SIMCON - Grup de Recerca de Simulació per Ordinador en Matèria Condensada
http://hdl.handle.net/2117/394
2016-05-27T22:14:08ZFree energy landscapes of sodium ions bound to DMPC–cholesterol membrane surfaces at infinite dilution
http://hdl.handle.net/2117/86798
Free energy landscapes of sodium ions bound to DMPC–cholesterol membrane surfaces at infinite dilution
Yang, Jing; Bonomi, Massimiliano; Calero Borrallo, Carles; Martí Rabassa, Jordi
Exploring the free energy landscapes of metal cations on phospholipid membrane surfaces is important for the understanding of chemical and biological processes in cellular environments. Using metadynamics simulations we have performed systematic free energy calculations of sodium cations bound to DMPC phospholipid membranes with cholesterol concentration varying between 0% (cholesterol-free) and 50% (cholesterol-rich) at infinite dilution. The resulting free energy landscapes reveal the competition between binding of sodium to water and to lipid head groups. Moreover, the binding competitiveness of lipid head groups is diminished by cholesterol contents. As cholesterol concentration increases, the ionic affinity to membranes decreases. When cholesterol concentration is greater than 30%, the ionic binding is significantly reduced, which coincides with the phase transition point of DMPC–cholesterol membranes from a liquid-disordered phase to a liquid-ordered phase. We have also evaluated the contributions of different lipid head groups to the binding free energy separately. The DMPC's carbonyl group is the most favorable binding site for sodium, followed by DMPC's phosphate group and then the hydroxyl group of cholesterol.
2016-05-09T17:46:07ZYang, JingBonomi, MassimilianoCalero Borrallo, CarlesMartí Rabassa, JordiExploring the free energy landscapes of metal cations on phospholipid membrane surfaces is important for the understanding of chemical and biological processes in cellular environments. Using metadynamics simulations we have performed systematic free energy calculations of sodium cations bound to DMPC phospholipid membranes with cholesterol concentration varying between 0% (cholesterol-free) and 50% (cholesterol-rich) at infinite dilution. The resulting free energy landscapes reveal the competition between binding of sodium to water and to lipid head groups. Moreover, the binding competitiveness of lipid head groups is diminished by cholesterol contents. As cholesterol concentration increases, the ionic affinity to membranes decreases. When cholesterol concentration is greater than 30%, the ionic binding is significantly reduced, which coincides with the phase transition point of DMPC–cholesterol membranes from a liquid-disordered phase to a liquid-ordered phase. We have also evaluated the contributions of different lipid head groups to the binding free energy separately. The DMPC's carbonyl group is the most favorable binding site for sodium, followed by DMPC's phosphate group and then the hydroxyl group of cholesterol.The role of nickel in radiation damage of ferritic alloys
http://hdl.handle.net/2117/86565
The role of nickel in radiation damage of ferritic alloys
Osetsky, Yuri; Anento Moreno, Napoleón; Serra Tort, Ana María; Terentyev, Dimitry
According to modern theory, damage evolution under neutron irradiation depends on the fraction of self-interstitial atoms (SIAs) produced in the form of one-dimensional glissile clusters. These clusters, having a low interaction cross-section with other defects, are absorbed mainly by grain boundaries and dislocations, creating the so-called production bias. It is known empirically that the addition of certain alloying elements influences many radiation effects, including swelling; however, the mechanisms are unknown in many cases. In this paper we report the results of an extensive multi-technique atomistic level modeling study of SIA clusters mobility in body-centered cubic Fe-Ni alloys. We have found that Ni interacts strongly with the periphery of clusters, affecting their mobility. The total effect is defined by the number of Ni atoms interacting with the cluster at the same time and can be significant, even in low-Ni alloys. Thus a 1 nm (37SIAs) cluster is practically immobile at T < 500 K in the Fe-0.8 at.% Ni alloy. Increasing cluster size and Ni content enhances cluster immobilization. This effect should have quite broad consequences in void swelling, matrix damage accumulation and radiation induced hardening and the results obtained help to better understand and predict the effects of radiation in Fe-Ni ferritic alloys. Published by Elsevier Ltd. on behalf of Acta Materialia Inc.
