Brownian dynamics simulation of polymer collapse in a poor solvent: influence of implicit hydrodynamic interactions

Pham, Tri; Bajaj, Mohit; Prakash, J. Ravi

doi:10.1039/b717350d

Cited by 54 publications

(102 citation statements)

References 44 publications

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“…Thus during the coarsening process, S n (t) ∼ t 0.95±0.08 . We note that similar results were also obtained in the work of Pham et al, 19 but not in other previous works. We also note that the growth exponents for S n (t) is larger than Klushin's 9 and Byrne et al's 15 theoretical predictions.…”

Section: B Kinetics Of the Transitionsupporting

confidence: 80%

“…This is probably the reason that, in implicit solvent models, the conformation of the polymer is frequently trapped in the sausage-like metastable state. 10,19,27,39 The duration of this stage roughly scales as τ 3 6/5 which has a larger exponent than our results. As a result of the coarsening process including second and third stages, the number of clusters decreases and their sizes increase.…”

Section: B Kinetics Of the Transitioncontrasting

confidence: 50%

“…6(b) shows the case at a P S = 60.0k B T /r c .). We note that some other simulation methods, such as Lee and Kapral, 22 Pham et al 19 also reported linear scaling. Lee and Kapral.…”

Section: B Kinetics Of the Transitionmentioning

confidence: 99%

“…However, using the same method, Kikuchi et al 10 obtained τ c ∼ N 4/3 , which agreed well with their own phenomenological model. Pham et al 19 used Brownian dynamics also obtained τ c ∼ N 1.01 , but only for shallow quenches when there is no trapping at the sausage-like stage. We do not have a clear understanding of the discrepancy between the various previous studies.…”

Section: B Kinetics Of the Transitionmentioning

confidence: 99%

“…in which s is the cluster size, i.e., the number of beads in the cluster; n(s) denotes the number of clusters of size s. We follow the same way as other authors to define a cluster, 15,19 i.e., non-bonded beads are considered to be in the same cluster when the separation between each pair of them is less than the cutoff radius r c .…”

Section: Definition Of a Clustermentioning

confidence: 99%

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Coil-to-globule transition by dissipative particle dynamics simulation

Guo

Liang

Wang

2011

The Journal of Chemical Physics

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The dynamics of a collapsing polymer under a temperature quench in dilute solution is investigated by dissipative particles dynamics. Hydrodynamic interactions and many-body interaction are preserved naturally by incorporating explicit solvent particles in this approach. Our simulation suggests a four-stage collapse pathway: localized clusters formation, cluster coarsening in situ, coarsening involving global backbone conformation change into a crumpled globule, and compaction of the globule. For all the quench depths and chain lengths used in our study, collapse proceeds without the chain getting trapped in a metastable "sausage" configuration, as reported in some earlier studies. We obtain the time scales for each of the first three stages, as well as its scaling with the quench depths ξ and chain lengths N . The total collapse time scales as τ c ∼ ξ −0.46±0.04 N 0.98±0.09 , with the quench depth and degree of polymerization.

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Section: B Kinetics Of the Transitionsupporting

confidence: 80%

Section: B Kinetics Of the Transitioncontrasting

confidence: 50%

“…6(b) shows the case at a P S = 60.0k B T /r c .). We note that some other simulation methods, such as Lee and Kapral, 22 Pham et al 19 also reported linear scaling. Lee and Kapral.…”

Section: B Kinetics Of the Transitionmentioning

confidence: 99%

Section: B Kinetics Of the Transitionmentioning

confidence: 99%

Section: Definition Of a Clustermentioning

confidence: 99%

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Coil-to-globule transition by dissipative particle dynamics simulation

Guo

Liang

Wang

2011

The Journal of Chemical Physics

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A multifunctional polymer for optimization of the cement spacers: oil-based drilling fluid removal and rheology regulation

Meng,

Xia,

et al. 2024

Colloid Polym Sci

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Probing solvation decay length in order to characterize hydrophobicity-induced bead–bead attractive interactions in polymer chains

Das

Chakraborty

2010

J Mol Model

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In this paper, we quantitatively demonstrate that exponentially decaying attractive potentials can effectively mimic strong hydrophobic interactions between monomer units of a polymer chain dissolved in aqueous solvent. Classical approaches to modeling hydrophobic solvation interactions are based on invariant attractive length scales. However, we demonstrate here that the solvation interaction decay length may need to be posed as a function of the relative separation distances and the sizes of the interacting species (or beads or monomers) to replicate the necessary physical interactions. As an illustrative example, we derive a universal scaling relationship for a given solute-solvent combination between the solvation decay length, the bead radius, and the distance between the interacting beads. With our formalism, the hydrophobic component of the net attractive interaction between monomer units can be synergistically accounted for within the unified framework of a simple exponentially decaying potential law, where the characteristic decay length incorporates the distinctive and critical physical features of the underlying interaction. The present formalism, even in a mesoscopic computational framework, is capable of incorporating the essential physics of the appropriate solute-size dependence and solvent-interaction dependence in the hydrophobic force estimation, without explicitly resolving the underlying molecular level details.

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Brownian dynamics simulation of polymer collapse in a poor solvent: influence of implicit hydrodynamic interactions

Cited by 54 publications

References 44 publications

Coil-to-globule transition by dissipative particle dynamics simulation

Coil-to-globule transition by dissipative particle dynamics simulation

A multifunctional polymer for optimization of the cement spacers: oil-based drilling fluid removal and rheology regulation

Probing solvation decay length in order to characterize hydrophobicity-induced bead–bead attractive interactions in polymer chains

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