bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis and characterization of core–shell structured M@Pd/SnO2–graphene [M = Co, Ni or Cu] electrocatalysts for ethanol oxidation in alkaline solution
Authors: Fahim Ahmed E. , Abdel Hameed R. M. , Allam Nageh K.
Published: March 2018

Core–shell structured M@Pd/SnO2–graphene (Gr), [M = Co, Ni or Cu] electrocatalysts were synthesized using ethylene glycol as a reducing agent with the aid of microwave irradiation in a two-step process.
Laser direct structuring and electroless plating applicable super-engineering plastic PPS based thermal conductive composite with particle surface modification
Authors: Kim Kiho , Lee Jinseong , Ryu Seokgyu , Kim Jooheon
Published: March 2018

Boron nitride (BN) and laser activate particles (LAPs) which used for electroless plating were surface-modifiedviabase treatment and by using a silane coupling agent in order to confer functionality and enhance the interfacial affinity of these particles for a polymer matrix.
Negative thermal expansion and electronic structure variation of chalcopyrite type LiGaTe2
Authors: Atuchin V. V. , Liang Fei , Grazhdannikov S. , Isaenko L. I. , Krinitsin P. G. , Molokeev M. S. , Prosvirin I. P. , Jiang Xingxing , Lin Zheshuai
Published: March 2018

The LiGaTe2crystals were grown by the Bridgman–Stockbarger technique and the cell parameter dependence on temperature in the range of 303–563 K was evaluated by the X-ray diffraction analysis and first principles calculations.
High performance nanostructured bismuth oxide–cobaltite as a durable oxygen electrode for reversible solid oxide cells
Authors: Ai Na , Chen Minle , He Shuai , Chen Kongfa , Zhang Teng , Jiang San Ping
Published: March 2018

Nanostructured bismuth oxide–cobaltite is developed as a high performance and durable oxygen electrode for reversible solid oxide cells.
Enhanced charge carrier separation of manganese(ii)-doped graphitic carbon nitride: formation of N–Mn bonds through redox reactions
Authors: Li Haiping , Xia Yuguo , Hu Tingxia , Deng Quanhua , Du Na , Hou Wanguo
Published: March 2018

MnII-doped g-C3N4obtained through redox reactions between a permanganate and urea upon calcination in an inert gas exhibits enhanced photogenerated charge carrier separation.
Solution-processed broadband polymer photodetectors with a spectral response of up to 2.5 μm by a low bandgap donor–acceptor conjugated copolymer
Authors: Zheng Luyao , Zhu Tao , Xu Wenzhan , Liu Lei , Zheng Jie , Gong Xiong , Wudl Fred
Published: March 2018

Solution-processed polymer PDs with a spectral response ranging from 350 nm to 2500 nm.
Transcriptome profiling of HepG2 cells exposed to the flame retardant 9,10-dihydro-9-oxa-10-phosphaphenanthrene 10-oxide (DOPO)
Authors: Krivoshiev Boris V. , Beemster Gerrit T. S. , Sprangers Katrien , Cuypers Bart , Laukens Kris , Blust Ronny , Husson Steven J.
Published: March 2018

The first omics study of DOPO in a human-relevant model to identify toxicity.
Human relevance of rodent liver tumour formation by constitutive androstane receptor (CAR) activators
Authors: Lake Brian G.
Published: March 2018

A large number of nongenotoxic chemicals have been shown to increase the incidence of liver tumours in rats and/or mice by a mode of action (MOA) involving activation of the constitutive androstane receptor (CAR). Studies with the model CAR activator phenobarbital (PB) and its sodium salt (sodium phenobarbital; NaPB) have demonstrated that the key and associative events for rat and mouse liver tumour formation include CAR activation, increased hepatocyte replicative DNA synthesis (RDS), induction of cytochrome P450 CYP2B subfamily enzymes, liver hypertrophy, increased altered hepatic foci and hepatocellular adenomas/carcinomas. The key species difference between the rat and mouse compared to humans, is that human hepatocytes are refractory to the mitogenic effects of PB/NaPB and other CAR activators. While PB/NaPB and other CAR activators stimulate RDS in rat and mouse hepatocytes in both in vitro and in vivo studies, such compounds do not stimulate RDS in cultured human hepatocytes and in in vivo studies performed in chimeric mice with humanised livers. In terms of species differences in RDS, unlike the rat and mouse, humans are similar to other species such as the Syrian hamster and guinea pig in being nonresponsive to the mitogenic effects of CAR activators. Overall, the MOA for rat and mouse liver tumour formation by PB/NaPB and other CAR activators is considered qualitatively not plausible for humans. This conclusion is supported by data from a number of epidemiological studies, which demonstrate that chronic treatment with PB does not increase the incidence of liver cancer in humans.
Les lois de Wolff. Conséquences cliniques 1re partie
Authors: BERT Marc
Published: March 2018

