First assembly times and equilibration in stochastic coagulation-fragmentation

D’Orsogna, Maria R.; Lei, Qi; Chou, Tom

doi:10.1063/1.4923002

Cited by 9 publications

(7 citation statements)

References 39 publications

(54 reference statements)

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“…3(d)) and the system is prone to depletion traps. A similar broadening of the size distribution has been reported in the context of stochastic coagulation-fragmentation of identical particles 38 .…”

Section: Resultssupporting

confidence: 80%

Stochastic Yield Catastrophes and Robustness in Self-Assembly

Gartner

Graf

Wilke

et al. 2019

Preprint

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A guiding principle in self-assembly is that, for high production yield, nucleation of structures must be significantly slower than their growth. However, details of the mechanism that impedes nucleation are broadly considered irrelevant. Here, we analyze self-assembly into finite-sized target structures employing mathematical modeling. We investigate two key scenarios to delay nucleation: (i) by introducing a slow activation step for the assembling constituents and, (ii) by decreasing the dimerization rate. These scenarios have widely different characteristics. While the dimerization scenario exhibits robust behavior, the activation scenario is highly sensitive to demographic fluctuations. These demographic fluctuations ultimately disfavor growth compared to nucleation and can suppress yield completely. The occurrence of this stochastic yield catastrophe does not depend on model details but is generic as soon as number fluctuations between constituents are taken into account. On a broader perspective, our results reveal that stochasticity is an important limiting factor for self-assembly and that the specific implementation of the nucleation process plays a significant role in determining the yield.

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Section: Resultssupporting

confidence: 80%

Stochastic Yield Catastrophes and Robustness in Self-Assembly

Gartner

Graf

Wilke

et al. 2019

Preprint

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“…A number of generalization of this model could be considered and will be relevant to tackle new biophysical problems. One could generalize this study to allow general coagulation-fragmentation between any two clusters 48 . This extension as well as the treatment of heterogeneous nucleation and secondary pathways will be considered in future work.…”

Section: Discussionmentioning

confidence: 99%

First passage times in homogeneous nucleation: Dependence on the total number of particles

Yvinec

Bernard

Hingant

et al. 2016

The Journal of Chemical Physics

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Motivated by nucleation and molecular aggregation in physical, chemical, and biological settings, we present an extension to a thorough analysis of the stochastic self-assembly of a fixed number of identical particles in a finite volume. We study the statistics of times required for maximal clusters to be completed, starting from a pure-monomeric particle configuration. For finite volumes, we extend previous analytical approaches to the case of arbitrary size-dependent aggregation and fragmentation kinetic rates. For larger volumes, we develop a scaling framework to study the first assembly time behavior as a function of the total quantity of particles. We find that the mean time to first completion of a maximum-sized cluster may have a surprisingly weak dependence on the total number of particles. We highlight how higher statistics (variance, distribution) of the first passage time may nevertheless help to infer key parameters, such as the size of the maximum cluster. Finally, we present a framework to quantify formation of macroscopic sized clusters, which are (asymptotically) very unlikely and occur as a large deviation phenomenon from the mean-field limit. We argue that this framework is suitable to describe phase transition phenomena, as inherent infrequent stochastic processes, in contrast to classical nucleation theory.

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“…A more recent stochastic treatment has revealed interesting digitization phenomena (20) that persist even when Eq. 1 is extended to include coagulation and fragmentation (21). Cooperativity was not considered in these studies, and importantly, the impact of signaling noise and the ensuing effects on signaling fidelity remain unexplored.…”

Section: Methodsmentioning

confidence: 99%

Cooperative Clustering Digitizes Biochemical Signaling and Enhances its Fidelity

Roob

Trendel

Wolde

et al. 2016

Biophysical Journal

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Many membrane-bound molecules in cells form small clusters. It has been hypothesized that these clusters convert an analog extracellular signal into a digital intracellular signal and that this conversion increases signaling fidelity. However, the mechanism by which clusters digitize a signal and the subsequent effects on fidelity remain poorly understood. Here we demonstrate using a stochastic model of cooperative cluster formation that sufficient cooperation leads to digital signaling. We show that despite reducing the number of output states, which decreases fidelity, digitization also reduces noise in the system, which increases fidelity. The tradeoff between these effects leads to an optimal cluster size that agrees with experimental measurements.

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First assembly times and equilibration in stochastic coagulation-fragmentation

Cited by 9 publications

References 39 publications

Stochastic Yield Catastrophes and Robustness in Self-Assembly

Stochastic Yield Catastrophes and Robustness in Self-Assembly

First passage times in homogeneous nucleation: Dependence on the total number of particles

Cooperative Clustering Digitizes Biochemical Signaling and Enhances its Fidelity

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