Hybrid theoretical models for molecular nanoplasmonics.

The multidisciplinary nature of the research in molecular nanoplasmonics, i.e., the use of plasmonic nanostructures to enhance, control, or suppress properties of molecules interacting with light, led to contributions from different theory communities over the years, with the aim of understanding, interpreting, and predicting the physical and chemical phenomena occurring at molecular- and nano-scale in the presence of light. Multiscale hybrid techniques, using a different level of description for the molecule and the plasmonic nanosystems, permit a reliable representation of the atomistic details and of collective features, such as plasmons, in such complex systems. Here, we focus on a selected set of topics of current interest in molecular plasmonics (control of electronic excitations in light-harvesting systems, polaritonic chemistry, hot-carrier generation, and plasmon-enhanced catalysis). We discuss how their description may benefit from a hybrid modeling approach and what are the main challenges for the application of such models. In doing so, we also provide an introduction to such models and to the selected topics, as well as general discussions on their theoretical descriptions.

Solid state effects on the electronic structure of H2OEP.

We present the results of a joint experimental and theoretical investigation concerning the effect of crystal packing on the electronic properties of the H2OEP molecule. Thin films, deposited in ultra high vacuum on metal surfaces, are investigated by combining valence band photoemission, inverse photoemission, and X-ray absorption spectroscopy. The spectra of the films are compared, when possible, with those measured in the gas phase. Once many-body effects are included in the calculations through the GW method, the electronic structure of H2OEP in the film and gas phase are accurately reproduced for both valence and conduction states. Upon going from an isolated molecule to the film phase, the electronic gap shrinks significantly and the lowest unoccupied molecular orbital (LUMO) and LUMO + 1 degeneracy is removed. The calculations show that the reduction of the transport gap in the film is entirely addressable to the enhancement of the electronic screening.

Excited state properties of formamide in water solution: an ab initio study.

We present ab initio quantum calculation of the optical properties of formamide in vapor phase and in water solution. We employ time dependent density functional theory for the isolated molecule and many-body perturbation theory methods for the system in solution. An average over several molecular dynamics snapshots is performed to take into account the disorder of the liquid. We find that the excited state properties of the gas-phase formamide are strongly modified by the presence of the water solvent: the geometry of the molecule is distorted and the electronic and optical properties are severely modified. The important interaction among the formamide and the water molecules forces us to use fully quantum methods for the calculation of the excited state properties of this system. The excitonic wave function is localized both on the solute and on part of the solvent.

Time-Resolved Excited-State Analysis of Molecular Electron Dynamics by TDDFT and Bethe-Salpeter Equation Formalisms.

In this work, a theoretical and computational set of tools to study and analyze time-resolved electron dynamics in molecules, under the influence of one or more external pulses, is presented. By coupling electronic-structure methods with the resolution of the time-dependent Schrödinger equation, we developed and implemented the time-resolved induced density of the electronic wavepacket, the time-resolved formulation of the differential projection density of states (ΔPDOS), and of transition contribution map (TCM) to look at the single-electron orbital occupation and localization change in time. Moreover, to further quantify the possible charge transfer, we also defined the energy-integrated ΔPDOS and the fragment-projected TCM. We have used time-dependent density-functional theory (TDDFT), as implemented in ADF software, and the Bethe-Salpeter equation, as provided by MolGW package, for the description of the electronic excited states. This suite of postprocessing tools also provides the time evolution of the electronic states of the system of interest. To illustrate the usefulness of these postprocessing tools, excited-state populations have been computed for HBDI (the chromophore of GFP) and DNQDI molecules interacting with a sequence of two pulses. Time-resolved descriptors have been applied to study the time-resolved electron dynamics of HBDI, DNQDI, LiCN (being a model system for dipole switching upon highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) electronic excitation), and Ag22. The computational analysis tools presented in this article can be employed to help the interpretation of fast and ultrafast spectroscopies on molecular, supramolecular, and composite systems.

Many-body perturbation theory calculations using the yambo code.

yambo is an open source project aimed at studying excited state properties of condensed matter systems from first principles using many-body methods. As input, yambo requires ground state electronic structure data as computed by density functional theory codes such as Quantum ESPRESSO and Abinit. yambo's capabilities include the calculation of linear response quantities (both independent-particle and including electron-hole interactions), quasi-particle corrections based on the GW formalism, optical absorption, and other spectroscopic quantities. Here we describe recent developments ranging from the inclusion of important but oft-neglected physical effects such as electron-phonon interactions to the implementation of a real-time propagation scheme for simulating linear and non-linear optical properties. Improvements to numerical algorithms and the user interface are outlined. Particular emphasis is given to the new and efficient parallel structure that makes it possible to exploit modern high performance computing architectures. Finally, we demonstrate the possibility to automate workflows by interfacing with the yambopy and AiiDA software tools.

