Including Polarization Effects Research Articles

Rovibrational excitation of rare-gas dimers by electron impact

Electron scattering by rare-gas dimers is studied for very low incident energies using the zero range potential (ZRP) method. Beyond the traditional ZRP, we consider an alternative formulation accounting for the atomic polarization, inspired in the modified effective range theory. The scattering calculations are reported in fixed nuclei, rigid rotor, and rovibrational approximations, the first two being analytical. An expression for the electron-molecule scattering length is obtained. We find that short-range interactions are the dominant mechanism for rotational transitions in electron scattering by rare-gas dimers, while the long-range interactions may be neglected. Our results show how the elastic, rotational, and rovibrational cross sections depend on the electron-atom scattering length, on the molecular parameters, and also on the inclusion of polarization effects. The principle of detailed balance is discussed in the context of the ZRP method. Finally, we show that the rovibrational coupling considerably affects the rotational cross sections when the rotational constant becomes comparable to the vibrational constant.

Electronic excitation cross section in positron scattering by H2 molecules using distorted-wave method

In this work we have applied for the first time the distorted-wave approximation (DWA) combined with Schwinger Variational Iterative Method (SVIM) to describe electronic excitation of H2 molecules by positron collisions. The integral (ICS) and differential (DCS) excitation cross sections for X1Σg+ → B1Σu+ transition of H2 molecule, in the range from near threshold up to 45 eV of positron energies, were reported in static (ST) and static-correlation-polarization (STPOL) levels. Our two-state ICS in DWA-ST level have quantitative agreement with experimental measurement at energies from threshold up to 18 eV and the inclusion of polarization effects increases the cross sections. Comparison with 2-state close-coupling approximation (CCA), 2-state Schwinger Multichannel (SMC), 5-state SMC and 1013-state from Convergent Close-Coupling (CCC) methods are done and is encouraging. The relative steeper drop above 22 eV in experimental ICS was not observed by any theoretical calculations indicating that new measurements would be interesting for this transition in this energy range.

Computational Study of PCSK9-EGFA Complex with Effective Polarizable Bond Force Field.

Inhibiting of Proprotein Convertase Subtilisin/Kexin-type 9 (PCSK9) and Low Density Lipoprotein Receptor (LDLR) binding is an effective way for reducing Low Density Lipoprotein cholesterol (LDL-C). Understanding the interaction between PCSK9 and LDLR is useful for PCSK9 inhibitor design. In this work, MD simulations with the standard (non-polarizable) AMBER force field and effective polarizable bond (EPB) force field were performed for wild type and four mutants of PCSK9 and EGFA (Epidermal Growth Factor-like repeat A) domain of LDLR complexes. These four mutants are gain-of-function mutants. The analysis of hydrogen bond dynamics and the relative binding free energy indicates that EPB is more reliable in simulating protein dynamics and predicting relative binding affinity. Structures sampled from MD simulations with the standard AMBER force field deviate too far away from crystal structures. Many important interaction components between of PCSK9 and EGFA no longer exist in the simulation with the Amber force field. For comparison, simulation using EPB force field gives more stable structures as shown by hydrogen bond analysis and produced relative binding free energies that are consistent with experimental results. Our study suggests that inclusion of polarization effects in MD simulation is important for studying the protein-protein interaction.

Elastic electron scattering from nitrobenzene.

We present integral, momentum transfer, and differential cross sections for an elastic scattering of electrons by nitrobenzene. Our calculations employed the Schwinger multichannel method with pseudopotentials and were performed in the static-exchange and static-exchange plus polarization approximations. The cross sections were computed for impact energies up to 10 eV. We observed four resonances in the static-exchange calculations, and three when polarization effects were included. This result indicates that the low-lying resonance in the B1 symmetry of C2v group, observed in the static-exchange calculation, became a bound state when polarization was taken into account. Our calculations including polarization effects assigned the low-lying resonance located at 0.92 eV to the A2 symmetry and the other two resonances, located at 2.07 eV and 6 eV, to the B1 symmetry. These results compare well with the attachment energies obtained through electron transmission spectroscopy data and with dissociative electron attachment results for the NO2- sub-product, suggesting for the latter that the π* resonances mediate the dissociation process.