L’anatomie osseuse n’est pas une structure figée,
mais évolue selon les charges subies par l’os.
Énoncées en 1892 par Julius Wolff, un chirurgien,
et se basant sur l’observation clinique, ces lois
vont permettre non plus d’apprendre l’anatomie
des os maxillaires, comme habituellement,
mais de la comprendre et d’anticiper leur
évolution en réaction aux traitements qu’ils
subissent : perte des dents, mise en place
d’implants. Les mécanismes de perception
des contraintes et de leur transmission
aux centres supérieurs sont évoqués, mettant
en avant le rôle particulièrement important
des ostéocytes, cellules que l’on a cru longtemps
être quiescentes.
Fertilitätserhalt bei Patientinnen mit Mammakarzinom – eine aktuelle Übersicht
Authors: Guenther Veronika , Alkatout Ibrahim , Junkers Wiebe , Bauerschlag Dirk , Maass Nicolai , von Otte Soere
Published: March 2018

Bei vielen prämenopausalen Patientinnen, die an einem Mammakarzinom erkranken, ist die Familienplanung noch nicht abgeschlossen, sodass für den Erhalt des fertilen Potenzials Maßnahmen der Fertilitätsprotektion sinnvoll sind. Durch eine Polychemotherapie – unabhängig ob im neoadjuvanten oder adjuvanten Setting – kommt es zu einer irreversiblen Schädigung der Follikel, was unter Umständen zu einer permanenten Infertilität führen kann. Abhängig von den verwendeten Zytostatika und der altersabhängigen Ovarialreserve der Frau, muss das gonadotoxische Risiko als niedrig, mittel oder hoch eingeschätzt werden. Möglichkeiten des Fertilitätserhalts sind: a) die Kryokonservierung von fertilisierten oder unfertilisierten Oozyten. Hierbei werden nach ovarieller Hyperstimulation reife Oozyten mittels transvaginaler Follikelaspiration gewonnen und im Anschluss entweder unfertilisiert oder nach erfolgter IVF- oder ICSI-Behandlung kryokonserviert. Bei b) der Kryokonservierung von Ovarialgewebe wird mithilfe eines laparoskopischen Eingriffs etwa 50 % des Ovarkortex eines Ovars reseziert und kryokonserviert. Die Verwendung von c) GnRH-Agonisten als medikamentöse Therapieoption unternimmt den Versuch einer endokrinen Ovarialsuppression, um Oozyten, Granulosa- und Thekazellen vor dem zytotoxischen Einfluss der Chemotherapie zu schützen.
Frequency of Blood Pressure and Estimated Glomerular Filtration Rate Testing in Type 2 Diabetes Mellitus: A Retrospective Study with 43,509 Patients
Authors: Kostev Karel , Lucas Alexander , Jacob Louis
Published: March 2018

Background The goal of this study was to analyze the frequency of blood pressure (BP) and estimated glomerular filtration rate (eGFR) testing in type 2 diabetes mellitus (T2DM) patients followed in general and diabetological practices in Germany.

Methods The study included individuals who had at least two concultations due to T2DM diagnosis (ICD-10: E11) between January and December 2016. Patients were followed in 557 general and diabetological practices. The primary outcome was the frequency of BP and eGFR testing in T2DM patients in 2016. The association between several demographic and clinical variables and the odds of receiving≥2 BP and≥1 eGFR tests in the year 2016 was analyzed using multivariate logistic regression models.

Results A total of 43,509 individuals were available for analysis. The mean age of the population was 68.6 years (SD=12.4 years). The mean number of measurements was 2.9 (SD=3.5) for BP and 0.4 (SD=1.1) for eGFR. 52.3% of patients were tested at least twice for BP and 15.3% of them at least once for eGFR in 2016. Older patients, individuals followed in diabetological practices, people receiving antihyperglycemic medications, and those affected by chronic conditions (i. e. hypertension, renal complications, or neuropathy) displayed higher odds of receiving≥2 BP and≥1 eGFR tests, whereas patients with a diabetes duration of>1 year displayed lower odds.

Conclusions The frequency of BP and eGFR testing was low in T2DM patients in Germany in 2016. Several demographic and clinical variables were associated with this frequency.
Intravenous Injection of miR-34a Inhibitor Alleviates Diabetes Mellitus-Induced Vascular Endothelial Dysfunction by Targeting NOTCH1
Authors: Zhao Di , Wang Na-Sui , Chen Fu , Li Zheng-Bing , Li Xi-Tao , Zhu Xu-Xin
Published: March 2018

Background miR-34a is a multifunctional post-translational modulator, which is involved in several diabetes-related complications. However, miR-34a remains to be fully elucidated in the diabetic endothelium from rats. In this study, the role of miR-34a/NOTCH1 signaling in the progression of hyperglycemia-vascular endothelial dysfunction was investigated.

Methods In intravenous injection of miR-34a mimics and inhibitors in streptozotocin (STZ)-induced diabetic rats, the biomarkers of endothelial dysfunction was measured. The targeted genes were predicted by a bioinformatics algorithm and confirmed by a dual luciferase reporter assay. The mRNA and protein levels were assayed by qRT-PCR and western blotting, respectively. Immunohistochemical staining was performed to measure NOTCH1 expression in the diabetic endothelium.

Results miR-34a was significantly up-regulated, and NOTCH1 down-regulated, in the thoracic aorta from STZ-induced diabetic rats compared with control group. As compared to model group, the mRNA of NOTCH1 was significantly decreased or increased by miR-34a mimics or inhibitors ex vivo, respectively. Bioinformatics methods further demonstrated that NOTCH1 was a potential target of miR-34a, which was confirmed by dual-luciferase reporter assay. Moreover, both serum ET and NO were significantly increased in diabetic rats as compared to control group. miR-34a inhibitors ex vivo treatment resulted in significant down-regulation ofserum ET and NO levels in diabetic rats as compared to model group.

