Calculations of the free energy of interaction of the c-Fos−c-Jun coiled coil: Effects of the solvation model and the inclusion of polarization effects

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein−protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson−Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos−c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos−c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.

Beam polarization effects in the radiative production of lightest neutralinos in e(+)e(-) collisions in supersymmetric grand unified models

We study the production of the lightest neutralinos in the process e(+)e(-) -> chi(0)(1)chi(0)(1)gamma in supersymmetric grand unified models for the International Linear Collider energies with longitudinally polarized beams. We consider cases where the standard model gauge group is unified into the grand unified gauge groups SU(5), or SO(10). We have carried out a comprehensive study of this process in the SU(5) and SO(10) grand unified theories which includes the QED radiative corrections. We compare and contrast the dependence of the signal cross section on the grand unified gauge group, and on the different representations of the grand unified gauge group, when the electron and positron beams are longitudinally polarized. To assess the feasibility of experimentally observing the radiative production process, we have also considered in detail the background to this process coming from the radiative neutrino production process e(+)e(-)-> nu(nu) over bar gamma with longitudinally polarized electron and positron beams. In addition we have also considered the supersymmetric background coming from the radiative production of scalar neutrinos in the process e(+)e(-) -> (nu) over tilde(nu) over tilde*gamma with longitudinally polarized beams. The process can be a major background to the radiative production of neutralinos when the scalar neutrinos decay invisibly.

Polarization effects simulation of AlGaN/GaN heterojunction by using a symbolistic delta-doping layer

Polarization effects in AlGaN/GaN heterojunction are simulated based on a traditional semiconductor device simulator. A delta doping layer is purposely inserted at the interface of the heterojunction in the simulation, so the ionized donors or acceptors can represent polarization-induced positive or negative fixed charges. The free electron distribution of single AlGaN/GaN heterostructures with Ga-face and N-face growth is compared, and the results of the simulation show that carrier confinement takes place only in the former structure. The dependence of sheet density of free electrons at the interface of Ga-face growth AlGaN/GaN on Al composition and the thickness of AlGaN is also investigated. The consistency of simulation results with the experiments and calculations reported by other researchers shows that this method can be effectively used to deal with the polarization effects in the simulation of GaN-based heterojunction devices. (C) 2004 Elsevier Ltd. All rights reserved.

Simulation of polarization effects in AlGaN/GaN heterojunction

A method for introducing polarization effects in the simulation of GaN-based heterojunction devices is proposed. A delta doping layer is inserted at the interface of heterojunction and the ionized donors or acceptors act as polarization induced fixed charges. Thus polarization effects can be taken into account in a traditional device simulator. Ga-face and N-face single AlGaN/GaN heterostructures are simulated, and the simulation results show that carrier confinement takes place only in the former structure while not in the latter one. The sheet density of free electrons at the interface of Ga-face AlGaN/GaN increases with the Al composition and the thickness of AlGaN. The consistence of simulation results with the experiments and calculations reported elsewhere shows that this method can effectively introduce polarization effects in the simulation of GaN-based heterojunction devices.

Theory of elasticity and electric polarization effects in the group-III nitrides

In this work, the properties of strained tetrahedrally bonded materials are explored theoretically, with special focus on group-III nitrides. In order to do so, a multiscale approach is taken: accurate quantitative calculations of material properties are carried out in a quantum first-principles frame, for small systems. These properties are then extrapolated and empirical methods are employed to make predictions for larger systems, such as alloys or nanostructures. We focus our attention on elasticity and electric polarization in semiconductors. These quantities serve as input for the calculation of the optoelectronic properties of these systems. Regarding the methods employed, our first-principles calculations use highly- accurate density functional theory (DFT) within both standard Kohn-Sham and generalized (hybrid functional) Kohn-Sham approaches. We have developed our own empirical methods, including valence force field (VFF) and a point-dipole model for the calculation of local polarization and local polarization potential. Our local polarization model gives insight for the first time to local fluctuations of the electric polarization at an atomistic level. At the continuum level, we have studied composition-engineering optimization of nitride nanostructures for built-in electrostatic field reduction, and have developed a highly efficient hybrid analytical-numerical staggered-grid computational implementation of continuum elasticity theory, that is used to treat larger systems, such as quantum dots.

