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The scientific paper is devoted to the electrochemical reduction of bismuth ions from citrate electrolytes. The kinetics and mechanism of the process and the influence of various factors on the electroreduction process of bismuth ions were studied by recording cyclic and linear polarization curves on Pt, Ni and Ni/Bi electrodes. The effective activation energy and diffusion coefficient were calculated according to the obtained data. The results of the calculation show that the electroreduction process of the bismuth ions from citrate solutions is accompanied by diffusion polarization. [ABSTRACT FROM AUTHOR]

Large low-frequency polarization noise is found in some perovskite relaxor ferroelectrics when they are partially polarized, regardless of whether the polarization is accompanied by an applied electric field. The noise appears both in the ferroelectric and relaxor states, including the nominally ergodic paraelectric state at temperatures above the susceptibility peak. Since it is present whenever the samples have non-zero average piezoelectric coefficients, but not otherwise evident, it appears to be a response to mechanical strain changes. Dependence of the noise on sample thermal history indicates that non-equilibrium strain relaxation is the source, even in the temperature range for which the sample is nominally ergodic. Non-equilibrium noise in the absence of net piezoelectricity is found at somewhat higher frequencies. Related materials lacking a metastable non-equilibrium cubic bulk phase and a symmetry-broken surface layer show very little of the anomalous low-frequency noise. The implications for a non-equilibrium origin of the skin effect are discussed. [ABSTRACT FROM AUTHOR]

Large low-frequency polarization noise is found in some perovskite relaxor ferroelectrics when they are partially polarized, regardless of whether the polarization is accompanied by an applied electric field. The noise appears both in the ferroelectric and relaxor states, including the nominally ergodic paraelectric state at temperatures above the susceptibility peak. Since it is present whenever the samples have non-zero average piezoelectric coefficients, but not otherwise evident, it appears to be a response to mechanical strain changes. Dependence of the noise on sample thermal history indicates that non-equilibrium strain relaxation is the source, even in the temperature range for which the sample is nominally ergodic. Non-equilibrium noise in the absence of net piezoelectricity is found at somewhat higher frequencies. Related materials lacking a metastable non-equilibrium cubic bulk phase and a symmetry-broken surface layer show very little of the anomalous low-frequency noise. The implications for a non-equilibrium origin of the skin effect are discussed. [ABSTRACT FROM AUTHOR]

A lithium-air battery based on lithium oxide (Li2O) formation can theoretically deliver an energy density that is comparable to that of gasoline. Lithium oxide formation involves a four-electron reaction that is more difficult to achieve than the one- and two-electron reaction processes that result in lithium superoxide (LiO2O ) and lithium peroxide (Li2O2), respectively. By using a composite polymer electrolyte based on Li10GeP2S12 nanoparticles embedded in a modified polyethylene oxide polymer matrix, we found that Li2O is the main product in a room temperature solid-state lithium-air battery. The battery is rechargeable for 1000 cycles with a low polarization gap and can operate at high rates. The four-electron reaction is enabled by a mixed ion-electron-conducting discharge product and its interface with air. [ABSTRACT FROM AUTHOR]

Using the decoction extraction method, we obtained twice crude aqueous extracts of Artemisia absinthium or (wormwood) that was made to start a comparative study, between the first extract which corresponds to the leaves of our plant (AQL) and the second which belongs to the stems (AQS). The inhibitory activity of the twice extracts of Artemisia absinthium was studied by weight loss, potentiodynamic polarization and electrochemistry impedance spectroscopy. The morphology of the mild steel surface was examined by SEM. The inhibitory efficiency increased with the increase of the concentration, we reach an efficiency of 85% for AQL and 82% for AQS at 308 K for a concentration of 0.2 g/L. Two Artemisia absinthium extracts used to prevent corrosion in mild steel adhere to the Langmuir adsorption isotherm during adsorption. The majority compound is 3,4-dihydroxybenzoic acid in the case of extracts with percentages of 42.4% for AQL and 42.2% for AQS. The DFT results of the majority of compounds allowed us to have an idea on the power of adsorption of these last ones on the surface of the metal, indeed there can be a combined effect of the various molecules constituting the extracts on the corrosion inhibition. [ABSTRACT FROM AUTHOR]

In this paper, the design, fabrication, and measurement of a high-performance metamaterial absorber (MMA) have been presented. The three major concerns of MMA's are narrow bandwidth, angle sensitivity, and uncontrollable polarization. By smartly controlling the proposed design, the solutions to these three concerns of MMA are given in this paper. By integrating the design with varactor diodes, we make the MMA tunable to wide frequency ranges. Frequency tunability ranges from 4.2 to 7 GHz. By using circular sectors in the resonator, wide incident angle insensitivity has been achieved. The presented MMA exhibits more than 80% absorptivity up to 70° incident angles. With the proposed design, it is possible to control either TM or TE polarization resonant frequency by fixing the resonant frequency of other polarization. Also, a biasing technique which is simple and effective to control both TM and TE resonant frequencies simultaneously is given in this paper. Moreover, all these advantages have been achieved by using a single layer low cost FR4 material having thickness 0.6 mm as a substrate. By using a standard parameter retrieval technique, the real and imaginary parts of both permittivity and permeability of the presented MMA are calculated. It is expected that the presented work improves the state-of-the-art in the smart metamaterial absorber domain. [ABSTRACT FROM AUTHOR]

