SIMCON - Grup de Recerca de Simulació per Ordinador en Matèria Condensada
http://hdl.handle.net/2117/394
2017-07-29T11:57:38ZMolecular dynamics of di-palmitoyl-phosphatidyl-choline biomembranes in ionic solution: adsorption of the precursor neurotransmitter tryptophan
http://hdl.handle.net/2117/105364
Molecular dynamics of di-palmitoyl-phosphatidyl-choline biomembranes in ionic solution: adsorption of the precursor neurotransmitter tryptophan
Martí Rabassa, Jordi; Lu, Huixia
Microscopic structure of a fully hydrated di-palmytoil-phosphatidyl-choline lipid bilayer membrane in the liquid-crystalline phase has been analyzed with all-atom molecular dynamics simulations based on the recently parameterized CHARMM36 force field. Within the membrane, a single molecule of the a-aminoacid tryptophan (precursor of important neurotransmitters such as serotonin and melatonin) has been embedded and its structure and binding sites to water and lipids have been explored. In addition, properties such as radial distribution functions, hydrogen-bonding, energy and pressure profiles and the potentials of mean force of water-tryptophan and lipid-tryptophan have been evaluated. It has been observed that tryptophan usually has a tendency to place itself close to the lipid headgroups but that it can be fully hydrated during short time intervals of the order of a few nanoseconds. This would indicate that, for tryptophan, both hydrophobic forces as well as the attraction to polar sites of the lipids play a significant role in the definition of its structure and binding states.
2017-06-12T15:26:54ZMartí Rabassa, JordiLu, HuixiaMicroscopic structure of a fully hydrated di-palmytoil-phosphatidyl-choline lipid bilayer membrane in the liquid-crystalline phase has been analyzed with all-atom molecular dynamics simulations based on the recently parameterized CHARMM36 force field. Within the membrane, a single molecule of the a-aminoacid tryptophan (precursor of important neurotransmitters such as serotonin and melatonin) has been embedded and its structure and binding sites to water and lipids have been explored. In addition, properties such as radial distribution functions, hydrogen-bonding, energy and pressure profiles and the potentials of mean force of water-tryptophan and lipid-tryptophan have been evaluated. It has been observed that tryptophan usually has a tendency to place itself close to the lipid headgroups but that it can be fully hydrated during short time intervals of the order of a few nanoseconds. This would indicate that, for tryptophan, both hydrophobic forces as well as the attraction to polar sites of the lipids play a significant role in the definition of its structure and binding states.Scale-free networks emerging from multifractal time series
http://hdl.handle.net/2117/105316
Scale-free networks emerging from multifractal time series
Budroni, Marcello A.; Baronchelli, Andrea; Pastor Satorras, Romualdo
Methods connecting dynamical systems and graph theory have attracted increasing interest in the past few years, with applications ranging from a detailed comparison of different kinds of dynamics to the characterization of empirical data. Here we investigate the effects of the (multi)fractal properties of a signal, common in time series arising from chaotic dynamics or strange attractors, on the topology of a suitably projected network. Relying on the box-counting formalism, we map boxes into the nodes of a network and establish analytic expressions connecting the natural measure of a box with its degree in the graph representation. We single out the conditions yielding to the emergence of a scale-free topology and validate our findings with extensive numerical simulations. We finally present a numerical analysis on the properties of weighted and directed network projections.
