arXiv subjects

Jenny M. Poulton

Publications and source records attributed to Jenny M. Poulton.

3 recordsLinked to original sources

arXiv2025

Thermodynamic limits on general far-from-equilibrium molecular templating networks

Cells produce RNA and proteins via molecular templating networks. We show that information transmission in such networks is bounded by functions of a simple thermodynamic property of the network, regardless of complexity. Surprisingly, putative systems operating at this bound do not have a high flux around the network. Instead, they have low entropy production, with each product in a ``pseudo-equilibrium'' determined by a single pathway. These pseudo-equilibrium limits constrain information transmission for the overall network, even if individual templates are arbitrarily specific.

physics.bio-ph↗

arXiv2023

Evolution with recombination as a Metropolis-Hastings sampling procedure

This work presents a population genetic model of evolution, which includes haploid selection, mutation, recombination, and drift. The mutation-selection equilibrium can be expressed exactly in closed form for arbitrary fitness functions without resorting to diffusion approximations. Tractability is achieved by generating new offspring using n-parent rather than 2-parent recombination. While this enforces linkage equilibrium among offspring, it allows analysis of the whole population under linkage disequilibrium. We derive a general and exact relationship between fitness fluctuations and response to selection. Our assumptions allow analytical calculation of the stationary distribution of the model for a variety of non-trivial fitness functions. These results allow us to speak to genetic architecture, i.e., what stationary distributions result from different fitness functions. This paper presents methods for exactly deriving stationary states for finite and infinite populations. This method can be applied to many fitness functions, and we give exact calculations for four of these. These results allow us to investigate metastability, tradeoffs between fitness functions, and even consider error-correcting codes

q-bio.PE↗

arXiv2023

A Universal Method for Analysing Copolymer Growth

Polymers consisting of more than one type of monomer, known as copolymers, are vital to both living and synthetic systems. Copolymerisation has been studied theoretically in a number of contexts, often by considering a Markov process in which monomers are added or removed from the growing tip of a long copolymer. To date, the analysis of the most general models of this class has necessitated simulation. We present a general method for analysing such processes without resorting to simulation. Our method can be applied to models with an arbitrary network of sub-steps prior to addition or removal of a monomer, including non-equilibrium kinetic proofreading cycles. Moreover, the approach allows for a dependency of addition and removal reactions on the neighbouring site in the copolymer, and thermodynamically self-consistent models in which all steps are assumed to be microscopically reversible. Using our approach, thermodynamic quantities such as chemical work; kinetic quantities such as time taken to grow; and statistical quantities such as the distribution of monomer types in the growing copolymer can be derived either analytically or numerically directly from the model definition.

physics.chem-ph↗