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http://hdl.handle.net/2117/394
2014-10-24T08:36:36ZThe force matching approach to multiscale simulations: merits, shortcomings, and future perspectives
http://hdl.handle.net/2117/23978
Title: The force matching approach to multiscale simulations: merits, shortcomings, and future perspectives
Authors: Masia, Marco; Guàrdia Manuel, Elvira; Nicolini, Paolo
Abstract: Among the various approaches to multiscale simulations, in recent years, force matching has been known for a quick growth. The method is based on a least-square fit of reference properties obtained from simulations at a certain scale, to parameterize the force field for coarser-grained scale simulations. Its advantage with respect to conventional schemes used for parameterizing force fields, lies in that only physically accessible configurations are sampled, and that the number of reference data per configuration is large. In this perspective article, we discuss some recent findings on the tailoring of the objective function, on the choice of the empirical potential, and on the way to improve the quality of the reference calculations. We present pros and cons of the algorithm, and we propose a road map to future developments. (C) 2014 Wiley Periodicals, Inc.2014-09-03T15:14:58ZAtomic monolayer deposition on the surface of nanotube mechanical resonators
http://hdl.handle.net/2117/23221
Title: Atomic monolayer deposition on the surface of nanotube mechanical resonators
Authors: Tavernarakis, Alexandros; Chaste, Julien; Eichler, Alexander; Ceballo, Gustavo; Gordillo Bargueño, Maria Carmen; Boronat Medico, Jordi; Bachtold, Adrian
Abstract: We study monolayers of noble gas atoms (Xe, Kr, Ar, and Ne) deposited on individual ultraclean suspended nanotubes. For this, we record the resonance frequency of the mechanical motion of the nanotube, since it provides a direct measure of the coverage. The latter is the number of adsorbed atoms divided by the number of the carbon atoms of the suspended nanotube. Monolayers form when the temperature is lowered in a constant pressure of noble gas atoms. The coverage of Xe monolayers remains constant at 1/6 over a large temperature range. This finding reveals that Xe monolayers are solid phases with a triangular atomic arrangement, and are commensurate with the underlying carbon nanotube. By comparing our measurements to theoretical calculations, we identify the phases of Ar and Ne monolayers as fluids, and we tentatively describe Kr monolayers as solid phases. These results underscore that mechanical resonators made from single nanotubes are excellent probes for surface science.2014-06-13T17:24:45ZDynamical aspects of intermolecular proton transfer in liquid water and low-density amorphous ices
http://hdl.handle.net/2117/23020
Title: Dynamical aspects of intermolecular proton transfer in liquid water and low-density amorphous ices
Authors: Tahat, Amani; Martí Rabassa, Jordi
Abstract: The microscopic dynamics of an excess proton in water and in low-density amorphous ices has been studied by means of a series of molecular dynamics simulations. Interaction of water with the proton species was modelled using a multistate empirical valence bond Hamiltonian model. The analysis of the effects of low temperatures on proton diffusion and transfer rates has been considered for a temperature range between 100 and 298 K at the constant density of 1 g cm -3 . We observed a marked slowdown of proton transfer rates at low temperatures, but some episodes are still seen at 100 K. In a similar fashion, mobility of the lone proton gets significantly reduced when temperature decreases below 273 K. The proton transfer in low-density amorphous ice is an activated process with energy barriers between 1–10 kJ/mol depending of the temperature range considered and eventually showing Arrhenius-like behavior. Spectroscopic data indicated the survival of both Zundel and Eigen structures along the whole temperature range, revealed by significant spectral frequency shifts.2014-05-20T15:34:20ZMolecular dynamics simulation study of methanesulfonic acid
http://hdl.handle.net/2117/22794
Title: Molecular dynamics simulation study of methanesulfonic acid
Authors: Canales Gabriel, Manel; Alemán Llansó, Carlos
