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.

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.

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.

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.

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.

Time-dependent information transmission in a model regulatory circuit.

Many biological regulatory systems respond with a physiological delay when processing signals. A simple model of regulation which respects these features shows how the ability of a delayed output to transmit information is limited: at short times by the time scale of the dynamic input, at long times by that of the dynamic output. We find that topologies of maximally informative networks correspond to commonly occurring biological circuits linked to stress response and that circuits functioning out of steady state may exploit absorbing states to transmit information optimally.

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.

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.

Managing intensive supports. The attitudes of the health care workers of five Italian Hospitals to institution of CPR and admission to the ICU.

AIM: The aim of the paper was to examine the attitudes of the health care workers (HCW) of five Italian Hospitals towards intensive supports, in the hypothesis that a large involvement could help to solve the problems of a more adequate management of vital supports. DESIGN: Hospital HCWs' attitudes towards cardiopulmonary resuscitation (CPR) and ICU admission were investigated using a self-administered questionnaire. SETTING: five Italian Hospitals. PARTICIPANTS: all the doctors (MD) and nurses (RN), except those working in obstetrics and in paediatrics. INTERVENTION: a questionnaire was offered to all eligible participants (4903 HCW) and 2466 analysable files (50.3%) were obtained. RESULTS: In spite of a great variation in responses among health care givers, the majority of answers is almost in line with current professional and bioethical documents, at both international and national level. This, also when the proposed solution is not clearly recognised by the Italian laws. The statistically significant differences depend on profession (RN/MD), on working area and experiential working characteristics. A strict minority of workers would trust their colleagues in case of hypothetical personal critical illness. CONCLUSIONS: Our data confirm both the importance of communication among HCW, in order to reach the best decision for every patient, and the great need of continuous educational programs which could compensate for lack of experience and help to create/maintain a strong bioethical and patient-oriented attitude.

Mean platelet volume trend in sepsis: is it a useful parameter?

AIM: Sepsis, as an uncontrolled generalized inflammatory response, involves also the haemostatic mechanisms. Mean platelet volume (MPV) measurement has been available since 1970s, but neither its relationship with platelet count nor the clinical meaning of this relation has been understood in sepsis yet. This study aimed to evaluate both the trend and the relationship between platelet count (PC) and their MPV and to explore their significance in the course of sepsis. METHODS: Seventy septic patients, were recruited in this prospective study. The PC and MPV were measured repeatedly at the enrollment and, thereafter, whenever patient's sequential organ failure assessment (SOFA) score changed by +/-8% up to 5 samples. Standard correlation test, ANOVA for repeated measures, logistic regression and Wilcoxon test were used. RESULTS: The relationship between PC and MPV, expressed as means and frequency distributions, showed a negative correlation (95% CI; r -0.34; P<0.0001) with an inverse trend during sepsis course. The logistic regression showed a three times increase in death probability (95% CI; OR=3.04; P<0.05) of patients with a MPV<9.7 fL at the recruitment time. CONCLUSIONS: The behaviour of platelets and their respective MPV could be an indirect sign of disturbance in platelet production and activity, and bone marrow response in sepsis. Our results could suggest that routine concomitant measurement of PC and MPV trend could be considered as a quick and reliable guide in the assessment of bone marrow response to sepsis evolution.

Role of patient posture during puncture on successful unilateral spinal anaesthesia in outpatient lower abdominal surgery.

BACKGROUND AND OBJECTIVE: Unilateral spinal anaesthesia is a useful anaesthesia technique in lower abdominal surgery, especially in an outpatient setting. Patient posture is pivotal in the achievement of unilateral anaesthesia. Nevertheless, no studies have elucidated the influence of patient posture during the anaesthetic injection on unilaterality. Thus, the aim was to compare the effect of patient posture, during the induction phase of spinal anaesthesia, on block characteristics. METHODS: Eighty patients, ASA I-II, scheduled for unilateral hernioplasty were randomized into two groups. Anaesthesia was performed in lateral position in Group 1 (G1) with operative side down and in sitting position in Group 2 (G2) whose patients were then immediately turned on their lateral side. All patients were maintained for 20 min in lateral position with their operative side down. Hyperbaric bupivacaine 1% 10 mg were used. RESULTS: Unilateral anaesthesia was seen in 80% (32/40) and 12.5% (5/40) of G1 and G2, respectively. The readiness for surgery was faster in G1 (P < 0.0001). The motor block in the non-operative side was stronger in G2 (P < 0.0001). The offset of sensory block was faster in G1 (P = 0.0001). The offset of motor block was slower in G1 (P = 0.0008). The time for voiding was shorter in G1, although not significant. CONCLUSIONS: Lateral posture during the induction of spinal anaesthesia is pivotal for a higher success of unilateral block, a fast readiness to surgery, and a fast recovery. Therefore, this technique can be considered feasible and time-saving for lower abdominal surgery.

