Articles de revista
http://hdl.handle.net/2117/395
Mon, 20 Nov 2017 04:09:29 GMT2017-11-20T04:09:29ZFree-energy surfaces of ionic adsorption in cholesterol-free and cholesterol-rich phospholipid membranes
http://hdl.handle.net/2117/110069
Free-energy surfaces of ionic adsorption in cholesterol-free and cholesterol-rich phospholipid membranes
Martí Rabassa, Jordi
Free energy surfaces associated to the adsorption of metal cations ((Formula presented.), (Formula presented.), (Formula presented.), and (Formula presented.)) in biological environments have been computed by metadynamics simulations. In all cases, the systems were modelled using the CHARMM36 force field. The free-energy landscapes unveil specific binding behaviour of metal cations. So, (Formula presented.) and (Formula presented.) are more likely to stay in the aqueous solution, and can easily bind to a few lipid oxygens by overcoming low free-energy barriers. Differently, (Formula presented.) is most stable when bound to four lipid oxygens of the membranes, rather than being hydrated in the aqueous solution. Finally, (Formula presented.) is tightly hydrated, and can hardly lose a hydration water and bind directly to the membranes. When cholesterol is included inside the membrane at concentration up to 50%, the resulting free-energy landscapes reveal the competition between binding of sodium to water and to lipid head groups, although the binding competitiveness of lipid head groups is diminished by cholesterol contents. 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.
Mon, 06 Nov 2017 19:42:35 GMThttp://hdl.handle.net/2117/1100692017-11-06T19:42:35ZMartí Rabassa, JordiFree energy surfaces associated to the adsorption of metal cations ((Formula presented.), (Formula presented.), (Formula presented.), and (Formula presented.)) in biological environments have been computed by metadynamics simulations. In all cases, the systems were modelled using the CHARMM36 force field. The free-energy landscapes unveil specific binding behaviour of metal cations. So, (Formula presented.) and (Formula presented.) are more likely to stay in the aqueous solution, and can easily bind to a few lipid oxygens by overcoming low free-energy barriers. Differently, (Formula presented.) is most stable when bound to four lipid oxygens of the membranes, rather than being hydrated in the aqueous solution. Finally, (Formula presented.) is tightly hydrated, and can hardly lose a hydration water and bind directly to the membranes. When cholesterol is included inside the membrane at concentration up to 50%, the resulting free-energy landscapes reveal the competition between binding of sodium to water and to lipid head groups, although the binding competitiveness of lipid head groups is diminished by cholesterol contents. 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.Composite boson description of a low-density gas of excitons
http://hdl.handle.net/2117/110068
Composite boson description of a low-density gas of excitons
Golomedov, A. E.; Lozovik, Yu. E.; Astrakharchik, Grigori; Boronat Medico, Jordi
Ground-state properties of a fermionic Coulomb gas are calculated using the fixed-node diffusion Monte Carlo method. The validity of the composite boson description is tested for different densities. We extract the exciton–exciton s-wave scattering length by solving the four-body problem in a harmonic trap and mapping the energy to that of two trapped bosons. The equation of state is consistent with the Bogoliubov theory for composite bosons interacting with the obtained s-wave scattering length. The perturbative expansion at low density has contributions physically coming from (a) exciton binding energy, (b) mean-field Gross–Pitaevskii interaction between excitons, and (c) quantum depletion of the excitonic condensate (Lee–Huang–Yang terms for composite bosons). In addition, for low densities we find a good agreement with the Bogoliubov bosonic theory for the condensate fraction of excitons. The equation of state in the opposite limit of large density is found to be well described by the perturbative theory including (a) mixture of two ideal Fermi gases and (b) exchange energy. We find that for low densities both energetic and coherent properties are correctly described by the picture of composite bosons (excitons).
