Identifying reaction pathways in phase space via asymptotic trajectories.

In this paper, we revisit the concepts of the reactivity map and the reactivity bands as an alternative to the use of perturbation theory for the determination of the phase space geometry of chemical reactions. We introduce a reformulated metric, called the asymptotic trajectory indicator, and an efficient algorithm to obtain reactivity boundaries. We demonstrate that this method has sufficient accuracy to reproduce phase space structures such as turnstiles for a 1D model of the isomerization of ketene in an external field. The asymptotic trajectory indicator can be applied to higher dimensional systems coupled to Langevin baths as we demonstrate for a 3D model of the isomerization of ketene.

Implications of grey zone results for routine hepatitis C virus screening with the ARCHITECT HCV-Ag assay.

AIMS: Hepatitis C virus antigen (HCV-Ag) detection requires retesting for samples with grey zone results (GzR), adding cost and time and decreasing reliability. Our aim in this study was to evaluate the frequency and significance of GzR during the use of the automated Architect HCV-Ag assay in routine clinical practice. METHODS AND RESULTS: We studied HCV-Ag levels in 952 serum samples using the ARCHITECT HCV-Ag assay. GzR were detected in 33 samples; 25 were reactive on retesting and 19 were anti-HCV positive. Seventeen of these 19 samples were tested for HCV-RNA and were all reactive (viral loads <104  IU ml-1 ). The remaining six samples were anti-HCV nonreactive and had undetectable HCV-RNA. Eight GzR samples were nonreactive on retesting, seven were anti-HCV nonreactive (three underwent HCV-RNA quantification and were all nonreactive), and one was anti-HCV reactive (HCV-RNA nonreactive). No significant differences were found on comparing HCV-Ag values. CONCLUSIONS: Grey zone results found to be negative on retesting do not need additional technique testing, except in donor screening scenarios, where the use of molecular methods would be advisable. SIGNIFICANCE AND IMPACT OF THE STUDY:  The proposed diagnostic algorithm confirms that, eventhough GzR occur, hepatitis C virus antigen is a robust alternative to HCV-RNA detection in the active detection of infections.

Water phase transitions from the perspective of hydrogen-bond network analysis.

We analyze the water vapour-liquid and solid-liquid phase transitions from the perspective of hydrogen bond networks. Using molecular dynamics simulation data for the TIP4P/2005 and TIP4P/ice water models, we built hydrogen bond networks in the neighbourhood of the transitions. We studied the behaviour of some topological network properties: the average degree, clustering coefficient, and average path length. We found that these properties exhibit a discontinuity while approaching a phase transition region, similar to those that appear for some thermodynamic properties in the same region. This approach can be extended to characterize other water phase transitions. Besides, it can also be applied to study the phase transitions of other hydrogen-bonded substances or to other scenarios whose relevant "interaction" could be identified together with a "proper criterion" defined in an analogous way as in the case of hydrogen bonded systems.

Above Saddle-Point Regions of Order in a Sea of Chaos in the Vibrational Dynamics of KCN.

The dynamical characteristics of a region of regular vibrational motion in the sea of chaos above the saddle point corresponding to the linear C-N-K configuration is examined in detail. To explain the origin of this regularity, the associated phase space structures were characterized using suitably defined Poincaré surfaces of section, identifying the different resonances between the stretching and bending modes, as a function of excitation energy. The corresponding topology is elucidated by means of periodic orbit analysis.

Semiclassical basis sets for the computation of molecular vibrational states.

In this paper, we extend a method recently reported [F. Revuelta et al., Phys. Rev. E 87, 042921 (2013)] for the calculation of the eigenstates of classically highly chaotic systems to cases of mixed dynamics, i.e., those presenting regular and irregular motions at the same energy. The efficiency of the method, which is based on the use of a semiclassical basis set of localized wave functions, is demonstrated by applying it to the determination of the vibrational states of a realistic molecular system, namely, the LiCN molecule.

Transition state theory for activated systems with driven anharmonic barriers.