Abstract: A molecular dynamics simulation study of methanesulfonic acid has been carried out using a reliable force field in a large range of temperatures. Several thermodynamic, structural, and dynamical properties have been calculated and compared with the available experimental data. The density, the shear viscosity, the heat of vaporization, and the melting temperature results, calculated from this force field, are in a good agreement with the experimental data. Analysis of the influence of the hydrogen bonds in structural and dynamical properties has also been performed. The continuous and interrupted methodologies to compute hydrogen bonding lifetimes have been applied. The interrupted hydrogen bond lifetimes values are consistent with the diffusion and viscosity coefficients. The activation energies of the self-diffusion, the reorientational motions, and the hydrogen bonding lifetimes are coincident.2014-04-30T15:55:44ZSpin-polarized hydrogen adsorbed on the surface of superfluid He-4
http://hdl.handle.net/2117/22078
Title: Spin-polarized hydrogen adsorbed on the surface of superfluid He-4
Authors: Marín, J. M.; Vranješ Markic, Leandra; Boronat Medico, Jordi
Abstract: The experimental realization of a thin layer of spin-polarized hydrogen H double down arrow adsorbed on top of the surface of superfluid He-4 provides one of the best examples of a stable, nearly two-dimensional(2D) quantum Bose gas. We report a theoretical study of this system using quantum Monte Carlo methods in the limit of zero temperature. Using the full Hamiltonian of the system, composed of a superfluid He-4 slab and the adsorbed H double down arrow layer, we calculate the main properties of its ground state using accurate models for the pair interatomic potentials. Comparing the results for the layer with the ones obtained for a strictly 2D setup, we analyze the departure from the 2D character when the density increases. Only when the coverage is rather small the use of a purely 2D model is justified. The condensate fraction of the layer is significantly larger than in 2D at the same surface density, being as large as 60% at the largest coverage studied. (c) 2013 AIP Publishing LLC. [http://dx.doi.org/10.1063/1.4843375]2014-03-14T15:12:24ZDiffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes
http://hdl.handle.net/2117/21998
Title: Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes
Authors: Yang, Jing; Calero Borrallo, Carles; Martí Rabassa, Jordi
Abstract: Microscopic structure and dynamics of water and lipids in a fully hydrated dimyristoylphosphatidylcholine phospholipid lipid bilayer membrane in the liquid-crystalline phase have been analyzed with all-atom molecular dynamics simulations based on the recently parameterized CHARMM36 force field. The diffusive dynamics of the membrane lipids and of its hydration water, their reorientational motions as well as their corresponding spectral densities, related to the absorption of radiation, have been considered for the first time using the present force field. In addition, structural properties such as density and pressure profiles, a deuterium-order parameter, surface tension, and the extent of water penetration in the membrane have been analyzed. Molecular self-diffusion, reorientational motions, and spectral densities of atomic species reveal a variety of time scales playing a role in membrane dynamics. The mechanisms of lipid motion strongly depend on the time scale considered, from fast ballistic translation at the scale of picoseconds (effective diffusion coefficients of the order of 10-5 cm2/s) to diffusive flow of a few lipids forming nanodomains at the scale of hundreds of nanoseconds (diffusion coefficients of the order of 10-8 cm2/s). In the intermediate regime of sub-diffusion, collisions with nearest neighbors prevent the lipids to achieve full diffusion. Lipid reorientations along selected directions agree well with reported nuclear magnetic resonance data and indicate two different time scales, one about 1 ns and a second one in the range of 2–8 ns. We associated the two time scales of reorientational motions with angular distributions of selected vectors. Calculated spectral densities corresponding to lipid and water reveal an overall good qualitative agreement with Fourier transform infrared spectroscopy experiments. Our simulations indicate a blue-shift of the low frequency spectral bands of hydration water as a result of its interaction with lipids. We have thoroughly analyzed the physical meaning of all spectral features from lipid atomic sites and correlated them with experimental data. Our findings include a “wagging of the tails” frequency around 30 cm-1, which essentially corresponds to motions of the tail-group along the instantaneous plane formed by the two lipid tails, i.e., in-plane oscillations are clearly of bigger importance than those along the normal-to-the plane direction.2014-03-11T15:30:00ZWM Program manual
http://hdl.handle.net/2117/21798
Title: WM Program manual
Authors: Tahat, Amani; Martí Rabassa, Jordi; Tahat, Mohammed
Abstract: This manual describes how to run the new produced GUI C++ program that so called
'WM' program. Section two describes the instructions of the program installation.