Conclusion These results provide evidence to support the use of miR-34a inhibitors as a therapeutic approach attenuating hyperglycemia-induced vascular endothelial dysfunction.
Computation of the bluff-body sound generation by a self-consistent mean flow formulation
Authors: Fani A. , Citro V. , Giannetti F. , Auteri F.
Published: March 2018

The sound generated by the flow around a circular cylinder is numerically investigated by using a finite-element method. In particular, we study the acoustic emissions generated by the flow past the bluff body at low Mach and Reynolds numbers. We perform a global stability analysis by using the compressible linearized Navier-Stokes equations. The resulting direct global mode provides detailed information related to the underlying hydrodynamic instability and data on the acoustic field generated. In order to recover the intensity of the produced sound, we apply the self-consistent model for non-linear saturation proposed by Mantič-Lugo, Arratia, and Gallaire [“Self-consistent mean flow description of the nonlinear saturation of the vortex shedding in the cylinder wake,” Phys. Rev. Lett. 113, 084501 (2014)]. The application of this model allows us to compute the amplitude of the resulting linear mode and the effects of saturation on the mode structure and acoustic field. Our results show excellent agreement with those obtained by a full compressible simulation direct numerical simulation and those derived by the application of classical acoustic analogy formulations.
Anomalous amplified and bound-state-like optical transmissions via unidirectional interaction in parity-time symmetric metamaterials
Authors: Zhang Yan-Rong , Wang Wei , Wang Lu-Qi , Guo Rui-Peng , Cao Xuewei , Chen Jing
Published: March 2018

We develop a coupled-mode theory on the optical transmission in parity-time (PT) symmetric coaxial metamaterials. Modeled by coupled lossy Lorentzian oscillators, the theory provides a good fit to numerical full-wave simulation. In the scenario of unidirectional coupling, two polarization-sensitive anomalies are obtained: an amplified transmission and an ultra-narrow one analogous to bound states in continuum. We argue that these phenomena are associated with either a unidirectional-field-transfer process or an indirect unidirectional-field-trapping resonance. The broadening effect is shown to determine the magnitude and polarization of the transmission. Our theory and analysis provide a deep understanding on the importance of PT symmetry and dark helical modes and would contribute to applications such as light storage, field amplification, and even lasing.
Peaked dielectric responses in Ti3C2 MXene nanosheets enabled composites with efficient microwave absorption
Authors: Luo Heng , Feng Wanlin , Liao Congwei , Deng Lianwen , Liu Sheng , Zhang Haibin , Xiao Peng
Published: March 2018

The microwave dielectric behavior of sandwich-like Ti3C2 MXene nanosheets with efficient microwave absorption was investigated by a combination of experiments and simulations. The obvious frequency dispersion effect and the double-peaked feature of dielectric spectra in Ti3C2 MXene nanosheets could be observed over the frequency range of 2–18 GHz, giving rise to superior microwave attenuation capability. Furthermore, a revised Drude-Lorentz model was proposed to explain the peaked feature of permittivity, and simulated results were demonstrated to agree well with the experimental measurements. It was concluded that the hopping migration between Ti3C2 MXene nanosheets with longer relaxation time than “micro-dipole” relaxation within nanosheets makes a superior contribution to overall absorbing performance.
Phase field model of the nanoscale evolution during the explosive crystallization phenomenon
Authors: Lombardo S. F. , Boninelli S. , Cristiano F. , Deretzis I. , Grimaldi M. G. , Huet K. , Napolitani E. , La Magna A.
Published: March 2018

Explosive crystallization is a well known phenomenon occurring due to the thermodynamic instability of strongly under-cooled liquids, which is particularly relevant in pulsed laser annealing processes of amorphous semiconductor materials due to the globally exothermic amorphous-to-liquid-to-crystal transition pathway. In spite of the assessed understanding of this phenomenon, quantitative predictions of the material kinetics promoted by explosive crystallization are hardly achieved due to the lack of a consistent model able to simulate the concurrent kinetics of the amorphous-liquid and liquid-crystal interfaces. Here, we propose a multi-well phase-field model specifically suited for the simulation of explosive crystallization induced by pulsed laser irradiation in the nanosecond time scale. The numerical implementation of the model is robust despite the discontinuous jumps of the interface speed induced by the phenomenon. The predictive potential of the simulations is demonstrated by means of comparisons of the modelling predictions with experimental data in terms of in situ reflectivity measurements and ex-situ micro-structural and chemical characterization.
Dynamics of proteins aggregation. II. Dynamic scaling in confined media
Authors: Zheng Size , Shing Katherine S. , Sahimi Muhammad
Published: March 2018