Mon, 06 Nov 2017 19:27:49 GMThttp://hdl.handle.net/2117/1100682017-11-06T19:27:49ZGolomedov, A. E.Lozovik, Yu. E.Astrakharchik, GrigoriBoronat Medico, JordiGround-state properties of a fermionic Coulomb gas are calculated using the fixed-node diffusion Monte Carlo method. The validity of the composite boson description is tested for different densities. We extract the exciton–exciton s-wave scattering length by solving the four-body problem in a harmonic trap and mapping the energy to that of two trapped bosons. The equation of state is consistent with the Bogoliubov theory for composite bosons interacting with the obtained s-wave scattering length. The perturbative expansion at low density has contributions physically coming from (a) exciton binding energy, (b) mean-field Gross–Pitaevskii interaction between excitons, and (c) quantum depletion of the excitonic condensate (Lee–Huang–Yang terms for composite bosons). In addition, for low densities we find a good agreement with the Bogoliubov bosonic theory for the condensate fraction of excitons. The equation of state in the opposite limit of large density is found to be well described by the perturbative theory including (a) mixture of two ideal Fermi gases and (b) exchange energy. We find that for low densities both energetic and coherent properties are correctly described by the picture of composite bosons (excitons).Grain boundary mediated plasticity: the role of grain boundary atomic structure and thermal activation
http://hdl.handle.net/2117/109068
Grain boundary mediated plasticity: the role of grain boundary atomic structure and thermal activation
Terentyev, Dimitry; Bakaev, A.; Serra Tort, Ana María; Pavia, F.; Baker, K. L.; Anento Moreno, Napoleón
The interaction of dislocation pile-ups with several tilt grain boundaries (GB) is studied in copper by using a hybrid continuum-atomistic approach. The effects of temperature, pile-up intensity and GB structure on absorption and transmission of slip as a function of local stress state are explored. By considering several high-angle GBs with different misorientation angles, we demonstrate that GB atomic structure primarily defines its ability to accommodate incoming pile-up dislocations, thus limiting the direct transmission of pile-ups through the interface.
Tue, 24 Oct 2017 15:35:10 GMThttp://hdl.handle.net/2117/1090682017-10-24T15:35:10ZTerentyev, DimitryBakaev, A.Serra Tort, Ana MaríaPavia, F.Baker, K. L.Anento Moreno, NapoleónThe interaction of dislocation pile-ups with several tilt grain boundaries (GB) is studied in copper by using a hybrid continuum-atomistic approach. The effects of temperature, pile-up intensity and GB structure on absorption and transmission of slip as a function of local stress state are explored. By considering several high-angle GBs with different misorientation angles, we demonstrate that GB atomic structure primarily defines its ability to accommodate incoming pile-up dislocations, thus limiting the direct transmission of pile-ups through the interface.Lepton flavor changing Higgs decays in the littlest Higgs model with T-parity
http://hdl.handle.net/2117/108150
Lepton flavor changing Higgs decays in the littlest Higgs model with T-parity
del Aguila Jiménez, Francisco; Ametller Congost, Lluís; Illana, José Ignacio; Santiago, Jose; Talavera, Pere; Vega-Morales, Roberto
We calculate loop induced lepton flavor violating Higgs decays in the Littlest
Higgs model with T-parity. We find that a finite amplitude is obtained only when all
contributions from the T-odd lepton sector are included. This is in contrast to lepton fla-
vor violating processes mediated by gauge bosons where the partners of the right-handed
mirror leptons can be decoupled from the spectrum. These partners are necessary to can-
cel the divergence in the Higgs mass introduced by the mirror leptons but are otherwise
unnecessary and assumed to be decoupled in previous phenomenological studies. Further-
more, as we emphasize, including the partner leptons in the spectrum also introduces a
new source of lepton flavor violation via their couplings to the physical pseudo-Goldstone
electroweak triplet scalar. Although this extra source also affects lepton flavor changing
gauge transitions, it decouples from these amplitudes in the limit of heavy mass for the
partner leptons. We find that the corresponding Higgs branching ratio into taus and muons
can be as large as ~ 0.2 × 10 -6 for T-odd masses of the order a few TeV, a demanding
challenge even for the high luminosity LHC.