2017-06-09T15:54:57ZBudroni, Marcello A.Baronchelli, AndreaPastor Satorras, RomualdoMethods connecting dynamical systems and graph theory have attracted increasing interest in the past few years, with applications ranging from a detailed comparison of different kinds of dynamics to the characterization of empirical data. Here we investigate the effects of the (multi)fractal properties of a signal, common in time series arising from chaotic dynamics or strange attractors, on the topology of a suitably projected network. Relying on the box-counting formalism, we map boxes into the nodes of a network and establish analytic expressions connecting the natural measure of a box with its degree in the graph representation. We single out the conditions yielding to the emergence of a scale-free topology and validate our findings with extensive numerical simulations. We finally present a numerical analysis on the properties of weighted and directed network projections.Effect of nickel on point defects diffusion in Fe – Ni alloys
http://hdl.handle.net/2117/104785
Effect of nickel on point defects diffusion in Fe – Ni alloys
Anento Moreno, Napoleón; Serra Tort, Ana María; Osetsky, Yuri
Iron-Nickel alloys are perspective alloys as nuclear energy structural materials because of their good radiation damage tolerance and mechanical properties. Understanding of experimentally observed features such as the effect of Ni content to radiation defects evolution is essential for developing predictive models of radiation. Recently an atomic-scale modelling study has revealed one particular mechanism of Ni effect related to the reduced mobility of clusters of interstitial atoms in Fe-Ni alloys. In this paper we present results of the microsecond-scale molecular dynamics study of point defects, i.e. vacancies and self-interstitial atoms, diffusion in Fe-Ni alloys. It is found that the addition of Ni atoms affects diffusion processes: diffusion of vacancies is enhanced in the presence of Ni, whereas diffusion of interstitials is reduced and these effects increase at high Ni concentration and low temperature. The role of Ni solutes in radiation damage evolution in Fe-Ni ferritic alloys is discussed
2017-05-23T14:47:34ZAnento Moreno, NapoleónSerra Tort, Ana MaríaOsetsky, YuriIron-Nickel alloys are perspective alloys as nuclear energy structural materials because of their good radiation damage tolerance and mechanical properties. Understanding of experimentally observed features such as the effect of Ni content to radiation defects evolution is essential for developing predictive models of radiation. Recently an atomic-scale modelling study has revealed one particular mechanism of Ni effect related to the reduced mobility of clusters of interstitial atoms in Fe-Ni alloys. In this paper we present results of the microsecond-scale molecular dynamics study of point defects, i.e. vacancies and self-interstitial atoms, diffusion in Fe-Ni alloys. It is found that the addition of Ni atoms affects diffusion processes: diffusion of vacancies is enhanced in the presence of Ni, whereas diffusion of interstitials is reduced and these effects increase at high Ni concentration and low temperature. The role of Ni solutes in radiation damage evolution in Fe-Ni ferritic alloys is discussedObservation of dynamic atom-atom correlation in liquid helium in real space
http://hdl.handle.net/2117/104604
Observation of dynamic atom-atom correlation in liquid helium in real space
Dmowski, W.; Diallo, S. O.; Lokshin, K.; Ehlers, G.; Ferré Porta, Guillem; Boronat Medico, Jordi; Egami, T.
Liquid He-4 becomes superfluid and flows without resistance below temperature 2.17 K. Superfluidity has been a subject of intense studies and notable advances were made in elucidating the phenomenon by experiment and theory. Nevertheless, details of the microscopic state, including dynamic atom-atom correlations in the superfluid state, are not fully understood. Here using a technique of neutron dynamic pair-density function (DPDF) analysis we show that He-4 atoms in the Bose-Einstein condensate have environment significantly different from uncondensed atoms, with the interatomic distance larger than the average by about 10%, whereas the average structure changes little through the superfluid transition. DPDF peak not seen in the snap-shot pair-density function is found at 2.3 angstrom, and is interpreted in terms of atomic tunnelling. The real space picture of dynamic atom-atom correlations presented here reveal characteristics of atomic dynamics not recognized so far, compelling yet another look at the phenomenon.
2017-05-18T13:43:46ZDmowski, W.Diallo, S. O.Lokshin, K.Ehlers, G.Ferré Porta, GuillemBoronat Medico, JordiEgami, T.Liquid He-4 becomes superfluid and flows without resistance below temperature 2.17 K. Superfluidity has been a subject of intense studies and notable advances were made in elucidating the phenomenon by experiment and theory. Nevertheless, details of the microscopic state, including dynamic atom-atom correlations in the superfluid state, are not fully understood. Here using a technique of neutron dynamic pair-density function (DPDF) analysis we show that He-4 atoms in the Bose-Einstein condensate have environment significantly different from uncondensed atoms, with the interatomic distance larger than the average by about 10%, whereas the average structure changes little through the superfluid transition. DPDF peak not seen in the snap-shot pair-density function is found at 2.3 angstrom, and is interpreted in terms of atomic tunnelling. The real space picture of dynamic atom-atom correlations presented here reveal characteristics of atomic dynamics not recognized so far, compelling yet another look at the phenomenon.He-3 on preplated graphite
http://hdl.handle.net/2117/104458
He-3 on preplated graphite
Gordillo Bargueño, Maria Carmen; Boronat Medico, Jordi
By using the diffusion Monte Carlo method, we obtained the full phase diagram of He3 on top of graphite preplated with a solid layer of He4. All the He4 atoms of the substrate were explicitly considered and allowed to move during the simulation. We found that the ground state is a liquid of density 0.007±0.001 Å-2, in good agreement with available experimental data. This is significantly different from the case of He3 on clean graphite, in which both theory and experiment agree on the existence of a gas-liquid transition at low densities. Upon an increase in He3 density, we predict a first-order phase transition between a dense liquid and a registered 7/12 phase, the 4/7 phase being found metastable in our calculations. At larger second-layer densities, a final transition is produced to an incommensurate triangular phase.
