Condensed Matter Physics Center

Madrid, Spain

Condensed Matter Physics Center

Madrid, Spain
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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.


Dominguez F.,Condensed Matter Physics Center | Dominguez F.,Autonomous University of Madrid | Yeyati A.L.,Condensed Matter Physics Center | Yeyati A.L.,Autonomous University of Madrid
Physica E: Low-Dimensional Systems and Nanostructures | Year: 2016

New generation of Cooper pair splitters defined on hybrid nanostructures are devices with high tunable coupling parameters. Transport measurements through these devices revealed clear signatures of interference effects and motivated us to introduce a new model, called the 3-sites model. These devices provide an ideal playground to tune the Cooper pair splitting (CPS) efficiency on demand, and displays a rich variety of physical phenomena. In the present work we analyze theoretically the conductance of the 3-sites model in the linear and non-linear regimes and characterize the most representative features that arise by the interplay of the different model parameters. In the linear regime we find that the local processes typically exhibit Fano-shape resonances, while the CPS contribution exhibits Lorentzian-shapes. Remarkably, we find that under certain conditions, the transport is blocked by the presence of a dark state. In the non-linear regime we established a hierarchy of the model parameters to obtain the conditions for optimal efficiency. © 2016.


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.


Dominguez F.,Condensed Matter Physics Center | Dominguez F.,Autonomous University of Madrid | Yeyati A.L.,Condensed Matter Physics Center
Physica E: Low-Dimensional Systems and Nanostructures | Year: 2016

New generation of Cooper pair splitters defined on hybrid nanostructures are devices with high tunable coupling parameters. Transport measurements through these devices revealed clear signatures of interference effects and motivated us to introduce a new model, called the 3-sites model. These devices provide an ideal playground to tune the Cooper pair splitting (CPS) efficiency on demand, and displays a rich variety of physical phenomena. In the present work we analyze theoretically the conductance of the 3-sites model in the linear and non-linear regimes and characterize the most representative features that arise by the interplay of the different model parameters. In the linear regime we find that the local processes typically exhibit Fano-shape resonances, while the CPS contribution exhibits Lorentzian-shapes. Remarkably, we find that under certain conditions, the transport is blocked by the presence of a dark state. In the non-linear regime we established a hierarchy of the model parameters to obtain the conditions for optimal efficiency. © 2015 Elsevier B.V. All rights reserved.


Balboa Usabiaga F.,Condensed Matter Physics Center | Delgado-Buscalioni R.,Condensed Matter Physics Center | Griffith B.E.,New York University | Griffith B.E.,Courant Institute of Mathematical Sciences | Donev A.,Courant Institute of Mathematical Sciences
Computer Methods in Applied Mechanics and Engineering | Year: 2014

We develop an inertial coupling method for modeling the dynamics of point-like "blob" particles immersed in an incompressible fluid, generalizing previous work for compressible fluids (Balboa Usabiaga et al., 2013 [42]). The coupling consistently includes excess (positive or negative) inertia of the particles relative to the displaced fluid, and accounts for thermal fluctuations in the fluid momentum equation. The coupling between the fluid and the blob is based on a no-slip constraint equating the particle velocity with the local average of the fluid velocity, and conserves momentum and energy. We demonstrate that the formulation obeys a fluctuation-dissipation balance, owing to the non-dissipative nature of the no-slip coupling. We develop a spatio-temporal discretization that preserves, as best as possible, these properties of the continuum formulation. In the spatial discretization, the local averaging and spreading operations are accomplished using compact kernels commonly used in immersed boundary methods. We find that the special properties of these kernels allow the blob to provide an effective model of a particle; specifically, the volume, mass, and hydrodynamic properties of the blob are remarkably grid-independent. We develop a second-order semi-implicit temporal integrator that maintains discrete fluctuation-dissipation balance, and is not limited in stability by viscosity. Furthermore, the temporal scheme requires only constant-coefficient Poisson and Helmholtz linear solvers, enabling a very efficient and simple FFT-based implementation on GPUs. We numerically investigate the performance of the method on several standard test problems. In the deterministic setting, we find the blob to be a remarkably robust approximation to a rigid sphere, at both low and high Reynolds numbers. In the stochastic setting, we study in detail the short and long-time behavior of the velocity autocorrelation function and observe agreement with all of the known behavior for rigid sphere immersed in a fluctuating fluid. The proposed inertial coupling method provides a low-cost coarse-grained (minimal resolution) model of particulate flows over a wide range of time-scales ranging from Brownian to convection-driven motion. © 2013 Elsevier B.V.


Delong S.,Courant Institute of Mathematical Sciences | Usabiaga F.B.,Condensed Matter Physics Center | Delgado-Buscalioni R.,Condensed Matter Physics Center | Griffith B.E.,Courant Institute of Mathematical Sciences | And 2 more authors.
Journal of Chemical Physics | Year: 2014

We develop a Fluctuating Immersed Boundary (FIB) method for performing Brownian dynamics simulations of confined particle suspensions. Unlike traditional methods which employ analytical Green's functions for Stokes flow in the confined geometry, the FIB method uses a fluctuating finite-volume Stokes solver to generate the action of the response functions "on the fly." Importantly, we demonstrate that both the deterministic terms necessary to capture the hydrodynamic interactions among the suspended particles, as well as the stochastic terms necessary to generate the hydrodynamically correlated Brownian motion, can be generated by solving the steady Stokes equations numerically only once per time step. This is accomplished by including a stochastic contribution to the stress tensor in the fluid equations consistent with fluctuating hydrodynamics. We develop novel temporal integrators that account for the multiplicative nature of the noise in the equations of Brownian dynamics and the strong dependence of the mobility on the configuration for confined systems. Notably, we propose a random finite difference approach to approximating the stochastic drift proportional to the divergence of the configuration-dependent mobility matrix. Through comparisons with analytical and existing computational results, we numerically demonstrate the ability of the FIB method to accurately capture both the static (equilibrium) and dynamic properties of interacting particles in flow. © 2014 AIP Publishing LLC.


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.


PubMed | CSIC - Institute of Materials Science and Condensed Matter Physics Center
Type: | Journal: 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 (0.01-1M), 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.

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