Browsing by Author "Martí Rabassa, Jordi"

1H nuclear spin relaxation of liquid water from molecular dynamics simulations

Calero Borrallo, Carles; Martí Rabassa, Jordi; Guàrdia Manuel, Elvira (2015-01-13)
Article
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We 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

Videla, Pablo; Sala Viñas, Jonàs; Martí Rabassa, Jordi; Guàrdia Manuel, Elvira; Laria, Daniel (2011-09-09)
Article
Open Access

Molecular 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

Khwaldeh, Ali; Tahat, Amani; Martí Rabassa, Jordi; Tahat, Mofleh (2013-02-27)
Article
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This 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 and dynamics of melatonin at the interface of phosphatidylcholine-cholesterol membranes

Huixia, Lu; Martí Rabassa, Jordi (Public Library of Science (PLOS), 2019-11-07)
Article
Open Access

The characterization of interactions between melatonin, one main ingredient of medicines regulating sleeping rhythms, and basic components of cellular plasma membranes (phospholipids, cholesterol, metal ions and water) ...

Binding free energies of small-molecules in phospholipid membranes: aminoacids, serotonin and melatonin

Lu, Huixia; Martí Rabassa, Jordi (2018-10-04)
Article
Open Access

Free 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

Calero Borrallo, Carles; Martí Rabassa, Jordi; Guàrdia Manuel, Elvira; Masia, Marco (2013-09-17)
Article
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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 ...

Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes

Yang, Jing; Calero Borrallo, Carles; Martí Rabassa, Jordi (2014-03-10)
Article
Open Access

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 ...

Dynamical aspects of intermolecular proton transfer in liquid water and low-density amorphous ices

Tahat, Amani; Martí Rabassa, Jordi (2014-05-19)
Article
Open Access

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 ...

Effects of cholesterol on the binding of the precursor neurotransmitter tryptophan to zwitterionic membranes

Lu, Huixia; Martí Rabassa, Jordi (American Institute of Physics (AIP), 2018-10-25)
Article
Open Access

The 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

Sala Viñas, Jonàs; Guàrdia Manuel, Elvira; Martí Rabassa, Jordi (American Institute of Physics (AIP), 2010-06-03)
Article
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The 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

Semino, Rocío; Martí Rabassa, Jordi; Guàrdia Manuel, Elvira; Laria, Daniel (2012-11-19)
Article
Open Access

We 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

RODRIGUEZ, J; Martí Rabassa, Jordi; Guàrdia Manuel, Elvira; Laria, D (2008-07)
Article
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We 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

Sala Viñas, Jonàs; Guàrdia Manuel, Elvira; Martí Rabassa, Jordi; Spangberg, Daniel; Masia, Marco (2012-02-02)
Article
Restricted access - publisher's policy

In 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 ...

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