SIMCON - Grup de Recerca de Simulació per Ordinador en Matèria Condensada
http://hdl.handle.net/2117/394
2016-09-24T22:50:08ZThe structure of liquid water beyond the first hydration shell
http://hdl.handle.net/2117/90080
The structure of liquid water beyond the first hydration shell
Henao Aristizábal, Andrés; Busch, Sebastian; Guàrdia Manuel, Elvira; Tamarit Mur, José Luis; Pardo Soto, Luis Carlos
To date there is a general consensus on the structure of the first coordination shells of liquid water, namely tetrahedral short range order of molecules. In contrast, little is known about the structure at longer distances and the influence of the tetrahedral molecular arrangement of the first shells on the order at these length scales. An expansion of the distance dependent excess entropy is used in this contribution to find out which molecular arrangements are important at each distance range. This was done by splitting the excess entropy into two parts: one connected to the relative position of two molecules and the other one related to their relative orientation. A transition between two previously unknown regimes in liquid water is identified at a distance of about similar to 6 angstrom: from a predominantly orientational order at shorter distances to a regime at larger distances of up to similar to 9 angstrom where the order is predominantly positional and molecules are distributed with the same tetrahedral symmetry as the very first molecules.
2016-09-20T14:24:47ZHenao Aristizábal, AndrésBusch, SebastianGuàrdia Manuel, ElviraTamarit Mur, José LuisPardo Soto, Luis CarlosTo date there is a general consensus on the structure of the first coordination shells of liquid water, namely tetrahedral short range order of molecules. In contrast, little is known about the structure at longer distances and the influence of the tetrahedral molecular arrangement of the first shells on the order at these length scales. An expansion of the distance dependent excess entropy is used in this contribution to find out which molecular arrangements are important at each distance range. This was done by splitting the excess entropy into two parts: one connected to the relative position of two molecules and the other one related to their relative orientation. A transition between two previously unknown regimes in liquid water is identified at a distance of about similar to 6 angstrom: from a predominantly orientational order at shorter distances to a regime at larger distances of up to similar to 9 angstrom where the order is predominantly positional and molecules are distributed with the same tetrahedral symmetry as the very first molecules.Br diffusion in molten NaBr explored by coherent quasielastic neutron scattering
http://hdl.handle.net/2117/88971
Br diffusion in molten NaBr explored by coherent quasielastic neutron scattering
Demmel, F; Alcaraz Sendra, Olga; Trullàs Simó, Joaquim
Molten sodium bromide has been investigated by quasielastic neutron scattering focusing on the wave vector range around the first structure factor peak. The linewidth of the scattering function shows a narrowing around the wave number of the structure factor peak, known as deGennes narrowing. In a monatomic system, this narrowing or in the time domain slowing down, has been related to a self-diffusion process of the caged particle. Here we show that this methodology can be applied to the molten alkali halide NaBr. The incoherent scattering from the sodium ions at small wave vectors provides the self-diffusion coefficient of sodium and the dynamics of bromine ions can be studied at wave numbers around the structure factor peak. With input from molecular dynamics simulations on the partial structure factors, diffusion coefficients of the bromine ions can be obtained. These experimentally derived diffusion coefficients are in good agreement with molecular dynamics simulation results. This methodology to extract self-diffusion coefficients from coherent quasielastic neutron scattering is applicable to binary fluids in general when one particle dominates the scattering response at the structure factor maximum.
2016-07-20T12:05:25ZDemmel, FAlcaraz Sendra, OlgaTrullàs Simó, JoaquimMolten sodium bromide has been investigated by quasielastic neutron scattering focusing on the wave vector range around the first structure factor peak. The linewidth of the scattering function shows a narrowing around the wave number of the structure factor peak, known as deGennes narrowing. In a monatomic system, this narrowing or in the time domain slowing down, has been related to a self-diffusion process of the caged particle. Here we show that this methodology can be applied to the molten alkali halide NaBr. The incoherent scattering from the sodium ions at small wave vectors provides the self-diffusion coefficient of sodium and the dynamics of bromine ions can be studied at wave numbers around the structure factor peak. With input from molecular dynamics simulations on the partial structure factors, diffusion coefficients of the bromine ions can be obtained. These experimentally derived diffusion coefficients are in good agreement with molecular dynamics simulation results. This methodology to extract self-diffusion coefficients from coherent quasielastic neutron scattering is applicable to binary fluids in general when one particle dominates the scattering response at the structure factor maximum.One dimensional H-1, H-2 and H-3
http://hdl.handle.net/2117/88635
One dimensional H-1, H-2 and H-3
Vidal, A.J.; Astrakharchik, Grigori; Vranješ Markic, Leandra; Boronat, J.
