L’activitat investigadora del grup està centrada en la simulació per ordinador de sistemes de N-cosos i en la seva aplicació a l’estudi de líquids i sòlids així com a diferents sistemes complexos. Els mètodes emprats són bàsicament la Dinàmica Molecular, els Mètode de Monte Carlo i els autòmates cel•lulars. Els sistemes que actualment s'estudien són, entre altres, sals foses, líquids moleculars, dissolucions iòniques, fluids i sòlids quàntics, metalls en fases cristal•lines, sistemes i xarxes complexes.
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.
The role of edge dislocations as sinks for small radiation induced defects in bcc-Fe is investigated by means of atomistic computer simulation. In this work we investigate by Molecular Statics (T = 0K) the interaction between an immobile dislocation line and defect clusters of small sizes invisible experimentally. The study highlights in particular the anisotropy of the interaction and distinguishes between absorbed and trapped defects. When the considered defect intersects the dislocation glide plane and the distance from the dislocation line to the defect is on the range between 2 nm and 4 nm, either total or partial absorption of the cluster takes place leading to the formation of jogs. Residual defects produced during partial absorption pin the dislocation. By the calculation of stress-strain curves we have assessed the strength of those residues as obstacles for the motion of the dislocation, which is reflected on the unpinning stresses and the binding energies obtained. When the defect is outside this range, but on planes close to the dislocation glide plane, instead of absorption we have observed a capture process. Finally, with a view to introducing explicitly in kinetic Monte Carlo models a sink with the shape of a dislocation line, we have summarized our findings on a table presenting the most relevant parameters, which define the interaction of the dislocation with the defects considered.
We study the superfluid properties of a system of fully polarized dipolar bosons moving in the
XY plane. We focus on the general case where the polarization field forms an arbitrary angle a with respect to the Z axis, while the system is still stable. We use the diffusion Monte Carlo and the path integral ground state methods to evaluate the one-body density matrix and the superfluid fractions in the region of the phase diagram where the system forms stripes. Despite its oscillatory behavior, the presence of a finite large-distance asymptotic value in the s-wave component of the one-body density matrix indicates the existence of a Bose condensate. The superfluid fraction along the stripes direction is always close to 1, while in the Y direction decreases to a small value that is nevertheless different from zero. These two facts confirm that the stripe phase of the dipolar Bose system is a clear candidate for an intrinsic supersolid without the presence of defects as described by the Andreev-Lifshitz mechanism.
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.
The cryptocurrency market surpassed the barrier of $100 billion market capitalization in June 2017, after months of steady growth. Despite its increasing relevance in the financial world, a comprehensive analysis of the whole system is still lacking, as most studies have focused exclusively on the behaviour of one (Bitcoin) or few cryptocurrencies. Here, we consider the history of the entire market and analyse the behaviour of 1469 cryptocurrencies introduced between April 2013 and May 2017. We reveal that, while new cryptocurrencies appear and disappear continuously and their market capitalization is increasing (super-)exponentially, several statistical properties of the market have been stable for years. These include the number of active cryptocurrencies, market share distribution and the turnover of cryptocurrencies. Adopting an ecological perspective, we show that the so-called neutral model of evolution is able to reproduce a number of key empirical observations, despite its simplicity and the assumption of no selective advantage of one cryptocurrency over another. Our results shed light on the properties of the cryptocurrency market and establish a first formal link between ecological modelling and the study of this growing system. We anticipate they will spark further research in this direction.
The largest eigenvalue of a network’s adjacency matrix and its associated principal eigenvector are key elements for determining the topological structure and the properties of dynamical processes mediated by it. We present a physically grounded expression relating the value of the largest eigenvalue of a given network to the largest eigenvalue of two network subgraphs, considered as isolated: the hub with its immediate neighbors and the densely connected set of nodes with maximum
-core index. We validate this formula by showing that it predicts, with good accuracy, the largest eigenvalue of a large set of synthetic and real-world topologies. We also present evidence of the consequences of these findings for broad classes of dynamics taking place on the networks. As a by-product, we reveal that the spectral properties of heterogeneous networks built according to the linear preferential attachment model are qualitatively different from those of their static counterparts.