In this paper, the second in a series devoted to molecular modeling of protein aggregation, a mesoscale model of proteins together with extensive discontinuous molecular dynamics simulation is used to study the phenomenon in a confined medium. The medium, as a model of a crowded cellular environment, is represented by a spherical cavity, as well as cylindrical tubes with two aspect ratios. The aggregation process leads to the formation of β sheets and eventually fibrils, whose deposition on biological tissues is believed to be a major factor contributing to many neuro-degenerative diseases, such as Alzheimer’s, Parkinson’s, and amyotrophic lateral sclerosis diseases. Several important properties of the aggregation process, including dynamic evolution of the total number of the aggregates, the mean aggregate size, and the number of peptides that contribute to the formation of the β sheets, have been computed. We show, similar to the unconfined media studied in Paper I [S. Zheng et al., J. Chem. Phys. 145, 134306 (2016)], that the computed properties follow dynamic scaling, characterized by power laws. The existence of such dynamic scaling in unconfined media was recently confirmed by experiments. The exponents that characterize the power-law dependence on time of the properties of the aggregation process in spherical cavities are shown to agree with those in unbounded fluids at the same protein density, while the exponents for aggregation in the cylindrical tubes exhibit sensitivity to the geometry of the system. The effects of the number of amino acids in the protein, as well as the size of the confined media, have also been studied. Similarities and differences between aggregation in confined and unconfined media are described, including the possibility of no fibril formation, if confinement is severe.
Microwave assisted scalable synthesis of titanium ferrite nanomaterials
Authors: Shukla Abhishek , Bhardwaj Abhishek K. , Singh S. C. , Uttam K. N. , Gautam Nisha , Himanshu A. K. , Shah Jyoti , Kotnala R. K. , Gopal R.
Published: March 2018

Titanium ferrite magnetic nanomaterials are synthesized by one-step, one pot, and scalable method assisted by microwave radiation. Effects of titanium content and microwave exposure time on size, shape, morphology, yield, bonding nature, crystalline structure, and magnetic properties of titanium ferrite nanomaterials are studied. As-synthesized nanomaterials are characterized by X-ray diffraction (XRD), ultraviolet-visible absorption spectroscopy (UV-Vis), attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), Raman spectroscopy, transmission electron microscopy (TEM), and vibrating sample magnetometer measurements. XRD measurements depict the presence of two phases of titanium ferrite into the same sample, where crystallite size increases from ∼33 nm to 37 nm with the increase in titanium concentration. UV-Vis measurement showed broad spectrum in the spectral range of 250–600 nm which reveals that its characteristic peaks lie between ultraviolet and visible region; ATR-FTIR and Raman measurements predict iron-titanium oxide structures that are consistent with XRD results. The micrographs of TEM and selected area electron diffraction patterns show formation of hexagonal shaped particles with a high degree of crystallinity and presence of multi-phase. Energy dispersive spectroscopy measurements confirm that Ti:Fe compositional mass ratio can be controlled by tuning synthesis conditions. Increase of Ti defects into titanium ferrite lattice, either by increasing titanium precursor or by increasing exposure time, enhances its magnetic properties.
Near shot-noise limited time-resolved circular dichroism pump-probe spectrometer
Authors: Stadnytskyi Valentyn , Orf Gregory S. , Blankenship Robert E. , Savikhin Sergei
Published: March 2018

We describe an optical near shot-noise limited time-resolved circular dichroism (TRCD) pump-probe spectrometer capable of reliably measuring circular dichroism signals in the order of μdeg with nanosecond time resolution. Such sensitivity is achieved through a modification of existing TRCD designs and introduction of a new data processing protocol that eliminates approximations that have caused substantial nonlinearities in past measurements and allows the measurement of absorption and circular dichroism transients simultaneously with a single pump pulse. The exceptional signal-to-noise ratio of the described setup makes the TRCD technique applicable to a large range of non-biological and biological systems. The spectrometer was used to record, for the first time, weak TRCD kinetics associated with the triplet state energy transfer in the photosynthetic Fenna-Matthews-Olson antenna pigment-protein complex.
Generating intrinsically disordered protein conformational ensembles from a Markov chain
Authors: Cukier Robert I.
Published: March 2018

Intrinsically disordered proteins (IDPs) sample a diverse conformational space. They are important to signaling and regulatory pathways in cells. An entropy penalty must be payed when an IDP becomes ordered upon interaction with another protein or a ligand. Thus, the degree of conformational disorder of an IDP is of interest. We create a dichotomic Markov model that can explore entropic features of an IDP. The Markov condition introduces local (neighbor residues in a protein sequence) rotamer dependences that arise from van der Waals and other chemical constraints. A protein sequence of length N is characterized by its (information) entropy and mutual information, MIMC, the latter providing a measure of the dependence among the random variables describing the rotamer probabilities of the residues that comprise the sequence. For a Markov chain, the MIMC is proportional to the pair mutual information MI which depends on the singlet and pair probabilities of neighbor residue rotamer sampling. All 2N sequence states are generated, along with their probabilities, and contrasted with the probabilities under the assumption of independent residues. An efficient method to generate realizations of the chain is also provided. The chain entropy, MIMC, and state probabilities provide the ingredients to distinguish different scenarios using the terminologies: MoRF (molecular recognition feature), not-MoRF, and not-IDP. A MoRF corresponds to large entropy and large MIMC (strong dependence among the residues’ rotamer sampling), a not-MoRF corresponds to large entropy but small MIMC, and not-IDP corresponds to low entropy irrespective of the MIMC. We show that MorFs are most appropriate as descriptors of IDPs. They provide a reasonable number of high-population states that reflect the dependences between neighbor residues, thus classifying them as IDPs, yet without very large entropy that might lead to a too high entropy penalty.
Linear approximations of global behaviors in nonlinear systems with moderate or strong noise
Authors: Liang Junhao , Din Anwarud , Zhou Tianshou
Published: March 2018