The ground-state properties of one-dimensional electron-spin-polarized hydrogen H-1, deuterium H-2, and tritium 3 Hare obtained by means of quantum Monte Carlo methods. The equations of state of the three isotopes are calculated for a wide range of linear densities. The pair correlation function and the static structure factor are obtained and interpreted within the framework of the Luttinger liquid theory. We report the density dependence of the Luttinger parameter and use it to identify different physical regimes: Bogoliubov Bose gas, super-Tonks-Girardeau gas, and quasi-crystal regimes for bosons; repulsive, attractive Fermi gas, and quasi-crystal regimes for fermions. We find that the tritium isotope is the one with the richest behavior. Our results show unambiguously the relevant role of the isotope mass in the properties of this quantum system.
2016-07-08T16:41:50ZVidal, A.J.Astrakharchik, GrigoriVranješ Markic, LeandraBoronat, J.The ground-state properties of one-dimensional electron-spin-polarized hydrogen H-1, deuterium H-2, and tritium 3 Hare obtained by means of quantum Monte Carlo methods. The equations of state of the three isotopes are calculated for a wide range of linear densities. The pair correlation function and the static structure factor are obtained and interpreted within the framework of the Luttinger liquid theory. We report the density dependence of the Luttinger parameter and use it to identify different physical regimes: Bogoliubov Bose gas, super-Tonks-Girardeau gas, and quasi-crystal regimes for bosons; repulsive, attractive Fermi gas, and quasi-crystal regimes for fermions. We find that the tritium isotope is the one with the richest behavior. Our results show unambiguously the relevant role of the isotope mass in the properties of this quantum system.Multistate empirical valence bond study of temperature and confinement effects on proton transfer in water inside hydrophobic nanochannels
http://hdl.handle.net/2117/88634
Multistate empirical valence bond study of temperature and confinement effects on proton transfer in water inside hydrophobic nanochannels
Tahat, Amani; Martí Rabassa, Jordi
Microscopic characteristics of an aqueous excess proton in a wide range of thermodynamic states, from low density amorphous ices (down to 100 K) to high temperature liquids under the critical point (up to 600 K), placed inside hydrophobic graphene slabs at the nanometric scale (with interplate distances between 3.1 and 0.7 nm wide) have been analyzed by means of molecular dynamics simulations. Water-proton and carbon-proton forces were modeled with a multistate empirical valence bond method. Densities between 0.07 and 0.02 1/Å^3 have been considered. As a general trend, we observed a competition between effects of confinement and temperature on structure and dynamical properties of the lone proton. Confinement has strong influence on the local structure of the proton, whereas the main effect of temperature on proton properties is observed on its dynamics, with significant variation of proton transfer rates, proton diffusion coefficients, and characteristic frequencies of vibrational motions. Proton transfer is an activated process with energy barriers between 1 and 10 kJ/mol for both proton transfer and diffusion, depending of the temperature range considered and also on the interplate distance. Arrhenius-like behavior of the transfer rates and of proton diffusion are clearly observed for states above 100 K. Spectral densities of proton species indicated that in all states Zundel-like and Eigen-like complexes survive at some extent.
