An Implicit Solvent Ionic Strength (ISIS) Method to Model Polyelectrolyte Systems with Dissipative Particle Dynamics

Li, Nan K.; Fuss, William H.; Yingling, Yaroslava G.

doi:10.1002/mats.201400043

Cited by 16 publications

(18 citation statements)

References 35 publications

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“…As an attempt to address this issue, the polarizable MARTINI water model was developed by including a positively charged particle and a negatively charged particle inside each CG bead, similar to that of the Drude oscillator . Explicit CG water models can also be used with implicit ions, as in the implicit solvent ionic strength method for DPD simulations that is capable of modeling large‐scale salt responsive morphology of polyeletrolytes …”

Section: Coarse‐grained Water Modelsmentioning

confidence: 99%

Water models for biomolecular simulations

Onufriev

Izadi²

2017

WIREs Comput Mol Sci

176

225

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Modern simulation and modeling approaches to investigation of biomolecular structure and function rely heavily on a variety of methods—water models—to approximate the influence of solvent. We give a brief overview of several distinct classes of available water models, with the emphasis on the conceptual basis at each level of approximation. The main focus is on classes of models most widely used in atomistic simulations, including popular implicit and explicit solvent models. Among the latter, nonpolarizable N‐point models are covered in most detail, including some recent methodological advances and nuances. Notes on practical availability and usage in biomolecular simulations are included. Atomistic simulations that were hardly possible only a short while ago have revealed significant problems that can be traced to deficiencies of most commonly used N‐point water models. Recently developed models of this class approximate experimental properties of liquid water much closer than before, and show promise in practical biomolecular simulations. Obstacles to wider adoption of these more accurate water models, both technical and conceptual, are discussed. It is argued that verifying robustness of simulation results to the choice of water model can be of immediate benefit even in the absence of a clear replacement for older models; a specific strategy is proposed. The review is concluded with a discussion on how force‐field development efforts can benefit from better solvent models, and vice versa. WIREs Comput Mol Sci 2018, 8:e1347. doi: 10.1002/wcms.1347 This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods

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Section: Coarse‐grained Water Modelsmentioning

confidence: 99%

Water models for biomolecular simulations

Onufriev

Izadi²

2017

WIREs Comput Mol Sci

176

225

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“…The properties of a single polyelectrolyte chain in an infinitely diluted situation were parameterized to produce scaling relations of

R_{normalg} \approx c_{normals}^{- 0.18}

D_{ee} \approx c_{normals}^{- 0.20}

, and

l_{normalp} \approx c_{normals}^{- 0.375}

, where R g is the radius of gyration, D ee is the end‐to‐end distance, l p is the persistence length, and c s is the solvent ionic strength. These scaling relations agree with the results from previous studies . Initially, triblock chains were randomly homogeneously mixed with solvent at a desired volume fraction.…”

Section: Resultsmentioning

confidence: 99%

“…Initially, triblock chains were randomly homogeneously mixed with solvent at a desired volume fraction. Within the framework of the ISIS‐DPD model, the solvent ionic strength is represented by repulsive parameters between polyelectrolyte beads a pp = a ii + a elec , where a ii = 25 and a elec is inversely proportional to salt concentration (

c_{normals}^{- 1})

. In our study, a pp was varied between 25 (high solvent ionic strength) and 90 (low solvent ionic strength), which corresponds to the salt‐dominated regime …”

Section: Resultsmentioning

confidence: 99%

“…Further decrease in solvent ionic strength (at a pp ≥ 45) leads, however, to an increase in the percentage of bridge chains up to 55%. In our previous study, a scaling relation between persistence length ( l p ) and solvent ionic strength ( c s ) for a single polyelectrolyte was obtained as

l_{normalp} \propto c_{normals}^{- 0.375}

. At low solvent ionic strength, the polyelectrolyte block is semi‐flexible due to the electrostatic repulsion between charged monomers, which prevents the chain from adopting a loop‐like conformation, and consequently more bridges are formed.…”

Section: Resultsmentioning

confidence: 99%

“…Only a few studies are available in which the canonical molecular simulation techniques, including molecular dynamics, Monte Carlo, and density functional theory, were used to probe the polyelectrolyte network structure during the gelation process . To overcome these limitations we have recently developed an implicit solvent ionic strength model for dissipative particle dynamics (ISIS‐DPD) which permits large‐scale simulation of polyelectrolytes self‐assembly . Our model was successfully applied to the prediction of salt‐induced morphological changes of diblock polyelectrolyte copolymers and their scaling relations between micellar size parameters and solvent ionic strength or block length .…”

Section: Introductionmentioning

confidence: 99%

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Salt Responsive Morphologies of ssDNA‐Based Triblock Polyelectrolytes in Semi‐Dilute Regime: Effect of Volume Fractions and Polyelectrolyte Length

Kuang

Fuss

et al. 2017

Macromol. Rapid Commun.

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A comprehensive study is reported on the effect of salt concentration, polyelectrolyte block length, and polymer concentration on the morphology and structural properties of nanoaggregates self-assembled from BAB single-strand DNA (ssDNA) triblock polynucleotides in which A represents polyelectrolyte blocks and B represents hydrophobic neutral blocks. A morphological phase diagram above the gelation point is developed as a function of solvent ionic strength and polyelectrolyte block length utilizing an implicit solvent ionic strength method for dissipative particle dynamics simulations. As the solvent ionic strength increases, the self-assembled DNA network structures shrinks considerably, leading to a morphological transition from a micellar network to worm-like or hamburger-shape aggregates. This study provides insight into the network morphology and its changes by calculating the aggregation number, number of hydrophobic cores, and percentage of bridge chains in the network. The simulation results are corroborated through cryogenic transmission electron microscopy on the example of the self-assembly of ssDNA triblocks.

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Simulation Study of the Conformational Properties of Diblock Polyelectrolytes in Salt Solutions

Dabhade

Chaudhury

2021

Chemistry An Asian Journal

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Coarse‐grained molecular dynamics simulations are performed to understand the behavior of diblock polyelectrolytes in solutions of divalent salt by studying the conformations of chains over a wide range of salt concentrations. The polymer molecules are modeled as bead spring chains with different charged fractions and the counterions and salt ions are incorporated explicitly. Upon addition of a divalent salt, the salt cations replace the monovalent counterions, and the condensation of divalent salt cations onto the polyelectrolyte increases, and the chains favor to collapse. The condensation of ions changes with the salt concentration and depends on the charged fraction. Also, the degree of collapse at a given salt concentration changes with the increasing valency of the counterion due to the bridging effect. As a quantitative measure of the distribution of counterions around the polyelectrolyte chain, we study the radial distribution function between monomers on different polyelectrolytes and the counterions inside the counterion worm surrounding a polymer chain at different concentrations of the divalent salt. Our simulation results show a strong dependence of salt concentration on the conformational properties of diblock copolymers and indicate that it can tune the self‐assembly behaviors of such charged polyelectrolyte block copolymers.

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An Implicit Solvent Ionic Strength (ISIS) Method to Model Polyelectrolyte Systems with Dissipative Particle Dynamics

Cited by 16 publications

References 35 publications

Water models for biomolecular simulations

Water models for biomolecular simulations

Salt Responsive Morphologies of ssDNA‐Based Triblock Polyelectrolytes in Semi‐Dilute Regime: Effect of Volume Fractions and Polyelectrolyte Length

Simulation Study of the Conformational Properties of Diblock Polyelectrolytes in Salt Solutions

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