Mobile impurity atoms immersed in Bose–Einstein condensates provide a new platform for exploring Bose polarons. Recent experimental advances in the field of ultracold atoms make it possible to realize such systems with highly tunable microscopic parameters and to explore equilibrium and dynamical properties of polarons using a rich toolbox of atomic physics. In this paper we present a detailed theoretical analysis of Bose polarons in one-dimensional systems of ultracold atoms. By combining a non-perturbative renormalization group approach with numerically exact diffusion Monte Carlo calculations we obtain not only detailed numerical results over a broad range of parameters but also qualitative understanding of different regimes of the system. We find that an accurate description of Bose polarons requires the inclusion of two-phonon scattering terms which go beyond the commonly used Fröhlich model. Furthermore we show that when the Bose gas is in the strongly interacting regime, one needs to include interactions between the phonon modes. We use several theoretical approaches to calculate the polaron energy and its effective mass. The former can be measured using radio-frequency spectroscopy and the latter can be studied experimentally using impurity oscillations in a harmonic trapping potential. We compare our theoretical results for the effective mass to the experiments by Catani et al (2012 Phys. Rev. A 85 023623). In the weak-to-intermediate coupling regimes we obtain excellent quantitative agreement between theory and experiment, without any free fitting parameter. We supplement our analysis by full dynamical simulations of polaron oscillations in a shallow trapping potential. We also use our renormalization group approach to analyze the full phase diagram and identify regions that support repulsive and attractive polarons, as well as multi-particle bound states.
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.
Golomedov, A.; Lozovik, Y.; Astrakharchik, G.; Boronat, J. Journal of low temperature physics Vol. 189, num. 5-6, p. 300-311 DOI: 10.1007/s10909-017-1814-y Data de publicació: 2017-10-13 Article en revista
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).
L'objectiu principal d'aquesta tesi es l'estudi de propietats estàtiques i dinàmiques de diferents fluids quàntics utilitzant tècniques de Monte Carlo quàntiques, principalment emprant el formalisme de path integrals per obtenir results tan a temperatura zero com a temperatura finita. Primer de tot, presentem els mètodes de Monte Carlo quàntics més importants, i introduïm el mètode de Path Integral Monte Carlo (PIMC), que fem servir al llarg de tota la tesi, i el mètode de Path Integral Ground State (PIGS), que es una extensió del primer pero a temperatura zero. Després d'introduir el formalisme bàsic, comentem les diferents aproximacions necesaries i aportem una comparació entre elles. També expliquem un posible mètode de paral·lelització i tècniques de mostreig avançat.Els primers resultats que mostrem en aquesta tesi son pel diagrama de fases d'un gas de Coulomb unidimensional, que hem obtingut emprant PIMC. Hem construit el diagrama de fases mitjançant el càlcul de propietats energètiques i estructurals. Els nostres resultats amplien estudis previs que s'havien realitzat pel mateix sistema a temperatura zero. Els nostres resultats mostren l'existencia d'un règim de cristall de Wigner quàntic i un d'un gas de Fermi ideal a temperatures baixes. Incrementant la temperatura obtenim un cristall de Wigner clàssic i un gas clàssic.En el següent capítol ensenyem els resultats per un sistema quasi-unidimensional de parahidrogen. L'objectiu d'aquest estudi es veure si la quasi-unidimensionalitat afecta al paràmetre de Luttinger quan el comparem pel cas purament unidimensional. Això ho fem a temperatura zero utilitzant PIGS. Sent el parahidrogen un fort candidat a ser superfluid, la idea principal es veure si reduint la dimensionalitat del sistema podem alleugerir suficient la interacció intermolecular. Per fer-ho, provem diferents potentials externs per controlar l'obertura del sistema en dues de les dimensions. Tot i l'increment del paràmetre de Luttinger respecte al cas unidimensional, aquest no arriba als valors esperats per mostrar superfluidesa.El següents resultats són del nostre estudi sobre el factor d'estructura dinàmic per 4He. Utilitzant PIMC, calculem la funció de dispersió a diferents temperatures i fem una inversió per tal d'accedir a les propietats dinàmiques del sistema. Tot i la naturalesa de problema mal posat d'aquesta inversió, obtenim resultats qualitativament bons en comparació amb els experimentals, i provem que el nostre mètode d'inversió obté resultats superiors per 4He a temperatura finita que els obtinguts previament utilitzant altres mètodes. En aquest sentit, aportem una comparació amb el mètode de màxima entropia i amb resultats experimentals. L'estudi