Identification of the invariant manifolds of the LiCN molecule using Lagrangian descriptors.

In this paper, we apply Lagrangian descriptors to study the invariant manifolds that emerge from the top of two barriers existing in the LiCN⇌LiNC isomerization reaction. We demonstrate that the integration times must be large enough compared with the characteristic stability exponents of the periodic orbit under study. The invariant manifolds manifest as singularities in the Lagrangian descriptors. Furthermore, we develop an equivalent potential energy surface with 2 degrees of freedom, which reproduces with a great accuracy previous results [F. Revuelta, R. M. Benito, and F. Borondo, Phys. Rev. E 99, 032221 (2019)2470-004510.1103/PhysRevE.99.032221]. This surface allows the use of an adiabatic approximation to develop a more simplified potential energy with solely 1 degree of freedom. The reduced dimensional model is still able to qualitatively describe the results observed with the original 2-degrees-of-freedom potential energy landscape. Likewise, it is also used to study in a more simple manner the influence on the Lagrangian descriptors of a bifurcation, where some of the previous invariant manifolds emerge, even before it takes place.

Correspondence between classical and quantum resonances.

Bifurcations take place in molecular Hamiltonian nonlinear systems as the excitation energy increases, leading to the appearance of different classical resonances. In this paper, we study the quantum manifestations of these classical resonances in the isomerizing system CN-Li⇆Li-CN. By using a correlation diagram of eigenenergies versus Planck constant, we show the existence of different series of avoided crossings, leading to the corresponding series of quantum resonances, which represent the quantum manifestations of the classical resonances. Moreover, the extrapolation of these series to ℏ=0 unveils the correspondence between the bifurcation energy of classical resonances and the energy of the series of quantum resonances in the semiclassical limit ℏ→0. Additionally, in order to obtain analytical expressions for our results, a semiclassical theory is developed.

A multi-technique approach to understanding delithiation damage in LiCoO2 thin films.

We report on the delithiation of LiCoO2 thin films using oxalic acid (C2H2O4) with the goal of understanding the structural degradation of an insertion oxide associated with Li chemical extraction. Using a multi-technique approach that includes synchrotron radiation X-ray diffraction, scanning electron microscopy, micro Raman spectroscopy, photoelectron spectroscopy and conductive atomic force microscopy we reveal the balance between selective Li extraction and structural damage. We identify three different delithiation regimes, related to surface processes, bulk delithiation and damage generation. We find that only a fraction of the grains is affected by the delithiation process, which may create local inhomogeneities. However, the bulk delithiation regime is effective to delithiate the LCO film. All experimental evidence collected indicates that the delithiation process in this regime mimics the behavior of LCO upon electrochemical delithiation. We discard the formation of Co oxalate during the chemical extraction process. In conclusion, the chemical route to Li extraction provides additional opportunities to investigate delithiation while avoiding the complications associated with electrolyte breakdown and simplifying in-situ measurements.

SARS-CoV-2 immunochromatographic IgM/IgG rapid test in pregnancy: A false friend?

BACKGROUND: An increasing body of evidence has revealed that SARS-CoV-2 infection in pregnant women could increase the risk of adverse maternal and fetal outcomes. Careful monitoring of pregnancies with COVID-19 and measures to prevent neonatal infection are warranted. Therefore, rapid antibody tests have been suggested as an efficient screening tool during pregnancy. CASES: We analysed the clinical performance during pregnancy of a rapid, lateral-flow immunochromatographic assay for qualitative detection of SARS-CoV-2 IgG/IgM antibodies. We performed a universal screening including 169 patients during their last trimester of pregnancy. We present a series of 14 patients with positive SARS-CoV-2 immunochromatographic assay rapid test result. Immunochromatographic assay results were always confirmed by chemiluminescent microparticle immunoassays for quantitative detection of SARS-CoV-2 IgG and IgM+IgA antibodies as the gold standard. We observed a positive predictive value of 50% and a false positive rate of 50% in pregnant women, involving a significantly lower diagnostic performance than reported in non-pregnant patients. DISCUSSION: Our data suggest that although immunochromatographic assay rapid tests may be a fast and profitable screening tool for SARS-CoV-2 infection, they may have a high false positive rate and low positive predictive value in pregnant women. Therefore, immunochromatographic assay for qualitative detection of SARS-CoV-2 IgG/IgM antibodies must be verified by other test in pregnant patients.