Classical transition state theory has been extended to address chemical reactions across barriers that are driven and anharmonic. This resolves a challenge to the naive theory that necessarily leads to recrossings and approximate rates because it relies on a fixed dividing surface. We develop both perturbative and numerical methods for the computation of a time-dependent recrossing-free dividing surface for a model anharmonic system in a solvated environment that interacts strongly with an oscillatory external field. We extend our previous work, which relied either on a harmonic approximation or on periodic force driving. We demonstrate that the reaction rate, expressed as the long-time flux of reactive trajectories, can be extracted directly from the stability exponents, namely, Lyapunov exponents, of the moving dividing surface. Comparison to numerical results demonstrates the accuracy and robustness of this approach for the computation of optimal (recrossing-free) dividing surfaces and reaction rates in systems with Markovian solvation forces. The resulting reaction rates are in strong agreement with those determined from the long-time flux of reactive trajectories.

Design and application of a 23-gene panel by next-generation sequencing for inherited coagulation bleeding disorders.

INTRODUCTION: Molecular testing of Inherited bleeding coagulation disorders (IBCDs) not only offers confirmation of diagnosis but also aids in genetic counselling, prenatal diagnosis and in certain cases genotype-phenotype correlations are important for predicting the clinical course of the disease and to allow tailor-made follow-up of individuals. Until recently, genotyping has been mainly performed by Sanger sequencing, a technique known to be time consuming and expensive. Currently, next-generation sequencing (NGS) offers a new potential approach that enables the simultaneous investigation of multiple genes at manageable cost. AIM: The aim of this study was to design and to analyse the applicability of a 23-gene NGS panel in the molecular diagnosis of patients with IBCDs. METHODS: A custom target enrichment library was designed to capture 31 genes known to be associated with IBCDs. Probes were generated for 296 targets to cover 86.3 kb regions (all exons and flanking regions) of these genes. Twenty patients with an IBCDs phenotype were studied using NGS technology. RESULTS: In all patients, our NGS approach detected causative mutations. Twenty-one pathogenic variants were found; while most of them were missense (18), three deletions were also identified. Six novel mutations affecting F8, FGA, F11, F10 and VWF genes, and 15 previously reported variants were detected. NGS and Sanger sequencing were 100% concordant. CONCLUSION: Our results demonstrate that this approach could be an accurate, reproducible and reliable tool in the rapid genetic diagnosis of IBCDs.

Transition state geometry of driven chemical reactions on time-dependent double-well potentials.

Reaction rates across time-dependent barriers are difficult to define and difficult to obtain using standard transition state theory approaches because of the complexity of the geometry of the dividing surface separating reactants and products. Using perturbation theory (PT) or Lagrangian descriptors (LDs), we can obtain the transition state trajectory and the associated recrossing-free dividing surface. With the latter, we are able to determine the exact reactant population decay and the corresponding rates to benchmark the PT and LD approaches. Specifically, accurate rates are obtained from a local description regarding only direct barrier crossings and to those obtained from a stability analysis of the transition state trajectory. We find that these benchmarks agree with the PT and LD approaches for obtaining recrossing-free dividing surfaces. This result holds not only for the local dynamics in the vicinity of the barrier top, but also for the global dynamics of particles that are quenched at the reactant or product wells after their sojourn over the barrier region. The double-well structure of the potential allows for long-time dynamics related to collisions with the outside walls that lead to long-time returns in the low-friction regime. This additional global dynamics introduces slow-decay pathways that do not result from the local transition across the recrossing-free dividing surface associated with the transition state trajectory, but can be addressed if that structure is augmented by the population transfer of the long-time returns.

Scar Functions, Barriers for Chemical Reactivity, and Vibrational Basis Sets.

The performance of a recently proposed method to efficiently calculate scar functions is analyzed in problems of chemical interest. An application to the computation of wave functions associated with barriers relevant for the LiNC ⇄ LiCN isomerization reaction is presented as an illustration. These scar functions also constitute excellent elements for basis sets suitable for quantum calculation of vibrational energy levels. To illustrate their efficiency, a calculation of the LiNC/LiCN eigenfunctions is also presented.

Frequency analysis of the laser driven nonlinear dynamics of HCN.

We study the vibrational dynamics of a model for the HCN molecule in the presence of a monochromatic laser field. The variation of the structural behavior of the system as a function of the laser frequency is analyzed in detail using the smaller alignment index, frequency maps, and diffusion coefficients. It is observed that the ergodicity of the system depends on the frequency of the excitation field, especially in its transitions from and into chaos. This provides a roadmap for the possibility of bond excitation and dissociation in this molecule.