Passive compensation of laser-induced higher-order aberrations in high-power NIR optics.

We report a method for passive compensation of thermally induced focal shifts and higher-order aberrations of NIR laser processing optics. Theoretical considerations are made on the elimination of aberrations including polarization effects using a multi-stage compensation element with optical flats of both positive and negative dn/dT. A compensation layout is designed and optimized utilizing numerical simulations of thermo-optic effects. Based on these findings, optical elements for compensation of an F-Theta objective are manufactured. By means of wavefront measurements and beam caustic measurements the feasibility of simultaneous passive compensation of focal shifts and higher-order aberrations is demonstrated.

Electron collisions with F2CO molecules

In this paper we present elastic differential, integral, and momentum-transfer cross sections for electron collisions with carbonyl fluoride $({\mathrm{F}}_{2}\mathrm{CO})$ molecules for the incident electron's energy from 0.5 eV to 20 eV. The Schwinger multichannel method with pseudopotentials was employed to obtain the cross sections in the static-exchange and static-exchange plus polarization approximations. The present results were compared with the available data in the literature, in particular, with the results of Kaur, Mason, and Antony [Phys. Rev. A 92, 052702 (2015)] for the differential, total, and momentum-transfer cross sections. We have found a ${\ensuremath{\pi}}^{*}$ shape resonance centered at 2.6 eV in the ${B}_{1}$ symmetry and other resonance, in the ${B}_{2}$ symmetry, located at around 9.7 eV. A systematic study of the inclusion of polarization effects was performed in order to have a well balanced description of this negative-ion transient state. The effects of the long-range electric dipole potential were included by the Born closure scheme. Electronic structure calculations were also performed to help in the interpretation of the scattering results, and associate the transient states to the unoccupied orbitals.

Theoretical investigations of nonlinear optical properties of two crystalline acetamides structures including polarization effects of their environment

We determined the nonlinear optical properties of two organic crystals 2-(4-chlorophenyl)-N-(2-iodophenyl)acetamide and 2-(4-chlorophenyl)-N-(pyrazin-2-yl)acetamide, to understand their linear and nonlinear optical behavior in the static and dynamic cases. A new approach treating the supermolecule is employed in combination with an interactive electrostatic system in which the atoms of neighboring molecules are considered as point charges. The ab initio computational results of (hyper) polarizabilities are derived from an iterative process and confirm these crystals as good candidates for photonic devices, such as optical switches, modulators, pyrazoline derivatives and optical energy applications.

A wave-based model for cross-beam energy transfer in direct-drive inertial confinement fusion

Cross-beam energy transfer (CBET) is thought to be responsible for a 30% reduction in hydrodynamic coupling efficiency on OMEGA and up to 50% at the ignition scale for direct-drive (DD) implosions. These numbers are determined by ray-based models that have been developed and integrated within the radiation–hydrodynamics codes LILAC (1-D) and DRACO (2-D). However, ray-based modeling of CBET in an inhomogeneous plasma assumes a steady-state plasma response, does not include the effects of beam speckle, and treats ray caustics in an ad hoc manner. The validity of the modeling for ignition-scale implosions has not yet been determined. To address the physics shortcomings, which have important implications for DD inertial confinement fusion, a new wave-based model has been developed. It solves the time-enveloped Maxwell equations in three dimensions, including polarization effects, plasma inhomogeneity, and open-boundary conditions with the ability to prescribe beams incident at arbitrary angles. Beams can be made realistic with respect to laser speckle, polarization smoothing, and laser bandwidth. This, coupled to a linearized low-frequency plasma response that does not assume a steady state, represents the most-complete model of CBET to date.

Understanding the interfacial behavior of lysozyme on Au (111) surfaces with multiscale simulations

The understanding of the adsorption and interfacial behavior of proteins is crucial to the development of novel biosensors and biomaterials. By using bottom-up atomistic multiscale simulations, we study here the adsorption of lysozyme on Au(111) surfaces in an aqueous environment. Atomistic simulations are used to calculate the inhomogeneous polarization of the gold surface, which is induced by the protein adsorption, and by the presence of an interfacial layer of water molecules and monovalent salts. The corresponding potential of mean force between the protein and the gold surface including polarization effects is used in Langevin Dynamics simulations to study the time dependent behavior of proteins at finite concentration. These simulations display a rapid adsorption and formation of a first-layer of proteins at the interface. Proteins are initially adsorbed directly on the gold surface due to the strong protein-surface attractive interaction. A subsequent interfacial weak aggregation of proteins leading to multilayer build-up is also observed at long times.