The integration of ferroelectric materials with semiconductor heterostructures can greatly enhance the functionality of electronic devices, provided the ferroelectric material retains a significant part of its switchable polarization. This work reports polarization switching in epitaxial PbZr0.2Ti0.8O3/ZnO/GaN heterostructures grown on c-cut sapphire single-crystal substrates. The electrical measurements of PbZr0.2Ti0.8O3/ZnO ferroelectric/semiconductor capacitors reveal an unexpected difference between a counterclockwise ferroelectric hysteresis loop and a clockwise C-V loop. A non-linear hysteretic behavior of the capacitance is observed in the voltage range that is at least 3 times narrower than the range of ferroelectric polarization switching voltages. This difference can be explained by charge injection effects at the interface between ferroelectrics and semiconductors. The interaction between electric polarization and the electronic structure of the heterojunction leads to capacitance and charge carrier concentrations that are switchable by polarization of the ferroelectric layer. These findings are important for both fundamental and applied research of switchable and highly tunable ferroelectric/semiconductor heterostructures. [ABSTRACT FROM AUTHOR]

Molecular dynamics (MD) simulations of peptides and proteins offer atomic-level detail into many biological processes, although the degree of insight depends on the accuracy of the force fields used to represent them. Protein folding is a key example in which the accurate reproduction of folded-state conformations of proteins and kinetics of the folding processes in simulation is a longstanding goal. Although there have been a number of recent successes, challenges remain in capturing the full complexity of folding for even secondary-structure elements. In the present work, we have used all-atom MD simulations to study the folding properties of one such element, the C-terminal β-hairpin of the B1 domain of streptococcal protein G (GB1). Using replica-exchange umbrella sampling simulations, we examined the folding free energy of two fixed-charge CHARMM force fields, CHARMM36 and CHARMM22*, as well as a polarizable force field, the CHARMM Drude-2013 model, which has previously been shown to improve the folding properties of α-helical peptides. The CHARMM22* and Drude-2013 models are in rough agreement with experimental studies of GB1 folding, while CHARMM36 overstabilizes the β-hairpin. Additional free-energy calculations show that small adjustments to the atomic polarizabilities in the Drude-2013 model can improve both the backbone solubility and folding properties of GB1 without significantly affecting the model’s ability to properly fold α-helices. We also identify a non-native salt bridge in the β-turn region that overstabilizes the β-hairpin in the C36 model. Finally, we demonstrate that tryptophan fluorescence is insufficient for capturing the full β-hairpin folding pathway. [ABSTRACT FROM AUTHOR]

Supercell modeling of an electrical double layer (EDL) at electrified solid-electrolyte interfaces is a challenge. The net polarization of EDLs arising from the fixed chemical composition setup leads to uncompensated EDLs under periodic boundary condition and convolutes the calculation of the Helmholtz capacitance [C. Zhang and M. Sprik, Phys. Rev. B 94, 245309 (2016)]. Here we provide a new formula based on the supercell polarization at zero electric field Ē = 0 (i.e., standard Ewald boundary condition) to calculate the Helmholtz capacitance of charged insulator-electrolyte interfaces and validate it using atomistic simulations. Results are shown to be independent of the supercell size. This formula gives a shortcut to compute the Helmholtz capacitance without locating the zero net charge state of EDL and applies directly to any standard molecular dynamics code where the electrostatic interactions are treated by the Ewald summation or its variants. [ABSTRACT FROM AUTHOR]

Studies on ion pairing at interfaces have been intensified recently because of their importance in many chemical reactive phenomena, such as ion–ion interactions that are affected by interfaces and their influence on kinetic processes. In this study, we performed simulations to examine the thermodynamics and kinetics of small polarizable sodium iodide ions in the bulk and near the water liquid–vapor interface. Using classical transition state theory, we calculated the dissociation rates and corrected them with transmission coefficients obtained from the reactive flux formalism and Grote-Hynes theory. Our results show that in addition to affecting the free energy of ions in solution, the interfacial environments significantly influence the kinetics of ion pairing. The results on the relaxation time obtained using the reactive flux formalism and Grote-Hynes theory present an unequivocal picture that the interface suppresses ion dissociation. The effects of the use of molecular models on the ion interactions as well as the ion-pair configurations at the interface are also quantified and discussed. [ABSTRACT FROM AUTHOR]

We present efficient methods to calculate beyond random phase approximation (RPA) correlation energies for molecular systems with up to 500 atoms. To reduce the computational cost, we employ the resolution-of-the-identity and a double-Laplace transform of the non-interacting polarization propagator in conjunction with an atomic orbital formalism. Further improvements are achieved using integral screening and the introduction of Cholesky decomposed densities. Our methods are applicable to the dielectric matrix formalism of RPA including second-order screened exchange (RPA-SOSEX), the RPA electron-hole time-dependent Hartree-Fock (RPA-eh-TDHF) approximation, and RPA renormalized perturbation theory using an approximate exchange kernel (RPA-AXK). We give an application of our methodology by presenting RPA-SOSEX benchmark results for the L7 test set of large, dispersion dominated molecules, yielding a mean absolute error below 1 kcal/mol. The present work enables calculating beyond RPA correlation energies for significantly larger molecules than possible to date, thereby extending the applicability of these methods to a wider range of chemical systems. [ABSTRACT FROM AUTHOR]

