Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models

2018 ◽  
Vol 149 (4) ◽  
pp. 044104 ◽  
Author(s):  
Yining Han ◽  
James F. Dama ◽  
Gregory A. Voth
Keyword(s):  
Coarse Grained ◽  
Atomistic Models

Development of hybrid coarse-grained atomistic models for rapid assessment of local structuring of polymeric semiconductors

2022 ◽  
Author(s):  
Maryam Reisjalali ◽  
Rex Manurung ◽  
Paola Carbone ◽  
Alessandro Troisi
Keyword(s):  
Computational Study ◽  
Rapid Assessment ◽  
Semiconducting Polymers ◽  
Coarse Grained ◽  
Atomistic Models

Decades of work in the field of computational study of semiconducting polymers using atomistic models illustrate the challenges of generating equilibrated models for this class of materials. While adopting a...

Towards a Mechanical Model of Skin: Insights into Stratum Corneum Mechanical Properties from Hierarchical Models of Lipid Organisation

2004 ◽  
Vol 844 ◽  
Author(s):  
Brendan O'Malley ◽  
David J. Moore ◽  
Massimo Noro ◽  
Jamshed Anwar ◽  
Becky Notman ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Stratum Corneum ◽  
Mechanical Model ◽  
The Body ◽  
Coarse Grained ◽  
Lipid Matrix ◽  
Lipid Species ◽  
Atomistic Models ◽  
Mesoscale Simulations

ABSTRACTThe stratum corneum (SC), the outermost layer of the skin, provides the body with a physiologically essential barrier to unregulated water loss and the influx of exogenous substances. Furthermore, the 10–20 micron thick SC, composed of overlapping protein-rich corneocytes surrounded by a heterogeneous multilamellar lipid matrix, displays tremendous mechanical cohesion and thermal integrity. To understand the contribution of these components to SC mechanical properties requires building a complete mechanical model of the skin. In this study we focus on modelling the hierarchical microstructure of the lipid phase and its relation to mechanical properties using a combination of atomistic and mesoscale simulations. The modelling approaches are parameterised with experimental data from FT-IR spectroscopy, X-ray scattering and, in the case of the mesoscale simulations, with detailed density profiles derived from atomic models. The atomistic models are used to probe the role of specific lipid species in maintaining the thermal and structural stability of the SC extracellular lipid matrix and to investigate the role of hydrogen bonding networks in SC lipid cohesion. Mesoscale models are used to investigate domain formation and lipid bilayer organisation on length and time scales inaccessible with atomistic models. These coarse grained models display transitions between ordered hexagonal gel phases and fluid phases, reproducing the experimentally observed ordering of the hydrophilic and hydrophobic regions.

Beyond-Mean-Field Treatments of Island Formation during Submonolayer Deposition: Island Size Distributions for Large Critical Sizes

2004 ◽  
Vol 859 ◽  
Author(s):  
Maozhi Li ◽  
Maria C. Bartelt ◽  
J. W. Evans
Keyword(s):  
Critical Size ◽  
Kinetic Monte Carlo ◽  
Mean Field ◽  
Coarse Grained ◽  
Size Distributions ◽  
Island Size ◽  
Island Formation ◽  
Scaling Properties ◽  
Cpu Time ◽  
Atomistic Models

ABSTRACTKinetic Monte Carlo (KMC) simulation of atomistic models reveals the failure of mean-field treatments of the island size distribution (ISD) for islands formed by homogeneous nucleation during submonolayer deposition on perfect surfaces. KMC also facilitates analysis of scaling properties of the ISD, although here some misperceptions persist which we attempt to clarify. However, KMC becomes inefficient for highly reversible island formation (e.g., for large values of a critical size, i, above which islands are stable) due to the high density of diffusing adatoms on the surface. This reduced efficiency is quantified here with results for CPU time versus i. This feature has motivated development of alternative beyond-mean-field coarse-grained approaches which should be more efficient for large i. We provide results for the ISD for a range of i = 1, 2, 3, and 6 using one such approach, a stochastic geometry-based simulation (GBS) strategy.