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.

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.

Haemostatic molecular markers in patients undergoing radical retropubic prostatectomy for prostate cancer and submitted to prophylaxis with unfractioned or low molecular weight heparin.

BACKGROUND: Deep vein thrombosis and subsequently pulmonary embolism are the most common causes of increased post-operative morbidity and mortality in patients with pelvic or abdominal cancer. Aim of the study was to evaluate variations in coagulative parameters induced by two accepted primary prophylaxis patterns: standardized low doses of unfractioned heparin (UFH) or single doses of low molecular weight heparin (LMWH) in cancer patients submitted to radical retropubic prostatectomy. METHODS: Fifty patients (45-75 yr) were randomly assigned two groups. Group 1 received UFH (5000 units s.c. x 3 daily); group 2 received calcium nadroparin (single daily dose of 0.3 ml s.c.). In both groups prophylaxis began preoperatively and was maintained throughout the entire hospital-stay. Blood cell, platelet count, coagulative system exploring tests, thrombotic molecular markers, and physiological inhibitors of coagulation were determined at baseline conditions and on the first and seventh day after surgery. RESULTS: Preoperative values of fibrinogen, F1+2 fragment, TAT and D-dimer resulted over normal range in both groups. A significant increase of these markers was observed also during the post-operative period. PT, aPTT, ATIII, PC, total and free PS showed the most substantial changes on the 1st post operative day, though their values ranged within normal levels on the three sampling times. The levels of haemostatic markers demonstrated a baseline hypercoagulability, probably related to cancer and thrombin activation caused by prostatectomy. Despite this thrombophylic state, neither of the two groups presented symptomatic bleeding or thromboembolic complications. CONCLUSIONS: These results prove that a single daily dose of nadroparin has been safe and efficient as a thrice-daily dose of UFH, with a better risk/benefit relationship.

Learning to coordinate in a complex and nonstationary world.

We study analytically and by computer simulations a complex system of adaptive agents with finite memory. Borrowing the framework of the minority game and using the replica formalism we show the existence of an equilibrium phase transition as a function of the ratio between the memory lambda and the learning rates Gamma of the agents. We show that, starting from a random configuration, a dynamic phase transition also exists, which prevents agents from reaching optimal coordination. Furthermore, in a nonstationary environment, we show by numerical simulations that the phase transition becomes discontinuous.

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.

First-order phase transition in a nonequilibrium growth process

We introduce a simple continuous model for nonequilibrium surface growth. The dynamics of the system is defined by the Kardar-Parisi-Zhang equation with a Morse-like potential representing a short range interaction between the surface and the substrate. The mean field solution displays a nontrivial phase diagram with a first-order transition between a growing and a bound surface, associated with a region of coexisting phases, and a tricritical point where the transition becomes second order. Numerical simulations in three dimensions show quantitative agreement with mean field results, and the features of the phase space are preserved even in two dimensions.

Relevance of memory in minority games

By considering diffusion on De Bruijn graphs, we study in detail the dynamics of the histories in the minority game, a model of competition between adaptative agents. Such graphs describe the structure of the temporal evolution of M bit strings, each node standing for a given string, i.e., a history in the minority game. We show that the frequency of visit of each history is not given by 1/2(M) in the limit of large M when the transition probabilities are biased. Consequently, all quantities of the model do significantly depend on whether the histories are real or uniformly and randomly sampled. We expose a self-consistent theory of the case of real histories, which turns out to be in very good agreement with numerical simulations.