Glucans monomer-exchange dynamics as an open chemical network

Self Cite

Kinetic theory and thermodynamics of reaction networks are extended to the out-of-equilibrium dynamics of continuous-flow stirred tank reactors (CSTR) and serial transfers. On the basis of their stoichiometry matrix, the conservation laws and the cycles of the network are determined for both dynamics. It is shown that the CSTR and serial transfer dynamics are equivalent in the limit where the time interval between the transfers tends to zero proportionally to the ratio of the fractions of fresh to transferred solutions. These results are illustrated with a finite cross-catalytic reaction network and an infinite reaction network describing mass exchange between polymers. Serial transfer dynamics is typically used in molecular evolution experiments in the context of research on the origins of life. The present study is shedding a new light on the role played by serial transfer parameters in these experiments.

Section: Example With An Infinite Networkmentioning

confidence: 71%

“…We now move to a more complex reaction network, namely the model of polymers undergoing a massexchange process taken from Ref. 28. In this model, two polymers of mass n and m interact with the reaction…”

Section: Example With An Infinite Networkmentioning

confidence: 99%

Reaction kinetics in open reactors and serial transfers between closed reactors

Blokhuis

Lacoste

Gaspard

2018

Self Cite

“…Concerning (iii), one way to describe the coupling of a system to an environment is to introduce chemostats which impose that the concentration of certain polymers be fixed. We have found in previous work that such models have a rich dynamics even for polymers which have no sequences 41 . Such an approach based on Stochastic Thermodynamics was extended for general chemical networks in Ref 20 .…”

Section: Discussionmentioning

confidence: 99%

“…This list is updated for every subsequent reaction step and changes in ∆s L and ∆s ω are calculated from Eq. (41).…”

Section: Simulations With Energetically Neutral Reactionsmentioning

confidence: 99%

Length and sequence relaxation of copolymers under recombination reactions

Blokhuis

Lacoste

2017

Self Cite

We describe the kinetics and thermodynamics of copolymers undergoing recombination reactions, which are important for prebiotic chemistry. We use two approaches: the first one, based on chemical rate equations and the mass-action law describes the infinite size limit, while the second one, based on the chemical master equation, describes systems of finite size. We compare the predictions of both approaches for the relaxation of thermodynamic quantities towards equilibrium. We find that for some choice of initial conditions, the entropy of the sequence distribution can be lowered at the expense of increasing the entropy of the length distribution. We consider mainly energetically neutral reactions, except for one simple case of non-neutral reactions.

“…Remark For CRN with infinite number of species and reactions-e.g. aggregation-fragmentation and polymerization processes [46][47][48]-the CRN may undergo steady growth regimes in which ∆G is not subextensive in time and cannot be neglected in long-time limit. TABLE II.…”

Section: A Entropy Productionmentioning

confidence: 99%

Conservation laws and work fluctuation relations in chemical reaction networks

Rao

Esposito

2018

Self Cite

We formulate a nonequilibrium thermodynamic description for open chemical reaction networks (CRN) described by a chemical master equation. The topological properties of the CRN and its conservation laws are shown to play a crucial role. They are used to decompose the entropy production into a potential change and two work contributions, the first due to time dependent changes in the externally controlled chemostats concentrations and the second due to flows maintained across the system by nonconservative forces. These two works jointly satisfy a Jarzynski and Crooks fluctuation theorem. In absence of work, the potential is minimized by the dynamics as the system relaxes to equilibrium and its equilibrium value coincides with the maximum entropy principle. A generalized Landauer's principle also holds: the minimal work needed to create a nonequilibrium state is the relative entropy of that state to its equilibrium value reached in absence of any work.