Parameterization of a coarse-grained model with short-ranged interactions for modeling fuel cell membranes with controlled water uptake

2017 ◽  
Vol 19 (27) ◽  
pp. 17698-17707 ◽  
Author(s):  
Jibao Lu ◽  
Chance Miller ◽  
Valeria Molinero
Keyword(s):  
Fuel Cell ◽  
Activity Coefficient ◽  
Water Uptake ◽  
Coarse Grained ◽  
Fuel Cell Membranes ◽  
Coarse Grained Model ◽  
Experimental Activity ◽  
Tetramethylammonium Chloride ◽  
Atomistic Models ◽  
Wide Range

The coarse-grained model FFpvap reproduces the experimental activity coefficient of water in tetramethylammonium chloride solutions over a wide range of concentrations, with a hundred-fold gain in computing efficiency with respect to atomistic models.

scholarly journals The Automated Optimisation of a Coarse-Grained Force Field Using Free Energy Data

2021 ◽  
Author(s):  
Javier Caceres-Delpiano ◽  
Lee-Ping Wang ◽  
Jonathan Wynne Essex
Keyword(s):  
Free Energy ◽  
Force Field ◽  
Coarse Grained ◽  
Energy Data ◽  
Molecular Systems ◽  
Atomistic Models ◽  
Large Systems ◽  
Long Timescales

Atomistic models provide a detailed representation of molecular systems, but are sometimes inadequate for simulations of large systems over long timescales. Coarse-grained models enable accelerated simulations by reducing the number...

Mesoscale modeling of cement matrix using the concept of building block

2015 ◽  
Vol 1759 ◽  
Author(s):  
Denvid Lau ◽  
Zechuan Yu ◽  
Oral Buyukozturk
Keyword(s):  
Cement Paste ◽  
Building Block ◽  
Time Scale ◽  
Modeling Technique ◽  
Coarse Grained ◽  
Cement Matrix ◽  
Computing Power ◽  
Coarse Grained Model ◽  
Atomistic Models ◽  
Extended Length

ABSTRACTCalcium silicate hydrate (C-S-H) gel is the cohesive phase in cement paste and critically controls the cement hydration. Atomistic models can reproduce reasonable structural and mechanical properties of C-S-H gel at the nano scale. However, the length and time scale of such all-atom modeling technique are restrained by limited computing power. Under this context, coarse-grained modeling technique emerges as a useful alternative for investigating cement paste at extended length and time scale. Here, we regard the building block of cement as ellipsoid and develop a coarse-grained model of cement matrix based on the Gay-Berne (GB) potential. Emphasis of the present paper is on the parameterization and interpretation of the GB potential formula.

scholarly journals The Automated Optimisation of a Coarse-Grained Force Field Using Free Energy Data

2020 ◽  
Author(s):  
Javier Caceres-Delpiano ◽  
Lee-Ping Wang ◽  
Jonathan W. Essex
Keyword(s):  
Free Energy ◽  
Force Field ◽  
Degrees Of Freedom ◽  
Coarse Grained ◽  
Free Energies ◽  
Energy Data ◽  
Molecular Systems ◽  
Atomistic Models ◽  
The Cost ◽  
Long Timescales

AbstractAtomistic models provide a detailed representation of molecular systems, but are sometimes inadequate for simulations of large systems over long timescales. Coarse-grained models enable accelerated simulations by reducing the number of degrees of freedom, at the cost of reduced accuracy. New optimisation processes to parameterise these models could improve their quality and range of applicability. We present an automated approach for the optimisation of coarse-grained force fields, by reproducing free energy data derived from atomistic molecular simulations. To illustrate the approach, we implemented hydration free energy gradients as a new target for force field optimisation in ForceBalance and applied it successfully to optimise the un-charged side-chains and the protein backbone in the SIRAH protein coarse-grain force field. The optimised parameters closely reproduced hydration free energies of atomistic models and gave improved agreement with experiment.

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