Browsing by Subject "Dinàmica molecular"
Now showing items 1-20 of 127
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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 hypothesis to explain direct and inverse co-morbidities between Alzheimer’s Disease, Glioblastoma and Lung cancer
(Nature Publishing Group, 2017-06-30)
Article
Open AccessEpidemiological 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
(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 ... -
Atomic processes of shear-coupled migration in {112} twins and vicinal grain boundaries in bcc-Fe
(American Physical Society (APS), 2020-07)
Article
Open AccessTilt {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
(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
(2018-10-04)
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 ... -
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 ... -
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 ... -
Comment on
(2010-01-15)
Article
Restricted access - publisher's policy -
Competing structures within the first shell of liquid C2Cl6: a molecular dynamics study
(2014-02-28)
Article
Open AccessWe 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
(1991-01)
Article
Restricted access - publisher's policyA 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
(2023-05-01)
Article
Open AccessClassical 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
(American Chemical Society, 2016-06-20)
Article
Open AccessTo 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
(2021-08-15)
Article
Restricted access - publisher's policyThe 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 ... -
Design and development of an interactive visualization tools for molecular dynamics simulation data
(Universitat Politècnica de Catalunya, 2019-01-29)
Master thesis
Open Access
Covenantee: Università degli Studi di MilanoThe 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 ...
