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Michael A. Seaton

Publications and source records attributed to Michael A. Seaton.

5 recordsLinked to original sources

Highly coarse-grained polarisable water models for mesoscopic simulations

Modelling micro- and meso-scopic scale thermodynamic and transport properties of soft condensed matter hinges upon its representation. This is especially relevant for polar solvents such as water, since these require effective representation of their dielectric nature as driven by molecular charge distributions and molecular network structuring. The dielectric nature of a medium leads to complex phenomena such as local polarisability response and restructuring near interfaces in reaction to changes in local charge distributions. Inclusion of such phenomena when using larger-than-atomistic techniques such as coarse-grained molecular dynamics (CG-MD) and dissipative particle dynamics (DPD) is still an open question, to which we provide a novel way to consider and justify the necessary and suitable coarse-graining level, enabling us to compare new polar CG models' performance against that of an underlying atomistic model. We polarise our previous non-polar nDPD water model to prepare it for use in simulations of liquid electrolytes as well as solvated organic membranes and measure its fitness to serve as a dielectric medium by comparing its properties to those of the TIP3P water model, while simultaneously observing changes to properties already represented well by the non-polar model.

cond-mat.soft↗

Polarisable soft solvent models with applications in dissipative particle dynamics

We critically examine a broad class of explicitly polarisable soft solvent models aimed at applications in dissipative particle dynamics. We obtain the dielectric permittivity using the fluctuating box dipole method in linear response theory, and verify the models in relation to several test cases including demonstrating ion desorption from an oil-water interface due to image charge effects. We additionally compute the Kirkwood factor and find it uniformly lies in the range gK approx 0.7-0.8, indicating that dipole-dipole correlations are not negligible in these models. This is supported by measurements of dipole-dipole correlation functions. As a consequence, Onsager theory over-predicts the dielectric permittivity by approximately 20-30 percent. On the other hand, the mean square molecular dipole moment can be accurately estimated with a first-order Wertheim perturbation theory.

cond-mat.soft↗

Semantic interoperability based on the European Materials and Modelling Ontology and its ontological paradigm: Mereosemiotics

The European Materials and Modelling Ontology (EMMO) has recently been advanced in the computational molecular engineering and multiscale modelling communities as a top-level ontology, aiming to support semantic interoperability and data integration solutions, e.g., for research data infrastructures. The present work explores how top-level ontologies that are based on the same paradigm - the same set of fundamental postulates - as the EMMO can be applied to models of physical systems and their use in computational engineering practice. This paradigm, which combines mereology (in its extension as mereotopology) and semiotics (following Peirce's approach), is here referred to as mereosemiotics. Multiple conceivable ways of implementing mereosemiotics are compared, and the design space consisting of the possible types of top-level ontologies following this paradigm is characterized.

cs.AI↗

Ontologies for the Virtual Materials Marketplace

The Virtual Materials Marketplace (VIMMP) project, which develops an open platform for providing and accessing services related to materials modelling, is presented with a focus on its ontology development and data technology aspects. Within VIMMP, a system of marketplace-level ontologies is developed to characterize services, models, and interactions between users; the European Materials and Modelling Ontology (EMMO) is employed as a top-level ontology. The ontologies are used to annotate data that are stored in the ZONTAL Space component of VIMMP and to support the ingest and retrieval of data and metadata at the VIMMP marketplace frontend.

cs.DB↗

Electronic effects in high-energy radiation damage in tungsten

Although the effects of the electronic excitations during high-energy radiation damage processes are not currently understood, it is shown that their role in the interaction of radiation with matter is important. We perform molecular dynamics simulations of high-energy collision cascades in bcc-tungsten using the coupled two-temperature molecular dynamics (2T-MD) model that incorporates both the effects of electronic stopping and electron-phonon interaction. We compare the combination of these effects on the induced damage with only the effect of electronic stopping, and conclude in several novel insights. In the 2T-MD model, the electron-phonon coupling results in less damage production in the molten region and in faster relaxation of the damage at short times. These two effects lead to significantly smaller amount of the final damage at longer times.

cond-mat.mtrl-sci↗