Chacon E.,CSIC - Institute of Materials Science |
Chacon E.,Autonomous University of Madrid |
Tarazona P.,Autonomous University of Madrid |
Tarazona P.,Condensed Matter Physics Center
Journal of Physics Condensed Matter | Year: 2016
We study the link between the density functional (DF) formalism and the capillary wave theory (CWT) for liquid surfaces, focused on the Landau-Ginzburg-Wilson (LGW) model, or square gradient DF expansion, with a symmetric double parabola free energy, which has been extensively used in theoretical studies of this problem. We show the equivalence between the non-local DF results of Parry and coworkers and the direct evaluation of the mean square fluctuations of the intrinsic surface, as is done in the intrinsic sampling method for computer simulations. The definition of effective wave-vector dependent surface tensions is reviewed and we obtain new proposals for the LGW model. The surface weight proposed by Blokhuis and the surface mode analysis proposed by Stecki provide consistent and optimal effective definitions for the extended CWT Hamiltonian associated to the DF model. A non-local, or coarse-grained, definition of the intrinsic surface provides the missing element to get the mesoscopic surface Hamiltonian from the molecular DF description, as had been proposed a long time ago by Dietrich and coworkers. © 2016 IOP Publishing Ltd.
Marcos-Alcalde I.,Molecular Modelling Group |
Setoain J.,Complutense University of Madrid |
Mendieta-Moreno J.I.,Molecular Modelling Group |
Mendieta-Moreno J.I.,Condensed Matter Physics Center |
And 3 more authors.
Bioinformatics | Year: 2015
From conformational studies to atomistic descriptions of enzymatic reactions, potential and free energy landscapes can be used to describe biomolecular systems in detail. However, extracting the relevant data of complex 3D energy surfaces can sometimes be laborious. In this article, we present MEPSA (Minimum Energy Path Surface Analysis), a cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective. Some of its most relevant features are: identification of all the barriers and minima of the landscape at once, description of maxima edge profiles, detection of the lowest energy path connecting two minima and generation of transition state theory diagrams along these paths. In addition to a built-in plotting system, MEPSA can save most of the generated data into easily parseable text files, allowing more versatile uses of MEPSA's output such as the generation of molecular dynamics restraints from a calculated path. © The Author 2015. Published by Oxford University Press. All rights reserved.
Martin F.,Autonomous University of Madrid |
Martin F.,Condensed Matter Physics Center |
Martin F.,Instituto Madrileno Of Estudios Avanzados En Nanociencia |
Cheng Y.,University of Central Florida |
And 7 more authors.
Journal of Physics: Conference Series | Year: 2015
We extend attosecond transient absorption spectroscopy (ATAS) to the study of hydrogen molecules, demonstrating the potential of the technique to resolve-simultaneously and with state resolution-both the electronic and nuclear dynamics. © Published under licence by IOP Publishing Ltd.
Martin-Jimenez D.,CSIC - Institute of Materials Science |
Chacon E.,CSIC - Institute of Materials Science |
Tarazona P.,Condensed Matter Physics Center |
Garcia R.,CSIC - Institute of Materials Science
Nature Communications | Year: 2016
Interfacial liquid layers play a central role in a variety of phenomena ranging from friction to molecular recognition. Liquids near a solid surface form an interfacial layer where the molecular structure is different from that of the bulk. Here we report atomic resolution three-dimensional images of electrolyte solutions near a mica surface that demonstrate the existence of three types of interfacial structures. At low concentrations (0.01-1 M), cations are adsorbed onto the mica. The cation layer is topped by a few hydration layers. At higher concentrations, the interfacial layer extends several nanometres into the liquid. It involves the alternation of cation and anion planes. Fluid Density Functional calculations show that water molecules are a critical factor for stabilizing the structure of the interfacial layer. The interfacial layer stabilizes a crystal-like structure compatible with liquid-like ion and solvent mobilities. At saturation, some ions precipitate and small crystals are formed on the mica.
Sablic J.,Slovenian National Institute of Chemistry |
Praprotnik M.,Slovenian National Institute of Chemistry |
Praprotnik M.,University of Ljubljana |
Delgado-Buscalioni R.,Autonomous University of Madrid |
Delgado-Buscalioni R.,Condensed Matter Physics Center
Soft Matter | Year: 2016
Open boundary molecular dynamics (OBMD) simulations of a sheared star polymer melt under isothermal conditions are performed to study the rheology and molecular structure of the melt under a fixed normal load. Comparison is made with the standard molecular dynamics (MD) in periodic (closed) boxes at a fixed shear rate (using the SLLOD dynamics). The OBMD system exchanges mass and momentum with adjacent reservoirs (buffers) where the external pressure tensor is imposed. Insertion of molecules in the buffers is made feasible by implementing there a low resolution model (blob-molecules with soft effective interactions) and then using the adaptive resolution scheme (AdResS) to connect with the bulk MD. Straining with increasing shear stress induces melt expansion and a significantly different redistribution of pressure compared with the closed case. In the open sample, the shear viscosity is also a bit lowered but more stable against the viscous heating. At a given Weissenberg number, molecular deformations and material properties (recoverable shear strain and normal stress ratio) are found to be similar in both setups. We also study the modelling effect of normal and tangential friction between monomers implemented in a dissipative particle dynamics (DPD) thermostat. Interestingly, the tangential friction substantially enhances the elastic response of the melt due to a reduction of the kinetic stress viscous contribution. © The Royal Society of Chemistry 2016.