Free Energy Contribution Analysis Using Response Kernel Approximation: Insights into the Acylation Reaction of a Beta-Lactamase.

A widely applicable free energy contribution analysis (FECA) method based on the quantum mechanical/molecular mechanical (QM/MM) approximation using response kernel approaches has been proposed to investigate the influences of environmental residues and/or atoms in the QM region on the free energy profile. This method can evaluate atomic contributions to the free energy along the reaction path including polarization effects on the QM region within a dramatically reduced computational time. The rate-limiting step in the deactivation of the β-lactam antibiotic cefalotin (CLS) by β-lactamase was studied using this method. The experimentally observed activation barrier was successfully reproduced by free energy perturbation calculations along the optimized reaction path that involved activation by the carboxylate moiety in CLS. It was found that the free energy profile in the QM region was slightly higher than the isolated energy and that two residues, Lys67 and Lys315, as well as water molecules deeply influenced the QM atoms associated with the bond alternation reaction in the acyl-enzyme intermediate. These facts suggested that the surrounding residues are favorable for the reactant complex and prevent the intermediate from being too stabilized to proceed to the following deacylation reaction. We have demonstrated that the free energy contribution analysis should be a useful method to investigate enzyme catalysis and to facilitate intelligent molecular design.

No-core configuration-interaction model for the isospin- and angular-momentum-projected states

[Background] Single-reference density functional theory is very successful in reproducing bulk nuclear properties like binding energies, radii, or quadrupole moments throughout the entire periodic table. Its extension to the multi-reference level allows for restoring symmetries and, in turn, for calculating transition rates. [Purpose] We propose a new no-core-configuration-interaction (NCCI) model treating properly isospin and rotational symmetries. The model is applicable to any nucleus irrespective of its mass and neutron- and proton-number parity. It properly includes polarization effects caused by an interplay between the long- and short-range forces acting in the atomic nucleus. [Methods] The method is based on solving the Hill-Wheeler-Griffin equation within a model space built of linearly-dependent states having good angular momentum and properly treated isobaric spin. The states are generated by means of the isospin and angular-momentum projection applied to a set of low-lying (multi)particle-(multi)hole deformed Slater determinants calculated using the self-consistent Skyrme-Hartree-Fock approach. [Results] The theory is applied to calculate energy spectra in N~Z nuclei that are relevant from the point of view of a study of superallowed Fermi beta-decays. In particular, a new set of the isospin-symmetry-breaking corrections to these decays is given. [Conclusions] It is demonstrated that the NCCI model is capable to capture main features of low-lying energy spectra in light and medium-mass nuclei using relatively small model space and without any local readjustment of its low-energy coupling constants. Its flexibility and a range of applicability makes it an interesting alternative to the conventional nuclear shell model.

On the internal quantum efficiency for InGaN/GaN light-emitting diodes grown on insulating substrates

The internal quantum efficiency (IQE) for InGaN/GaN light-emitting diodes (LEDs) grown on [0001] sapphire substrates is strongly affected by various factors including polarization effect in the InGaN/GaN multiple quantum wells (MQWs), insufficient electron and hole injections, low p-type GaN doping efficiency, carrier loss due to the Auger recombination, and current crowding effect especially for the hole current in the p-GaN region. In this work, the remedies taken by the scientific community to enhance the IQE are reviewed, compared and summarized. Meanwhile, this review also discusses alternative ways including polarization self-screening effect, polarization cooling, hole accelerator, and hole modulator. The structural solutions we propose in this work can better improve the device performance without increasing the processing difficulty significantly, and their effectiveness in improving the IQE is further supported by the numerical and experimental studies. For example, on the contrary to common belief, the polarizations in the [0001] oriented InGaN/GaN LEDs can be advantageously used to improve the device performance based on our designs.

Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning.