First-principles study of silicon nanocrystals: structural and electronic properties, absorption, emission, and doping.

Total energy calculations within the Density Functional Theory have been carried out in order to investigate the structural, electronic, and optical properties of un-doped and doped silicon nanostructures of different size and different surface terminations. In particular the effects induced by the creation of an electron-hole pair on the properties of hydrogenated silicon nanoclusters as a function of dimension are discussed in detail showing the strong interplay between the structural and optical properties of the system. The distortion induced on the structure by an electronic excitation of the cluster is analyzed and considered in the evaluation of the Stokes shift between absorption and emission energies. Besides we show how many-body effects crucially modify the absorption and emission spectra of the silicon nanocrystals. Starting from the hydrogenated clusters, different Si/O bonding at the cluster surface have been considered. We found that the presence of a Si--O--Si bridge bond originates significative excitonic luminescence features in the near-visible range. Concerning the doping, we consider B and P single- and co-doped Si nanoclusters. The neutral impurities formation energies are calculated and their dependence on the impurity position within the nanocrystal is discussed. In the case of co-doping the formation energy is strongly reduced, favoring this process with respect to the single doping. Moreover the band gap and the optical threshold are clearly red-shifted with respect to that of the pure crystals showing the possibility of an impurity based engineering of the absorption and luminescence properties of Si nanocrystals.

Advanced capabilities for materials modelling with Quantum ESPRESSO.

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

Hybrid resistance to BALB/c plasmacytomas: F1 hybrid anti-MPC-11 immunological responses correlated with resistance to tumor challenge.

BALB/cJ X C57BL/10Sn F1 (hereafter called B10F1) hybrids resist challenge with the BALB/c plasmacytoma, MPC-11, by a radiation-sensitive, silica-insensitive mechanism, whereas BALB/cJ X BALB.B F1 (hereafter called BALB.BF1) hybrids are as susceptible to MPC-11 as are homozygous BALB/c mice themselves. To investigate the mechanism of resistance, we have compared anti-MPC-11 immune responses by these F1 hybrids both before and at various times after tumor challenge. Resistance is not determined by natural killer cell reactivity inasmuch as neither hybrid harbors splenic natural killer cells with lytic activity directed against MPC-11. Nor is it determined by antibody-dependent cell-mediated cytotoxicity since neither hybrid produces an appropriate anti-MPC-11 antibody. Spleen cells and lymph node cells from both hybrids are capable of generating high levels of anti-MPC-11 cytotoxic T-lymphocyte activity in both primary and secondary mixed-lymphocyte tumor cell cultures. Such cytotoxic T-lymphocytes protect susceptible hybrids from tumor growth in Winn assays. The susceptible but not the resistant hybrids lose the ability to generate high levels of cytotoxic T-lymphocytes activity in spleen mixed lymphocyte tumor cell cultures by 28 days, and in lymph node mixed-lymphocyte tumor cell cultures by 14 days postchallenge. The reduction in spleen cell reactivity is due to suppression mainly by adherent cells and can be abrogated by pretreatment of the susceptible hybrids with a low dose of Cytoxan 2 days before challenge. This pretreatment does not, however, protect the mice. They develop tumor at the same rate and die at the same time as do controls. Both the late appearance of suppression and the lack of effect on survival of its ablation suggest it to be a concomitant of tumor growth rather than its cause. Resistance to tumor growth in this model system may reflect an enhanced ability of the resistant hybrid to deliver effector cells to the site of tumor implantation.

Elimination of L5178Y cells from tumor-dormant DBA/2 mice by specific active immunotherapy.

Cytolytic T-lymphocytes (CTL) can be repeatedly stimulated in L5178Y cell tumor-dormant DBA/2 mice by the i.p. inoculation of 2 X 10(6) X-irradiated L5178Y cells. The restimulated CTL activity has the same kinetics of generation and decline and the same target cell specificity as does the CTL response generated during establishment of the L5178Y cell tumor dormant state. No increase in adherent cell-mediated cytolytic activity or cytolytic or cytophilic anti-L5178Y antibody can be detected after inoculation of irradiated L5178Y cells. The repeated stimulation of CTL activity in tumor-dormant DBA/2 mice results in the elimination of L5178Y cells from a significant number of tumor-dormant mice.

Statistical mechanics of systems with heterogeneous agents: minority games

We study analytically a simple game theoretical model of heterogeneous interacting agents. We show that the stationary state of the system is described by the ground state of a disordered spin model which is exactly solvable within the simple replica symmetric ansatz. Such a stationary state differs from the Nash equilibrium where each agent maximizes her own utility. The latter turns out to be characterized by a replica symmetry broken structure. Numerical results fully agree with our analytical findings.