a diferents temperatures ens deixa veure la desaparició del pic del rotó quan creuem T=2.17K desde el règim superfluid al fluid normal. També observem una curvatura extranya en la distribució de moments en el règim de superfluidesa que desapareix a temperatures més elevades, i pel qual no existeix cap explicació teòrica.Finalment, mostrem un mètode per calcular funcions de correlació en temps complex, l'objectiu del qual es obtenir factors d'estructura dinàmic superiors als obtinguts en temps purament imaginari. Aquest model ha sigut provat amb èxit en sistemes d'una sola partícula. El nostre objectiu es veure si obtenim resultats bons en sistemes amb més partícules, i si el temps complex màxim al que podem accedir no es redueix amb aquest increment. Tot i el increment en la variança, obtenim bons resultats pel factor dinàmic i, comparant-los amb els obtinguts amb temps imaginari, podem veure com el temps complex ofereix resultats més pròxims als exactes.
The main objective of the thesis is to study static and/or dynamic properties of a set of quantum fluids by means of quantum Monte Carlo techniques, mainly using the path integral formalism to obtain results both at zero temperature and finite temperature. First, we present briefly some of the more important quantum Monte Carlo methods, and introduce the Path Integral Monte Carlo (PIMC) method, which has been used during all this thesis, as well as the Path Integral Ground State (PIGS), which is an extension of the first at ground state. After introducing the basic formalism, we comment on the approximations needed and provide a comparison between different actions. We also comment on parallelization schemes and advanced sampling techniques.
The first results shown in this thesis are for the phase diagram of a one-dimensional Coulomb gas, which have been obtained using the PIMC method. The phase diagram have been constructed mainly by calculating energetic and structural properties. The obtained results extend previous knowledge of different phases in the one-dimensional Coulomb gas at zero temperature. Our results show the existence of a quantum Wigner crystal regime and a Ideal Fermi gas regime at low temperatures. As temperature increases, we reach a classic Wigner crystal regime and a classical gas.
In the following chapter we show the results of a quasi-one-dimensional para-H2. The aim of this work is to see how the quasi-one-dimensionality affects the Luttinger parameter when comparing it with the pure one-dimensional case. This is done at zero temperature using PIGS. As para-hydrogen is an important candidate to superfluidity, the main idea behind study a quasi-one-dimensional system is to reduce dimensionality in order to soften intermolecular interaction. For that, we try different external potentials to control the opening of the system in two dimensions. Despite an increase in the Luttinger parameter in the various quasi-one-dimensional cases, it still does not reach the values displaying superfluidity.
The next work shown in the thesis is our extensive study of the dynamic structure factor for the 4He. Using Path Integral Monte Carlo, we compute the intermediate scattering function at different temperatures and perform an inversion in order to gain access at the dynamics of the system. Despite the ill-posed problem of this inversion, we obtain results in a qualitative agreement with the experiments and prove that our method of inversion, despite having to yield with inversion problems achieves to obtain better numerical results for 4He at finite temperature than the ones previously reported. In this sense, we provide comparisons with the Maximum Entropy method and with experimental results. The study at different temperatures shows us the dissappearance of the roton peak when we cross T=2.17K from the superfluid regime to the normal fluid. We also observe a kink in the momentum distribution at the superfluid regime that dissappears at higher temperatures, for which does not exist an explanation in the theory.
In the final chapter of the thesis we provide a method to sample complex-time correlation functions whose aim is to obtain better dynamic structure factor functions than the ones obtained via pure imaginary-time correlation functions. This model has already been tested for single-particle systems. Our aim is to test it for multi-particle systems, and to see if we can still recover good results at a reasonable high complex-time when the number of particles is closer to the typical simulation values of real systems. We tested it with particles interacting with an harmonic potential. Despite an increased variance compared with the one-particle case, we obtain good results that allow us to obtain the dynamic structure factor. Comparing the results with ones obtained at pure-imaginary time, we show how the complex-time inversion is superior and provides results closer to the exact ones.