2016-05-04T12:08:54ZOsetsky, YuriAnento Moreno, NapoleónSerra Tort, Ana MaríaTerentyev, DimitryAccording to modern theory, damage evolution under neutron irradiation depends on the fraction of self-interstitial atoms (SIAs) produced in the form of one-dimensional glissile clusters. These clusters, having a low interaction cross-section with other defects, are absorbed mainly by grain boundaries and dislocations, creating the so-called production bias. It is known empirically that the addition of certain alloying elements influences many radiation effects, including swelling; however, the mechanisms are unknown in many cases. In this paper we report the results of an extensive multi-technique atomistic level modeling study of SIA clusters mobility in body-centered cubic Fe-Ni alloys. We have found that Ni interacts strongly with the periphery of clusters, affecting their mobility. The total effect is defined by the number of Ni atoms interacting with the cluster at the same time and can be significant, even in low-Ni alloys. Thus a 1 nm (37SIAs) cluster is practically immobile at T < 500 K in the Fe-0.8 at.% Ni alloy. Increasing cluster size and Ni content enhances cluster immobilization. This effect should have quite broad consequences in void swelling, matrix damage accumulation and radiation induced hardening and the results obtained help to better understand and predict the effects of radiation in Fe-Ni ferritic alloys. Published by Elsevier Ltd. on behalf of Acta Materialia Inc.Competing structures within the first shell of liquid C2Cl6: a molecular dynamics study
http://hdl.handle.net/2117/86473
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
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 as the main phenomenology. Particular attention is paid to the first neighbor structure studying the distance of the center of mass (CM) and relative orientation arrangements. The distance dependence of the orientation and location of closer neighbors is studied up to the fourth neighbor (the maximum of first peak of the CM radial distribution function). An unusual arrangement in the first neighbor is seen.
2016-05-02T11:40:12ZHenao Aristizábal, AndrésPothoczki, SzilviaCanales Gabriel, ManelGuàrdia Manuel, ElviraPardo Soto, Luis CarlosWe 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 as the main phenomenology. Particular attention is paid to the first neighbor structure studying the distance of the center of mass (CM) and relative orientation arrangements. The distance dependence of the orientation and location of closer neighbors is studied up to the fourth neighbor (the maximum of first peak of the CM radial distribution function). An unusual arrangement in the first neighbor is seen.Phase diagram of a quantum Coulomb wire
http://hdl.handle.net/2117/85102
Phase diagram of a quantum Coulomb wire
Ferré Porta, Guillem; Astrakharchik, Grigori; Boronat Medico, Jordi
2016-04-04T10:20:09ZFerré Porta, GuillemAstrakharchik, GrigoriBoronat Medico, JordiOne-dimensional Bose gas in optical lattices of arbitrary strength
http://hdl.handle.net/2117/84244
One-dimensional Bose gas in optical lattices of arbitrary strength
Astrakharchik, Grigori; Krutitsky, K.V.; Lewenstein, Maciej; Mazzanti Castrillejo, Fernando Pablo
One-dimensional Bose gas with contact interaction in optical lattices at zero temperature is investigated by means of the exact diffusion Monte Carlo algorithm. The results obtained from the fundamental continuous model are compared with those obtained from the lattice (discrete) Bose-Hubbard model, using exact diagonalization, and from the quantum sine-Gordon model. We map out the complete phase diagram of the continuous model and determine the regions of applicability of the Bose-Hubbard model. Various physical quantities characterizing the systems are calculated, and it is demonstrated that the sine-Gordon model used for shallow lattices is inaccurate.
2016-03-11T17:29:02ZAstrakharchik, GrigoriKrutitsky, K.V.Lewenstein, MaciejMazzanti Castrillejo, Fernando PabloOne-dimensional Bose gas with contact interaction in optical lattices at zero temperature is investigated by means of the exact diffusion Monte Carlo algorithm. The results obtained from the fundamental continuous model are compared with those obtained from the lattice (discrete) Bose-Hubbard model, using exact diagonalization, and from the quantum sine-Gordon model. We map out the complete phase diagram of the continuous model and determine the regions of applicability of the Bose-Hubbard model. Various physical quantities characterizing the systems are calculated, and it is demonstrated that the sine-Gordon model used for shallow lattices is inaccurate.Distinct types of eigenvector localization in networks
http://hdl.handle.net/2117/83693
Distinct types of eigenvector localization in networks
Pastor Satorras, Romualdo; Castellano, Claudio
The spectral properties of the adjacency matrix provide a trove of information about the structure and function of complex networks. In particular, the largest eigenvalue and its associated principal eigenvector are crucial in the understanding of nodes' centrality and the unfolding of dynamical processes. Here we show that two distinct types of localization of the principal eigenvector may occur in heterogeneous networks. For synthetic networks with degree distribution P(q) ~ q -'¿, localization occurs on the largest hub if ¿ > 5/2; for ¿ < 5/2 a new type of localization arises on a mesoscopic subgraph associated with the shell with the largest index in the K-core decomposition. Similar evidence for the existence of distinct localization modes is found in the analysis of real-world networks. Our results open a new perspective on dynamical processes on networks and on a recently proposed alternative measure of node centrality based on the non-backtracking matrix.
