Browsing by Author "Martí Rabassa, Jordi"
Now showing items 1-20 of 62
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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 ... -
A well-tempered metadynamics study on free energy landscapes of melatonin bound to DMPC-cholesterol bilayers
(2019)
Conference report
Restricted access - publisher's policySmall molecules, such as melatonin (MEL, C 13 H 16 N 2 O 2 ),are essential compo- nents in biological environments. MEL’s main applications are: (1) helping to control brain function; (2) immunotherapeutic potential in ... -
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 and dynamics of melatonin at the interface of phosphatidylcholine-cholesterol membranes
(Public Library of Science (PLOS), 2019-11-07)
Article
Open AccessThe 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 and dynamics of melatonin at the interface of phosphatidylcholine-cholesterol membranes
(Public Library of Science (PLOS), 2019-11-07)
Article
Open AccessThe characterization of interactions between melatonin, one main ingredient of medicines regulating sleeping rhythms, and basic components of cellular plasma membranes (phos- pholipids, cholesterol, metal ions and water) ... -
Binding free energies of small-molecules in phospholipid membranes: Aminoacids, serotonin and melatonin
(2018-11-16)
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 ... -
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 ... -
Cellular absorption of small molecules: free energy landscapes of melatonin binding at phospholipid membranes
(Nature, 2020-06-08)
Article
Open AccessFree energy calculations are essential to unveil mechanisms at the atomic scale such as binding of small solutes and their translocation across cell membranes, eventually producing cellular absorption. Melatonin regulates ... -
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 ... -
Discovering and targeting dynamic drugging pockets of oncogenic proteins: the role of magnesium in conformational changes of the G12D mutated Kirsten Rat Sarcoma-guanosine diphosphate complex
(2022-11-10)
Article
Open AccessKRAS-G12D mutations are the one of most frequent oncogenic drivers in human cancers. Unfortunately, no therapeutic agent directly targeting KRAS-G12D has been clinically approved yet, with such mutated species remaining ... -
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), 2018-10-28)
Article
Open AccessThe characterization of the microscopical forces between the essential a-amino-acid tryptophan, pre- cursor of the neurotransmitter serotonin and of the hormone melatonin, and the basic components of cell membranes and ... -
Effects of cholesterol on the binding of the precursor neurotransmitter tryptophan to zwitterionic membranes
(American Institute of Physics (AIP), 2018-10-25)
Article
Open AccessThe 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 ... -
Efficient recursive Adams–Bashforth methods in molecular dynamics simulations of N-body systems interacting through pairwise potentials
(2020-09-09)
Article
Open AccessA recursive multistep Adams–Bashforth method applied to the Molecular Dynamics simulations of N-body systems interacting through pairwise force fields is introduced and analysed. Equations of motion are obtained using a ... -
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 ...