Solvated molecular dynamics of LiCN isomerization: All-atom argon solvent versus a generalized Langevin bath.

The reaction rate rises and falls with increasing density or friction when a molecule is activated by collisions with the solvent particles. This so-called Kramers turnover has recently been observed in the isomerization reaction of LiCN in an argon bath. In this paper, we demonstrate by direct comparison with those results that a reduced-dimensional (generalized) Langevin description gives rise to similar reaction dynamics as the corresponding (computationally expensive) full molecular dynamics calculations. We show that the density distributions within the Langevin description are in direct agreement with the full molecular dynamics results and that the turnover in the reaction rates is reproduced qualitatively and quantitatively at different temperatures.

Agricultural activity shapes the communication and migration patterns in Senegal.

The communication and migration patterns of a country are shaped by its socioeconomic processes. The economy of Senegal is predominantly rural, as agriculture employs over 70% of the labor force. In this paper, we use mobile phone records to explore the impact of agricultural activity on the communication and mobility patterns of the inhabitants of Senegal. We find two peaks of phone calls activity emerging during the growing season. Moreover, during the harvest period, we detect an increase in the migration flows throughout the country. However, religious holidays also shape the mobility patterns of the Senegalese people. Hence, in the light of our results, agricultural activity and religious holidays are the primary drivers of mobility inside the country.

Peptic Ulcer Bleeding Risk. The Role of Helicobacter Pylori Infection in NSAID/Low-Dose Aspirin Users.

OBJECTIVES: Helicobacter pylori (H. pylori) infection and NSAID/low-dose aspirin (ASA) use are associated with peptic ulcer disease. The risk of peptic ulcer bleeding (PUB) associated with the interaction of these factors remains unclear. The objective of this study was to determine the risk of PUB associated with the interaction between H. pylori infection and current nonsteroidal anti-inflammatory drugs (NSAIDs) or low-dose ASA use. METHODS: This was a case-control study of consecutive patients hospitalized because of PUB. Controls were matched by age, sex, and month of admission. H. pylori infection status was determined in all cases and controls by serology. Drug use was determined by structured questionnaire. Adjusted relative risk (RR) associated with different factors, and the interaction between NSAID/ASA and H. pylori infection was estimated by logistic regression analysis. RESULTS: The study included 666 cases of PUB and 666 controls; 74.3% cases and 54.8% controls (RR: 2.6; 95% confidence interval (CI): 2.0-3.3) tested positive for H. pylori infection; 34.5% of cases had current NSAID use compared with 13.4% of controls (RR: 4.0; 95% CI: 3.0-5.4). Respective proportions for low-dose ASA use were 15.8 and 12%, respectively (RR: 1.9; 95% CI: 1.3-2.7). The RR of PUB for concomitant NSAID use and H. pylori infection suggested an additive effect (RR: 8.0; 95% CI: 5.0-12.8), whereas no interaction was observed with ASA use (RR: 3.5; 95% CI: 2.0-6.1). CONCLUSIONS: NSAID, low-dose ASA use, and H. pylori infection are three independent risk factors for the development of PUB, but there were differences in the interaction effect between low-dose ASA (no interaction) or NSAID (addition) use and H. pylori infection, which may have implications for clinical practice in prevention strategies.

Measuring political polarization: Twitter shows the two sides of Venezuela.

We say that a population is perfectly polarized when divided in two groups of the same size and opposite opinions. In this paper, we propose a methodology to study and measure the emergence of polarization from social interactions. We begin by proposing a model to estimate opinions in which a minority of influential individuals propagate their opinions through a social network. The result of the model is an opinion probability density function. Next, we propose an index to quantify the extent to which the resulting distribution is polarized. Finally, we apply the proposed methodology to a Twitter conversation about the late Venezuelan president, Hugo Chávez, finding a good agreement between our results and offline data. Hence, we show that our methodology can detect different degrees of polarization, depending on the structure of the network.

The role of the CN vibration in the activated dynamics of LiNC<−>LiCN isomerization in an argon solvent at high temperatures.

