Applications of computational geometry to the molecular simulation of interfaces

Usabiaga, Florencio Balboa; Duque, Daniel

doi:10.1103/physreve.79.046709

Cited by 18 publications

(11 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Usually, this implies applying some criteria to decide which atoms belong to the liquid phase, followed by a decision as to which of such atoms lie on the surface (pivot atoms). 15,46,54,56,57 This task cannot be done at atomic scale resolution without some degree of arbitrariness. 57 In this work, we have adopted the ISM, 46 which is quite time-consuming but provides results that are very much consistent with the capillary wave theory.…”

Section: Characterization Of Adsorbed Interfaces Using Computer Simulmentioning

confidence: 99%

Nanocapillarity and Liquid Bridge-Mediated Force between Colloidal Nanoparticles

et al. 2018

View full text Add to dashboard Cite

In this work, we probe the concept of interface tension for ultrathin adsorbed liquid films on the nanoscale by studying the surface fluctuations of films down to the monolayer. Our results show that the spectrum of film height fluctuations of a liquid–vapor surface may be extended to ultrathin films provided we take into account the interactions of the substrate with the surface. Global fluctuations of the film height are described in terms of disjoining pressure, whereas surface deformations that are proportional to the interface area are accounted for by a film thickness-dependent surface tension. As a proof of concept, we model the capillary forces between colloidal nanoparticles held together by liquid bridges. Our results indicate that the classical equations for capillarity follow very precisely down to the nanoscale provided we account for the film height dependence of the surface tension.

show abstract

Section: Characterization Of Adsorbed Interfaces Using Computer Simulmentioning

confidence: 99%

Nanocapillarity and Liquid Bridge-Mediated Force between Colloidal Nanoparticles

et al. 2018

View full text Add to dashboard Cite

show abstract

“…The new GITIM method consistently reproduces the results of ITIM in the planar case while retaining the ability to describe arbitrarily shaped surfaces. To the best of our knowledge, the concept of α-shapes has been employed in the determination of intrinsic densities at fluid interfaces only once before, by Usabiaga and Duque, 36 who also noticed the formal similarities between the α-shapes algorithm and ITIM.…”

Section: Introductionmentioning

confidence: 99%

The generalized identification of truly interfacial molecules (ITIM) algorithm for nonplanar interfaces

Sega¹,

Kantorovich²,

Jedlovszky³

et al. 2013

The Journal of Chemical Physics

112

View full text Add to dashboard Cite

We present a generalized version of the ITIM algorithm for the identification of interfacial molecules, which is able to treat arbitrarily shaped interfaces. The algorithm exploits the similarities between the concept of probe sphere used in ITIM and the circumsphere criterion used in the α-shapes approach, and can be regarded either as a reference-frame independent version of the former, or as an extended version of the latter that includes the atomic excluded volume. The new algorithm is applied to compute the intrinsic orientational order parameters of water around a dodecylphosphocholine and a cholic acid micelle in aqueous environment, and to the identification of solvent-reachable sites in four model structures for soot. The additional algorithm introduced for the calculation of intrinsic density profiles in arbitrary geometries proved to be extremely useful also for planar interfaces, as it allows to solve the paradox of smeared intrinsic profiles far from the interface.

show abstract

“…[34][35][36][37][38][39][40][41][42][43][44][45] Other typical examples of the utility of the Voronoi construction are the analysis of solvation shells, [46][47][48][49] clustering and chemical association. 36,[50][51][52] The Voronoi construction has also been employed to define the interface between two systems [53][54][55] and to obtain structural information of pure water. 50,[56][57][58][59][60][61][62] and water solutions 36,[63][64][65][66][67][68][69] More closely related with the goals of this work is its application to detect different types of cavities such as pores, pockets, clefts, channels and docking sites.…”

Section: Introductionmentioning

confidence: 99%

Homogeneous bubble nucleation in water at negative pressure: A Voronoi polyhedra analysis

Abascal

Gonzalez

Aragonés

et al. 2013

The Journal of Chemical Physics

View full text Add to dashboard Cite

We investigate vapor bubble nucleation in metastable TIP4P/2005 water at negative pressure via the Mean First Passage Time (MFPT) technique using the volume of the largest bubble as a local order parameter. We identify the bubbles in the system by means of a Voronoi-based analysis of the molecular dynamics trajectories. By comparing the features of the tessellation of liquid water at ambient conditions to those of the same system with an empty cavity we are able to discriminate vapor (or interfacial) molecules from the bulk ones. This information is used to follow the time evolution of the largest bubble until the system cavitates at 280 K above and below the spinodal line. At the pressure above the spinodal line, the MFPT curve shows the expected shape for a moderately metastable liquid from which we estimate the bubble nucleation rate and the size of the critical cluster. The nucleation rate estimated using Classical Nucleation Theory turns out to be about 8 order of magnitude lower than the one we compute by means of MFPT. The behavior at the pressure below the spinodal line, where the liquid is thermodynamically unstable, is remarkably different, the MFPT curve being a monotonous function without any inflection point.

show abstract

Applications of computational geometry to the molecular simulation of interfaces

Cited by 18 publications

References 47 publications

Nanocapillarity and Liquid Bridge-Mediated Force between Colloidal Nanoparticles

Nanocapillarity and Liquid Bridge-Mediated Force between Colloidal Nanoparticles

The generalized identification of truly interfacial molecules (ITIM) algorithm for nonplanar interfaces

Homogeneous bubble nucleation in water at negative pressure: A Voronoi polyhedra analysis

Contact Info

Product

Resources

About