Fri, 29 Sep 2017 09:56:05 GMThttp://hdl.handle.net/2117/1081502017-09-29T09:56:05Zdel Aguila Jiménez, FranciscoAmetller Congost, LluísIllana, José IgnacioSantiago, JoseTalavera, PereVega-Morales, RobertoWe calculate loop induced lepton flavor violating Higgs decays in the Littlest
Higgs model with T-parity. We find that a finite amplitude is obtained only when all
contributions from the T-odd lepton sector are included. This is in contrast to lepton fla-
vor violating processes mediated by gauge bosons where the partners of the right-handed
mirror leptons can be decoupled from the spectrum. These partners are necessary to can-
cel the divergence in the Higgs mass introduced by the mirror leptons but are otherwise
unnecessary and assumed to be decoupled in previous phenomenological studies. Further-
more, as we emphasize, including the partner leptons in the spectrum also introduces a
new source of lepton flavor violation via their couplings to the physical pseudo-Goldstone
electroweak triplet scalar. Although this extra source also affects lepton flavor changing
gauge transitions, it decouples from these amplitudes in the limit of heavy mass for the
partner leptons. We find that the corresponding Higgs branching ratio into taus and muons
can be as large as ~ 0.2 × 10 -6 for T-odd masses of the order a few TeV, a demanding
challenge even for the high luminosity LHC.Local structural fluctuations, hydrogen bonding and structural transitions in supercritical water
http://hdl.handle.net/2117/108130
Local structural fluctuations, hydrogen bonding and structural transitions in supercritical water
Skarmoutsos, Ioannis; Guàrdia Manuel, Elvira; Samios, Jannis
The contribution of hydrogen bonding interactions to the formation of local density inhomogeneities in supercritical water at near-critical conditions has been extensively studied by means of molecular dynamics simulations. The results obtained have revealed the strong effect of water molecules forming one and two hydrogen bonds on the determination of the local density augmentation in the fluid. The local structural order has also been studied in terms of the trigonal and tetrahedral order parameters, revealing the correlation between local orientational order and hydrogen bonding. The dynamics of the structural order parameters exhibit similarities with local density ones. The local structural analysis performed in terms of nearest neighbors around the individual molecules provides additional significant evidence about the existence of a liquid-like to gas-like structural transition in supercritical water at the density range close to 0.2 ¿c, further supporting previous suggestions based on the interpretation of experimental thermodynamic data.
Thu, 28 Sep 2017 18:17:02 GMThttp://hdl.handle.net/2117/1081302017-09-28T18:17:02ZSkarmoutsos, IoannisGuàrdia Manuel, ElviraSamios, JannisThe contribution of hydrogen bonding interactions to the formation of local density inhomogeneities in supercritical water at near-critical conditions has been extensively studied by means of molecular dynamics simulations. The results obtained have revealed the strong effect of water molecules forming one and two hydrogen bonds on the determination of the local density augmentation in the fluid. The local structural order has also been studied in terms of the trigonal and tetrahedral order parameters, revealing the correlation between local orientational order and hydrogen bonding. The dynamics of the structural order parameters exhibit similarities with local density ones. The local structural analysis performed in terms of nearest neighbors around the individual molecules provides additional significant evidence about the existence of a liquid-like to gas-like structural transition in supercritical water at the density range close to 0.2 ¿c, further supporting previous suggestions based on the interpretation of experimental thermodynamic data.Optical lattices as a tool to study defect-induced superfluidity
http://hdl.handle.net/2117/108074
Optical lattices as a tool to study defect-induced superfluidity
Astrakharchik, Grigori; Krutitsky, K.V.; Lewenstein, Maciej; Mazzanti Castrillejo, Fernando Pablo; Boronat Medico, Jordi
We study the superfluid response, the energetic and structural properties of a one-dimensional ultracold Bose gas in an optical lattice of arbitrary strength. We use the Bose-Fermi mapping in the limit of infinitely large repulsive interaction and the diffusion Monte Carlo method in the case of finite interaction. For slightly incommensurate fillings we find a superfluid behavior, which is discussed in terms of vacancies and interstitials. It is shown that both the excitation spectrum and static structure factor are different for the cases of microscopic and macroscopic fractions of defects. This system provides an extremely well-controlled model for studying defect-induced superfluidity.
Wed, 27 Sep 2017 16:45:13 GMThttp://hdl.handle.net/2117/1080742017-09-27T16:45:13ZAstrakharchik, GrigoriKrutitsky, K.V.Lewenstein, MaciejMazzanti Castrillejo, Fernando PabloBoronat Medico, JordiWe study the superfluid response, the energetic and structural properties of a one-dimensional ultracold Bose gas in an optical lattice of arbitrary strength. We use the Bose-Fermi mapping in the limit of infinitely large repulsive interaction and the diffusion Monte Carlo method in the case of finite interaction. For slightly incommensurate fillings we find a superfluid behavior, which is discussed in terms of vacancies and interstitials. It is shown that both the excitation spectrum and static structure factor are different for the cases of microscopic and macroscopic fractions of defects. This system provides an extremely well-controlled model for studying defect-induced superfluidity.Thermodynamic behavior of a one-dimensional Bose gas at low temperature
http://hdl.handle.net/2117/108073
Thermodynamic behavior of a one-dimensional Bose gas at low temperature
de Rosi, Giulia; Astrakharchik, Grigori; Stringari, Sandro
We show that the chemical potential of a one-dimensional (1D) interacting Bose gas exhibits a nonmonotonic temperature dependence which is peculiar of superfluids. The effect is a direct consequence of the phononic nature of the excitation spectrum at large wavelengths exhibited by 1D Bose gases. For low temperatures T, we demonstrate that the coefficient in T^2 expansion of the chemical potential is entirely defined by the zero-temperature density dependence of the sound velocity. We calculate that coefficient along the crossover between the Bogoliubov weakly interacting gas and the Tonks-Girardeau gas of impenetrable bosons. Analytic expansions are provided in the asymptotic regimes. The theoretical predictions along the crossover are confirmed by comparison with the exactly solvable Yang-Yang model in which the finite-temperature equation of state is obtained numerically by solving Bethe-ansatz equations. A 1D ring geometry is equivalent to imposing periodic boundary conditions and arising finite-size effects are studied in detail. At T=0 we calculated various thermodynamic functions, including the inelastic structure factor, as a function of the number of atoms, pointing out the occurrence of important deviations from the thermodynamic limit.