The isomerization between CN-Li and Li-CN in an argon bath provides a paradigmatic example of a reaction in a solvent with tunable coupling. In previous work, we found that the rates exhibited a turnover with the density of the argon bath in the limit that the CN bond was held fixed [P. L. Garcia-Muller, R. Hernandez, R. M. Benito, and F. Borondo, J. Chem. Phys. 137, 204301 (2012)]. Here, we report the effect of the CN bond vibration on the dynamics and the persistence of the turnover. As hypothesized earlier, the CN bond is indeed weakly coupled with the reaction path despite the presence of the argon cage.

Ab initio potential energy surface for the highly nonlinear dynamics of the KCN molecule.

An accurate ab initio quantum chemistry study at level of quadratic configuration interaction method of the electronic ground state of the KCN molecule is presented. A fitting of the results to an analytical series expansion was performed to obtain a global potential energy surface suitable for the study of the associated vibrational dynamics. Additionally, classical Poincaré surfaces of section for different energies and quantum eigenstates were calculated, showing the highly nonlinear behavior of this system.

Reaction rate calculation with time-dependent invariant manifolds.

The identification of trajectories that contribute to the reaction rate is the crucial dynamical ingredient in any classical chemical reactivity calculation. This problem often requires a full scale numerical simulation of the dynamics, in particular if the reactive system is exposed to the influence of a heat bath. As an efficient alternative, we propose here to compute invariant surfaces in the phase space of the reactive system that separate reactive from nonreactive trajectories. The location of these invariant manifolds depends both on time and on the realization of the driving force exerted by the bath. These manifolds allow the identification of reactive trajectories simply from their initial conditions, without the need of any further simulation. In this paper, we show how these invariant manifolds can be calculated, and used in a formally exact reaction rate calculation based on perturbation theory for any multidimensional potential coupled to a noisy environment.

Communication: transition state theory for dissipative systems without a dividing surface.

Transition state theory is a central cornerstone in reaction dynamics. Its key step is the identification of a dividing surface that is crossed only once by all reactive trajectories. This assumption is often badly violated, especially when the reactive system is coupled to an environment. The calculations made in this way then overestimate the reaction rate and the results depend critically on the choice of the dividing surface. In this Communication, we study the phase space of a stochastically driven system close to an energetic barrier in order to identify the geometric structure unambiguously determining the reactive trajectories, which is then incorporated in a simple rate formula for reactions in condensed phase that is both independent of the dividing surface and exact.

Detailed study of the direct numerical observation of the Kramers turnover in the LiNC⇌LiCN isomerization rate.

According to Kramers, rates of molecular process are expected to follow a rise and fall from low friction (at little to no interaction with the environment) to high friction (at typical liquid densities and above). This so-called Kramers turnover was recently observed and delineated in the case of the LiNC⇌LiCN isomerization reaction in the presence of an argon bath [P. García-Müller, R. Hernandez, R. M. Benito, and F. Borondo, Phys. Rev. Lett. 101, 178302 (2008)]. The rates were obtained using direct molecular dynamics of an all-atom representation and the Langevin dynamics of a projected representation. We now provide further evidence that the forward and backward rates are indeed exhibiting the turnover. The rates are also seen to agree remarkably well with the Pollak-Grabert-Hänggi rate formulas in regimes satisfying the theory underlying assumptions. At higher temperatures, when the theory is expected to fail, the solvated LiCN isomerization continues to exhibit activated dynamics following the turnover.

Characterizing and modeling an electoral campaign in the context of Twitter: 2011 Spanish Presidential election as a case study.

Transmitting messages in the most efficient way as possible has always been one of politicians' main concerns during electoral processes. Due to the rapidly growing number of users, online social networks have become ideal platforms for politicians to interact with their potential voters. Exploiting the available potential of these tools to maximize their influence over voters is one of politicians' actual challenges. To step in this direction, we have analyzed the user activity in the online social network Twitter, during the 2011 Spanish Presidential electoral process, and found that such activity is correlated with the election results. We introduce a new measure to study political sentiment in Twitter, which we call the relative support. We have also characterized user behavior by analyzing the structural and dynamical patterns of the complex networks emergent from the mention and retweet networks. Our results suggest that the collective attention is driven by a very small fraction of users. Furthermore, we have analyzed the interactions taking place among politicians, observing a lack of debate. Finally, we develop a network growth model to reproduce the interactions taking place among politicians.