2016-03-02T10:56:42ZPastor Satorras, RomualdoCastellano, ClaudioThe spectral properties of the adjacency matrix provide a trove of information about the structure and function of complex networks. In particular, the largest eigenvalue and its associated principal eigenvector are crucial in the understanding of nodes' centrality and the unfolding of dynamical processes. Here we show that two distinct types of localization of the principal eigenvector may occur in heterogeneous networks. For synthetic networks with degree distribution P(q) ~ q -'¿, localization occurs on the largest hub if ¿ > 5/2; for ¿ < 5/2 a new type of localization arises on a mesoscopic subgraph associated with the shell with the largest index in the K-core decomposition. Similar evidence for the existence of distinct localization modes is found in the analysis of real-world networks. Our results open a new perspective on dynamical processes on networks and on a recently proposed alternative measure of node centrality based on the non-backtracking matrix.First-principles modeling of three-body interactions in highly compressed solid helium
http://hdl.handle.net/2117/83684
First-principles modeling of three-body interactions in highly compressed solid helium
Cazorla Silva, Claudio; Boronat Medico, Jordi
We present a set of three-body interaction models based on the Slater-Kirkwood (SK) potential that are suitable for the study of the energy, structural, and elastic properties of solid He4 at high pressure. Our effective three-body potentials are obtained from the fit to total energies and atomic forces computed with the van der Waals density functional theory method due to Grimme, and represent an improvement with respect to previously reported three-body interaction models. In particular, we show that some of the introduced SK three-body potentials reproduce closely the experimental equation of state and bulk modulus of solid helium up to a pressure of ~60 GPa, when used in combination with standard pairwise interaction models in diffusion Monte Carlo simulations. Importantly, we find that recent predictions reporting a surprisingly small variation of the kinetic energy and Lindeman ratio on quantum crystals under increasing pressure are likely to be artifacts deriving from the use of incomplete interaction models. Also, we show that the experimental variation of the shear modulus, C44, at pressures 0=P=25 GPa can be quantitatively described by our set of SK three-body potentials. At higher compression, however, the agreement between our C44 calculations and experiments deteriorates and thus we argue that higher order many-body terms in the expansion of the atomic interactions probably are necessary in order to better describe elasticity in very dense solid He4.
2016-03-02T09:15:05ZCazorla Silva, ClaudioBoronat Medico, JordiWe present a set of three-body interaction models based on the Slater-Kirkwood (SK) potential that are suitable for the study of the energy, structural, and elastic properties of solid He4 at high pressure. Our effective three-body potentials are obtained from the fit to total energies and atomic forces computed with the van der Waals density functional theory method due to Grimme, and represent an improvement with respect to previously reported three-body interaction models. In particular, we show that some of the introduced SK three-body potentials reproduce closely the experimental equation of state and bulk modulus of solid helium up to a pressure of ~60 GPa, when used in combination with standard pairwise interaction models in diffusion Monte Carlo simulations. Importantly, we find that recent predictions reporting a surprisingly small variation of the kinetic energy and Lindeman ratio on quantum crystals under increasing pressure are likely to be artifacts deriving from the use of incomplete interaction models. Also, we show that the experimental variation of the shear modulus, C44, at pressures 0=P=25 GPa can be quantitatively described by our set of SK three-body potentials. At higher compression, however, the agreement between our C44 calculations and experiments deteriorates and thus we argue that higher order many-body terms in the expansion of the atomic interactions probably are necessary in order to better describe elasticity in very dense solid He4.Quantum versus mean-field collapse in a many-body system
http://hdl.handle.net/2117/83079
Quantum versus mean-field collapse in a many-body system
Astrakharchik, Grigori; Malomed, Boris A.
The recent analysis, based on the mean-field approximation (MFA), has predicted that the critical quantum collapse of the bosonic wave function, pulled to the center by the inverse-square potential in the three-dimensional space, is suppressed by the repulsive cubic nonlinearity in the bosonic gas, the collapsing ground state being replaced by a regular one. We demonstrate that a similar stabilization acts in a quantum many-body system, beyond the MFA. While the collapse remains possible, repulsive two-particle interactions give rise to a metastable gaseous state, which is separated by a potential barrier from the collapsing regime. The stability of this state improves with the increase of the number of particles. The results are produced by calculations of the variational energy, with the help of the Monte Carlo method.