Polarization effects in fiber-optic communication systems

In this thesis we perform a detailed analysis of the state of polarization (SOP) of light scattering process using a concatenation of ber-coil based polarization controllers (PCs). We propose a polarization-mode dispersion (PMD) emulator, built through the concatenation of bercoil based PCs and polarization-maintaining bers (PMFs), capable of generate accurate rst- and second-order PMD statistics. We analyze the co-propagation of two optical waves inside a highbirefringence ber. The evolution along the ber of the relative SOP between the two signals is modeled by the de nition of the degree of co-polarization parameter. We validate the model for the degree of co-polarization experimentally, exploring the polarization dependence of the four-wave mixing e ect into a ber with high birefringence. We also study the interaction between signal and noise mediated by Kerr e ect in optical bers. A model accurately describing ampli ed spontaneous emission noise in systems with distributed Raman gain is derived. We show that the noise statistics depends on the propagation distance and on the signal power, and that for distances longer than 120 km and signal powers higher than 6 mW it deviates signi catively from the Gaussian distribution. We explore the all-optical polarization control process based on the stimulated Raman scattering e ect. Mapping parameters like the degree of polarization (DOP), we show that the preferred ampli cation of one particular polarization component of the signal allows a polarization pulling over a wavelength range of 60 nm. The e ciency of the process is higher close to the maximum Raman gain wavelength, where the DOP is roughly constant for a wavelength range of 15 nm. Finally, we study the polarization control in quantum key distribution (QKD) systems with polarization encoding. A model for the quantum bit error rate estimation in QKD systems with time-division multiplexing and wavelength-division multiplexing based polarization control schemes is derived.

Pairing with polarization effects in low-density neutron matter

We study the properties of the 1S0 pairing gap in low-density neutron matter. Different corrections to the lowest-order scattering length approximation are explored, resulting in a strong suppression with respect to the BCS result.

Finite size effects on the electrical properties of sol–gel synthesized CoFe2O4 powders: deviation from Maxwell–Wagner theory and evidence of surface polarization effects

Fine particles of cobalt ferrite were synthesized by the sol–gel method. Subsequent heat treatment at different temperatures yielded cobalt ferrites having different grain sizes. X-ray diffraction studies were carried out to elucidate the structure of all the samples. Dielectric permittivity and ac conductivity of all the samples were evaluated as a function of frequency, temperature and grain size. The variation of permittivity and ac conductivity with frequency reveals that the dispersion is due to Maxwell–Wagner type interfacial polarization in general, with a noted variation from the expected behaviour for the cold synthesized samples. High permittivity and conductivity for small grains were explained on the basis of the correlated barrier-hopping model

VACUUM POLARIZATION EFFECTS ON QUASINORMAL MODES IN ELECTRICALLY CHARGED BLACK HOLE SPACE-TIMES

We investigate the influence of vacuum polarization of quantum massive fields on the scalar sector of quasinormal modes in spherically symmetric black holes. We consider the evolution of a massless scalar field on the space-time corresponding to a charged semiclassical black hole, consisting of the quantum-corrected geometry of a Reissner-Nordstrom black hole dressed by a quantum massive scalar field in the large mass limit. Using a sixth order WKB approach we find a shift in the quasinormal mode frequencies due to vacuum polarization.