While many physical or chemical systems can be modeled by nonlinear Langevin equations (LEs), dynamical analysis of these systems is challenging in the cases of moderate and strong noise. Here we develop a linear approximation scheme, which can transform an often intractable LE into a linear set of binomial moment equations (BMEs). This scheme provides a feasible way to capture nonlinear behaviors in the sense of probability distribution and is effective even when the noise is moderate or big. Based on BMEs, we further develop a noise reduction technique, which can effectively handle tough cases where traditional small-noise theories are inapplicable. The overall method not only provides an approximation-based paradigm to analysis of the local and global behaviors of nonlinear noisy systems but also has a wide range of applications.
Solvent-assisted multistage nonequilibrium electron transfer in rigid supramolecular systems: Diabatic free energy surfaces and algorithms for numerical simulations
Authors: Feskov Serguei V. , Ivanov Anatoly I.
Published: March 2018

An approach to the construction of diabatic free energy surfaces (FESs) for ultrafast electron transfer (ET) in a supramolecule with an arbitrary number of electron localization centers (redox sites) is developed, supposing that the reorganization energies for the charge transfers and shifts between all these centers are known. Dimensionality of the coordinate space required for the description of multistage ET in this supramolecular system is shown to be equal to N − 1, where N is the number of the molecular centers involved in the reaction. The proposed algorithm of FES construction employs metric properties of the coordinate space, namely, relation between the solvent reorganization energy and the distance between the two FES minima. In this space, the ET reaction coordinate znn′ associated with electron transfer between the nth and n′th centers is calculated through the projection to the direction, connecting the FES minima. The energy-gap reaction coordinates znn′ corresponding to different ET processes are not in general orthogonal so that ET between two molecular centers can create nonequilibrium distribution, not only along its own reaction coordinate but along other reaction coordinates too. This results in the influence of the preceding ET steps on the kinetics of the ensuing ET. It is important for the ensuing reaction to be ultrafast to proceed in parallel with relaxation along the ET reaction coordinates. Efficient algorithms for numerical simulation of multistage ET within the stochastic point-transition model are developed. The algorithms are based on the Brownian simulation technique with the recrossing-event detection procedure. The main advantages of the numerical method are (i) its computational complexity is linear with respect to the number of electronic states involved and (ii) calculations can be naturally parallelized up to the level of individual trajectories. The efficiency of the proposed approach is demonstrated for a model supramolecular system involving four redox centers.
Investigation of nucleation kinetics in H2SO4 vapor through modeling of gas phase kinetics coupled with particle dynamics
Authors: Carlsson Philip T. M. , Zeuch Thomas
Published: March 2018

We have developed a new model utilizing our existing kinetic gas phase models to simulate experimental particle size distributions emerging in dry supersaturated H2SO4 vapor homogeneously produced by rapid oxidation of SO2 through stabilized Criegee-Intermediates from 2-butene ozonolysis. We use a sectional method for simulating the particle dynamics. The particle treatment in the model is based on first principles and takes into account the transition from the kinetic to the diffusion-limited regime. It captures the temporal evolution of size distributions at the end of the ozonolysis experiment well, noting a slight underrepresentation of coagulation effects for larger particle sizes. The model correctly predicts the shape and the modes of the experimentally observed particle size distributions. The predicted modes show an extremely high sensitivity to the H2SO4 evaporation rates of the initially formed H2SO4 clusters (dimer to pentamer), which were arbitrarily restricted to decrease exponentially with increasing cluster size. In future, the analysis presented in this work can be extended to allow a direct validation of quantum chemically predicted stabilities of small H2SO4 clusters, which are believed to initiate a significant fraction of atmospheric new particle formation events. We discuss the prospects and possible limitations of the here presented approach.
Composition, morphology, and growth of clusters in a gas of particles with random interactions
Authors: Azizi Itay , Rabin Yitzhak
Published: March 2018

We use Langevin dynamics simulations to study the growth kinetics and the steady-state properties of condensed clusters in a dilute two-dimensional system of particles that are all different (APD) in the sense that each particle is characterized by a randomly chosen interaction parameter. The growth exponents, the transition temperatures, and the steady-state properties of the clusters and of the surrounding gas phase are obtained and compared with those of one-component systems. We investigate the fractionation phenomenon, i.e., how particles of different identities are distributed between the coexisting mother (gas) and daughter (clusters) phases. We study the local organization of particles inside clusters, according to their identity—neighbourhood identity ordering (NIO)—and compare the results with those of previous studies of NIO in dense APD systems.
Implicit and explicit host effects on excitons in pentacene derivatives
Authors: Charlton R. J. , Fogarty R. M. , Bogatko S. , Zuehlsdorff T. J. , Hine N. D. M. , Heeney M. , Horsfield A. P. , Haynes P. D.
Published: March 2018