2016-07-08T15:50:09ZTahat, AmaniMartí Rabassa, JordiMicroscopic characteristics of an aqueous excess proton in a wide range of thermodynamic states, from low density amorphous ices (down to 100 K) to high temperature liquids under the critical point (up to 600 K), placed inside hydrophobic graphene slabs at the nanometric scale (with interplate distances between 3.1 and 0.7 nm wide) have been analyzed by means of molecular dynamics simulations. Water-proton and carbon-proton forces were modeled with a multistate empirical valence bond method. Densities between 0.07 and 0.02 1/Å^3 have been considered. As a general trend, we observed a competition between effects of confinement and temperature on structure and dynamical properties of the lone proton. Confinement has strong influence on the local structure of the proton, whereas the main effect of temperature on proton properties is observed on its dynamics, with significant variation of proton transfer rates, proton diffusion coefficients, and characteristic frequencies of vibrational motions. Proton transfer is an activated process with energy barriers between 1 and 10 kJ/mol for both proton transfer and diffusion, depending of the temperature range considered and also on the interplate distance. Arrhenius-like behavior of the transfer rates and of proton diffusion are clearly observed for states above 100 K. Spectral densities of proton species indicated that in all states Zundel-like and Eigen-like complexes survive at some extent.Pair interactions among ternary DPPC/POPC/cholesterol mixtures in liquid-ordered and liquid-disordered phases
http://hdl.handle.net/2117/88633
Pair interactions among ternary DPPC/POPC/cholesterol mixtures in liquid-ordered and liquid-disordered phases
Yang, Jing; Martí Rabassa, Jordi; Calero Borrallo, Carles
Saturated phospholipids, unsaturated phospholipids, and cholesterol are essential components of cell membranes, making the understanding of their mutual interactions of great significance. We have performed microsecond molecular dynamics simulations on the ternary mixtures of DPPC/POPC/cholesterol to systematically examine lipid-lipid and cholesterol-lipid interactions in the liquid-ordered and the liquid-disordered phases. The results show that there exists a competition between the tighter packing of cholesterol-lipid and the looser packing of lipid-lipid as the membrane changes from the liquid-disordered phase to the liquid-ordered phase. Depending on the lipid saturation, the favor of lipid-lipid interactions is in the order of saturated-saturated > monounsaturated-monounsaturated > saturated-monounsaturated. Cholesterol-saturated lipid interactions are more favorable than cholesterol-monounsaturated lipid ones. The results are consistent with the push-pull forces derived from experiments and give general insights into the interactions among membrane components.
2016-07-08T15:21:15ZYang, JingMartí Rabassa, JordiCalero Borrallo, CarlesSaturated phospholipids, unsaturated phospholipids, and cholesterol are essential components of cell membranes, making the understanding of their mutual interactions of great significance. We have performed microsecond molecular dynamics simulations on the ternary mixtures of DPPC/POPC/cholesterol to systematically examine lipid-lipid and cholesterol-lipid interactions in the liquid-ordered and the liquid-disordered phases. The results show that there exists a competition between the tighter packing of cholesterol-lipid and the looser packing of lipid-lipid as the membrane changes from the liquid-disordered phase to the liquid-ordered phase. Depending on the lipid saturation, the favor of lipid-lipid interactions is in the order of saturated-saturated > monounsaturated-monounsaturated > saturated-monounsaturated. Cholesterol-saturated lipid interactions are more favorable than cholesterol-monounsaturated lipid ones. The results are consistent with the push-pull forces derived from experiments and give general insights into the interactions among membrane components.Collective versus hub activation of epidemic phases on networks
http://hdl.handle.net/2117/88179
Collective versus hub activation of epidemic phases on networks
Ferreira, Silvio C.; Salvador, Renan; Pastor Satorras, Romualdo
We consider a general criterion to discern the nature of the threshold in epidemic models on scale-free (SF) networks. Comparing the epidemic lifespan of the nodes with largest degrees with the infection time between them, we propose a general dual scenario, in which the epidemic transition is either ruled by a hub activation process, leading to a null threshold in the thermodynamic limit, or given by a collective activation process, corresponding to a standard phase transition with a finite threshold. We validate the proposed criterion applying it to different epidemic models, with waning immunity or heterogeneous infection rates in both synthetic and real SF networks. In particular, a waning immunity, irrespective of its strength, leads to collective activation with finite threshold in scale-free networks with large degree exponent, at odds with canonical theoretical approaches.