Wed, 27 Sep 2017 15:39:23 GMThttp://hdl.handle.net/2117/1080732017-09-27T15:39:23Zde Rosi, GiuliaAstrakharchik, GrigoriStringari, SandroWe show that the chemical potential of a one-dimensional (1D) interacting Bose gas exhibits a nonmonotonic temperature dependence which is peculiar of superfluids. The effect is a direct consequence of the phononic nature of the excitation spectrum at large wavelengths exhibited by 1D Bose gases. For low temperatures T, we demonstrate that the coefficient in T^2 expansion of the chemical potential is entirely defined by the zero-temperature density dependence of the sound velocity. We calculate that coefficient along the crossover between the Bogoliubov weakly interacting gas and the Tonks-Girardeau gas of impenetrable bosons. Analytic expansions are provided in the asymptotic regimes. The theoretical predictions along the crossover are confirmed by comparison with the exactly solvable Yang-Yang model in which the finite-temperature equation of state is obtained numerically by solving Bethe-ansatz equations. A 1D ring geometry is equivalent to imposing periodic boundary conditions and arising finite-size effects are studied in detail. At T=0 we calculated various thermodynamic functions, including the inelastic structure factor, as a function of the number of atoms, pointing out the occurrence of important deviations from the thermodynamic limit.Simulation and understanding of atomic and molecular quantum crystals
http://hdl.handle.net/2117/107841
Simulation and understanding of atomic and molecular quantum crystals
Cazorla, Claudio; Boronat Medico, Jordi
Quantum crystals abound in the whole range of solid-state species. Below a certain threshold temperature the physical behavior of rare gases (4He and Ne), molecular solids (H2 and CH4), and some ionic (LiH), covalent (graphite), and metallic (Li) crystals can be explained only in terms of quantum nuclear effects (QNE). A detailed comprehension of the nature of quantum solids is critical for achieving progress in a number of fundamental and applied scientific fields such as planetary sciences, hydrogen storage, nuclear energy, quantum computing, and nanoelectronics. This review describes the current physical understanding of quantum crystals formed by atoms and small molecules, as well as the wide palette of simulation techniques that are used to investigate them. Relevant aspects in these materials such as phase transformations, structural properties, elasticity, crystalline defects, and the effects of reduced dimensionality are discussed thoroughly. An introduction to quantum Monte Carlo techniques, which in the present context are the simulation methods of choice, and other quantum simulation approaches (e.g., path-integral molecular dynamics and quantum thermal baths) is provided. The overarching objective of this article is twofold: first, to clarify in which crystals and physical situations the disregard of QNE may incur in important bias and erroneous interpretations. And second, to promote the study and appreciation of QNE, a topic that traditionally has been treated in the context of condensed matter physics, within the broad and interdisciplinary areas of materials science.
Wed, 20 Sep 2017 17:05:24 GMThttp://hdl.handle.net/2117/1078412017-09-20T17:05:24ZCazorla, ClaudioBoronat Medico, JordiQuantum crystals abound in the whole range of solid-state species. Below a certain threshold temperature the physical behavior of rare gases (4He and Ne), molecular solids (H2 and CH4), and some ionic (LiH), covalent (graphite), and metallic (Li) crystals can be explained only in terms of quantum nuclear effects (QNE). A detailed comprehension of the nature of quantum solids is critical for achieving progress in a number of fundamental and applied scientific fields such as planetary sciences, hydrogen storage, nuclear energy, quantum computing, and nanoelectronics. This review describes the current physical understanding of quantum crystals formed by atoms and small molecules, as well as the wide palette of simulation techniques that are used to investigate them. Relevant aspects in these materials such as phase transformations, structural properties, elasticity, crystalline defects, and the effects of reduced dimensionality are discussed thoroughly. An introduction to quantum Monte Carlo techniques, which in the present context are the simulation methods of choice, and other quantum simulation approaches (e.g., path-integral molecular dynamics and quantum thermal baths) is provided. The overarching objective of this article is twofold: first, to clarify in which crystals and physical situations the disregard of QNE may incur in important bias and erroneous interpretations. And second, to promote the study and appreciation of QNE, a topic that traditionally has been treated in the context of condensed matter physics, within the broad and interdisciplinary areas of materials science.Translational versus rotational energy flow in water solvation dynamics
http://hdl.handle.net/2117/107837
Translational versus rotational energy flow in water solvation dynamics
Rey Oriol, Rosendo; Hynes, James T.