2017-05-15T16:21:37ZGordillo Bargueño, Maria CarmenBoronat Medico, JordiBy using the diffusion Monte Carlo method, we obtained the full phase diagram of He3 on top of graphite preplated with a solid layer of He4. All the He4 atoms of the substrate were explicitly considered and allowed to move during the simulation. We found that the ground state is a liquid of density 0.007±0.001 Å-2, in good agreement with available experimental data. This is significantly different from the case of He3 on clean graphite, in which both theory and experiment agree on the existence of a gas-liquid transition at low densities. Upon an increase in He3 density, we predict a first-order phase transition between a dense liquid and a registered 7/12 phase, the 4/7 phase being found metastable in our calculations. At larger second-layer densities, a final transition is produced to an incommensurate triangular phase.Phase diagram of quasi-two-dimensional bosons in a laser-speckle potential
http://hdl.handle.net/2117/104376
Phase diagram of quasi-two-dimensional bosons in a laser-speckle potential
Astrakharchik, Grigori; Krutitsky, K.V.; Navez, Patrick
We have studied the phase diagram of a quasi-two-dimensional interacting Bose gas at zero temperature in the presence of random potential created by laser speckles. The superfluid fraction and the fraction of particles with zero momentum are obtained within the mean-field Gross-Pitaevskii theory and in diffusion Monte Carlo simulations. We find a transition from the superfluid to the insulating state when the strength of the disorder grows. Estimations of the critical parameters are compared with the predictions of the percolation theory in the Thomas-Fermi approximation. Analytical expressions for the zero-momentum fraction and the superfluid fraction are derived in the limit of weak disorder and weak interactions within the framework of the Bogoliubov theory. Limits of validity of various approximations are discussed.
2017-05-12T13:35:21ZAstrakharchik, GrigoriKrutitsky, K.V.Navez, PatrickWe have studied the phase diagram of a quasi-two-dimensional interacting Bose gas at zero temperature in the presence of random potential created by laser speckles. The superfluid fraction and the fraction of particles with zero momentum are obtained within the mean-field Gross-Pitaevskii theory and in diffusion Monte Carlo simulations. We find a transition from the superfluid to the insulating state when the strength of the disorder grows. Estimations of the critical parameters are compared with the predictions of the percolation theory in the Thomas-Fermi approximation. Analytical expressions for the zero-momentum fraction and the superfluid fraction are derived in the limit of weak disorder and weak interactions within the framework of the Bogoliubov theory. Limits of validity of various approximations are discussed.Solvation dynamics in liquid water: III: energy fluxes and structural changes
http://hdl.handle.net/2117/103729
Solvation dynamics in liquid water: III: energy fluxes and structural changes
Rey Oriol, Rosendo; Hynes, James T.
In previous installments it has been shown how a detailed analysis of energy fluxes induced by electronic excitation of a solute can provide a quantitative understanding of the dominant molecular energy flow channels characterizing solvation—and in particular, hydration— relaxation dynamics. Here this work and power approach is complemented with a detailed characterization of the changes induced by such energy fluxes. We first examine the water solvent’s spatial and orientational distributions and the assorted energy fluxes in the various hydration shells of the solute to provide a molecular picture of the relaxation. The latter analysis is also used to address the issue of a possible “inverse snowball” effect, an ansatz concerning the time scales of the different hydration shells to reach equilibrium. We then establish a link between the instantaneous torque, exerted on the water solvent neighbors’ principal rotational axes immediately after excitation and the final energy transferred into those librational motions, which are the dominant short-time energy receptor.
2017-04-25T16:17:30ZRey Oriol, RosendoHynes, James T.In previous installments it has been shown how a detailed analysis of energy fluxes induced by electronic excitation of a solute can provide a quantitative understanding of the dominant molecular energy flow channels characterizing solvation—and in particular, hydration— relaxation dynamics. Here this work and power approach is complemented with a detailed characterization of the changes induced by such energy fluxes. We first examine the water solvent’s spatial and orientational distributions and the assorted energy fluxes in the various hydration shells of the solute to provide a molecular picture of the relaxation. The latter analysis is also used to address the issue of a possible “inverse snowball” effect, an ansatz concerning the time scales of the different hydration shells to reach equilibrium. We then establish a link between the instantaneous torque, exerted on the water solvent neighbors’ principal rotational axes immediately after excitation and the final energy transferred into those librational motions, which are the dominant short-time energy receptor.Structure of halo and quasi-halo helium–helium–alkali trimers
http://hdl.handle.net/2117/103533
Structure of halo and quasi-halo helium–helium–alkali trimers
Stipanovic, P.; Vranješ Markic, Leandra; Boronat Medico, Jordi
We report a diffusion Monte Carlo study of A4He2 and A4He3He trimers’ structural properties, were A is one of the alkali atoms 6,7Li, 23Na, 39K, 85Rb or 133Cs. Some of them are in a pure halo state, characterized by large spatial extent and universality, while some are close to the halo limit. The theoretical analysis of these trimers enables insight on how structural properties of weakly bound systems change when approaching the halo edge. For that purpose, two-variable distributions of inter-particle separations and angles were calculated. Extreme spatial extensions of some trimers with 3He confirm their halo nature. Although all the considered systems are floppy, trimers with all bound dimer subsystems are less spread and have significantly lower percentage of quasi-linear configurations than those which have at least one unbound dimer subsystem.