L'objectiu principal d'aquesta tesi es l'estudi de propietats estàtiques i dinàmiques de diferents fluids quàntics utilitzant tècniques de Monte Carlo quàntiques, principalment emprant el formalisme de path integrals per obtenir resultats tan a temperatura zero com a temperatura finita. Primer de tot, presentem els mètodes de Monte Carlo quàntics més importants, i introduïm el mètode de Path Integral Monte Carlo (PIMC), que fem servir al llarg de tota la tesi, i el mètode de Path Integral Ground State (PIGS), que es una extensió del primer però a temperatura zero. Després d'introduir el formalisme bàsic, comentem les diferents aproximacions necessàries i aportem una comparació entre elles. També expliquem un possible mètode de paral·lelització i tècniques de mostreig avançat. Els primers resultats que mostrem en aquesta tesi son pel diagrama de fases d'un gas de Coulomb unidimensional, que hem obtingut emprant PIMC. Hem construït el diagrama de fases mitjançant el càlcul de propietats energètiques i estructurals. Els nostres resultats amplien estudis previs que s'havien realitzat pel mateix sistema a temperatura zero. Els nostres resultats mostren l'existència d'un règim de cristall de Wigner quàntic i un d'un gas de Fermi ideal a temperatures baixes. Incrementant la temperatura obtenim un cristall de Wigner clàssic i un gas clàssic. En el següent capítol ensenyem els resultats per un sistema quasi-unidimensional de parahidrogen. L'objectiu d'aquest estudi es veure si la quasi-unidimensionalitat afecta al paràmetre de Luttinger quan el comparem pel cas purament unidimensional. Això ho fem a temperatura zero utilitzant PIGS. Sent el parahidrogen un fort candidat a ser superfluid, la idea principal es veure si reduint la dimensionalitat del sistema podem alleugerir suficient la interacció intermolecular. Per fer-ho, provem diferents potencials externs per controlar l'obertura del sistema en dues de les dimensions. Tot i l'increment del paràmetre de Luttinger respecte al cas unidimensional, aquest no arriba als valors esperats per mostrar superfluïdesa. El següents resultats són del nostre estudi sobre el factor d'estructura dinàmic per 4He. Utilitzant PIMC, calculem la funció de dispersió a diferents temperatures i fem una inversió per tal d'accedir a les propietats dinàmiques del sistema. Tot i la naturalesa de problema mal posat d'aquesta inversió, obtenim resultats qualitativament bons en comparació amb els experimentals, i provem que el nostre mètode d'inversió obté resultats superiors per 4He a temperatura finita que els obtinguts prèviament utilitzant altres mètodes. En aquest sentit, aportem una comparació amb el mètode de màxima entropia i amb resultats experimentals. L'estudi a diferents temperatures ens deixa veure la desaparició del pic del rotó quan creuem T=2.17K des de el règim superfluid al fluid normal. També observem una curvatura estranya en la distribució de moments en el règim de superfluïdesa que desapareix a temperatures més elevades, i pel qual no existeix cap explicació teòrica. Finalment, mostrem un mètode per calcular funcions de correlació en temps complex, l'objectiu del qual es obtenir factors d'estructura dinàmic superiors als obtinguts en temps purament imaginari. Aquest model ha sigut provat amb èxit en sistemes d'una sola partícula. El nostre objectiu es veure si obtenim resultats bons en sistemes amb més partícules, i si el temps complex màxim al que podem accedir no es redueix amb aquest increment. Tot i l'increment en la variança, obtenim bons resultats pel factor dinàmic i, comparant-los amb els obtinguts amb temps imaginari, podem veure com el temps complex ofereix resultats més pròxims als exactes.
Astrakharchik, G.; Krutitsky, K.V.; Lewenstein, M.; Mazzanti, F.; Boronat, J. Physical Review A Vol. 96, num. 3, p. 1-13 DOI: 10.1103/PhysRevA.96.033606 Data de publicació: 2017-09-05 Article en revista
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.
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.