Molecular mechanics force fields, which are commonly used in biomolecular modeling and computer-aided drug design, typically treat nonbonded interactions using a limited library of empirical parameters that are developed for small molecules. This approach does not account for polarization in larger molecules or proteins, and the parametrization process is labor-intensive. Using linear-scaling density functional theory and atoms-in-molecule electron density partitioning, environment-specific charges and Lennard-Jones parameters are derived directly from quantum mechanical calculations for use in biomolecular modeling of organic and biomolecular systems. The proposed methods significantly reduce the number of empirical parameters needed to construct molecular mechanics force fields, naturally include polarization effects in charge and Lennard-Jones parameters, and scale well to systems comprised of thousands of atoms, including proteins. The feasibility and benefits of this approach are demonstrated by computing free energies of hydration, properties of pure liquids, and the relative binding free energies of indole and benzofuran to the L99A mutant of T4 lysozyme.

DFT-based polarizable force field for TiO2 and SiO2

TiO2 and SiO2 are materials with unique importance in materials science. They are often modelled using conventional force fields, but including polarization effects is compulsory for enhancing the accuracy of the simulations. Here we parameterize a force field for the two materials in the framework of the polarizable ion model. The parameterization is performed via a generalized force-fitting methodology using DFT calculations as reference data. We show that it is possible to generate a force field in which the same parameters are used for the oxide ion in both SiO2 and TiO2, and which is able to reproduce accurately the equilibrium structure of their various crystalline polymorphs, as well as glassy silica.

Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) via Water-Mediated Hydrogen Bonding.

Recently, we reported the differential impact of the monovalent cations Li(+), Na(+), K(+), and Rb(+) on DNA conformational properties. These were identified from variations in the calculated solution-state X-ray DNA spectra as a function of the ion type in solvation buffer in MD simulations using our recently developed polarizable force field based on the classical Drude oscillator. Changes in the DNA structure were found to mainly involve variations in the minor groove width. Because minor groove dimensions vary significantly in protein-DNA complexes and have been shown to play a critical role in both specific and nonspecific DNA readout, understanding the origins of the observed differential DNA modulation by the first-group monovalent ions is of great biological importance. In the present study, we show that the primary microscopic mechanism for the phenomenon is the formation of water-mediated hydrogen bonds between solvated cations located inside the minor groove and simultaneously to two DNA strands, a process whose intensity and impact on DNA structure depends on both the type of ion and the DNA sequence. Additionally, it is shown that the formation of such ion-DNA hydrogen bond complexes appreciably modulates the conformation of the backbone by increasing the population of the BII substate. Notably, the differential impact of the ions on DNA conformational behavior is only predicted by the Drude polarizable model for DNA with virtually no effect observed from MD simulations utilizing the additive CHARMM36 model. Analysis of dipole moments of the water shows the Drude SWM4 model to possess high sensitivity to changes in the local environment, which indicates the important role of electronic polarization in the salt-dependent conformational properties. This also suggests that inclusion of polarization effects is required to model even relatively simple biological systems, such as DNA, in various ionic solutions.

Effects of ocean particles on the upwelling radiance and polarized radiance in the atmosphere-ocean system

Based on a vector radiative transfer model of the atmosphere-ocean system, the influence of oceanic components on radiation processes, including polarization effects, was investigated in the wavelength region ranging from 0.380 to 0.865 μm. The components considered were phytoplankton, inorganic suspended material (sediment), and colored, dissolved organic matter. Due to their important roles in oceanic radiation processes, the sensitivity of the bidirectional reflectance to the rough ocean surface, represented by the wind velocity 10 m above the ocean surface, and aerosol, were taken into account. The results demonstrated that both radiance and polarized radiance just below the ocean surface were sensitive to the change of the concentrations of the considered components, while the dependence of polarized radiance on the observation geometry was more sensitive than radiance. Significant differences in the specular plane existed between the impacts of the phytoplankton and sediment on the degree of polarization just above the ocean surface at 670 nm. At the top of the atmosphere (TOA), polarization was relatively insensitive to changing concentrations of ocean particles at longer wavelengths. Furthermore, the radiance at the TOA in the solar plane was more sensitive to the aerosol optical thickness than wind velocity. In contrast, wind velocity strongly influenced the radiance at the TOA in the sun glint region, while the polarization degree showed less dependence in that region. Finally, a nonlinear optimal inversion method was proposed to simultaneously retrieve the aerosol and wind velocity using radiance measurement.