In this work, we propose an immersion corrosion measurement method with E10 bioethanol-gasoline blend on austenitic steel (SS304) and aluminum (Al6061). Immersion tests were designed to simulate a weekly refuel cycle and were performed over 4, 8, and 12-week durations. Polarization resistance, surface morphology, and corrosion products were then observed after the immersion tests. Corrosion rates were estimated from polarization resistance measurements via electrochemical impedance spectroscopy. Afterwards, the surface morphology of exposed samples was studied using scanning electron microscopy. Lastly, the corrosion products were characterized using scanning electron microscopy with energy dispersive X-ray analysis. Surface staining was observed in both metal substrates. It was observed that the corrosion rate of SS304 remained relatively constant throughout the immersion time. In contrast, an increment in the corrosion rate of Al6061 was observed after four weeks of immersion due to the peeling of the protective oxide layer. [ABSTRACT FROM AUTHOR]

In this paper, we study electrostatic properties between two similar or oppositely charged surfaces immersed in an electrolyte solution by using the mean-field approach accounting for solvent polarization and non-uniform size effects. Applying a free energy formalism accounting for unequal ion sizes and orientational ordering of water dipoles, we derive coupled and self-consistent equations to calculate electrostatic properties between charged surfaces. Electrostatic properties for similarly charged surfaces depend on the counterion size but not on the coion size. Moreover, electrostatic potential and osmotic pressure between similarly charged surfaces are found to be increased with increasing counterion size. On the other hand, the corresponding ones between oppositely charged surfaces are related to both sizes of positive and negative ions. For oppositely charged surfaces, the electrostatic potential, number density of solvent molecules, and relative permittivity of an electrolyte having unequal ion sizes are not symmetric about the centerline between the charged surfaces. For either case, the consideration of solvent polarization results in a decrease in the electrostatic potential and the osmotic pressure compared to the case without the effect. [ABSTRACT FROM AUTHOR]

We present the simultaneous detection of the spectrum and the complete polarization state of a multiplex coherent anti-Stokes Raman scattering signal with a fast division-of-amplitude spectro-polarimeter. The spectro-polarimeter is based on a commercial imaging spectrograph, a birefringent wedge prism, and a segmented polarizer. Compared to the standard rotating-retarder fixed-analyzer spectro-polarimeter, only a single measurement is required and an up to 21-fold reduced acquisition time is shown. The measured Stokes parameters allow us to differentiate between vibrational symmetries and to determine the depolarization ratio ρ by data post-processing. [ABSTRACT FROM AUTHOR]

In a recent paper [F. Aviat et al., J. Chem. Theory Comput. 13, 180-190 (2017)], we proposed the Truncated Conjugate Gradient (TCG) approach to compute the polarization energy and forces in polarizable molecular simulations. The method consists in truncating the conjugate gradient algorithm at a fixed predetermined order leading to a fixed computational cost and can thus be considered "non-iterative." This gives the possibility to derive analytical forces avoiding the usual energy conservation (i.e., drifts) issues occurring with iterative approaches. A key point concerns the evaluation of the analytical gradients, which is more complex than that with a usual solver. In this paper, after reviewing the present state of the art of polarization solvers, we detail a viable strategy for the efficient implementation of the TCG calculation. The complete cost of the approach is then measured as it is tested using a multi-time step scheme and compared to timings using usual iterative approaches. We show that the TCG methods are more efficient than traditional techniques, making it a method of choice for future long molecular dynamics simulations using polarizable force fields where energy conservation matters. We detail the various steps required for the implementation of the complete method by software developers. [ABSTRACT FROM AUTHOR]

This work presents two extensions of our self-consistent polarization model for treating non-valence excess electron systems. The first extension is the implementation of analytical gradients, and the second extension is the implementation of a mixed real space plus momentum space approach combined with fast Fourier transforms to reduce the computational time compared to a purely real space discrete variable representation approach. The performance of the new algorithms is assessed in calculations of the excess electron states of various size water clusters and of the non-valence correlation-bound anion of the C240 fullerene. [ABSTRACT FROM AUTHOR]

Alkylphosphonic acids are well known for their ability to form self-assembled monolayers on hydroxide surfaces. A crucial step to understanding fundamentally how these surfaces are created is the elucidation of the interaction process that leads to such interface creation. In this study, we employed electrochemical impedance spectroscopy (EIS), Monte Carlo and molecular dynamics to understand this process. The interaction with the Cu(111) surface of three different alkylphosphonic acids (hexyl-, octyl- and decylphosphonic acids) is evaluated in an aqueous acidic and in an ethanol solution by Monte Carlo and molecular dynamics simulations, while EIS measurements are used to put in evidence the impact of the layer made in ethanol on copper protection. Nyquist diagrams of copper samples modified with an alkylphosphonic monolayer showed a higher polarization resistance that mitigates the copper corrosion in an aqueous acid medium. The phase–frequency Bode plots had higher and broader phase maxima for a modified copper surface with phosphonic moieties, which confirmed the ability of this organic layer to prevent copper corrosion. [ABSTRACT FROM AUTHOR]

We have developed a method for modeling spatial stochastic biochemical reactions in complex, threedimensional, and time-dependent domains using the reaction-diffusion master equation formalism. In particular, we look to address the fully coupled problems that arise in systems biology where the shape and mechanical properties of a cell are determined by the state of the biochemistry and vice versa. To validate our method and characterize the error involved, we compare our results for a carefully constructed test problem to those of a microscale implementation. We demonstrate the effectiveness of our method by simulating a model of polarization and shmoo formation during the mating of yeast. The method is generally applicable to problems in systems biology where biochemistry and mechanics are coupled, and spatial stochastic effects are critical. [ABSTRACT FROM AUTHOR]