Short-periodic-orbit method for excited chaotic eigenfunctions.

An alternative method for the calculation of excited chaotic eigenfunctions in arbitrary energy windows is presented. We demonstrate the feasibility of using wave functions localized on unstable periodic orbits as efficient basis sets for this task in classically chaotic systems. The number of required localized wave functions is only of the order of the ratio t_{H}/t_{E}, with t_{H} the Heisenberg time and t_{E} the Ehrenfest time. As an illustration, we present convincing results for a coupled two-dimensional quartic oscillator with chaotic dynamics.

Using correlation diagrams to study the vibrational spectrum of highly nonlinear floppy molecules: The K-CN case.

The correlation diagrams of vibrational energy levels considering the Planck constant as a variable parameter have proven as a very useful tool to study vibrational molecular states, and more specifically in relation to the quantum manifestations of chaos in such dynamical systems. In this paper, we consider the highly nonlinear K-CN molecule, showing how the regular classical structures, i.e., Kolmogorov-Arnold-Moser tori, existing in the mixed classical phase space appear in the quantum levels correlation diagram as emerging diabatic states, something that remains hidden when only the actual value of the Planck constant is considered. Additionally, a quantum transition from order to chaos is unveiled with the aid of these correlation diagrams, where it appears as a frontier of scarred functions.

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.

Shannon entropy at avoided crossings in the quantum transition from order to chaos.

Shannon entropy is studied for the series of avoided crossings that characterize the transition from order to chaos in quantum mechanics. In order to be able to study jointly this entropy for discrete and continuous probability, calculations have been performed on a quantized map, the kicked Harper map, resulting in a different behavior, as order-chaos transition takes place, for the discrete (position representation) and continuous (coherent state representation) cases. This different behavior is analyzed in terms of the distribution of zeros of the Husimi function.

Finite-barrier corrections for multidimensional barriers in colored noise.

The usual identification of reactive trajectories for the calculation of reaction rates requires very time-consuming simulations, particularly if the environment presents memory effects. In this paper, we develop a method that permits the identification of reactive trajectories in a system under the action of a stochastic colored driving. This method is based on the perturbative computation of the invariant structures that act as separatrices for reactivity. Furthermore, using this perturbative scheme, we have obtained a formally exact expression for the reaction rate in multidimensional systems coupled to colored noisy environments.

Unveiling the chaotic structure in phase space of molecular systems using Lagrangian descriptors.

We explore here the feasibility of using the recently introduced Lagrangian descriptors [A. M. Mancho et al., Commun. Nonlinear Sci. Numer. Simul. 18, 3530 (2013)1007-570410.1016/j.cnsns.2013.05.002] to unveil the usually rich dynamics taking place in the vibrations of molecular systems, especially if they are floppy. The principal novelty of our work is the inclusion of p norms in the definition of the descriptors in this kind of system, which greatly enhances their power to discern among the different structures existing in the phase space. As an illustration we use the LiCN molecule described by realistic potentials in two and three dimensions, which exhibits chaotic motion within a mixed phase space in the isomerization between the two wells corresponding to the linear isomer stable configurations, LiNC and LiCN. In particular, we pay special attention to the manifolds emerging from the unstable fixed point between the corresponding isomer wells, and also to the marginally stable structures around a parabolic point existing near the LiNC well.

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.

Role of short periodic orbits in quantum maps with continuous openings.

We apply a recently developed semiclassical theory of short periodic orbits to the continuously open quantum tribaker map. In this paradigmatic system the trajectories are partially bounced back according to continuous reflectivity functions. This is relevant in many situations that include optical microresonators and more complicated boundary conditions. In a perturbative regime, the shortest periodic orbits belonging to the classical repeller of the open map-a cantor set given by a region of exactly zero reflectivity-prove to be extremely robust in supporting a set of long-lived resonances of the continuously open quantum maps. Moreover, for steplike functions a significant reduction in the number needed is obtained, similarly to the completely open situation. This happens despite a strong change in the spectral properties when compared to the discontinuous reflectivity case. In order to give a more realistic interpretation of these results we compare with a Fresnel-type reflectivity function.

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.

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.

Two novel variants of the ABCG5 gene cause xanthelasmas and macrothrombocytopenia: a brief review of hematologic abnormalities of sitosterolemia.

