Macromol. Theory Simul. 7/2011

Kauzlarić, David; Español, Pep; Greiner, Andreas; Succi, Sauro

doi:10.1002/mats.201190014

Cited by 7 publications

(10 citation statements)

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“…Inorganic materials: DPD has also been used for the CG modeling of solid inorganic materials. Coarsegrained representation of graphene turns out to be essential for study of large scale resonator technology [170,278].…”

Section: Systems Studied With Dpdmentioning

confidence: 99%

Perspective: Dissipative particle dynamics

Español

Warren

2017

The Journal of Chemical Physics

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488

392

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Dissipative particle dynamics (DPD) belongs to a class of models and computational algorithms developed to address mesoscale problems in complex fluids and soft matter in general. It is based on the notion of particles that represent coarse-grained portions of the system under study and allow, therefore, reaching time and length scales that would be otherwise unreachable from microscopic simulations. The method has been conceptually refined since its introduction almost twenty five years ago. This perspective surveys the major conceptual improvements in the original DPD model, along with its microscopic foundation, and discusses outstanding challenges in the field. We summarize some recent advances and suggest avenues for future developments.

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Section: Systems Studied With Dpdmentioning

confidence: 99%

Perspective: Dissipative particle dynamics

Español

Warren

2017

The Journal of Chemical Physics

Self Cite

488

392

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“…with respect to the equilibrium distribution, for a generic function F = F (γ) acting on the phase space and for a specific value of the coarse-grained variables Γ(γ) = Γ [46]. An alternative approach, the so-called Mori projection [32], can be seen as a finite-dimensional linear approximation of the Zwanzig projection [47]; in certain cases it can be shown that the Mori projection and the Zwanzig projection are approximately equivalent [47].…”

Section: A the Mori-zwanzig Equationsmentioning

confidence: 99%

“…( 6)). Different ways to consider the friction matrix were reported [19,47] as well as to include memory effects in CG simulations, [37,[76][77][78].…”

Section: Markovian Approximation Of the Memory Kernelmentioning

confidence: 99%

Systematic derivation of hybrid coarse-grained models

2019

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“…Since identifying the projection with a conditional expectation will be useful for the following sections, we provide a more detailed discussion in the SM. An alternative approach, the so-called Mori projection [32], can be seen as a finite-dimensional linear approximation of the Zwanzig projection [45]; in certain cases it can be shown that the Mori projection and the Zwanzig projection are approximately equivalent [45].…”

Section: A the Mori-zwanzig Equationsmentioning

confidence: 99%

“…( 6)). Different ways to consider the friction matrix were reported [17,45] as well as to include memory effects in CG simulations, [37,[63][64][65].…”

Section: Markovian Approximation Of the Memory Kernelmentioning

confidence: 99%

Systematic derivation of hybrid coarse-grained models

Di Pasquale,

Hudson,

Icardi

2018

Preprint

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Molecular dynamics represents a key enabling technology for applications ranging from biology to the development of new materials. However, many real-world applications remain inaccessible to fully-resolved simulations due their unsustainable computational costs and must therefore rely on semi-empirical coarse-grained models. Significant efforts have been devoted in the last decade towards improving the predictivity of these coarse-grained models and providing a rigorous justification of their use, through a combination of theoretical studies and data-driven approaches. One of the most promising research effort is the (re)discovery of the Mori-Zwanzig projection as a generic, yet systematic, theoretical tool for deriving coarse-grained models. Despite its clean mathematical formulation and generality, there are still many open questions about its applicability and assumptions. In this work, we propose a detailed derivation of a hybrid multi-scale system, generalising and further investigating the approach developed in [Español, P., EPL, 88, 40008 (2009)]. Issues such as the general coexistence of atoms (fully-resolved degrees of freedom) and beads (larger coarse-grained units), the role of the fine-to-coarse mapping chosen, and the approximation of effective potentials are discussed. The theoretical discussion is supported by numerical simulations of a monodimensional nonlinear periodic benchmark system with an open-source parallel Julia code, easily extensible to arbitrary potential models and fine-to-coarse mapping functions. The results presented highlight the importance of introducing, in the macroscopic model, non-constant fluctuating and dissipative terms, given by the Mori-Zwanzig approach, to correctly reproduce the reference fine-grained results, without requiring ad-hoc calibration of interaction potentials and thermostats. a

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Macromol. Theory Simul. 7/2011

Cited by 7 publications

References 0 publications

Perspective: Dissipative particle dynamics

Perspective: Dissipative particle dynamics

Systematic derivation of hybrid coarse-grained models

Systematic derivation of hybrid coarse-grained models

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