Early molecular dynamics simulations discovered an important asymmetry in the speed of water solvation dynamics for charge extinction and charge creation for an immersed solute, a feature representing a first demonstration of the breakdown of linear response theory. The molecular level mechanism of this asymmetry is examined here via a novel energy flux theoretical approach coupled to geometric probes. The results identify the effect as arising from the translational motions of the solute-hydrating water molecules rather than their rotational/librational motions, even though the latter are more rapid and dominate the energy flow.
Wed, 20 Sep 2017 15:50:12 GMThttp://hdl.handle.net/2117/1078372017-09-20T15:50:12ZRey Oriol, RosendoHynes, James T.Early molecular dynamics simulations discovered an important asymmetry in the speed of water solvation dynamics for charge extinction and charge creation for an immersed solute, a feature representing a first demonstration of the breakdown of linear response theory. The molecular level mechanism of this asymmetry is examined here via a novel energy flux theoretical approach coupled to geometric probes. The results identify the effect as arising from the translational motions of the solute-hydrating water molecules rather than their rotational/librational motions, even though the latter are more rapid and dominate the energy flow.Surface behavior of aprotic mixtures: dimethyl sulfoxide/acetonitrile
http://hdl.handle.net/2117/107616
Surface behavior of aprotic mixtures: dimethyl sulfoxide/acetonitrile
Rodriguez, Javier; Elola, M. Dolores; Martí Rabassa, Jordi; Laria, Daniel
We present results from molecular dynamics simulations that examine microscopic characteristics of mixtures combining acetonitrile (ACN) and dimethyl sulfoxide (DMSO) at the vicinity of liquid/air and liquid/graphene interfaces. In the former interfaces, our simulations reveal a clear propensity of ACN to lie adjacent to the vapor phase at all concentrations. A simple model based on the consideration of a chemical equilibrium between bulk and surface states was found to be adequate to reproduce simulation results. Orientational correlations at the interface showed a mild tendency for dipolar aligments pointing toward the vapor phase in ACN-rich solutions; contrasting, in DMSOrich
mixtures, the preferential orientations looked mostly parallel to the interface.
Close to graphene plates, the local scenarios reverse and local concentrations of
DMSO are larger than the one observed in the bulk. Dynamical results reveal that
the characteristic time scales describing orientational relaxations and residence
times at the interfaces stretch as the concentration of ACN diminishes. For liquid/air interfaces residence times for ACN were found to be larger than those for DMSO. A classical treatment for the predictions of the C-H stretching band of the IR peaks in
the bulk and at the interfaces reveals shifts that agree with experimental measurements.
Wed, 13 Sep 2017 19:12:39 GMThttp://hdl.handle.net/2117/1076162017-09-13T19:12:39ZRodriguez, JavierElola, M. DoloresMartí Rabassa, JordiLaria, DanielWe present results from molecular dynamics simulations that examine microscopic characteristics of mixtures combining acetonitrile (ACN) and dimethyl sulfoxide (DMSO) at the vicinity of liquid/air and liquid/graphene interfaces. In the former interfaces, our simulations reveal a clear propensity of ACN to lie adjacent to the vapor phase at all concentrations. A simple model based on the consideration of a chemical equilibrium between bulk and surface states was found to be adequate to reproduce simulation results. Orientational correlations at the interface showed a mild tendency for dipolar aligments pointing toward the vapor phase in ACN-rich solutions; contrasting, in DMSOrich
mixtures, the preferential orientations looked mostly parallel to the interface.
Close to graphene plates, the local scenarios reverse and local concentrations of
DMSO are larger than the one observed in the bulk. Dynamical results reveal that
the characteristic time scales describing orientational relaxations and residence
times at the interfaces stretch as the concentration of ACN diminishes. For liquid/air interfaces residence times for ACN were found to be larger than those for DMSO. A classical treatment for the predictions of the C-H stretching band of the IR peaks in
the bulk and at the interfaces reveals shifts that agree with experimental measurements.