Essentials Diagnosis of sitosterolemia, a rare recessive or syndromic disorder, is usually delayed. Peripheral blood smear is extremely useful for establishing the suspicion of sitosterolemia. High-throughput sequencing technology enables the molecular diagnosis of inherited thrombocytopenias. Accurate characterization of sitosterolemia helps us determine appropriate management. SUMMARY: Background Sitosterolemia (STSL) is a recessive inherited disorder caused by pathogenic variants in the ABCG5 and ABCG8 genes. Increased levels of plasma plant sterols (PSs) usually result in xanthomas and premature coronary atherosclerosis, although hematologic abnormalities may occasionally be present. This clinical picture is unfamiliar to many physicians, and patients may be at high risk of misdiagnosis. Objectives To report two novel ABCG5 variants causing STSL in a Spanish patient, and review the clinical and mutational landscape of STSL. Patient/Methods A 46-year-old female was referred to us with lifelong macrothrombocytopenia. She showed familial hypercholesterolemia-related xanthomas. Molecular analysis was performed with high-throughput sequencing. Plasma PS levels were evaluated with gas-liquid chromatography. The STSL landscape was reviewed with respect to specific online databases and all reports published since 1974. Results A blood smear revealed giant platelets and stomatocytes. Novel compound heterozygous variants were detected in exons 7 (c.914C>G) and 13 (c.1890delT) of ABCG5. The patient showed an increased plasma level of sitosterol. These findings support the diagnosis of STSL. In our review, we identified only 25 unrelated STLS patients who presented with hematologic abnormalities including macrothrombocytopenia. It remains unknown why only some patients develop hematologic abnormalities. Conclusions This is the first Spanish STSL patient to be reported and molecularly characterized. The early diagnosis of STLS is strongly supported by the presence of stomatocytes in blood smears. The definitive diagnosis of STSL by measurement of serum PS levels and molecular analyses prompted the use of ezetimibe therapy.

Altered gene expression in human placenta after suspected preterm labour.

INTRODUCTION: Suspected preterm labour occurs in around 9% of pregnancies. However, almost two-thirds of women admitted for threatened preterm labour ultimately deliver at term and are considered risk-free for fetal development. METHODS: We examined placental and umbilical cord blood samples from preterm or term deliveries after threatened preterm labour as well as term deliveries without threatened preterm labour. We quantitatively analysed the mRNA expression of inflammatory markers (IL6, IFNγ, and TNFα) and modulators of angiogenesis (FGF2, PGF, VEGFA, VEGFB, and VEGFR1). RESULTS: A total of 132 deliveries were analysed. Preterm delivery and term delivery after suspected preterm labour groups showed similar increases in TNFα expression compared with the term delivery control group in umbilical cord blood samples. Placental samples from preterm and term deliveries after suspected preterm labour exhibited significantly increased expression of TNFα and IL6 and decreased expression of IFNγ. Suspected preterm labour was also associated with altered expression of angiogenic factors, although not all differences reached statistical significance. DISCUSSION: We found gene expression patterns indicative of inflammation in human placentas after suspected preterm labour regardless of whether the deliveries occurred preterm or at term. Similarly, a trend towards altered expression of angiogeneic factors was not limited to preterm birth. These findings suggest that the biological mechanisms underlying threatened preterm labour affect pregnancies independently of gestational age at birth.

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.

Theory of short periodic orbits for partially open quantum maps.

We extend the semiclassical theory of short periodic orbits [M. Novaes et al., Phys. Rev. E 80, 035202(R) (2009)PLEEE81539-375510.1103/PhysRevE.80.035202] to partially open quantum maps, which correspond to classical maps where the trajectories are partially bounced back due to a finite reflectivity R. These maps are representative of a class that has many experimental applications. The open scar functions are conveniently redefined, providing a suitable tool for the investigation of this kind of system. Our theory is applied to the paradigmatic partially open tribaker map. We find that the set of periodic orbits that belongs to the classical repeller of the open map (R=0) is able to support the set of long-lived resonances of the partially open quantum map in a perturbative regime. By including the most relevant trajectories outside of this set, the validity of the approximation is extended to a broad range of R values. Finally, we identify the details of the transition from qualitatively open to qualitatively closed behavior, providing an explanation in terms of short periodic orbits.