Section three illustrates test runs description including running the program WM,
sample of the input, output files, in addition to some generated graphs followed by the main form of the program created by using the Borland C++ Builder 6.
Description: Manual d'un codi obert relacionat amb l'article: Information technology journal, 11 (11#, 1553-1569 #2012) doi: 10.3923/itj.2012.1553.1569.2014-02-27T17:36:24ZPattern recognition and data mining software based on artificial neural networks applied to proton transfer in aqueous environments
http://hdl.handle.net/2117/21794
Title: Pattern recognition and data mining software based on artificial neural networks applied to proton transfer in aqueous environments
Authors: Tahat, Amani; Martí Rabassa, Jordi; Khwaldeh, Ali; Tahat, Kaher
Abstract: In computational physics proton transfer phenomena could be viewed as pattern classification problems based on a set of input features allowing to classify the proton motion into two categories: transfer‘occurred’and transfer‘not occurred’. The goal of this paper is to evaluate the use of artificial neural networks in the classification of proton transfer events, based on the feed-forward back propagation neural network, used as a classifier to distinguish between the two transfer cases. In this paper, we use a new developed data mining and pattern recognition tool for automating, controlling, and drawing charts of the output data of an Empirical Valence Bond existing code. The study analyzes the need of pattern recognition in aqueous proton transfer processes and how the learning approach in error back propagation (multilayer perceptron algorithms) could be satisfactorily employed in the present case. We present a tool for pattern recognition and validate the code including a real physical case study. The results of applying the artificial neural networks methodology to crowd patterns based upon selected physical properties (e.g., temperature, density) show the abilities of the network to learn proton transfer patterns corresponding to properties of the aqueous environments, which is in turn proved to be fully compatible with previous proton transfer studies.2014-02-27T14:47:41ZPossible superfluidity of molecular hydrogen in a two-dimensional crystal phase of sodium
http://hdl.handle.net/2117/21500
Title: Possible superfluidity of molecular hydrogen in a two-dimensional crystal phase of sodium
Authors: Cazorla Silva, Claudio; Boronat Medico, Jordi
Abstract: We theoretically investigate the ground-state properties of a molecular para-hydrogen (p-H 2 ) film in which crystallization is energetically frustrated by embedding sodium (Na) atoms periodically distributed in a triangular lattice. In order to fully deal with the quantum nature of p-H 2 molecules, we employ the diffusion Monte Carlo method and realistic semiempirical pairwise potentials describing the interactions between H 2 -H 2 and Na-H 2 species. In particular, we calculate the energetic, structural, and superfluid properties of two-dimensional Na-H 2 systems within a narrow density interval around equilibrium at zero temperature. In contrast to previous computational studies considering other alkali metal species such as rubidium and potassium, we find that the p-H 2 ground state is a liquid with a significantly large superfluid fraction of ρ s /ρ=0.29(2) . The appearance of p-H 2 superfluid response is due to the fact that the interactions between Na atoms and H 2 molecules are less attractive than between H 2 molecules. This induces a considerable reduction of the hydrogen density which favors the stabilization of the liquid phase.2014-02-10T16:17:42ZShortcomings of the standard Lennard-Jones dispersion term in water models, studied with force matching
http://hdl.handle.net/2117/21290
Title: Shortcomings of the standard Lennard-Jones dispersion term in water models, studied with force matching
Authors: Nicolini, Paolo; Guàrdia Manuel, Elvira; Masia, Marco
Abstract: In this work, ab initio parametrization of water force field is used to get insights into the functional form of empirical potentials to properly model the physics underlying dispersion interactions. We exploited the force matching algorithm to fit the interaction forces obtained with dispersion corrected density functional theory based molecular dynamics simulations. We found that the standard Lennard-Jones interaction potentials poorly reproduce the attractive character of dispersion forces. This drawback can be resolved by accounting for the distinctive short range behavior of dispersion interactions, multiplying the r −6 term by a damping function. We propose two novel parametrizations of the force field using different damping functions. Structural and dynamical properties of the new models are computed and compared with the ones obtained from the non-damped force field, showing an improved agreement with reference first principle calculations.2014-01-20T17:45:49ZTopology, hierarchy, and correlations in Internet graphs