Spin-polarization effects in homogeneous and non-homogeneous diluted magnetic semiconductor heterostructures

Spin polarization is a key characteristic in developing spintronic devices. Diluted magnetic heterostructures (DMH), where subsequent layers of conventional and diluted magnetic semiconductors (DMS) are alternate, are one of the possible ways to obtain it. Si being the basis of modern electronics, Si or other group-IV DMH can be used to build spintronic devices directly integrated with conventional ones. In this work we study the physical properties and the spin-polarization effects of p-type DMH based in group-IV semiconductors (Si, Ge, SiGe, and SiC), by performing self-consistent (k) over right arrow . (p) over right arrow calculations in the local spin density approximation. We show that high spin polarization can be maintained in these structures below certain values of the carrier concentrations. Full spin polarization is attained in the low carrier concentration regime for carrier concentrations in the DMS layer up to similar to 2.0 x 10(19) cm(-3) for Si and up to similar to 6.0 x 10(19) cm(-3) for SiC. Partial, but still important spin polarization can be achieved for all studied group-IV DMH, with the exception of Ge for carrier concentrations up to 6.0 x 10(19) cm(-3). The role played by the effective masses and the energy splitting of the spin-orbit split-off hole bands is also discussed throughout the paper.

Vacuum polarization effects in hyperon-rich dense matter - a nonperturbative treatment

We derive the equation of state (EOS) for electrically charged neutral dense matter using the quantum hadrodynamics (QHD) model. This is carried out in a non-perturbative manner including quantum corrections for baryons through a realignment of vacuum with baryon-antibaryon condensates. This yields the results of relativistic Hartree approximation of summing over baryonic tadpole diagrams. The quantum corrections from the scalar meson is also taken into account in a similar way. This leads to a softening of the EOS for the hyperonic matter. The formalism also allows Lis to make a self-consistent calculation of the in-medium sigma meson mass. The effects of such quantum corrections on the composition of charged neutral dense matter is considered. The effect of the resulting EOS on the structure of neutron stars is also studied.

Electrostatic potentials and polarization effects in proton-molecule interactions by means of multipoles from the quantum theory of atoms in molecules

Some atomic multipoles (charges, dipoles and quadrupoles) from the Quantum Theory of Atoms in Molecules (QTAIM) and CHELPG charges are used to investigate interactions between a proton and a molecule (F2, Cl2, BF, AlF, BeO, MgO, LiH, H2CO, NH3, PH3, BF3, and CO2). Calculations were done at the B3LYP/6-311G(3d,3p) level. The main aspect of this work is the investigation of polarization effects over electrostatic potentials and atomic multipoles along a medium to long range of interaction distances. Large electronic charge fluxes and polarization changes are induced by a proton mainly when this positive particle approaches the least electronegative atom of diatomic heteronuclear molecules. The search for simple equations to describe polarization on electrostatic potentials from QTAIM quantities resulted in linear relations with r-4 (r is the interaction distance) for many cases. Moreover, the contribution from atomic dipoles to these potentials is usually the most affected contribution by polarization what reinforces the need for these dipoles to a minimal description of purely electrostatic interactions. Finally, CHELPG charges provide a description of polarization effects on electrostatic potentials that is in disagreement with physical arguments for certain of these molecules. (c) 2012 Wiley Periodicals, Inc.

Polarization effects in polymer FBGs:study and use for transverse force sensing

Bragg gratings photo-inscribed in polymer optical fibers (POFs) are more sensitive to temperature and pressure than their silica counterparts, because of their larger thermo-optic coefficient and smaller Young's modulus. Polymer optical fiber Bragg gratings (POFBGs) are most often photo-written in poly(methylmethacrylate) (PMMA) based materials using a continuous-wave 325 nm HeCd laser. In this work, we present the first study about birefringence effects in POFBGs manufactured in different types of fiber. To achieve this, highly reflective (> 90%) gratings were produced with the phase mask technique. Their spectral response was then monitored in transmission with polarized light. Polarization dependent loss (PDL) and differential group delay (DGD) were computed from the Jones matrix eigenanalysis using an optical vector analyzer. Maximum values exceeding several dB and a few picoseconds were obtained for the PDL and DGD, respectively. An inverse scattering technique applied to the experimental data provided an estimate of the photo-induced birefringence value arising from the side fabrication process. The response to lateral force was finally investigated for various incident directions using the PDL response of FBGs manufactured in step-index POFs. As the force induced birefringence adds to the photo-induced one, a force dependent evolution of the PDL maximum value was noticed, with a good temperature-insensitivity.