The Martini Model in Materials Science

Alessandri, Riccardo; Grünewald, Fabian; Marrink, Siewert J.

doi:10.1002/adma.202008635

Cited by 66 publications

(71 citation statements)

References 316 publications

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“…MARTINI [69,76,77] is the most popular CG force field. Originally developed to simulate lipid systems [66], it has been extended to proteins [67], polysaccharides [68], nucleic acids [70] and materials science [126]. A major advantage of MARTINI is a standardized coarse-graining scheme, in which chain fragments are merged into sites comprising four non-hydrogen atoms on average, while rings are divided into three-atom fragments.…”

Section: Martinimentioning

confidence: 99%

Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

et al. 2021

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Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications of coarse-grained molecular dynamics. We demonstrate that the motion of coarse-grained sites is governed by the potential of mean force and the friction and stochastic forces, resulting from integrating out the secondary degrees of freedom. Consequently, Langevin dynamics is a natural means of describing the motion of a system at the coarse-grained level and the potential of mean force is the physical basis of the coarse-grained force fields. Moreover, the choice of coarse-grained variables and the fact that coarse-grained sites often do not have spherical symmetry implies a non-diagonal inertia tensor. We describe selected coarse-grained models used in molecular dynamics simulations, including the most popular MARTINI model developed by Marrink’s group and the UNICORN model of biological macromolecules developed in our laboratory. We conclude by discussing examples of the application of coarse-grained molecular dynamics to study biologically important processes.

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Section: Martinimentioning

confidence: 99%

Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

et al. 2021

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“…In the present study, we utilized the popular MARTINI force field for the coarsegrained simulations, which has proved itself as a useful tool for a variety of applications including investigations of interaction between chemical compounds of different nature and biological membranes, membrane pore formation, fusion and disruption, lipid phase transitions, effects of CPEs and detergents on membrane properties, and many more [54,55]. Despite certain limitations of this force field, which does not account explicitly for hydrogen bonds, proper distribution of partial charges, smoother stereochemical interactions resulting in faster diffusion [56], and stickier interactions between proteins (mostly relevant to soluble proteins [57]), it describes the interactions between amphiphilic compounds and biological membranes satisfactorily [58].…”

Section: Coarse-grained Models Of Ethanol Linoleic Acid Lidocaine and Sc Membranementioning

confidence: 99%

“…The resulting topologies are available at https://github.com/porekhov/cg_topologies. [54,55]. Despite certain limitations of this force field, which does not account explicitly for hydrogen bonds, proper distribution of partial charges, smoother stereochemical interactions resulting in faster diffusion [56], and stickier interactions between proteins (mostly relevant to soluble proteins [57]), it describes the interactions between amphiphilic compounds and biological membranes satisfactorily [58].…”

Section: Coarse-grained Models Of Ethanol Linoleic Acid Lidocaine and Sc Membranementioning

confidence: 99%

Synergistic Effect of Chemical Penetration Enhancers on Lidocaine Permeability Revealed by Coarse-Grained Molecular Dynamics Simulations

Bozdaganyan

Orekhov

2021

Membranes

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The search for new formulations for transdermal drug delivery (TDD) is an important field in medicine and cosmetology. Molecules with specific physicochemical properties which can increase the permeability of active ingredients across the stratum corneum (SC) are called chemical penetration enhancers (CPEs), and it was shown that some CPEs can act synergistically. In this study, we performed coarse-grained (CG) molecular dynamics (MD) simulations of the lidocaine delivery facilitated by two CPEs—linoleic acid (LA) and ethanol—through the SC model membrane containing cholesterol, N-Stearoylsphingosine (DCPE), and behenic acid. In our simulations, we probed the effects of individual CPEs as well as their combination on various properties of the SC membrane and the lidocaine penetration across it. We demonstrated that the addition of both CPEs decreases the membrane thickness and the order parameters of the DPCE hydrocarbon chains. Moreover, LA also enhances diffusion of the SC membrane components, especially cholesterol. The estimated potential of mean force (PMF) profiles for the lidocaine translocation across SC in the presence/absence of two individual CPEs and their combination demonstrated that while ethanol lowers the free energy barrier for lidocaine to enter SC, LA decreases the depth of the free energy minima for lidocaine inside SC. These two effects supposedly result in synergistic penetration enhancement of drugs. Altogether, the present simulations provide a detailed molecular picture of CPEs’ action and their synergistic effect on the penetration of small molecular weight therapeutics that can be beneficial for the design of novel drug and cosmetics formulations.

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“…As test cases for the micelle aggregates we selected two surfactant molecules, namely Dodecylphosphocholine (DPC), and Sodium-dodecylsulfate (SDS); both parametrized according to the standard Martini force-field. 52,71 The explicit solvent used for these lipid and surfactant systems was Martini water. The equilibrated structure of the surfactant micelles was obtained via spontaneous self-assembly from dispersed monomers, to obtain a size near the normal size distribution at our conditions.…”

Section: Micelles and Membranes (2d-assemblies)mentioning

confidence: 99%

Classifying soft self-assembled materials via unsupervised machine learning of defects

Gardin¹,

Perego²,

Doni³

et al. 2021

Preprint

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Unlike molecular crystals, soft self-assembled fibres, micelles, vesicles, etc., exhibit a certain order in the arrangement of their constitutive monomers, but also high structural dynamicity and variability. Defects and disordered local domains that continuously form-and-repair in their structures impart to such materials unique adaptive and dynamical properties, which make them, e.g., capable to communicate with each other. However, objective criteria to compare such complex dynamical features and to classify soft supramolecular materials are non-trivial to attain. Here we show a data-driven workflow allowing us to achieve this goal. Building on unsupervised clustering of Smooth Overlap of Atomic Position (SOAP) data obtained from equilibrium molecular dynamics simulations, we can compare a variety of soft supramolecular assemblies via a robust SOAP metric. This provides us with a data-driven "defectometer" to classify different types of supramolecular materials based on the structural dynamics of the ordered/disordered local molecular environments that statistically emerge within them.

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The Martini Model in Materials Science

Cited by 66 publications

References 316 publications

Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

Synergistic Effect of Chemical Penetration Enhancers on Lidocaine Permeability Revealed by Coarse-Grained Molecular Dynamics Simulations

Classifying soft self-assembled materials via unsupervised machine learning of defects

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