Nonequilibrium phase transition in a model for social influence

We present extensive numerical simulations of the Axelrod's model for social influence, aimed at understanding the formation of cultural domains. This is a nonequilibrium model with short range interactions and a remarkably rich dynamical behavior. We study the phase diagram of the model and uncover a nonequilibrium phase transition separating an ordered (culturally polarized) phase from a disordered (culturally fragmented) one. The nature of the phase transition can be continuous or discontinuous depending on the model parameters. At the transition, the size of cultural regions is power-law distributed.

Aspirin effect on early and late changes in acute lung injury in sheep.

OBJECTIVE: There have been several studies that have already explored the potential beneficial role of cyclo-oxygenase (CO) inhibitors on oleic acid (OA)-induced lung injury in different species. These studies report no significant effect of CO inhibition, though thromboxane B2 (TxB2) was effectively blocked. However, recent studies indicate that pre-treatment with aspirin (ASA) preserve gas exchange in OA lung injury in dogs. Aim of our study has been to evaluate the potential beneficial effects of the pre-treatment with low doses of ASA on gas exchange, hemodynamics, respiratory mechanics, prostanoids and lung histology in OA-induced lung injury in sheep. DESIGN: 0.09 ml/kg of OA was administered into the right atrium of 14 anaesthetized sheep. Six received a bolus of ASA (10 mg/kg i.v.) 30 min before OA, the others saline as placebo. MEASUREMENTS AND RESULTS: Pulmonary and tissue gas exchange, pulmonary and systematic hemodynamics, respiratory system mechanics, TxB2 and 6-keto-PGF1 alpha, leukocytes and platelets concentrations were measured throughout the subsequent 3 h and lung histology was effected at end-experiment. The principal findings of our study are: 1) ASA reduces OA-induced early pulmonary vasoconstriction and bronchoconstriction, parallelled by a suppression of TxB2 generation; 2) the late increase in pulmonary artery pressure and airway resistance due to OA is not inhibited by ASA; 3) the early disturbance in pulmonary gas exchange is reduced by ASA, whereas the late severe deterioration is exaggerated by ASA; 4) the stability of tissue exchange ratio (R) at approximately 1 in ASA-group compared to its fall to approximately 0.7 in controls. CONCLUSION: Our findings suggest that ASA: 1) is only effective to treat the very transient TxB2-induced pulmonary vasoconstriction resulting in hydrostatic edema, and it is ineffective, even accentuates, the subsequent major pulmonary endothelial cell injury leading to alveolar flooding that is unrelated to TxB2; 2) has a transient protective effect on the TxB2-induced early bronchospasm; 3) has a biphasic behaviour on gas exchange, with a benefit which lasts only one hour and then results in a worse gas exchange; 4) has an immediate, stabilizing, persisting effect on R, contrasting with its transient effect on pulmonary hemodynamics and PaO2.

The prominent role of thromboxane A2 formation on early pulmonary hypertension induced by oleic acid administration in sheep.

The early increase of pulmonary artery pressure observed in different models of experimentally induced lung injury have been shown to be associated with the release of vasoconstrictive agents by activated platelets. The aim of this study was to evaluate the pattern of these metabolites, in particular TxA2, and the effects of the inhibition of their production by ASA on the modifications of pulmonary hemodynamics induced by oleic acid administration in sheep. Group I (8 sheep) was infused with oleic acid (0.09 ml/kg at 0.02 ml/min) while in group II (6 sheep) ASA (10 mg/kg i.v.) was administered 30 minutes before oleic acid infusion. In group I pulmonary artery pressure (PAP) and pulmonary vascular resistance (PVR) were significantly higher at the end of the infusion while cardiac output (CO) significantly decreased in comparison to baseline values. A marked increase in plasma TxB2 levels paralleled pulmonary hemodynamic changes. Also plasma 6 keto PGF levels increased after OA infusion. The early increase in PAP and PVR was significantly lower in group II (p less than 0.005) while CO did not undergo any significant change. ASA pretreatment significantly blunted the rise of TxB2 concentrations and prevented the elevation of 6 keto PGFa. These results indicate that early pulmonary hypertension in oleic acid induced injury is mainly related to TxA2 released from platelets and leukocytes and that pulmonary hemodynamic changes are significantly inhibited by ASA pretreatment.

Pre-operative IL-2 immunoprophylaxis of cancer recurrence: long-term clinical results of a phase II study in radically operable colorectal cancer.