2016-02-17T15:33:53ZAstrakharchik, GrigoriMalomed, Boris A.The recent analysis, based on the mean-field approximation (MFA), has predicted that the critical quantum collapse of the bosonic wave function, pulled to the center by the inverse-square potential in the three-dimensional space, is suppressed by the repulsive cubic nonlinearity in the bosonic gas, the collapsing ground state being replaced by a regular one. We demonstrate that a similar stabilization acts in a quantum many-body system, beyond the MFA. While the collapse remains possible, repulsive two-particle interactions give rise to a metastable gaseous state, which is separated by a potential barrier from the collapsing regime. The stability of this state improves with the increase of the number of particles. The results are produced by calculations of the variational energy, with the help of the Monte Carlo method.Interaction of He and He-V clusters with self-interstitials and dislocations defects in bcc Fe
http://hdl.handle.net/2117/81803
Interaction of He and He-V clusters with self-interstitials and dislocations defects in bcc Fe
Terentyev, Dimitry; Anento Moreno, Napoleón; Serra Tort, Ana María; Ortiz, C. J.; zhurkin, E. E.
The understanding of helium effects in synergy with radiation damage is crucial for the development of structural steels for fusion applications. Recent investigations in ultra-pure iron, taken as a basic model, have shown a drastic impact of dual beam (helium and iron) exposure on the accumulation of radiation-induced dislocation loops in terms of strong bias towards a(0)/2 < 111 > loops, while a(0)< 100 > loops are mostly observed upon iron ion beam. In this work we perform a series of atomistic studies to rationalize possible mechanisms through which He could affect the evolution of microstructure and bias the population of a(0)/2 < 111 > loops. It is shown that He atoms are dragged by gliding a(0)/2 < 111 > loops. This strongly suppresses loop diffusivity and in turn it prohibits the mutual interaction of a(0)/2 < 111 > loops, being prerequisite of the formation of a(0)< 100 > loops, as well as it reduces the disappearance of a(0)/2 < 111 > loops at sinks. A scenario for the microstructural evolution in the single-and dual-beam conditions is discussed. (C) 2014 Elsevier B. V. All rights reserved.
2016-01-21T12:29:01ZTerentyev, DimitryAnento Moreno, NapoleónSerra Tort, Ana MaríaOrtiz, C. J.zhurkin, E. E.The understanding of helium effects in synergy with radiation damage is crucial for the development of structural steels for fusion applications. Recent investigations in ultra-pure iron, taken as a basic model, have shown a drastic impact of dual beam (helium and iron) exposure on the accumulation of radiation-induced dislocation loops in terms of strong bias towards a(0)/2 < 111 > loops, while a(0)< 100 > loops are mostly observed upon iron ion beam. In this work we perform a series of atomistic studies to rationalize possible mechanisms through which He could affect the evolution of microstructure and bias the population of a(0)/2 < 111 > loops. It is shown that He atoms are dragged by gliding a(0)/2 < 111 > loops. This strongly suppresses loop diffusivity and in turn it prohibits the mutual interaction of a(0)/2 < 111 > loops, being prerequisite of the formation of a(0)< 100 > loops, as well as it reduces the disappearance of a(0)/2 < 111 > loops at sinks. A scenario for the microstructural evolution in the single-and dual-beam conditions is discussed. (C) 2014 Elsevier B. V. All rights reserved.Evolution of matrix-twin interfaces of (101¯2) twin in magnesium
http://hdl.handle.net/2117/80919
Evolution of matrix-twin interfaces of (101¯2) twin in magnesium
Ostapovets, Andriy; Serra Tort, Ana María
Recently, the presence of basal-prismatic interfaces in hexagonal close packed metals became subject of intensive investigation. We model the {101¯2} twin in magnesium bounded by two types of boundaries, i.e. {101¯2} interface and basal-prismatic facets. The migration of all boundary types is mediated by the motion of interfacial disconnections. It was shown that basal-prismatic interfaces play an important role in twin growth. The lengths of basal-prismatic facets remain constant during migration independently of the applied strain. In contrast, the {101¯2} interfaces increase their lengths during growth.
2015-12-18T18:44:03ZOstapovets, AndriySerra Tort, Ana MaríaRecently, the presence of basal-prismatic interfaces in hexagonal close packed metals became subject of intensive investigation. We model the {101¯2} twin in magnesium bounded by two types of boundaries, i.e. {101¯2} interface and basal-prismatic facets. The migration of all boundary types is mediated by the motion of interfacial disconnections. It was shown that basal-prismatic interfaces play an important role in twin growth. The lengths of basal-prismatic facets remain constant during migration independently of the applied strain. In contrast, the {101¯2} interfaces increase their lengths during growth.