2017-04-18T17:45:04ZStipanovic, P.Vranješ Markic, LeandraBoronat Medico, JordiWe report a diffusion Monte Carlo study of A4He2 and A4He3He trimers’ structural properties, were A is one of the alkali atoms 6,7Li, 23Na, 39K, 85Rb or 133Cs. Some of them are in a pure halo state, characterized by large spatial extent and universality, while some are close to the halo limit. The theoretical analysis of these trimers enables insight on how structural properties of weakly bound systems change when approaching the halo edge. For that purpose, two-variable distributions of inter-particle separations and angles were calculated. Extreme spatial extensions of some trimers with 3He confirm their halo nature. Although all the considered systems are floppy, trimers with all bound dimer subsystems are less spread and have significantly lower percentage of quasi-linear configurations than those which have at least one unbound dimer subsystem.Two-dimensional domain structures in Lithium Niobate via domain inversion with ultrafast light
http://hdl.handle.net/2117/103122
Two-dimensional domain structures in Lithium Niobate via domain inversion with ultrafast light
Chen, Xin; Karpinski, Pawel; Shvedov, Vladlen; Wang, Bingxia; Trull Silvestre, José Francisco; Cojocaru, Crina; Boes, A.; Mitchell, A.; Krolikowski, Wieslaw; Sheng, Yan
Periodic inversion of ferroelectric domains is realized in a lithium niobate crystal by focused femtosecond near-infrared laser beam. One and two-dimensional domain patterns are fabricated. Quasi-phase matched frequency doubling of 815nm light is demonstrated in a channel waveguide with an inscribed periodic domain pattern with conversion efficiency as high as 17.45%.
2017-03-30T16:32:04ZChen, XinKarpinski, PawelShvedov, VladlenWang, BingxiaTrull Silvestre, José FranciscoCojocaru, CrinaBoes, A.Mitchell, A.Krolikowski, WieslawSheng, YanPeriodic inversion of ferroelectric domains is realized in a lithium niobate crystal by focused femtosecond near-infrared laser beam. One and two-dimensional domain patterns are fabricated. Quasi-phase matched frequency doubling of 815nm light is demonstrated in a channel waveguide with an inscribed periodic domain pattern with conversion efficiency as high as 17.45%.Droplets of trapped quantum dipolar bosons
http://hdl.handle.net/2117/103119
Droplets of trapped quantum dipolar bosons
Macia Rey, Adrián; Sánchez Baena, Juan; Boronat Medico, Jordi; Mazzanti Castrillejo, Fernando Pablo
Strongly interacting systems of dipolar bosons in three dimensions confined by harmonic traps are analyzed using the exact path integral ground-state Monte Carlo method. By adding a repulsive two-body potential, we find a narrow window of interaction parameters leading to stable ground-state configurations of droplets in a crystalline arrangement. We find that this effect is entirely due to the interaction present in the Hamiltonian without resorting to additional stabilizing mechanisms or specific three-body forces. We analyze the number of droplets formed in terms of the Hamiltonian parameters, relate them to the corresponding s-wave scattering length, and discuss a simple scaling model for the density profiles. Our results are in qualitative agreement with recent experiments showing a quantum Rosensweig instability in trapped Dy atoms.
2017-03-30T14:48:30ZMacia Rey, AdriánSánchez Baena, JuanBoronat Medico, JordiMazzanti Castrillejo, Fernando PabloStrongly interacting systems of dipolar bosons in three dimensions confined by harmonic traps are analyzed using the exact path integral ground-state Monte Carlo method. By adding a repulsive two-body potential, we find a narrow window of interaction parameters leading to stable ground-state configurations of droplets in a crystalline arrangement. We find that this effect is entirely due to the interaction present in the Hamiltonian without resorting to additional stabilizing mechanisms or specific three-body forces. We analyze the number of droplets formed in terms of the Hamiltonian parameters, relate them to the corresponding s-wave scattering length, and discuss a simple scaling model for the density profiles. Our results are in qualitative agreement with recent experiments showing a quantum Rosensweig instability in trapped Dy atoms.