The homonuclear radio-frequency driven recoupling (RFDR) experiment is commonly used in solid-state NMR spectroscopy to gain insight into the structure of biological samples due to its ease of implementation, stability towards fluctuations/missetting of radio-frequency (rf) field strength, and in general low rf requirements. A theoretical operator-based Floquet description is presented to appreciate the effect of having a temporal displacement of the π-pulses in the RFDR experiment. From this description, we demonstrate improved transfer efficiency for the RFDR experiment by generating an adiabatic passage through the zero-quantum recoupling condition. We have compared the performances of RFDR and the improved sequence to mediate efficient 13CO to 13Cα polarization transfer for uniformly 13C,15N-labeled glycine and for the fibril forming peptide SNNFGAILSS (one-letter amino acid codes) uniformly 13C,15N-labeled at the FGAIL residues. Using numerically optimized sweeps, we get experimental gains of approximately 20% for glycine where numerical simulations predict an improvement of 25% relative to the standard implementation. For the fibril forming peptide, using the same sweep parameters as found for glycine, we have gains in the order of 10%-20% depending on the spectral regions of interest. [ABSTRACT FROM AUTHOR]

Generally, the phase structure change of Pb(B' B'')O3–PZT solid solutions near a morphotropic phase boundary (MPB) can be originated from composition variations. Here our results show that the excess PbO and the sintering temperature can also result in the ferroelectric phase structure change in the Pb(Ni1/3Nb2/3)O3–Pb(Zr,Ti)O3 (PNN–PZT)-based ceramics near the MPB. The dielectric, piezoelectric, and ferroelectric properties are dependent on the tetragonal phase content (TP) which is closely associated with the excess PbO and the sintering temperature. The temperature dependence of the polarization (P)–electric field (E) hysteresis loops reveals that the tetragonal phase in the PNN–PZT-based ceramics has a lower activation energy (Ea) for domain wall movement than that of the rhombohedral phase, thus resulting in easier polarization rotation. This is responsible for the phase structure–electrical property relationships in the PNN–PZT-based ceramics, exhibiting the dependence of the tetragonal phase content (TP) on the electrical properties. [ABSTRACT FROM AUTHOR]

When a depolarizing event occurs across a cell membrane there is a remarkable change in its electrical properties. A complete depolarization event produces a considerably rapid increase in voltage that propagates longitudinally along the axon and is accompanied by changes in axial conductance. A dynamically changing magnetic field is associated with the passage of the action potential down the axon. Over 75 years of research has gone into the quantification of this phenomenon. To date, no unified model exist that resolves transmembrane polarization in a closed-form description. Here, a simple but formative description of propagated signaling phenomena in the membrane of an axon is presented in closed-form. The focus is on using both biophysics and mathematical methods for elucidating the fundamental mechanisms governing transmembrane polarization. The results presented demonstrate how to resolve electromagnetic and thermodynamic factors that govern transmembrane potential. Computational results are supported by well-established quantitative descriptions of propagated signaling phenomena in the membrane of an axon. The findings demonstrate how intracellular conductance, the thermodynamics of magnetization, and current modulation function together in generating an action potential in a unified closed-form description. The work presented in this paper provides compelling evidence that three basic factors contribute to the propagated signaling in the membrane of an axon. It is anticipated this work will compel those in biophysics, physical biology, and in the computational neurosciences to probe deeper into the classical and quantum features of membrane magnetization and signaling. It is hoped that subsequent investigations of this sort will be advanced by the computational features of this model without having to resort to numerical methods of analysis. [ABSTRACT FROM AUTHOR]

We propose a method to produce valley-polarized electron beams using a bilayer graphene npn junction. By analyzing the transmission properties of electrons through the junction with zigzag interface in the presence of trigonal warping, we observe that there exist a range of incident energies and barrier heights in which transmitted electrons are well polarized and collimated. From this observation and by performing numerical simulations, it is demonstrated that valley-dependent electronic currents with nearly perfect polarization can be generated. We also show that the peak-to-peak separation angle between the polarized currents is tunable either by incident energy or by barrier height each of which is controlled by using top and back gate voltages. The results can be used for constructing an electron beam splitter to produce valley-polarized currents. [ABSTRACT FROM AUTHOR]

We present calculations which aim to describe coherent ultrafast magneto-optical effects observed in time-resolved pump-probe experiments. Our approach is based on a nonlinear semi-classical Drude-Voigt model and is used to interpret experiments performed on nickel ferromagnetic thin film. Within this framework, a phenomenological light-induced coherent molecular mean-field depending on the polarizations of the pump and probe pulses is proposed whose microscopic origin is related to a spin-orbit coupling involving the electron spins of the material sample and the electric field of the laser pulses. Theoretical predictions are compared to available experimental data. The model successfully reproduces the observed experimental trends and gives meaningful insight into the understanding of magneto-optical rotation behavior in the ultrafast regime. Theoretical predictions for further experimental studies are also proposed. [ABSTRACT FROM AUTHOR]