An ab initio study of the effects of implicit and explicit hosts on the excited state properties of pentacene and its nitrogen-based derivatives has been performed using ground state density functional theory (DFT), time-dependent DFT, and ΔSCF. We observe a significant solvatochromic redshift in the excitation energy of the lowest singlet state (S1) of pentacene from inclusion in a p-terphenyl host compared to vacuum; for an explicit host consisting of six nearest neighbour p-terphenyls, we obtain a redshift of 65 meV while a conductor-like polarisable continuum model (CPCM) yields a 78 meV redshift. Comparison is made between the excitonic properties of pentacene and four of its nitrogen-based analogs, 1,8-, 2,9-, 5,12-, and 6,13-diazapentacene with the latter found to be the most distinct due to local distortions in the ground state electronic structure. We observe that a CPCM is insufficient to fully understand the impact of the host due to the presence of a mild charge-transfer (CT) coupling between the chromophore and neighbouring p-terphenyls, a phenomenon which can only be captured using an explicit model. The strength of this CT interaction increases as the nitrogens are brought closer to the central acene ring of pentacene.
Effects of the bond polarity on the structural and dynamical properties of silica-like liquids
Authors: Pafong Sanjon E. , Drossel B. , Vogel M.
Published: March 2018

Silica is a network-forming liquid that shares many properties with water due to its tetrahedral structure. It undergoes a transition from a fragile to a strong liquid as the temperature is decreased, which is accompanied by a structural change to lower density and higher tetrahedral order. In order to disentangle the effects of Coulomb and van der Waals interactions on the structure and dynamics of liquid silica, we modify the bond polarity by changing the partial charges assigned to each atom. Using molecular dynamics simulations, we show that density, tetrahedral order, and structural relaxation times decrease when reducing bond polarity. Moreover, we find that the density maximum and the fragile-to-strong transition move to lower temperatures until they eventually vanish when the partial charges are decreased below approximately 75% of their regular value. Irrespective of whether strong or fragile behavior exists, structural relaxation is governed by hopping motion at sufficiently low temperatures. As long as there is a strong regime, the energy barrier associated with strong dynamics decreases with decreasing partial charges, but the dependence on the bond polarity differs from that of the activation energy in the Arrhenius regime at high temperatures. We show that the fragile-to-strong transition is associated with structural changes occurring between the first and second coordination shells that lead to a decrease in density and an increase in tetrahedral order. In particular, independent of the value of the partial charges, the distribution of the local structures is the same at this dynamic crossover, but we find no evidence that the effect occurs upon crossing the Widom line. In the fragile regime at intermediate temperatures, the relaxation times are well described by a previously proposed model which decomposes the apparent activation energy into a constant single-particle contribution and a temperature-dependent collective contribution. However, our results for silica-like melts do not obey several common relations of the model parameters reported for molecular glass formers.
A theoretical study on the optical properties of black silicon
Authors: Ma Shijun , Liu Shuang , Xu Qinwei , Xu Junwen , Lu Rongguo , Liu Yong , Zhong Zhiyong
Published: March 2018

There is a wide application prospect in black silicon, especially in solar cells and photoelectric detectors. For further optimization of black silicon, it is important to study its optical properties. Especially, the influence of the surface nanostructures on these properties and the light propagation within the nanostructures are relevant. In this paper, two kinds of black silicon models are studied via the finite differences time domain method. The simulated reflectance spectra matches well with the measured curve. Also, the light intensity distribution within the nanostructures shows that near 80% of the incident light are redirected and subjected to internal reflection, which provides powerful support for the good light trapping properties of black silicon.
Photodissociation dynamics in the first absorption band of pyrrole. I. Molecular Hamiltonian and the Herzberg-Teller absorption spectrum for the A21(πσ*)←X̃1 A1(ππ) transition
Authors: Picconi David , Grebenshchikov Sergy Yu.
Published: March 2018

This paper opens a series in which the photochemistry of the two lowest πσ* states of pyrrole and their interaction with each other and with the ground electronic state X̃ are studied using ab initio quantum mechanics. New 24-dimensional potential energy surfaces for the photodissociation of the N–H bond and the formation of the pyrrolyl radical are calculated using the multiconfigurational perturbation theory (CASPT2) for the electronic states X̃(ππ), 11A2(πσ*), and 11B1(πσ*) and locally diabatized. In this paper, the ab initio calculations are described and the photodissociation in the state 11A2(πσ*) is analyzed. The excitation 11 A2←X̃ is mediated by the coordinate dependent transition dipole moment functions constructed using the Herzberg-Teller expansion. Nuclear dynamics, including 6, 11, and 15 active degrees of freedom, are studied using the multi-configurational time-dependent Hartree method. The focus is on the frequency resolved absorption spectrum as well as on the dissociation time scales and the resonance lifetimes. Calculations are compared with available experimental data. An approximate convolution method is developed and validated, with which absorption spectra can be calculated and assigned in terms of vibrational quantum numbers. The method represents the total absorption spectrum as a convolution of the diffuse spectrum of the detaching H-atom and the Franck-Condon spectrum of the heteroaromatic ring. Convolution calculation requires a minimal quantum chemical input and is a promising tool for studying the πσ* photodissociation in model biochromophores.
Binding free energy analysis of protein-protein docking model structures by evERdock
Authors: Takemura Kazuhiro , Matubayasi Nobuyuki , Kitao Akio
Published: March 2018