Modeling and analysis of polarization effects in Fourier domain mode-locked lasers.

We develop a theoretical model for Fourier domain mode-locked (FDML) lasers in a non-polarization-maintaining configuration, which is the most widely used type of FDML source. This theoretical approach is applied to analyze a widely wavelength-swept FDML setup, as used for picosecond pulse generation by temporal compression of the sweeps. We demonstrate that good agreement between simulation and experiment can only be obtained by including polarization effects due to fiber bending birefringence, polarization mode dispersion, and cross-phase modulation into the theoretical model. Notably, the polarization dynamics are shown to have a beneficial effect on the instantaneous linewidth, resulting in improved coherence and thus compressibility of the wavelength-swept FDML output.

A New Force Field of Formamide and the Effect of the Dielectric Constant on Miscibility

Current force fields underestimate significantly the dielectric constant of formamide at standard conditions. We present a derivation of an accurate potential for formamide, with a functional form based on the OPLS/AA force field. Our procedure follows the approach introduced by Salas et al. ( J. Chem. Theory Comput. 2015 , 11 , 683 - 693 ) that relies on ab initio calculations and molecular dynamics simulations. We consider several strategies to derive the atomic charges of formamide. We find that the inclusion of polarization effects in the quantum mechanical computations is essential to obtain reliable force fields. By varying the atomic charges and the Lennard-Jones parameters describing the dispersion interactions in the OPLS/AA force field, we derive an optimum set of parameters that provides accurate results for the dielectric constant, surface tension, and bulk density of liquid formamide in a wide range of thermodynamic states. We test the transferability of our parameters to investigate liquid/liquid mixtures. We have chosen as case study an equimolar mixture of formamide and hexan-2-one. This mixture involves two fluids with very different polar characteristics, namely, large differences in their dielectric constants and their performance as solvents. The new potential predicts a liquid/liquid phase separation, in good agreement with experimental data, and highlights the importance of the correct parametrization of the pure liquid phases to investigate liquid mixtures. Finally, we examine the microscopic origin of the observed inmiscibility between formamide and hexa-2-one.

Mixed-level optical simulations of light-emitting diodes based on a combination of rigorous electromagnetic solvers and Monte Carlo ray-tracing methods

Over the last two decades, extensive research has been done to improve light-emitting diodes (LEDs) designs. Increasingly complex designs have necessitated the use of computational simulations which have provided numerous insights for improving LED performance. Depending upon the focus of the design and the scale of the problem, simulations are carried out using rigorous electromagnetic (EM) wave optics-based techniques, such as finite-difference time-domain and rigorous coupled wave analysis, or through ray optics-based techniques such as Monte Carlo ray-tracing (RT). The former are typically used for modeling nanostructures on the LED die, and the latter for modeling encapsulating structures, die placement, back-reflection, and phosphor downconversion. This paper presents the use of a mixed-level simulation approach that unifies the use of EM wave-level and ray-level tools. This approach uses rigorous EM wave-based tools to characterize the nanostructured die and generates both a bidirectional scattering distribution function and a far-field angular intensity distribution. These characteristics are then incorporated into the RT simulator to obtain the overall performance. Such a mixed-level approach allows for comprehensive modeling of the optical characteristic of LEDs, including polarization effects, and can potentially lead to a more accurate performance than that from individual modeling tools alone.

CONSERT line-of-sight link budget simulator

In bistatic radar systems utilizing elliptical polarization on both the sending and receiving side, great care must be taken to correctly calculate the received power, as a mismatch in polarization may incur significant additional losses. In this paper, we present a method to simulate the link budget of the CONSERT instrument aboard the Rosetta mission, including polarization effects. The correctness of the simulation method is demonstrated by comparing with a state-of-the-art Method of Moments solver.The CONSERT instrument's components aboard the Philae lander and the Rosetta orbiter need to be synchronized before the actual sounding. This synchronization can only be performed in line-of-sight conditions. In order to maximize sounding time for the propagation through 67P's core, the synchronization should happen as close to the approximate point of occultation as possible. A statistical analysis is presented to determine the probability of sufficient received power for the synchronization regarding uncertainties in the orbiter's pointing accuracy.