MOLC. A reversible coarse grained approach using anisotropic beads for the modelling of organic functional materials

Ricci, Matteo; Roscioni, Otello Maria; Querciagrossa, Lara; Zannoni, Claudio

doi:10.1039/c9cp04120f

Cited by 27 publications

(55 citation statements)

References 72 publications

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“…The following table reports recent studies aimed at comparing the different force fields for studying Aβ peptides in explicit water, as recently summarized [206]. Considering the well-known limitations of all-atom MD simulations, research effort is being focused on the development of reliable coarse-grained forcefield for protein structures [214] and complex organic molecules [215]. Several manuscripts in literature have applied a coarse-grained or hybrid all-atom /coarse-grained approach to study the spontaneous oligomerization of AB 1-40 and AB 1-42 [61][62][63][64].…”

Section: Appropriate Selection Of Molecular Force Fieldmentioning

confidence: 99%

Molecular simulations of amyloid beta assemblies

Grasso

Danani

2020

Advances in Physics: X

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Several neurodegenerative disorders arise from the abnormal protein aggregation in the nervous tissue leading tointracellular inclusions or extracellular aggregates in specific brain areas. In case of Alzheimer Disease, the accumulation of the Amyloid Beta peptide in the brain is proposed to be an early important event in the pathogenesis. Despite significant research efforts in this field, the molecular mechanisms of protein misfolding and aggregation remain somewhat unrevealed.Within this framework, computer simulations represent a powerful tool able to connect macroscopic experimental findings to nanoscale molecular events.However, from the computational point of view, insufficient sampling often limits the ability of computer simulations to fully address this point. One of the main challenges of MD simulations is the ability to sample experimentally relevant millisecond to second timescales.The present review describes the applications of molecular dynamics techniques to elucidate the conformational states and the aggregation pathway of the Amyloid Beta peptide responsible for AD. Moreover, the computational studies focused on the impact of Amyloid Beta assemblies on cell membranes will be also described. Finally, the interaction mechanisms between promising small molecules and Amyloid Beta assemblies will be discussed within the field of designing new efficient drugs against neurodegenerative disorders.

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Section: Appropriate Selection Of Molecular Force Fieldmentioning

confidence: 99%

Molecular simulations of amyloid beta assemblies

Grasso

Danani

2020

Advances in Physics: X

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“…The MOLC force field has been described in detail elsewhere. 16 In the MOLC model, the electrostatic interactions are accounted for via virtual sites acting as point charges (see Figure 1 a,b). The sites are placed within a skin distance from the external surface of a parent CG particle, i.e., an ellipsoid.…”

Section: Methodsmentioning

confidence: 99%

“…This work explores the tantalizing possibility of carrying out CG-MD simulations of liquid water with near-atomistic quality using the MOLC model, 16 which is available as a user-defined package for the popular materials modeling code LAMMPS. 17 , 18 The CG models of water presented in this work use one site to represent the whole molecule but with the possibility to host an arbitrary number of virtual charges to account for realistic electrostatic interactions.…”

Section: Introductionmentioning

confidence: 99%

Anisotropic Electrostatic Interactions in Coarse-Grained Water Models to Enhance the Accuracy and Speed-Up Factor of Mesoscopic Simulations

Bellussi

Roscioni²,

Ricci³

et al. 2021

J. Phys. Chem. B

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Water models with realistic physical–chemical properties are essential to study a variety of biomedical processes or engineering technologies involving molecules or nanomaterials. Atomistic models of water are constrained by the feasible computational capacity, but calibrated coarse-grained (CG) ones can go beyond these limits. Here, we compare three popular atomistic water models with their corresponding CG model built using finite-size particles such as ellipsoids. Differently from previous approaches, short-range interactions are accounted for with the generalized Gay–Berne potential, while electrostatic and long-range interactions are computed from virtual charges inside the ellipsoids. Such an approach leads to a quantitative agreement between the original atomistic models and their CG counterparts. Results show that a timestep of up to 10 fs can be achieved to integrate the equations of motion without significant degradation of the physical observables extracted from the computed trajectories, thus unlocking a significant acceleration of water-based mesoscopic simulations at a given accuracy.

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“…LAMMPS also allows particles to have directional attributes as well as other custom attributes created by the user. In the MOLC model [31], large organic molecules are represented in terms of ellipsoidal beads connected by directional bonds.…”

Section: Particles With Custom Attributes Mesoscale Modeling Requirementioning

confidence: 99%

Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics

Jewett

Stelter

Lambert

et al. 2021

Journal of Molecular Biology

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256

144

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This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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MOLC. A reversible coarse grained approach using anisotropic beads for the modelling of organic functional materials

Abstract: We describe the development and implementation of a new reversible coarse grained model where complex organic molecules are described in terms of a set of connected biaxial Gay–Berne ellipsoidal beads, decorated with point charges.

Cited by 27 publications

References 72 publications

Molecular simulations of amyloid beta assemblies

Molecular simulations of amyloid beta assemblies

Anisotropic Electrostatic Interactions in Coarse-Grained Water Models to Enhance the Accuracy and Speed-Up Factor of Mesoscopic Simulations

Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics

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