To aid the evaluation of protein-protein complex model structures generated by protein docking prediction (decoys), we previously developed a method to calculate the binding free energies for complexes. The method combines a short (2 ns) all-atom molecular dynamics simulation with explicit solvent and solution theory in the energy representation (ER). We showed that this method successfully selected structures similar to the native complex structure (near-native decoys) as the lowest binding free energy structures. In our current work, we applied this method (evERdock) to 100 or 300 model structures of four protein-protein complexes. The crystal structures and the near-native decoys showed the lowest binding free energy of all the examined structures, indicating that evERdock can successfully evaluate decoys. Several decoys that show low interface root-mean-square distance but relatively high binding free energy were also identified. Analysis of the fraction of native contacts, hydrogen bonds, and salt bridges at the protein-protein interface indicated that these decoys were insufficiently optimized at the interface. After optimizing the interactions around the interface by including interfacial water molecules, the binding free energies of these decoys were improved. We also investigated the effect of solute entropy on binding free energy and found that consideration of the entropy term does not necessarily improve the evaluations of decoys using the normal model analysis for entropy calculation.
Intrinsic point defects in β-In2S3 studied by means of hybrid density-functional theory
Authors: Ghorbani Elaheh , Albe Karsten
Published: March 2018

We have employed first principles total energy calculations in the framework of density functional theory, with plane wave basis sets and screened exchange hybrid functionals to study the incorporation of intrinsic defects in bulk β-In2S3. The results are obtained for In-rich and S-rich experimental growth conditions. The charge transition level is discussed for all native defects, including VIn, VS, Ini, Si, SIn, and InS, and a comparison between the theoretically calculated charge transition levels and the available experimental findings is presented. The results imply that β-In2S3 shows n-type conductivity under both In-rich and S-rich growth conditions. The indium antiisite (InS), the indium interstitial (Ini), and the sulfur vacancy (VS′) are found to be the leading sources of sample's n-type conductivity. When going from the In-rich to the S-rich condition, the conductivity of the material decreases; however, the type of conductivity remains unchanged.
A new exactly integrable hypergeometric potential for the Schrödinger equation
Authors: Ishkhanyan T. A. , Manukyan V. A. , Harutyunyan A. H. , Ishkhanyan A. M.
Published: March 2018

We introduce a new exactly integrable potential for the Schrödinger equation for which the solution of the problem may be expressed in terms of the Gauss hypergeometric functions. This is a potential step with variable height and steepness. We present the general solution of the problem, discuss the transmission of a quantum particle above the barrier, and derive explicit expressions for the reflection and transmission coefficients.
Efficient implementation of one- and two-component analytical energy gradients in exact two-component theory
Authors: Franzke Yannick J. , Middendorf Nils , Weigend Florian
Published: March 2018

We present an efficient algorithm for one- and two-component analytical energy gradients with respect to nuclear displacements in the exact two-component decoupling approach to the one-electron Dirac equation (X2C). Our approach is a generalization of the spin-free ansatz by Cheng and Gauss [J. Chem. Phys. 135, 084114 (2011)], where the perturbed one-electron Hamiltonian is calculated by solving a first-order response equation. Computational costs are drastically reduced by applying the diagonal local approximation to the unitary decoupling transformation (DLU) [D. Peng and M. Reiher, J. Chem. Phys. 136, 244108 (2012)] to the X2C Hamiltonian. The introduced error is found to be almost negligible as the mean absolute error of the optimized structures amounts to only 0.01 pm. Our implementation in TURBOMOLE is also available within the finite nucleus model based on a Gaussian charge distribution. For a X2C/DLU gradient calculation, computational effort scales cubically with the molecular size, while storage increases quadratically. The efficiency is demonstrated in calculations of large silver clusters and organometallic iridium complexes.
“Divide-and-conquer” semiclassical molecular dynamics: An application to water clusters
Authors: Di Liberto Giovanni , Conte Riccardo , Ceotto Michele
Published: March 2018

We present an investigation of vibrational features in water clusters performed by means of our recently established divide-and-conquer semiclassical approach [M. Ceotto, G. Di Liberto, and R. Conte, Phys. Rev. Lett. 119, 010401 (2017)]. This technique allows us to simulate quantum vibrational spectra of high-dimensional systems starting from full-dimensional classical trajectories and projection of the semiclassical propagator onto a set of lower dimensional subspaces. The potential energy surface employed is a many-body representation up to three-body terms, in which monomers and two-body interactions are described by the high level Wang-Huang-Braams-Bowman (WHBB) water potential, while, for three-body interactions, calculations adopt a fast permutationally invariant ab initio surface at the same level of theory of the WHBB 3-body potential. Applications range from the water dimer up to the water decamer, a system made of 84 vibrational degrees of freedom. Results are generally in agreement with previous variational estimates in the literature. This is particularly true for the bending and the high-frequency stretching motions, while estimates of modes strongly influenced by hydrogen bonding are red shifted, in a few instances even substantially, as a consequence of the dynamical and global picture provided by the semiclassical approach.
Communication: Strong laser alignment of solvent-solute aggregates in the gas-phase
Authors: Trippel Sebastian , Wiese Joss , Mullins Terry , Küpper Jochen
Published: March 2018