Multi-layered networks represent a major advance in the description of natural complex systems, and their study has shed light on new physical phenomena. Despite its importance, however, the role of the temporal dimension in their structure and function has not been investigated in much detail so far. Here we study the temporal correlations between layers exhibited by real social multiplex networks. At a basic level, the presence of such correlations implies a certain degree of predictability in the contact pattern, as we quantify by an extension of the entropy and mutual information analyses proposed for the single-layer case. At a different level, we demonstrate that temporal correlations are a signature of a ‘multitasking’ behavior of network agents, characterized by a higher level of switching between different social activities than expected in a uncorrelated pattern. Moreover, temporal correlations significantly affect the dynamics of coupled epidemic processes unfolding on the network. Our work opens the way for the systematic study of temporal multiplex networks and we anticipate it will be of interest to researchers in a broad array of fields.
del Aguila , F.; Ametller, L.; Illana, J.I.; Santiago, J.; Talavera, P.; Vega-Morales, R. Journal of high energy physics Vol. 08, num. 028, p. 1-26 DOI: 10.1007/JHEP08(2017)028 Data de publicació: 2017-08-08 Article en revista
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.
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.
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.
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.
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 alpha-aminoacid tryptophan (precursor of important neurotransmitters such as serotonin and melatonin) has been embedded and his structure and binding sites have been explored. In addition, properties such as radial distribution functions, 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 tends to be close to the lipid headgroups but that it can be fully hydrated during short time intervals of the order of 1 ns. This would indicate that hydrophobic forces as well as the attraction of tryptophan to polar sites of the lipids play a significant role in the definition of the structure and binding states of tryptophan.
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.
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
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.
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.
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.
Marti, J.; Calero, C.; Franzese, G. Entropy: international and interdisciplinary journal of entropy and information studies Vol. 19, num. 3, p. 1-20 DOI: 10.3390/e19030135 Data de publicació: 2017-03-21 Article en revista
Water structure and dynamics are affected by the presence of a nearby interface. Here,
first we review recent results by molecular dynamics simulations about the effect of different carbon-based materials, including armchair carbon nanotubes and a variety of graphene sheets—flat and with corrugation—on water structure and dynamics. We discuss the calculations of binding energies, hydrogen bond distributions, water’s diffusion coefficients and their relation with surface’s geometries at different thermodynamical conditions. Next, we present new results of the crystallization and dynamics of water in a rigid graphene sieve. In particular, we show that the
diffusion of water confined between parallel walls depends on the plate distance in a non-monotonic way and is related to the water structuring, crystallization, re-melting and evaporation for decreasing inter-plate distance. Our results could be relevant in those applications where water is in contact with nanostructured carbon materials at ambient or cryogenic temperatures, as in man-made superhydrophobic materials or filtration membranes, or in techniques that take advantage of hydrated graphene interfaces, as in aqueous electron cryomicroscopy for the analysis of proteins adsorbed on graphene.
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.
We have studied the ground-state properties of para-hydrogen in one dimension and in quasi-one-dimensional configurations using the path-integral ground-state Monte Carlo method. This method produces zero-temperature exact results for a given interaction and geometry. The quasi-one-dimensional setup has been implemented in two forms: the inner channel inside a carbon nanotube coated with H2 and a harmonic confinement of variable strength. Our main result is the dependence of the Luttinger parameter on the density within the stable regime. Going from one dimension to quasi-one dimension, keeping the linear density constant, produces a systematic increase of the Luttinger parameter. This increase is, however, not enough to reach the superfluid regime and the system always remain in the quasicrystal regime, according to Luttinger liquid theory.
The generalized H(n) Hirsch index of order n has been recently introduced and shown to interpolate between the degree and the K-core centrality in networks. We provide a detailed analytic characterization of the properties of sets of nodes having the same H(n), within the annealed network approximation. The connection between the Hirsch indices and the degree is highlighted. Numerical tests in synthetic uncorrelated networks and real-world correlated ones validate the findings. We also test the use of the Hirsch index for the identification of influential spreaders in networks, finding that it is in general outperformed by the recently introduced nonbacktracking centrality.
