A Discrete Approximation to Gibbs Free Energy of Chemical Reactions is Needed for Accurately Calculating Entropy Production in Mesoscopic Simulations

Floyd, Carlos; Papoian, Garegin A.; Jarzynski, Christopher

doi:10.48550/arxiv.1901.10520

Cited by 1 publication

(2 citation statements)

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“…upon leveraging the sizes of N i,A and N i,B relative to 1. The derivation of the above results can be found in an accompanying paper [38].…”

Section: ∆G Of Chemical Reactionsmentioning

confidence: 92%

“…For the present purpose of measuring dissipation, we introduced into this simulation protocol a precise formula for the change in Gibbs free energy corresponding to the occurrence of various reactions as a function of the instantaneous compartment concentrations. In the Supplementary Information we establish this formula, while we present its derivation in an accompanying paper [38]. The set of chemical reactions used to describe actomyosin networks in this study is based on a previous model of actin polymerization dynamics that explicitly treats hydrolysis states of the nucleotide bound to each actin subunit [39,40].…”

Section: Measuring Dissipation In Medyanmentioning

confidence: 99%

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Quantifying dissipation in actomyosin networks

2019

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Quantifying entropy production in various active matter phases will open new avenues for probing self-organization principles in these far-from-equilibrium systems. It has been hypothesized that the dissipation of free energy by active matter systems may be optimized, leading to system trajectories with histories of large dissipation and an accompanying emergence of ordered dynamical states. This interesting idea has not been widely tested. In particular, it is not clear whether emergent states of actomyosin networks, which represent a salient example of biological active matter, self-organize following the principle of dissipation optimization. In order to start addressing this question using detailed computational modelling, we rely on the MEDYAN simulation platform, which allows simulating active matter networks from fundamental molecular principles. We have extended the capabilities of MEDYAN to allow quantification of the rates of dissipation resulting from chemical reactions and relaxation of mechanical stresses during simulation trajectories. This is done by computing precise changes in Gibbs free energy accompanying chemical reactions using a novel formula and through detailed calculations of instantaneous values of the system’s mechanical energy. We validate our approach with a mean-field model that estimates the rates of dissipation from filament treadmilling. Applying this methodology to the self-organization of small disordered actomyosin networks, we find that compact and highly cross-linked networks tend to allow more efficient transduction of chemical free energy into mechanical energy. In these simple systems, we observe that spontaneous network reorganizations tend to result in a decrease in the total dissipation rate to a low steady-state value. Future studies might carefully test whether the dissipation-driven adaptation hypothesis applies in this instance, as well as in more complex cytoskeletal geometries.

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“…upon leveraging the sizes of N i,A and N i,B relative to 1. The derivation of the above results can be found in an accompanying paper [38].…”

Section: ∆G Of Chemical Reactionsmentioning

confidence: 92%