Browsing by Author "Martí Rabassa, Jordi"
Now showing items 1-20 of 33
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1H nuclear spin relaxation of liquid water from molecular dynamics simulations
(2015-01-13)
Article
Restricted access - publisher's policyWe have investigated the nuclear spin relaxation properties of 1H in liquid water with the help of molecular dynamics simulations. We have computed the 1H nuclear spin relaxation times T1 and T2 and determined the contribution ... -
Aqueous electrolytes confined within functionalized silica nanopores
(2011-09-09)
Article
Open AccessMolecular dynamics simulations have been carried out to investigate structural and dynamical characteristics of NaCl aqueous solutions confined within silica nanopores in contact with a “bulk-like” reservoir. Two types of ... -
Atomic data mining numerical methods, source code SQlite with Python
(2013-02-27)
Article
Restricted access - publisher's policyThis paper introduces a recently published Python data mining book (chapters, topics, samples of Python source code written by its authors) to be used in data mining via world wide web and any specific database in several ... -
Binding free energies of small-molecules in phospholipid membranes: aminoacids, serotonin and melatonin
(2018-10-04)
Article
Open AccessFree energy barriers associated to the binding of small-molecules at phospholipid zwitterionic membranes have been computed at 323 K for a variety of species: tryptophan, histidine, tyrosine, serotonin and melatonin ... -
Characterization of the methane–graphene hydrophobic interaction in aqueous solution from ab initio simulations
(2013-09-17)
Article
Restricted access - publisher's policyIn 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 ... -
Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes
(2014-03-10)
Article
Open AccessMicroscopic 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 ... -
Dynamical aspects of intermolecular proton transfer in liquid water and low-density amorphous ices
(2014-05-19)
Article
Open AccessThe 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 ... -
Effects of cholesterol on the binding of the precursor neurotransmitter tryptophan to zwitterionic membranes
(American Institute of Physics (AIP), 2018-10-25)
Article
Restricted access - publisher's policyThe characterization of the microscopical forces between the essential a-amino-acid tryptophan, precursor of the neurotransmitter serotonin and of the hormone melatonin, and the basic components of cell membranes and their ... -
Effects of concentration on structure, dielectric, and dynamic properties of aqueous NaCl solutions using a polarizable model
(American Institute of Physics (AIP), 2010-06-03)
Article
Restricted access - publisher's policyThe study of NaCl solutions in water at finite concentration, explicitly including polarization in water molecules and ions, has been carried out by molecular dynamics simulations. A comparison of the RPOL polarizable model ... -
Excess protons in mesoscopic water-acetone nanoclusters
(2012-11-19)
Article
Open AccessWe carried out molecular dynamics simulation experiments to examine equilibrium and dynamical characteristics of the solvation of excess protons in mesoscopic, [m:n] binary polar clusters comprising m = 50 water molecules ... -
Exploring the picosecond time domain of the solvation dynamics of coumarin 153 within beta-cyclodextrins
(2008-07)
Article
Restricted access - publisher's policyWe report molecular dynamics simulation results of equilibrium and dynamical characteristics pertaining to the solvation of the dye coumarin 153 (C153) trapped within hydrophobic cavities of di- and trimethylated ß-cyclodextrins ... -
Fitting properties from density functional theory based molecular dynamics simulations to parameterize a rigid water force field
(2012-02-02)
Article
Restricted access - publisher's policyIn the quest towards coarse-grained potentials and new water models, we present an extension of the force matching technique to parameterize an all-atom force field for rigid water. The methodology presented here allows ... -
Free energy landscapes of sodium ions bound to DMPC–cholesterol membrane surfaces at infinite dilution
(2016-03-02)
Article
Open AccessExploring the free energy landscapes of metal cations on phospholipid membrane surfaces is important for the understanding of chemical and biological processes in cellular environments. Using metadynamics simulations we ... -
Free-energy surfaces of ionic adsorption in cholesterol-free and cholesterol-rich phospholipid membranes
(2017-10-23)
Article
Open AccessFree energy surfaces associated to the adsorption of metal cations ((Formula presented.), (Formula presented.), (Formula presented.), and (Formula presented.)) in biological environments have been computed by metadynamics ... -
Maintenance and reengineering of software: creating a Visual C++ graphical user interface to perform specific tasks related to soil structure interaction in poroelastic soil
(2012-08-27)
Article
Restricted access - publisher's policyIn this study, an interactive Graphical User Interface (GUI) application was introduced and tested. It worked as a utility program to facilitate and maximize the re-use of existing FORTRAN software. The GUI had been designed ... -
Molecular dynamics of di-palmitoyl-phosphatidyl-choline biomembranes in ionic solution: adsorption of the precursor neurotransmitter tryptophan
(Elsevier, 2017-06-09)
Article
Open AccessMicroscopic structure of a fully hydrated di-palmytoil-phosphatidyl-choline lipid bilayer membrane in the liquid-crystalline phase has been analyzed with all-atom molecular dynamics simulations based on the recently ... -
Molecular dynamics simulations of supercritical water confined within a carbon-slit pore
(2009-03)
Article
Open AccessWe report the results of a series of molecular dynamics simulations of water inside a carbon-slit pore at supercritical conditions. A range of densities corresponding from liquid 0.66 g cm−3 to gas environments 0.08 g ... -
Multistate empirical valence bond study of temperature and confinement effects on proton transfer in water inside hydrophobic nanochannels
(2016-05-17)
Article
Open AccessMicroscopic characteristics of an aqueous excess proton in a wide range of thermodynamic states, from low density amorphous ices (down to 100 K) to high temperature liquids under the critical point (up to 600 K), placed ... -
Pair interactions among ternary DPPC/POPC/cholesterol mixtures in liquid-ordered and liquid-disordered phases
(2016-04-12)
Article
Open AccessSaturated phospholipids, unsaturated phospholipids, and cholesterol are essential components of cell membranes, making the understanding of their mutual interactions of great significance. We have performed microsecond ... -
Pattern recognition and data mining software based on artificial neural networks applied to proton transfer in aqueous environments
(2014-02-10)
Article
Restricted access - publisher's policyIn 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 ...