Gallium nitride (GaN) is one of the most technologically important semiconductors and a fundamental component in many optoelectronic and power devices. Low-resistivity GaN wafers are in demand and actively being developed to improve the performance of vertical GaN power devices necessary for high-voltage and high-frequency applications. For the development of GaN devices, nondestructive characterization of electrical properties particularly for carrier densities in the order of 1019 cm−3 or higher is highly favorable. In this study, we investigated GaN single crystals with different carrier densities of up to 1020 cm−3 using THz time-domain ellipsometry in reflection configuration. The p- and s-polarized THz waves reflected off the GaN samples are measured and then corrected based on the analysis of multiple waveforms measured with a rotating analyzer. We show that performing such analysis leads to a ten times higher precision than by merely measuring the polarization components. As a result, the carrier density and mobility parameters can be unambiguously determined even at high conductivities. [ABSTRACT FROM AUTHOR]

Gallium nitride (GaN) is one of the most technologically important semiconductors and a fundamental component in many optoelectronic and power devices. Low-resistivity GaN wafers are in demand and actively being developed to improve the performance of vertical GaN power devices necessary for high-voltage and high-frequency applications. For the development of GaN devices, nondestructive characterization of electrical properties particularly for carrier densities in the order of 1019 cm−3 or higher is highly favorable. In this study, we investigated GaN single crystals with different carrier densities of up to 1020 cm−3 using THz time-domain ellipsometry in reflection configuration. The p- and s-polarized THz waves reflected off the GaN samples are measured and then corrected based on the analysis of multiple waveforms measured with a rotating analyzer. We show that performing such analysis leads to a ten times higher precision than by merely measuring the polarization components. As a result, the carrier density and mobility parameters can be unambiguously determined even at high conductivities. [ABSTRACT FROM AUTHOR]

We study the conformational behavior of polarizable polymer chain under an external homogeneous electric field within the Flory type self-consistent field theory. We consider the influence of electric field on the polymer coil as well as on the polymer globule. We show that when the polymer chain conformation is a coil, application of external electric field leads to its additional swelling. However, when the polymer conformation is a globule, a sufficiently strong field can induce a globule-coil transition. We show that such "field-induced" globule-coil transition at the sufficiently small monomer polarizabilities goes quite smoothly. On the contrary, when the monomer polarizability exceeds a certain threshold value, the globule-coil transition occurs as a dramatic expansion in the regime of first-order phase transition. The developed theoretical model can be applied to predicting polymer globule density change under external electric field in order to provide more efficient processes of polymer functionalization, such as sorption, dyeing, and chemical modification. [ABSTRACT FROM AUTHOR]

Polarization fluctuation behavior of lanthanum substituted Bi4Ti3O12 (Bi4-xLaxTi3O12, BLT) ferroelectric thin films has been examined. Remnant polarization exhibits an initial increase (Pup, 1-106 cycles) and a subsequent decrease (Pdown, 106-109 cycles) with switching cycles, whereas the dielectric constant exhibits a continuous decrease. By careful investigations on the effect of switching frequency and annealing atmosphere on the polarization fluctuation characteristics, we propose that this polarization fluctuation characteristic of BLT films is attributed to the competition between domain pinning and passive layer growing effect, due to the redistribution of oxygen vacancy related defect under external applied field. Pup behavior is dominated by the unpinning of pinned domain, while Pdown behavior is dominated by the reduction of applied field on BLT bulk layer, due to the growing of the passive layer between BLT and Pt electrode. By assuming the dielectric constant and initial thickness of passive layer, the passive layer was estimated to be about 2-5 times thicker than the initial state after 109 cycling. [ABSTRACT FROM AUTHOR]

We present a detailed analysis of a setup capable of arbitrary amplitude, phase, and polarization shaping of broadband visible femtosecond pulses at 1?kHz via a pair of actively phase stabilized acousto-optic programmable dispersive filters arranged in a Mach-Zehnder interferometer geometry. The setup features phase stability values around λ/225 at 580?nm as well as degrees of polarization of at least 0.9 for any polarization state. Both numbers are important metrics to evaluate a setup's potential for applications based on polarization-shaped femtosecond pulses, such as fully coherent multi-dimensional electronic spectroscopy. [ABSTRACT FROM AUTHOR]

Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that can be used to solvate biophysical systems of interest. Recently, a 4-to-1 mapping was used to couple the bundled-simple point charge water with the MARTINI model. Here, we extend the supramolecular mapping to coarse-grained models with explicit charges. In particular, the two tested models are the polarizable water and big multiple water models associated with the MARTINI force field. As corresponding coarse-grained representations consist of several interaction sites, we couple orientational degrees of freedom of the atomistic and coarse-grained representations via a harmonic energy penalty term. This additional energy term aligns the dipole moments of both representations. We test this coupling by studying the system under applied static external electric field. We show that our approach leads to the correct reproduction of the relevant structural and dynamical properties. [ABSTRACT FROM AUTHOR]

In the recently developed technique of X-ray Birefringence Imaging, molecular orientational order in anisotropic materials is studied by exploiting the birefringence of linearly polarized X-rays with energy close to an absorption edge of an element in the material. In the experimental setup, a vertically deflecting high-resolution double-crystal monochromator is used upstream from the sample to select the appropriate photon energy, and a horizontally deflecting X-ray polarization analyzer, consisting of a perfect single crystal with a Bragg reflection at Bragg angle of approximately 45°, is placed downstream from the sample to measure the resulting rotation of the X-ray polarization. However, if the experiment is performed on a synchrotron bending-magnet beamline, then the elliptical polarization of the X-rays out of the electron orbit plane affects the shape of the output beam. Also, because the monochromator introduces a correlation between vertical position and photon energy to the X-ray beam, the polarization analyzer does not select the entire beam, but instead selects a diagonal stripe, the slope of which depends on the Bragg angles of the monochromator and the polarization analyzer. In the present work, the final background intensity distribution is calculated analytically because the phase space sampling methods normally used in ray traces are too inefficient for this setup. X-ray Birefringence Imaging data measured at the Diamond Light Source beamline B16 agree well with the theory developed here. [ABSTRACT FROM AUTHOR]