The universality of quantum halo states enables a comparison of systems from different fields of physics, as demonstrated in two- and three-body clusters. In the present work, we studied weakly bound helium tetramers in order to test whether some of these four-body realistic systems qualify as halos. Their ground-state binding energies and structural properties were thoroughly estimated using the diffusion Monte Carlo method with pure estimators. Helium tetramer properties proved to be less sensitive on the potential model than previously evaluated trimer properties. We predict the existence of realistic four-body halo 4He23He2, whereas 4He4 and 4He33He are close to the border and thus can be used as prototypes of quasi-halo systems. Our results could be tested by the experimental determination of the tetramers’ structural properties using a setup similar to the one developed for the study of helium trimers.
Weakly bound triatomic molecules consisting of two helium atoms and one alkali metal atom are studied by means of the diffusion Monte Carlo method. We determined the stability of 4He2A, 4He3HeA, and 3He2A, where A is one of the alkali atoms Li, Na, K, Rb, or Cs. Some of the trimers with 3He are predicted to be self-bound for the first time, but this is observed to be dependent on the He–A interaction potential model. In addition to the ground-state energy of the trimers, we determined their density, radial, and angular distributions. Many of them are spatially very extended, which qualifies them as quantum halo states
We study the ground state of a bilayer system of dipolar bosons with dipoles oriented by an external field perpendicularly to the two parallel planes. By decreasing the interlayer distance, for a fixed value of the strength of the dipolar interaction, the system undergoes a quantum phase transition from an atomic to a pair superfluid. We investigate the excitation spectrum on both sides of this transition by using two microscopic approaches. Quantum Monte Carlo methods are employed to obtain the static structure factors and intermediate scattering functions in imaginary time. The dynamic response is calculated using both the correlated basis functions (CBF) method and the approximate inversion of the Laplace transform of the quantum Monte Carlo imaginary time data. In the atomic phase, both the density and spin excitations are gapless. However, in the pair-superfluid phase a gap opens in the excitation energy of the spin mode. For small separation between layers, the minimal spin excitation energy equals the binding energy of a dimer and is twice the gap value.
The molecular dynamics computer simulation method has been used to study sulfuric and methanesulfonic acids. Calculations have been carried out between 200 K and 400 K using reliable force fields. Thermodynamic properties, such as the density, the heat of vaporization and the melting temperature, have been computed. Moreover, structural and dynamical quantities, such as the radial distribution functions, the shear viscosity and the diffusion coefficients, have also been calculated. The results display a noticeable good agreement with the available experimental data. A hydrogen bond analysis has also been performed, which shows, on one hand, that sulfuric acid has a hydrogen bond network which resembles the one of water; and, on the other hand, that methanesulfonic acid has a hydrogen bond structure which, in some details, recalls the one of methanol, but with a more important presence of single bonds and, to a lesser extent, of branching. Finally, the dynamics of the formation and rupture of hydrogen bonds has also been analyzed. To this end, the interrupted or slow hydrogen bonding lifetimes have been calculated using two different procedures. Our findings suggest that the sulfuric acid hydrogen bond network is more labile than the methanesulfonic acid one.
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.
The static properties of the fundamental model for epidemics of diseases allowing immunity (susceptible-infected-removed model) are known to be derivable by an exact mapping to bond percolation. Yet when performing numerical simulations of these dynamics in a network a number of subtleties must be taken into account in order to correctly estimate the transition point and the associated critical properties. We expose these subtleties and identify the different quantities which play the role of criticality detector in the two dynamics.
This series’ first installment introduced an approach to solvation dynamics focused on expressing the emission frequency shift (following electronic excitation of, and resulting charge change or redistribution in, a solute) in terms of energy fluxes, a work and power perspective. This approach, which had been previously exploited for rotational and vibrational excitation-induced energy flow, has the novel advantage of providing a quantitative view and understanding of the molecular-level mechanisms involved in the solvation dynamics via tracing of the energy flow induced by the electronic excitation’s charge change or redistribution in the solute. This new methodology, which was illustrated for the case in which only the excited electronic state surface contributes to the frequency shift (ionization of a monatomic solute in water), is here extended to the general case in which both the excited and ground electronic states may contribute. Simple monatomic solute model variations allow a discussion of the (sometimes surprising) issues involved in assessing each surface’s contribution. The calculation of properly defined energy fluxes/work allows a more complete understanding of the solvation dynamics even when the real work for one of the surfaces does not directly contribute to the frequency shift, an aspect further emphasizing the utility of an energy flux approach.