2016-06-20T17:46:38ZFerreira, Silvio C.Salvador, RenanPastor Satorras, RomualdoWe consider a general criterion to discern the nature of the threshold in epidemic models on scale-free (SF) networks. Comparing the epidemic lifespan of the nodes with largest degrees with the infection time between them, we propose a general dual scenario, in which the epidemic transition is either ruled by a hub activation process, leading to a null threshold in the thermodynamic limit, or given by a collective activation process, corresponding to a standard phase transition with a finite threshold. We validate the proposed criterion applying it to different epidemic models, with waning immunity or heterogeneous infection rates in both synthetic and real SF networks. In particular, a waning immunity, irrespective of its strength, leads to collective activation with finite threshold in scale-free networks with large degree exponent, at odds with canonical theoretical approaches.Liquid and solid phases of He-3 on graphite
http://hdl.handle.net/2117/88150
Liquid and solid phases of He-3 on graphite
Gordillo Bargueño, Maria Carmen; Boronat Medico, Jordi
Recent heat-capacity experiments show quite unambiguously the existence of a liquid He-3 phase adsorbed on graphite. This liquid is stable at an extremely low density, possibly one of the lowest found in nature. Previous theoretical calculations of the same system, and in strictly two dimensions, agree with the result that this liquid phase is not stable and the system is in the gas phase. We calculated the phase diagram of normal He-3 adsorbed on graphite at T = 0 using quantum Monte Carlo methods. Considering a fully corrugated substrate, we observe that at densities lower than 0.006 angstrom(-2) the system is a very dilute gas that, at that density, is in equilibrium with a liquid of density 0.014 angstrom(-2). Our prediction matches very well the recent experimental findings on the same system. On the contrary, when a flat substrate is considered, no gas-liquid coexistence is found, in agreement with previous calculations. We also report results on the different solid structures, and on the corresponding phase transitions that appear at higher densities.
2016-06-17T17:24:16ZGordillo Bargueño, Maria CarmenBoronat Medico, JordiRecent heat-capacity experiments show quite unambiguously the existence of a liquid He-3 phase adsorbed on graphite. This liquid is stable at an extremely low density, possibly one of the lowest found in nature. Previous theoretical calculations of the same system, and in strictly two dimensions, agree with the result that this liquid phase is not stable and the system is in the gas phase. We calculated the phase diagram of normal He-3 adsorbed on graphite at T = 0 using quantum Monte Carlo methods. Considering a fully corrugated substrate, we observe that at densities lower than 0.006 angstrom(-2) the system is a very dilute gas that, at that density, is in equilibrium with a liquid of density 0.014 angstrom(-2). Our prediction matches very well the recent experimental findings on the same system. On the contrary, when a flat substrate is considered, no gas-liquid coexistence is found, in agreement with previous calculations. We also report results on the different solid structures, and on the corresponding phase transitions that appear at higher densities.Dynamic structure factor of liquid He 4 across the normal-superfluid transition
http://hdl.handle.net/2117/87562
Dynamic structure factor of liquid He 4 across the normal-superfluid transition
Ferré Porta, Guillem; Boronat Medico, Jordi
We have carried out a microscopic study of the dynamic structure factor of liquid He4 across the normal-superfluid transition temperature using the path integral Monte Carlo method. The ill-posed problem of the inverse Laplace transform, from the imaginary-time intermediate scattering function to the dynamic response, is tackled by stochastic optimization. Our results show a quasiparticle peak and a small and broad multiphonon contribution. In spite of the lack of strength in the collective peaks, we clearly identify the rapid dropping of the roton peak amplitude when crossing the transition temperature T¿. Other properties such as the static structure factor, static response, and one-phonon contribution to the response are also calculated at different temperatures. The changes of the phonon-roton spectrum with the temperature are also studied. An overall agreement with available experimental data is achieved.
2016-05-31T15:02:22ZFerré Porta, GuillemBoronat Medico, JordiWe have carried out a microscopic study of the dynamic structure factor of liquid He4 across the normal-superfluid transition temperature using the path integral Monte Carlo method. The ill-posed problem of the inverse Laplace transform, from the imaginary-time intermediate scattering function to the dynamic response, is tackled by stochastic optimization. Our results show a quasiparticle peak and a small and broad multiphonon contribution. In spite of the lack of strength in the collective peaks, we clearly identify the rapid dropping of the roton peak amplitude when crossing the transition temperature T¿. Other properties such as the static structure factor, static response, and one-phonon contribution to the response are also calculated at different temperatures. The changes of the phonon-roton spectrum with the temperature are also studied. An overall agreement with available experimental data is achieved.Free 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.