Strong quasi-adiabatic laser alignment of the indole-water-dimer clusters, an amino-acid chromophore bound to a single water molecule through a hydrogen bond, was experimentally realized. The alignment was visualized through ion and electron imaging following strong-field ionization. Molecular-frame photoelectron angular distributions showed a clear suppression of the electron yield in the plane of the ionizing laser’s polarization, which was analyzed as strong alignment of the molecular cluster with ⟨cos2 θ2D⟩ ≥ 0.9.
Nanoscale view of assisted ion transport across the liquid–liquid interface
Authors: Liang Zhu , Bu Wei , Schweighofer Karl J. , Walwark David J. , Harvey Jeffrey S. , Hanlon Glenn R. , Amoanu Daniel , Erol Cem , Benjamin Ilan , Schlossman Mark L.
Published: March 2018

Significance

The selective separation of targeted metal ions is utilized for environmental remediation, mining of rare earth and base metals, as well as the separation and isolation of long-lived radionuclides from nuclear waste. During the process of solvent extraction, organic extractant molecules complex with metal ions to assist their transfer from an aqueous to an organic phase. The structure of ion–extractant complexes at the interface, as well as the mechanism of ion transport across the interface, are generally unknown but are relevant for improving the kinetics and efficiency of this industrial process. Here, we describe experiments that reveal different ion–extractant complexes for divalent and trivalent ions, and discuss their consequences for the extraction process.
Empirical confidence interval calibration for population-level effect estimation studies in observational healthcare data
Authors: Schuemie Martijn J. , Hripcsak George , Ryan Patrick B. , Madigan David , Suchard Marc A.
Published: March 2018

Observational healthcare data, such as electronic health records and administrative claims, offer potential to estimate effects of medical products at scale. Observational studies have often been found to be nonreproducible, however, generating conflicting results even when using the same database to answer the same question. One source of discrepancies is error, both random caused by sampling variability and systematic (for example, because of confounding, selection bias, and measurement error). Only random error is typically quantified but converges to zero as databases become larger, whereas systematic error persists independent from sample size and therefore, increases in relative importance. Negative controls are exposure–outcome pairs, where one believes no causal effect exists; they can be used to detect multiple sources of systematic error, but interpreting their results is not always straightforward. Previously, we have shown that an empirical null distribution can be derived from a sample of negative controls and used to calibratePvalues, accounting for both random and systematic error. Here, we extend this work to calibration of confidence intervals (CIs). CIs require positive controls, which we synthesize by modifying negative controls. We show that our CI calibration restores nominal characteristics, such as 95% coverage of the true effect size by the 95% CI. We furthermore show that CI calibration reduces disagreement in replications of two pairs of conflicting observational studies: one related to dabigatran, warfarin, and gastrointestinal bleeding and one related to selective serotonin reuptake inhibitors and upper gastrointestinal bleeding. We recommend CI calibration to improve reproducibility of observational studies.
The Great Recession worsened blood pressure and blood glucose levels in American adults
Authors: Seeman Teresa , Thomas Duncan , Merkin Sharon Stein , Moore Kari , Watson Karol , Karlamangla Arun
Published: March 2018

Significance

Longitudinal data from the Multi-Ethnic Study of Atherosclerosis (MESA) document deleterious health impacts of the economic and social stresses associated with the Great Recession, with significant increases in blood pressure and glucose. Effects are independent of underlying age-related trends in these biomarkers. Larger effects are seen in population subgroups more severely hit by the recession: younger adults (i.e., those more likely still in the labor force) and older homeowners (whose declining home wealth likely reduced a key element of their financial security). Results also reveal greater impacts on blood pressure and glucose among those on medication, and a concomitant reduction in medication use and intensity of treatment—a potential pathway by which the Great Recession affected people on medications more.
Chemical control over membrane-initiated steroid signaling with a DNA nanocapsule
Authors: Veetil Aneesh T. , Jani Maulik S. , Krishnan Yamuna
Published: March 2018

Significance

Steroids execute their diverse biological functions through both membrane-initiated steroid signaling (MISS) and nuclear-initiated steroid signaling (NISS). NISS is much slower, occurring over hours to days accompanied by transcriptional changes in the nucleus and is well studied. In contrast MISS is more recently discovered––it is rapid, occurs within seconds upon binding the plasma membrane, and is much less studied. Despite its emerging importance, fundamental issues such as second messenger dynamics and downstream signaling molecules are still unknown because of the paucity of technologies available to manipulate signaling steroids. Here we describe a technology that offers a clean and controllable release of signaling steroids under chemical control that enables the study of MISS dynamics.
Reintroductions of birds and mammals involve evolutionarily distinct species at the regional scale
Authors: Thévenin Charles , Mouchet Maud , Robert Alexandre , Kerbiriou Christian , Sarrazin François
Published: March 2018

Significance

There are general acknowledgements that Earth’s sixth mass extinction event is more severe than perceived when looking at population extirpations (rather than focusing only on species extinctions) and that species extinctions are associated with the rapid loss of evolutionary history. In this study, we investigate how population reintroductions, a major conservation tool used to reverse population extirpations, can contribute to the preservation of evolutionary diversity within birds and mammals. Using data on reintroductions of terrestrial birds and mammals in Europe and North America, we show that, despite strong taxonomic biases leading to a poor representativeness of the regional phylogenetic diversity, reintroduction practitioners seem to have focused on highly evolutionarily distinct species.