Coarse grain models and the computer simulation of soft materials

Nielsen, Steven O.; López, Carlos F.; Srinivas, Goundla; Klein, Michael L.

doi:10.1088/0953-8984/16/15/r03

Cited by 456 publications

(418 citation statements)

References 161 publications

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“…By minimizing the residual (1) with respect to the elements of the force table, and employing the definitions in eq (7)-eq (9), a system of linear algebraic equations is obtained: (10) in which (11) and (12) The angular brackets denote an average over configurations sampled by the atomistic MD simulation. In the following analysis it will be assumed that this average over configurations is equivalent to the appropriate ensemble average: (13) The linear system in eq (10) is referred to as the "normal" MS-CG equations because G dd′ is a symmetric, i.e.…”

Section: Force-matching To a Central Pair Potentialmentioning

confidence: 99%

“…Since the j = k term has not been excluded from the triple sum in eq (12), the quantity G dd′ includes both two-and three-particle correlations, which may be explicitly separated and analyzed: (14) (15) (16) The quantity counts the number of distinct CG sites separated by a distance r d and is closely related to the radial distribution function for the CG sites. The quantity is a direct measure of three-particle correlations between CG sites in atomistic MD simulations.…”

Section: Force-matching To a Central Pair Potentialmentioning

confidence: 99%

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Multiscale Coarse-Graining and Structural Correlations: Connections to Liquid-State Theory

et al. 2007

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(2005)]. If no approximations are made, the MS-CG method yields a many-body multi-dimensional potential of mean force describing the interactions between CG sites. However, numerical applications of the MS-CG method typically employ a set of pair potentials to describe non-bonded interactions. The analogy between coarse-graining and the inverse problem of liquid state theory clarifies the general significance of three-particle correlations for the development of such CG pair potentials. It is demonstrated that the MS-CG methodology incorporates critical three-body correlation effects and that, for isotropic homogeneous systems evolving under a central pair potential, the MS-CG equations are a discretized representation of the well-known Yvon-Born-Green equation. Numerical calculations validate the theory and illustrate the role of these structural correlations in the MS-CG method.

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Section: Force-matching To a Central Pair Potentialmentioning

confidence: 99%

Section: Force-matching To a Central Pair Potentialmentioning

confidence: 99%

Multiscale Coarse-Graining and Structural Correlations: Connections to Liquid-State Theory

et al. 2007

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“…In order to simulate such systems efficiently and reasonably, researchers are increasingly turning to coarse-grained models [2,20]. Since the early works of Telo da Gama and Gubbins [21] and Smit [22], several researchers have proposed coarsegrained (CG) models with varying levels of detail.…”

Section: Coarse-grained Modelingmentioning

confidence: 99%

“…Since the early works of Telo da Gama and Gubbins [21] and Smit [22], several researchers have proposed coarsegrained (CG) models with varying levels of detail. A recent review outlines previous work, summarizes the consequences from coarse-graining and provides a sampling of typical results that can be expected [20]. One approach towards developing reasonable coarsegrained models is to limit the scope of the applicability.…”

Section: Coarse-grained Modelingmentioning

confidence: 99%

Equation of state for a coarse-grained DPPC monolayer at the air/water interface

Adhangale

Gaver

2006

Molecular Physics

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Pulmonary surfactant, a complex mixture of phospholipids and proteins, secreted by the type II epithelial cells in the lungs, is crucial to reducing the effort required for breathing. A lack of adequate amounts of pulmonary surfactant in underdeveloped lungs of premature infants results in infant respiratory distress syndrome (RDS). Surfactant replacement therapy (SRT) is the approved method of mitigating the effects of RDS. The development of new SRT regimens requires a fundamental understanding of the links between surfactant biochemistry and functionality. We use a coarse-grained (CG) model to predict the surface pressure-surface concentration relationship (equation of state) for pure DPPC, which is a major component of endogenous and synthetic pulmonary surfactant mixtures. We show that the model can be efficiently used to predict the equation of state in excellent agreement with experimental results. We also study the structure of the monolayer as a function of the surface tension of the system. We show that a decrease in the applied surface tension results in an increase in order in the head group region and a decrease in order in the tail region of DPPC. This technique may be useful in the prediction of equations of state for surfactant replacements.

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“…is far from trivial and it is still the norm that CG descriptions neglect some or all many-body effects [15][16][17][18]. Thus for polymers one might replace each chain by a set of one or more 'blobs' which interact via a pair potential such as the potential of mean force [19].…”

mentioning

confidence: 99%

Quantifying the effects of neglecting many-body interactions in coarse-grained models of complex fluids

Ashton

Wilding

2014

Phys. Rev. E

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We describe a general simulation scheme for assessing the thermodynamic consequences of neglecting many-body effects in coarse-grained models of complex fluids. The method exploits the fact that the asymptote of a simple-to-measure structural function provides direct estimates of virial coefficients. Comparing the virial coefficients of an atomistically detailed system with those of a coarse-grained version described by pair potentials, permits the role of many-body effects to be quantified. The approach is applied to two models: (i) a size-asymmetrical colloid-polymer mixture, and (ii) a solution of star polymers. In the latter case, coarse-graining to an effective fluid described by pair potentials is found to neglect important aspects of the true behaviour.Many-body forces occur when the net interaction between two particles is not simply pairwise additive, but depends on the presence of other particles. They appear in a wide range of physical systems including dense phases of noble gases [1], molecular systems [2], nuclear matter [3], superconductors [4] and complex fluids such as polymers [5], lipid membranes [6,7] and colloidal dispersions [8][9][10][11]. In seeking to make theoretical and computational progress with such systems one often attempts to simplify matters by "coarse-graining" ie. integrating over the degrees of freedom on small length or times scales. This leads to a description of the system in term of an effective Hamiltonian describing the interactions among the remaining degrees of freedom. These interactions are inherently many-body in character, even if the original system involves only pairwise interactions.To appreciate how many-body interactions arise in coarse-grained (CG) representations of complex fluids, consider the case of colloids dispersed in a sea of much smaller polymers. This system is commonly modelled as a highly size-asymmetrical mixture of spheres as shown in the simulation snapshot of Fig. 1(a). However, since dealing with components of disparate sizes is theoretically and computationally problematic, one typically seeks to integrate out the polymer degrees of freedom to yield an effective one-component model. But the colloidal interactions arise from the modulation of the polymer density distribution by all the colloids, and consequently, the effective one-component description is many-body in form. A second example is shown in Fig. 1(b) which depicts three star polymers in solution. A common CG model replaces each star by a single effective particle. However, the net interaction between two polymers depends on the proximity of a third, and hence the effective Hamiltonian has a many-body character [12].Computer simulation is a powerful route for designing CG models for complex fluids, which is currently receiving considerable attention. Indeed, in principle it can be used to determine a many-body potential for the CG coordinates which is consistent with the underlying atomistic model [13,14]. But implementing such approaches (Color online).(a) Snapshot of a highly siz...

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Coarse grain models and the computer simulation of soft materials

Cited by 456 publications

References 161 publications

Multiscale Coarse-Graining and Structural Correlations: Connections to Liquid-State Theory

Multiscale Coarse-Graining and Structural Correlations: Connections to Liquid-State Theory

Equation of state for a coarse-grained DPPC monolayer at the air/water interface

Quantifying the effects of neglecting many-body interactions in coarse-grained models of complex fluids

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