We study the dielectric dynamics of viscous glycerol in the presence of a large bias field. Apart from dielectric saturation and polarization anisotropy, we observe that the steady state structural relaxation time is longer by 2.7% in the presence of a 225 kV/cm dc-field relative to the linear response counterpart, equivalent to a field induced glass transition (Tg) shift of +84 mK. This result compares favorably with the 3.0% time constant increase predicted on the basis of a recent report [G. P. Johari, J. Chem. Phys. 138, 154503 (2013)], where the field induced reduction of the configurational entropy translates into slower dynamics by virtue of the Adam-Gibbs relation. Other models of field dependent glass transition temperatures are also discussed. Similar to observations related to the electro-optical Kerr effect, the rise time of the field induced effect is much longer than its collapse when the field is removed again. The orientational relaxation time of the plastic crystal cyclo-octanol is more sensitive to a bias field, showing a 13.5% increase at a field of 150 kV/cm, equivalent to an increase of Tg by 0.58 K. [ABSTRACT FROM AUTHOR]

The mean ionic activity coefficients of aqueous NaCl solutions of varying concentrations at 298.15 K and 1 bar have been obtained from molecular dynamics simulations by gradually turning on the interactions of an ion pair inserted into the solution. Several common non-polarizable water and ion models have been used in the simulations. Gibbs-Duhem equation calculations of the thermodynamic activity of water are used to confirm the thermodynamic consistency of the mean ionic activity coefficients. While the majority of model combinations predict the correct trends in mean ionic activity coefficients, they overestimate their values at high salt concentrations. The solubility predictions also suffer from inaccuracies, with all models underpredicting the experimental values, some by large factors. These results point to the need for further ion and water model development. [ABSTRACT FROM AUTHOR]

Long-lived nuclear spin states have a relaxation time much longer than the longitudinal relaxation time T1. Long-lived states extend significantly the time scales that may be probed with magnetic resonance, with possible applications to transport and binding studies, and to hyperpolarised imaging. Rapidly rotating methyl groups in solution may support a long-lived state, consisting of a population imbalance between states of different spin exchange symmetries. Here, we expand the formalism for describing the behaviour of long-lived nuclear spin states in methyl groups, with special attention to the hyperpolarisation effects observed in 13CH3 groups upon rapidly converting a material with low-barrier methyl rotation from the cryogenic solid state to a room-temperature solution [M. Icker and S. Berger, J. Magn. Reson. 219, 1 (2012)]. We analyse the relaxation properties of methyl long-lived states using semi-classical relaxation theory. Numerical simulations are supplemented with a spherical-tensor analysis, which captures the essential properties of methyl long-lived states. [ABSTRACT FROM AUTHOR]

We present a simple method to measure the dynamics of cross peaks in time-resolved two-dimensional vibrational spectroscopy. By combining suitably weighted dispersed pump-probe spectra, we eliminate the diagonal contribution to the 2D-IR response, so that the dispersed pump-probe signal contains the projection of only the cross peaks onto one of the axes of the 2D-IR spectrum. We apply the method to investigate the folding dynamics of an alpha-helical peptide in a temperature-jump experiment and find characteristic folding and unfolding time constants of 260 ± 30 and 580 ± 70 ns at 298 K. [ABSTRACT FROM AUTHOR]

The electric double layer (CD) and electrode quantum (CQ) capacitances of graphene-based supercapacitors are investigated using a combined molecular dynamics and density functional theory approach. In particular, we compare an approach that includes electronic polarization to one that is polarization-free by evaluating both CD and CQ using [EMIM][BF4] ionic liquid as a model electrolyte. Our results indicate that the inclusion of polarization effects can yield higher CD values--in this study by up to 40% around ±2 V--which we attribute primarily to the presence of charge smearing at the electrode-electrolyte interface. On the other hand, we find that the polarization-induced distortion of the electronic structure of graphene does not noticeably alter the predicted CQ. Our analysis suggests that an accurate description of the spatial charge distribution at the graphene interface due to polarization is necessary to improve our predictive capabilities, though more notably for CD. However, the conventional polarization-free approximation can serve as an efficient tool to study trends associated with both the CQ and CD at the interface of various graphene-like materials. [ABSTRACT FROM AUTHOR]

The properties of dipolar cubic lattices are studied and the paradox of how to obtain a long range polarization in such lattices is resolved by choosing a proper shape of the total system. It has been shown that large but finite number of aligned dipoles prefer to exist as needle shaped macroscopic particles [M. Yoon and D. Tománek, J. Phys.: Condens. Matter 22, 455105 (2010)]. The total energy for a particle in such a system has one short range contribution depending on the packing (the chosen lattice) and one long range term depending on the dipole density of the system. We show that the latter term corresponds exactly to the polarization term from a dielectric medium embedding a sphere of the considered system. There is no need to include a dielectric medium in this modeling and the "dielectric stabilization" is generated solely by the dipoles of the system. [ABSTRACT FROM AUTHOR]