This study evaluates retrospectively the outcome of 20 colorectal cancer patients radically operated (M/F 13/7; primary/recurrent 15/5; Dukes B=11; C=6; D=3) who received pre-operative IL-2 (18,000, 000 IU/daily s.c. for 3 days) and the outcome of 40 colorectal cancer (primary/recurrent 40/0) patients age, sex and stage-matched radically operated, as control group. After a median follow-up of 72 months, in the IL-2 pre-operative group we observed 6/20 recurrences (30%) vs. 19/40 (47.5%) in controls. Mean and median disease-free period in patients who relapsed were respectively 21 months and 20.5 months (range 6-36) in IL-2 group vs. 14.1 and 12 months in the control group (range 3-34). After a 5-year follow-up, 4/20 (20%) IL-2 treated patients were dead vs. 19/40 control patients (47.5%) (log-rank chi2=3.7, p=0.05). Pre-operative IL-2 administration is safe, active in preventing post-operative lymphocytopenia and seems to improve the clinical outcome in radically operated colorectal cancer patients.

A study of interactions among markers of macrophage functions in metastatic solid tumors: neopterin levels in relation to those of tumor necrosis factor-alpha and of soluble interleukin-2 receptors.

High levels of the macrophage activation marker neopterin have been described in metastatic cancer patients. Since macrophages may either counteract or stimulate tumor development, it is important to establish which macrophage activity is mainly related to neopterin release. The present study was carried out to evaluate neopterin levels in metastatic solid tumor patients in respect with the antitumor macrophage cytokine TNF and with soluble IL-2 receptor (SIL-2R), whose secretion is stimulated by macrophages and it is associated with the immunosuppressive status of cancer patients. The study included 35 patients with metastatic solid neoplasms. Serum levels of neopterin, TNF and SIL-2R were measured in blood samples collected during the morning. Abnormally high concentrations of neopterin were seen in 18/35 (51%) patients. Patients with high levels of neopterin showed significantly higher concentrations of SIL-2R than those with normal neopterin values, whereas no difference was found in TNF levels. This study would suggest that the increased secretion of neopterin may reflect macrophage-mediated immunosuppression in metastatic solid neoplasms, rather than to be associated with the antitumor activity of macrophages.

Continuum time limit and stationary states of the minority game.

We discuss in detail the derivation of stochastic differential equations for the continuum time limit of the minority game. We show that all properties of the minority game can be understood by a careful theoretical analysis of such equations. In particular, (i) we confirm that the stationary state properties are given by the ground state configurations of a disordered (soft) spin system, (ii) we derive the full stationary state distribution, (iii) we characterize the dependence on initial conditions in the symmetric phase, and (iv) we clarify the behavior of the system as a function of the learning rate. This leaves us with a complete and coherent picture of the collective behavior of the minority game. Strikingly we find that the temperaturelike parameter, which is introduced in the choice behavior of individual agents turns out to play the role, at the collective level, of the inverse of a thermodynamic temperature.

Data clustering and noise undressing of correlation matrices.

We discuss an approach to data clustering. We find that maximum likelihood leads naturally to an Hamiltonian of Potts variables that depends on the correlation matrix and whose low temperature behavior describes the correlation structure of the data. For random, uncorrelated data sets no correlation structure emerges. On the other hand, for data sets with a built-in cluster structure, the method is able to detect and recover efficiently that structure. Finally we apply the method to financial time series, where the low-temperature behavior reveals a nontrivial clustering.

Generalized minority games with adaptive trend-followers and contrarians.

We introduce a simple extension of the minority game in which the market rewards contrarian (respectively, trend-following) strategies when it is far from (respectively, close to) efficiency. The model displays a smooth crossover from a regime where contrarians dominate to one where trend-followers dominate. In the intermediate phase, the stationary state is characterized by non-Gaussian features as well as by the formation of sustained trends and bubbles.

Defibrotide in extracorporeal circulation on healthy rabbits.

Defibrotide, a partially depolymerized DNA fraction obtained from mammalian lung, was found to have significant antithrombotic and fibrinolytic activities. On the basis of this evidence defibrotide could be of clinical value during hemoperfusive treatment. The present study was designed to evaluate the biological tolerance of this technique in a model of extracorporeal circulation, using an original Silastic apparatus, with defibrotide (0.83 mg/kg-1/min-1 after a 50 mg/kg-1 bolus injection) and heparin (0.66 IU/kg-1/min-1 after a 400 IU/kg-1 bolus injection) in ten rabbits (Group 1) and heparin only in ten others (Group 2, control group). In this study defibrotide produced a significantly lower pressure inside the circuit compared to the control group and gave a protective effect against those pathological changes which appeared during extracorporeal circulation and that may be considered omens of a state of shock. However the use of defibrotide in addition to heparin seemed to have a poor effect on platelet and leukocyte count alterations during application of this technique.