Now showing items 1-20 of 134

    • 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 deep learning-based method for uncovering GPCR ligand-induced conformational states using interpretability techniques 

      Gutiérrez Mondragón, Mario Alberto; König, Caroline; Vellido Alcacena, Alfredo (Springer, 2022)
      Conference report
      Open Access
      There 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 

      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 ...
    • A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer’s Disease, Glioblastoma and Lung cancer 

      Sánchez-Valle, Jon; Tejero, Héctor; Ibáñez, Kristina; Portero, Jose L.; Krallinger, Martin; Al-Shahrour, Fátima; Tabarés Seisdedos, Rafael; Baudot, Anaïs; Valencia, Alfonso (Nature Publishing Group, 2017-06-30)
      Article
      Open Access
      Epidemiological studies indicate that patients suffering from Alzheimer’s disease have a lower risk of developing lung cancer, and suggest a higher risk of developing glioblastoma. Here we explore the molecular scenarios ...
    • 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
      Open Access
      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 ...
    • Atomic processes of shear-coupled migration in {112} twins and vicinal grain boundaries in bcc-Fe 

      Kvashin, Nikolai; García-Müller, Pablo Luis; Anento Moreno, Napoleón; Serra Tort, Ana María (American Physical Society (APS), 2020-07)
      Article
      Open Access
      Tilt {112} grain boundaries (GBs) in bcc metals perform shear-coupled grain-boundary migration by the creation and glide of disconnections. Disconnection dipoles may be created at the pristine GB at high stresses or may ...
    • Atomistic simulations and theoretical predictions of helium nucleation in liquid Pb-Li eutectic alloy 

      Al Awad, Abdulrahman; Batet Miracle, Lluís; Sedano Miguel, Luis Ángel (2022)
      Conference report
      Restricted access - publisher's policy
      Liquid 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 

      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 ...
    • 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 ...
    • 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 rapid and sustained insulin release from conducting hydrogels for glycemic control 

      Muñoz Galan, Helena; Molina, Brenda G.; Bertran Cànovas, Òscar; Pérez Madrigal, Maria del Mar; Alemán Llansó, Carlos (Elsevier, 2022-10-29)
      Article
      Restricted access - publisher's policy
      Innovative insulin delivery systems contemplate combining multi-pharmacokinetic profiles for glycemic control. Two device configurations have been designed for the controlled release of insulin using the same chemical ...
    • 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 study of ion-water and water-water hydrogen bonds in methanesulfonic acid solutions at room temperature 

      Canales Gabriel, Manel; Guàrdia Manuel, Elvira (2023-05-01)
      Article
      Open Access
      Classical molecular dynamics simulations of aqueous methanesulfonic acid solutions have been con- ducted at room temperature in the entire composition range. The dissociation of the acid has been con- sidered according to ...
    • 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 ...
    • Copper diffusion rates and hopping pathways in superionic Cu2Se 

      Sheik Md Kazi Nazrul, Islam; Mayank, Prince; Ouyang, Yulou; Chen, Jie; Sagotra, Arun K.; Li, Meng; Cortie, Michael B.; Mole, Richard; Cazorla Silva, Claudio; Yu, Dehong; Wang, Xiaolin; Robinson, Robert A.; Cortie, David Laurence (2021-08-15)
      Article
      Restricted access - publisher's policy
      The ultra-low thermal conductivity of Cu2Se is well established, but so far there is no consensus on the underlying mechanism. One proposal is that the fast-ionic diffusion of copper suppresses the acoustic phonons. The ...