Since the time of Kirkwood, observed deviations in magnitude of the dielectric constant of aqueous protein solution from that of neat water (~80) and slower decay of polarization have been subjects of enormous interest, controversy, and debate. Most of the common proteins have large permanent dipole moments (often more than 100 D) that can influence structure and dynamics of even distant water molecules, thereby affecting collective polarization fluctuation of the solution, which in turn can significantly alter solution's dielectric constant. Therefore, distance dependence of polarization fluctuation can provide important insight into the nature of biological water. We explore these aspects by studying aqueous solutions of four different proteins of different characteristics and varying sizes, chicken villin headpiece subdomain (HP-36), immunoglobulin binding domain protein G (GB1), hen-egg white lysozyme (LYS), and Myoglobin (MYO). We simulate fairly large systems consisting of single protein molecule and 20000-30000 water molecules (varied according to the protein size), providing a concentration in the range of ~2-3 mM. We find that the calculated dielectric constant of the system shows a noticeable increment in all the cases compared to that of neat water. Total dipole moment auto time correlation function of water (δMW(0)δMW(t)) is found to be sensitive to the nature of the protein. Surprisingly, dipole moment of the protein and total dipole moment of the water molecules are found to be only weakly coupled. Shellwise decomposition of water molecules around protein reveals higher density of first layer compared to the succeeding ones. We also calculate heuristic effective dielectric constant of successive layers and find that the layer adjacent to protein has much lower value (~50). However, progressive layers exhibit successive increment of dielectric constant, finally reaching a value close to that of bulk 4-5 layers away. We also calculate shellwise orientational correlation function and tetrahedral order parameter to understand the local dynamics and structural re-arrangement of water. Theoretical analysis providing simple method for calculation of shellwise local dielectric constant and implication of these findings are elaborately discussed in the present work. [ABSTRACT FROM AUTHOR]

We consider transport properties of a hybrid device composed by a quantum dot placed between normal and superconducting reservoirs, and coupled to a Majorana nanowire: a topological superconducting segment hosting Majorana bound states (MBSs) at the opposite ends. It is demonstrated that if highly nonlocal and nonoverlapping MBSs are formed in the system, the zero-bias Andreev conductance through the dot exhibits characteristic isoconductance profiles with the shape depending on the spin asymmetry of the coupling between the dot and the topological superconductor. Otherwise, for overlapping MBSs with less degree of nonlocality, the conductance is insensitive to the spin polarization and the isoconductance signatures disappear. This allows to propose an alternative experimental protocol for probing the nonlocality of the MBSs in Majorana nanowires. [ABSTRACT FROM AUTHOR]

Macromolecular crowding (MMC) in cells is a hot topic in biology; therefore, well-characterized measurement standards for the evaluation of the nano-environment in MMC solutions are necessary. We propose to use polarization-dependent fluorescence correlation spectroscopy (Pol-FCS) for evaluation of macromolecular crowding in solutions. Pol-FCS can simultaneously measure the relaxation times of rotational and translational diffusion of fluorescent molecules at the same position, even in living cells with low damage. In this report, the differences in the nano-environment among solutions of small molecules, gels, and MMC solutions were evaluated by comparing their rotational and translational diffusion using Pol-FCS. Moreover, this method could distinguish the phase shift in the polyethylene glycol solution. Finally, we separately evaluated the nano-environment in the cytosol and nucleus of living cells in different cell lines and cell cycles. We expect this evaluation method to be useful in characterizing the nano-environment in MMC studies. In addition, the proposed method may be useful for other nano-environments such as liquid–liquid phase separation. [ABSTRACT FROM AUTHOR]

Using first-principles calculations, we investigate the magnetic order in two-dimensional (2D) transition-metal-dichalcogenide (TMD) monolayers: MoS2, MoSe2, MoTe2, WSe2, and WS2 substitutionally doped with period four transition-metals (Ti, V, Cr, Mn, Fe, Co, Ni). We uncover five distinct magnetically ordered states among the 35 distinct TMD-dopant pairs: the non-magnetic (NM), the ferromagnetic with out-of-plane spin polarization (Z FM), the out-of-plane polarized clustered FMs (clustered Z FM), the in-plane polarized FMs (X–Y FM), and the anti-ferromagnetic (AFM) state. Ni and Ti dopants result in an NM state for all considered TMDs, while Cr dopants result in an anti-ferromagnetically ordered state for all the TMDs. Most remarkably, we find that Fe, Mn, Co, and V result in an FM ordered state for all the TMDs, except for MoTe2. Finally, we show that V-doped MoSe2 and WSe2, and Mn-doped MoS2, are the most suitable candidates for realizing a room-temperature FM at a 16–18% atomic substitution. [ABSTRACT FROM AUTHOR]

A two-dimensional electron gas (2DEG), which has recently been shown to develop in the central vertical plane of a wedge-shaped c-oriented GaN nanowall due to spontaneous polarization effect, offers a unique scenario, where the symmetry between the conduction and valence band is preserved over the entire confining potential. This results in the suppression of Rashba coupling even when the shape of the wedge is not symmetric. Here, for such a 2DEG channel, relaxation time for different spin projections is calculated as a function of donor concentration and gate bias. Our study reveals a strong dependence of the relaxation rate on the spin-orientation and density of carriers in the channel. Most interestingly, relaxation of spin oriented along the direction of confinement has been found to be completely switched off. Upon applying a suitable bias at the gate, the process can be switched on again. Exploiting this fascinating effect, an electrically driven spin-transistor has been proposed. [ABSTRACT FROM AUTHOR]