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.
Free energy barriers associated with the transfer of an excess proton in water and related to the potentials of mean force in proton transfer episodes have been computed in a wide range of thermodynamic states, from low-density amorphous ices to high-temperature liquids under the critical point for unconstrained and constrained systems. The latter were represented by set-ups placed inside hydrophobic graphene slabs at the nanometric scale allocating a few water layers, namely one or two in the narrowest case. Water–proton and carbon–proton forces were modelled with a Multi-State Empirical Valence Bond method. As a general trend, a competition between the effects of confinement and temperature is observed on the local hydrogen-bonded structures around the lone proton and, consequently, on the mean force exerted by its environment on the water molecule carrying the proton. Free energy barriers estimated from the computed potentials of mean force tend to rise with the combined effect of increasing temperatures and the packing effect due to a larger extent of hydrophobic confinement. The main reason observed for such enhancement of the free energy barriers was the breaking of the second coordination shell around the lone proton.
Empirical data on the dynamics of human face-to-face interactions across a variety of social venues have recently revealed a number of context-independent structural and temporal properties of human contact networks. This universality suggests that some basic mechanisms may be responsible for the unfolding of human interactions in the physical space. Here we discuss a simple model that reproduces the empirical distributions for the individual, group and collective dynamics of face-to-face contact networks. The model describes agents that move randomly in a two-dimensional space and tend to stop when meeting ‘attractive’ peers, and reproduces accurately the empirical distributions.
Muchos materiales de interés científico se presentan en fases desordenadas, donde las moléculas se encuentran desordenadas posicionalmente, orientacionalmente o ambas. Así mismo, procesos que son importantes para la vida se desarrollan en este tipo de fases. Un ejemplo de ello es el caso del agua líquida que está presente en muchos de los problemas importantes en bioquímica, como el plegamiento de proteínas. El estudio de estas fases desordenadas es inherentemente complejo debido a que no presentan periodicidad en la estructura como en el caso de sólidos cristalinos.En este trabajo se usa la simulación mediante dinámica molecular (MD) para estudiar dos fases desordenadas: el líquido y el cristal plástico. Las configuraciones obtenidas por MD son analizadas usando diferentes metodologías para entender el ordenamiento local y la dinámica de estas fases. El ordenamiento local de los sistemas se estudia usando el método de ángulos de Euler considerando las moléculas como cuerpos rígidos. Se obtienen distribuciones de probabilidad que describen el ordenamiento molecular posicional y orientacional. Estas distribuciones de probabilidad se analizan usando conceptos de teoría de la información que permiten entender mejor los resultados obtenidos.Se estudian dos sistemas de interés: hexacloroetano y agua. La estructura de las fases líquida y de cristal plástico en el hexacloroetano son investigadas y los resultados de MD y de los análisis de ordenamiento local son comparados con resultados previos de simulación y de difracción de neutrones. La estructura intra molecular del hexacloroetano se estudia usando análisis bayesiano haciendo un fit de los datos de difracción de neutrones, el conjunto de parámetros obtenidos mejoran resultados previos de experimentos de difracción por electrones respecto a la fase plástica.Se investiga el orden de corto alcance del agua a temperatura ambiente, contribuyendo al debate sobre su estructura local que es un tema aún abierto. El órden del agua para distancias más allá de los primeros vecinos también se estudia usando el enfoque de la teoría de la información. Los resultados encontrados dan soporte a experimentos y simulaciones recientes que muestran correlaciones de largo alcance en el agua. FInalmente, se estudian las fases plásticas del agua halladas recientemente por MD a altas presiones. Estas fases se comparan con una fase líquida a alta presión y con el hielo vii tanto en su ordenamiento local, como su dinámica.Las metodologías usadas en este trabajo constituyen una herramienta clave para el análisis de fases desordenadas y los resultados obtenidos contribuirán al entendimiento de la estructura de tales fases.