http://hdl.handle.net/2117/21109
Title: Topology, hierarchy, and correlations in Internet graphs
Authors: Pastor Satorras, Romualdo; Vázquez, Alexei; Vespignani, Alessandro
Abstract: We present a statistical analysis of different metrics characterizing the topological properties of Internet maps, collected at two different resolution scales: the router and the autonomous system level. The metrics we consider allow us to confirm the presence of scale-free signatures in several statistical distributions, as well as to show in a quantitative way the hierarchical nature of the Internet. Our findings are relevant for the development of more accurate Internet topology generators, which should include, along with the properties of the degree distribution, the hierarchical signatures reviewed in the present work.2013-12-31T09:34:07ZEpidemic spreading in complex networks with degree correlations
http://hdl.handle.net/2117/21105
Title: Epidemic spreading in complex networks with degree correlations
Authors: Boguñá, Marian; Pastor Satorras, Romualdo; Vespignani, Alessandro
Abstract: We review the behavior of epidemic spreading on complex networks in which there are explicit correlations among the degrees of connected vertices.2013-12-31T08:32:00ZZero-temperature phase diagram of D2 physisorbed on graphane
http://hdl.handle.net/2117/20842
Title: Zero-temperature phase diagram of D2 physisorbed on graphane
Authors: Carbonell Coronado, Carmen; De Soto Borrera, Feliciano Carlos; Cazorla Silva, Claudio; Boronat Medico, Jordi; Gordillo Bargueño, Maria Carmen
Abstract: We determined the zero-temperature phase diagram of D2 physisorbed on graphane using the diffusion Monte Carlo method. The substrate used was C-graphane, an allotropic form of the compound that has been experimentally obtained through hydrogenation of graphene. We found that the ground state is the δ phase, a commensurate structure observed experimentally when D2 is adsorbed on graphite, and not the registered structure characteristic of H2 on the same substrate.2013-11-28T17:56:18ZCharacterization of the methane–graphene hydrophobic interaction in aqueous solution from ab initio simulations
http://hdl.handle.net/2117/20817
Title: Characterization of the methane–graphene hydrophobic interaction in aqueous solution from ab initio simulations
Authors: Calero Borrallo, Carles; Martí Rabassa, Jordi; Guàrdia Manuel, Elvira; Masia, Marco
Abstract: In this article, the interaction between a methane molecule and a graphene plane in liquid water has been characterized employing DFT-based free energy Molecular Dynamics calculations. This system represents a good model to understand the generic interaction between a small hydrophobic solute (methane molecule) and an extense hydrophobic surface (graphene plane). The structural and dynamical properties of graphene and methane hydration water are analyzed and found to be closely related to the main features of the potential of mean force. The results could be used in coarse-grained models to take into account the effect of the hydrophobic interaction in realistic systems relevant to experiment.2013-11-27T14:39:00ZNon-mean-field behavior of the contact process on scale-free networks
http://hdl.handle.net/2117/20765
Title: Non-mean-field behavior of the contact process on scale-free networks
Authors: Castellano, Claudio; Pastor Satorras, Romualdo
Abstract: We present an analysis of the classical contact process on scale-free networks. A mean-field study, both for finite and infinite network sizes, yields an absorbing-state phase transition at a finite critical value of the control parameter, characterized by a set of exponents depending on the network structure. Since finite size effects are large and the infinite network limit cannot be reached in practice, a numerical study of the transition requires the application of finite size scaling theory. Contrary to other critical phenomena studied previously, the contact process in scale-free networks exhibits a nontrivial critical behavior that cannot be quantitatively accounted for by mean-field theory.2013-11-25T20:00:12Z