GaAs-based broad-area diode lasers are needed with improved lateral beam parameter product (BPPlat) at high power. An experimental study of the factors limiting BPPlat is therefore presented, using extreme double-asymmetric (EDAS) vertical structures emitting at 910 nm. Continuous wave, pulsed and polarization-resolved measurements are presented and compared to thermal simulation. The importance of thermal and packaging-induced effects is determined by comparing junction -up and -down devices. Process factors are clarified by comparing diodes with and without index-guiding trenches. We show that in all cases studied, BPPlat is limited by a non-thermal BPP ground-level and a thermal BPP, which depends linearly on self-heating. Measurements as a function of pulse width confirm that self-heating rather than bias-level dominates. Diodes without trenches show low BPP ground-level, and a thermal BPP which depends strongly on mounting, due to changes in the temperature profile. The additional lateral guiding in diodes with trenches strongly increases the BPP ground-level, but optically isolates the stripe from the device edges, suppressing the influence of the thermal profile, leading to a BPP-slope that is low and independent of mounting. Trenches are also shown to initiate strain fields that cause parasitic TM-polarized emission with large BPPlat, whose influence on total BPPlat remains small, provided the overall polarization purity is >95%. [ABSTRACT FROM AUTHOR]

Molecular dynamics (MD) simulations are employed to ascertain the relative importance of various electrostatic interaction contributions, including induction interactions, to the thermodynamics of dense, hot ion-dipole mixtures. In the absence of polarization, we find that an MD-constrained free energy term accounting for the ion-dipole interactions, combined with well tested ionic and dipolar contributions, yields a simple, fairly accurate free energy form that may be a better option for describing the thermodynamics of such mixtures than the mean spherical approximation (MSA). Polarization contributions induced by the presence of permanent dipoles and ions are found to be additive to a good approximation, simplifying the thermodynamic modeling. We suggest simple free energy corrections that account for these two effects, based in part on standard perturbative treatments and partly on comparisons with MD simulation. Even though the proposed approximations likely need further study, they provide a first quantitative assessment of polarization contributions at high densities and temperatures and may serve as a guide for future modeling efforts. [ABSTRACT FROM AUTHOR]

We present a generalized Kohn-Sham (KS) density functional theory (DFT) based effective fragment potential (EFP2-DFT) method for the treatment of solvent effects. Similar to the original Hartree-Fock (HF) based potential with fitted parameters for water (EFP1) and the generalized HF based potential (EFP2-HF), EFP2-DFT includes electrostatic, exchange-repulsion, polarization, and dispersion potentials, which are generated for a chosen DFT functional for a given isolated molecule. The method does not have fitted parameters, except for implicit parameters within a chosen functional and the dispersion correction to the potential. The electrostatic potential is modeled with a multipolar expansion at each atomic center and bond midpoint using Stone's distributed multipolar analysis. The exchange-repulsion potential between two fragments is composed of the overlap and kinetic energy integrals and the nondiagonal KS matrices in the localized molecular orbital basis. The polarization potential is derived from the static molecular polarizability. The dispersion potential includes the intermolecular D3 dispersion correction of Grimme et al. [J. Chem. Phys. 132, 154104 (2010)]. The potential generated from the CAMB3LYP functional has mean unsigned errors (MUEs) with respect to results from coupled cluster singles, doubles, and perturbative triples with a complete basis set limit (CCSD(T)/CBS) extrapolation, of 1.7, 2.2, 2.0, and 0.5 kcal/mol, for the S22, water-benzene clusters, water clusters, and n-alkane dimers benchmark sets, respectively. The corresponding EFP2-HF errors for the respective benchmarks are 2.41, 3.1, 1.8, and 2.5 kcal/mol. Thus, the new EFP2-DFT-D3 method with the CAMB3LYP functional provides comparable or improved results at lower computational cost and, therefore, extends the range of applicability of EFP2 to larger system sizes. [ABSTRACT FROM AUTHOR]

The difference between compositional and grain size effect on the dielectric nonlinearity was contrasted in Mn and V-doped BaTiO3 multilayer ceramic capacitors utilizing the first order reversal curve (FORC) distribution based on the Preisach model. The high field dielectric constants can be increased either by the adjustment of additive composition, that is, Ba concentration maintaining the same grain size, or by increasing its size. The former compositional effect caused an enhanced dielectric constant in both low and high field region, which can be associated with the increase in the saturation polarization, the reversible and the irreversible FORC distributions near zero bias. The latter grain growth effect, on the other hand, resulted in a decrease of the dielectric constants in the low field but a steep ac field dependence of them, which can be correlated with a decrease of the reversible FORC distribution and a significant increase of the irreversible FORC distribution near origin. These results show that the compositional effect is caused by the increase of the magnitude of the spontaneous polarization and the domain wall density, whereas the grain size effect is caused by the increase in the size of the domain and its wall, which increases the probability of domain pinning by weakly pinning centers but enables its long range motion beyond the threshold field. [ABSTRACT FROM AUTHOR]

The dynamics of water in aqueous solutions of glucose have been investigated using polarizationresolved femtosecond infrared spectroscopy of the hydroxyl stretch vibrations of water and glucose. Using reference measurements on solutions of glucose in dimethylsulfoxide and a spectral decomposition model, we are able to distinguish the reorientation dynamics of the glucose and water hydroxyl groups.We find that the water reorientation dynamics strongly slow down in the presence of glucose. [ABSTRACT FROM AUTHOR]