Many materials of scientific interest show a disordered phase, with their molecules presenting positional disorder, orientational disorder or both. Processes of interest to life also occur in these kind of phases as it is the case of liquid water present in many biochemical problems of interest such as protein folding. The study of these disordered phases is inherently difficult due to their lack of periodicity as in ordered crystals.
In this work, molecular dynamics simulations (MD) are used to study two disordered phases: the liquid and the plastic crystal. The configurations obtained by MD are analyzed using different methodologies to obtain insights into the local ordering of the molecules and into their dynamics. The local ordering of the systems is studied using the Euler angles method considering the molecules as rigid bodies. Probability distributions describing the positional and orientational molecular ordering are obtained. These probability distributions are analysed using information theory concepts that provide a deeper understanding of the results.
Two systems of interest are studied: hexachloroethane and water. The structure of the liquid and plastic crystal phases of hexacloroethane are investigated and the results from MD and the local ordering analyses are compared to previous works using simulations and neutron diffraction experiments. A Bayesian approach is used in order to obtain the intra-molecular structure of the molecule from the neutron diffraction experimental data, a set of parameters in better agreement with the plastic phase is obtained compared to previous electron diffraction experiments.
Liquid water at room conditions is studied on the short range order, presenting a contribution to the ongoing topic of its local structure. The ordering of water at distances beyond the first hydration shell is also studied using the information theory approach. Findings of this work support recent experimental and simulation data showing the existance of long range correlations in water. Finally, plastic crystals phases of water found at high pressures by MD are studied and compared to a high pressure liquid and the ice vii form by comparing their local ordering and dynamics.
The methodologies used in this work provide a powerful technique to analyse disordered phases and the results obtained will contribute to the understanding on the structure of such phases.
Muchos materiales de interés científico se presentan en fases desordenadas, donde las moléculas se encuentran desordenadas posicionalmente, orientacionalmente o ambas. Así mismo, procesos que son importantes para la vida se desarrollan en este tipo de fases. Un ejemplo de ello es el caso del agua líquida que está presente en muchos de los problemas importantes en bioquímica, como el plegamiento de proteínas. El estudio de estas fases desordenadas es inherentemente complejo debido a que no presentan periodicidad en la estructura como en el caso de sólidos cristalinos. En este trabajo se usa la simulación mediante dinámica molecular (MD) para estudiar dos fases desordenadas: el líquido y el cristal plástico. Las configuraciones obtenidas por MD son analizadas usando diferentes metodologías para entender el ordenamiento local y la dinámica de estas fases. El ordenamiento local de los sistemas se estudia usando el método de ángulos de Euler considerando las moléculas como cuerpos rígidos. Se obtienen distribuciones de probabilidad que describen el ordenamiento molecular posicional y orientacional. Estas distribuciones de probabilidad se analizan usando conceptos de teoría de la información que permiten entender mejor los resultados obtenidos. Se estudian dos sistemas de interés: hexacloroetano y agua. La estructura de las fases líquida y de cristal plástico en el hexacloroetano son investigadas y los resultados de MD y de los análisis de ordenamiento local son comparados con resultados previos de simulación y de difracción de neutrones. La estructura intra molecular del hexacloroetano se estudia usando análisis bayesiano haciendo un fit de los datos de difracción de neutrones, el conjunto de parámetros obtenidos mejoran resultados previos de experimentos de difracción por electrones respecto a la fase plástica. Se investiga el orden de corto alcance del agua a temperatura ambiente, contribuyendo al debate sobre su estructura local que es un tema aún abierto. El órden del agua para distancias más allá de los primeros vecinos también se estudia usando el enfoque de la teoría de la información. Los resultados encontrados dan soporte a experimentos y simulaciones recientes que muestran correlaciones de largo alcance en el agua. FInalmente, se estudian las fases plásticas del agua halladas recientemente por MD a altas presiones. Estas fases se comparan con una fase líquida a alta presión y con el hielo vii tanto en su ordenamiento local, como su dinámica. Las metodologías usadas en este trabajo constituyen una herramienta clave para el análisis de fases desordenadas y los resultados obtenidos contribuirán al entendimiento de la estructura de tales fases.