DOI: 10.5061/dryad.kh18932hr
title: Data from: Reciprocating thermochemical mediator of pre-biotic polymer decomposition on mineral surfaces

description: 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.  
description: 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. 
description: # Reciprocating thermochemical mediator: Open Source Script --- [Access
 this script via Dryad](https://doi.org/10.5061/dryad.kh18932hr) 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](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-&gt;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.