing frustration for origin of life scientists is that abiotic and, by extension, pre-biotic attempts to develop self-sustaining, evolving molecular systems tend to produce more dead-end substances than macromolecular products with the necessary potential for biostructure and function – the so-called 'tar problem'. Nevertheless, primordial life somehow emerged despite that presumed handicap. A resolution of this problem is important in emergence-of-life science because it would provide valuable guidance in choosing subsequent paths of investigation, such as identifying pre-biotic patterns on Mars. To study the problem we set up a simple non-equilibrium flow dynamical model for the coupled temperature and mass dynamics of the decomposition of a polymeric carbohydrate adsorbed on a mineral surface, with incident stochastic thermal fluctuations. Results show that the model system behaves as a reciprocating thermochemical oscillator. The output fluctuation distribution is bimodal, with a right-weighted component that guarantees a bias towards detachment and desorption of monomeric species such as ribose, even while tar is formed concomitantly. This fluctuating thermochemical reciprocator may ensure that non-performing polymers can be fractionated into a refractory carbon reservoir and active monomers which may be reincorporated into better-performing polymers with less vulnerability towards adsorptive tarring.
README: Reciprocating thermochemical mediator: Open Source Script
The XPPAUT script (reciprocator.ode) to generate Figure 3 and Figure 4 in 'Reciprocating thermochemical mediator of pre-biotic polymer decomposition on mineral surfaces' has been uploaded to Dryad.
The XPPAUT-generated file (reciprocator.ode.set) has been uploaded to Dryad.
Description of the open source software XPPAUT and the script reciprocator.ode and the file reciprocator.ode.set
XPPAUT is required to run the reciprocator.ode script.
XPPAUT is a powerful and capable software tool for solving differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations.
Download and install XPPAUT for your computer from https://sites.pitt.edu/~phase/bard/bardware/xpp/xpp.html
XPPAUT is easy to use. Read the documentation and run a few of the tutorial/example .ode files provided on the download site or in the downloaded package.
The reciprocator.ode script may be opened and edited in any text editor.
The script contains the equations in the form required by XPPAUT plus all of the associated parameter and variable definitions and necessary system settings.
If you run reciprocator.ode you may find it interesting to change the values of some of the parameters and see what happens, or change the integrator or time step, or investigate the numerics->stochast menu
The reciprocator.ode.set file is a data file that has been generated and output by XPPAUT on running the script reciprocator.ode. It is an ASCII file that is human and computer readable. It contains all the numerics and system settings data used for a run of reciprocator.ode.
All necessary documentation for the software package and many tutorials are accessible at the XPPAUT download site.
A useful published book reference is:
G. B. Ermentrout. Simulating, Analyzing, and Animating Dynamical Systems: A Guide to XPPAUT for Researchers and Students. SIAM, Philadelphia, 2002}. ISBN:978-0-89871-506-4.
Methods
The file reciprocator.ode is an XPPAUT script used to generate Figure 3 and Figure 4 in:
Ball, R. and Brindley, J. 2024. Reciprocating thermochemical mediator of pre-biotic polymer decomposition on mineral surfaces. J. R. Soc. Interface, accepted manuscript rsif-2024-0492.R2
The file reciprocator.ode.set was generated by running XPPAUT on reciprocator.ode and contains all numerical data and system settings for a particular run.