Now showing items 1-20 of 127

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

      Calero Borrallo, Carles; Martí Rabassa, Jordi; Guàrdia Manuel, Elvira (2015-01-13)
      Article
      Restricted access - publisher's policy
      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 ...
    • 3D structure of a Brucella melitensis porin: molecular modelling in lipid membranes 

      Lopes Rodrigues, Maximilien; Zanuy Gomara, David; Alemán Llansó, Carlos; Michaux, Catherine Anne Gisèle; Perpète, Eric A. (2018-01-01)
      Article
      Open Access
      Brucella 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 

      Sharma, Parul; Singh, Parvesh; Bisetty, Krishna; Pérez González, Juan Jesús (2011-09-15)
      Article
      Restricted access - publisher's policy
      A 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 molecular dynamics study on glucose molecular recognition by a non-enzymatic selective sensor based on a conducting polymer 

      Zanuy Gomara, David; Fabregat Jové, Georgina; Ferreira, Carlos Arthur; Alemán Llansó, Carlos (Royal Society of Chemistry (RSC), 2019-01-01)
      Article
      Open Access
      Poly(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 ...
    • Análisis y simulación de nuevos nanomateriales para la liberación de fármacos 

      Acero Narvaez, Joel (Universitat Politècnica de Catalunya, 2018-05)
      Bachelor thesis
      Open Access
      En 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 

      Valverde Salamanca, Abel; Gómez Gutiérrez, Patricia; Pérez González, Juan Jesús (2020-07-20)
      Article
      Restricted access - publisher's policy
      In 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 study of multimechanism diffusion by self-interstitial defects in ¿-Fe 

      Anento Moreno, Napoleón; Serra Tort, Ana María; Osetsky, Yuri N. (2010)
      Article
      Restricted access - publisher's policy
      We 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 

      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 ...
    • Binding free energies of small-molecules in phospholipid membranes: Aminoacids, serotonin and melatonin 

      Lu, Huixia; Martí Rabassa, Jordi (2018-11-16)
      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 ...
    • C60 solvate with (1,1,2)-trichloroethane: dynamic statistical disorder and mixed conformation 

      Mitsari, Efstratia; Romanini, Michela; Qureshi, Navid; Tamarit Mur, José Luis; Barrio Casado, María del; Macovez, Roberto (2016-05-27)
      Article
      Open Access
      We 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 

      Rosell, Mireia; Fernandez-Recio, Juan (Barcelona Supercomputing Center, 2015-05-05)
      Conference report
      Open Access
      Protein-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 

      Calero Borrallo, Carles; Martí Rabassa, Jordi; Guàrdia Manuel, Elvira; Masia, Marco (2013-09-17)
      Article
      Restricted access - publisher's policy
      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 ...
    • Charting molecular free-energy landscapes with an atlas of collective variables 

      Hashemian, B.; Millán, Raúl Daniel; Arroyo Balaguer, Marino (2016-11-07)
      Article
      Open Access
      Collective 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 

      Gilabert, Joan F.; Gracia Carmona, Oriol; Hogner, Anders; Guallar, Victor (American Chemical Society, 2020)
      Article
      Open Access
      We 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 

      Serra Tort, Ana María; Bacon, D.J.; Pond, R.C. (2010-01-15)
      Article
      Restricted access - publisher's policy
    • Competing structures within the first shell of liquid C2Cl6: a molecular dynamics study 

      Henao Aristizábal, Andrés; Pothoczki, Szilvia; Canales Gabriel, Manel; Guàrdia Manuel, Elvira; Pardo Soto, Luis Carlos (2014-02-28)
      Article
      Open Access
      We present a detailed study on the liquid structure of hexachloroethane (C2Cl6) within the first shell using the proper Euler-angles convention. Molecular dynamics is used and the van der Waals picture of a liquid is taken ...
    • Computer simulation of liquid methanol ii:system size effects 

      Casulleras Ambrós, Joaquín; Guàrdia Manuel, Elvira (1991-01)
      Article
      Restricted access - publisher's policy
      A series of molecular dynamics simulations of liquid methanol has been carried out on a supernode transputer array. Four system sizes from 125 to 512 molecules have been considered, in order to study the effect of system ...
    • Computer simulation of the atomic behaviour in condensed phases 

      Giró Roca, Antoni; Padró Càrdenas, Joan Àngel (Universitat Politècnica de Barcelona. Centre de Càlcul, 1987)
      Article
      Open Access
      Molecular dynamics simulation method for the study of condensed phases of matter is described in this paper. Computer programs for the simulation of atomic motion have been developed. Time-saving techniques, like the ...
    • Conformational Heterogeneity of Unbound Proteins Enhances Recognition in Protein–Protein Encounters 

      Pallara, Chiara; Rueda, Manuel; Abagyan, Ruben; Fernández-Recio, Juan (American Chemical Society, 2016-06-20)
      Article
      Open Access
      To understand cellular processes at the molecular level we need to improve our knowledge of protein−protein interactions, from a structural, mechanistic, and energetic point of view. Current theoretical studies and ...
    • Design and development of an interactive visualization tools for molecular dynamics simulation data 

      Garbin, Giacomo (Universitat Politècnica de Catalunya, 2019-01-29)
      Master thesis
      Open Access
      Covenantee:   Università degli Studi di Milano
      The research on molecular dynamics produces thousands of datasets pertaining the behavior of molecular compounds. The work aims to be a contribution toward the identification of effective ways to visualize the outcome of ...