Browsing by Subject "Molecular dynamics"
Now showing items 1-20 of 150
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{111} tilt grain boundaries as barriers for slip transfer in bcc Fe
(2022-02)
Article
Restricted access - publisher's policyWe have studied the interaction of an individual dislocation and a pile-up of dislocations with {111} tilt grain boundary in iron by means of atomistic simulations. The {111} tilt grain boundary, under externally applied ... -
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 ... -
3D structure of a Brucella melitensis porin: molecular modelling in lipid membranes
(2018-01-01)
Article
Open AccessBrucella melitensis is a pathogenic bacterium responsible for brucellosis in mammals and humans. Its outer membrane proteins (Omp) control the diffusion of solutes through the membrane, and they consequently have a crucial ... -
A computational study of Neuromedin B
(2011-09-15)
Article
Restricted access - publisher's policyA methodological study has been undertaken to assess the conformational profile of Neuromedin B (NMB) using classical molecular dynamics simulations (MD) and replica exchange molecular dynamics (REMD) simulations under ... -
A deep learning-based method for uncovering GPCR ligand-induced conformational states using interpretability techniques
(Springer, 2022)
Conference report
Restricted access - publisher's policyThere is increasing interest in the development of tools for investigating the protein ligand space. Understanding the underlying mechanisms of G protein-coupled receptors (GPCR) in the ligand-binding process is of particular ... -
A molecular dynamics study on glucose molecular recognition by a non-enzymatic selective sensor based on a conducting polymer
(Royal Society of Chemistry (RSC), 2019-01-01)
Article
Open AccessPoly(hydroxymethyl-3,4-ethylendioxythiophene) (PHMeDOT), a very electroactive polythiophene derivative bearing a dioxane ring fused onto the thiophene ring and an exocyclic hydroxymethyl substituent, is able to electrocatalyze ... -
A molecular simulation study on transport properties of FAMEs in high-pressure conditions
(Elsevier, 2022)
Article
Restricted access - publisher's policyTransport property prediction of fatty acid methyl esters (FAMEs) is essential to its utilisation as biodiesel and biolubricant which can work under high-pressure conditions. Equilibrium molecular simulation is performed ... -
Análisis y simulación de nuevos nanomateriales para la liberación de fármacos
(Universitat Politècnica de Catalunya, 2018-05)
Bachelor thesis
Open AccessEn el presente trabajo se ha realizado la simulación por Dinámica Molecular de dos ferritinas modificadas por medio del programa AMBER. Teniendo como objetivo comprobar la estabilidad de la estructura de dichas ferritinas, ... -
Assessment of the conformational profile of bombesin by computational methods
(2020-07-20)
Article
Open AccessIn the present work, the results of a computational study aimed at assessing the conformational profile of bombesin are reported. The conformational space of the peptide was sampled by means of a 4 µs accelerated molecular ... -
Atomistic simulations and theoretical predictions of helium nucleation in liquid Pb-Li eutectic alloy
(2022)
Conference report
Restricted access - publisher's policyLiquid Lead-Lithium Eutectic (LLE) alloy is a promising candidate coolant and/or breeder to attain tritium self-sufficiency in the EU DEMO breeding blanket design. Liquid metals are characterized with excellent heat-transport ... -
Atomistic study of multimechanism diffusion by self-interstitial defects in ¿-Fe
(2010)
Article
Restricted access - publisher's policyWe present the results of an extensive molecular dynamics study of selfinterstitial atom (SIA) clusters containing up to 37 defects over a wide range of temperatures in iron. A long simulation time and high statistics of ... -
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 ... -
BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
(Oxford University Press, 2022-07)
Article
Open AccessWe present BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) offering access to a collection of transversal pre-configured biomolecular simulation workflows assembled with the BioExcel Building ... -
C60 solvate with (1,1,2)-trichloroethane: dynamic statistical disorder and mixed conformation
(2016-05-27)
Article
Open AccessWe present a full characterization of the orientationally disordered cocrystal of C-60 with (1,1,2)-triChloroethane (C2H3Cl3), by means of X-ray diffraction, Raman spectroscopy, and broadband dielectric spectroscopy. Our ... -
Characteritzation of protein-protein interfaces and identification of transient cavities for its modulation
(Barcelona Supercomputing Center, 2015-05-05)
Conference report
Open AccessProtein-protein interactions (PPIs) play an essential role in many biological processes, including disease conditions. Strategies to modulate PPIs with small molecules have therefore attracted increasing interest over the ... -
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 ... -
Charting molecular free-energy landscapes with an atlas of collective variables
(2016-11-07)
Article
Open AccessCollective variables (CVs) are a fundamental tool to understand molecular flexibility, to compute free energy landscapes, and to enhance sampling in molecular dynamics simulations. However, identifying suitable CVs is ... -
Combining Monte Carlo and molecular dynamics simulations for enhanced binding free energy estimation through Markov State models
(American Chemical Society, 2020)
Article
Open AccessWe present a multistep protocol, combining Monte Carlo and molecular dynamics simulations, for the estimation of absolute binding free energies, one of the most significant challenges in computer-aided drug design. The ... -
Comment on
(2010-01-15)
Article
Restricted access - publisher's policy
