Simulated pathogenic conformational switch regions matched well with the biochemical findings

Pathogenic conformational conversion is a general causation of many disease, such as transmissible spon- giform encephalopathy (TSE) caused by misfolding of prion, sickle cell anemia, and etc. In such structural changes, misfolding occurs in regions important for the stability of native structure firstly. This destabi- lizes the normal conformation and leads to subsequent errors in folding pathway. Sites involved in the first stage can be deemed switch regions of the protein, and are vital for conformational conversion. Namely it could be a switch of disease at residue level. Here we report an algorithm that can identify such sites computationally with an accuracy of 93%, by calculating the probability of the native structure of a short segment jumping to a mistake one. Knowledge of such switch sites could be used to target clinical therapy, study physiological and pathologic mechanism of protein, and etc.

Splitting the fast and slow motions in molecular dynamics simulations based on the change of cold potential well bottom

Abstract. The atomic motion is coupled by the fast and slow components due to the high frequency vibration of atoms and the low frequency deformation of atomic lattice, respectively. A two-step approximate method was presented to determine the atomic slow motion. The first step is based on the change of the location of the cold potential well bottom and the second step is based on the average of the appropriate slow velocities of the surrounding atoms. The simple tensions of one-dimensional atoms and two-dimensional atoms were performed with the full molecular dynamics simulations. The conjugate gradient method was employed to determine the corresponding location of cold potential well bottom. Results show that our two-step approximate method is appropriate to determine the atomic slow motion under the low strain rate loading. This splitting method may be helpful to develop more efficient molecular modeling methods and simulations pertinent to realistic loading conditions of materials.

Part 1: Longitudinal static and dynamic effects in semiconductor lasers. Part II: Spectral characteristics of passively mode-locked quantum well lasers

In the first part of this thesis a study of the effect of the longitudinal distribution of optical intensity and electron density on the static and dynamic behavior of semiconductor lasers is performed. A static model for above threshold operation of a single mode laser, consisting of multiple active and passive sections, is developed by calculating the longitudinal optical intensity distribution and electron density distribution in a self-consistent manner. Feedback from an index and gain Bragg grating is included, as well as feedback from discrete reflections at interfaces and facets. Longitudinal spatial holeburning is analyzed by including the dependence of the gain and the refractive index on the electron density. The mechanisms of spatial holeburning in quarter wave shifted DFB lasers are analyzed. A new laser structure with a uniform optical intensity distribution is introduced and an implementation is simulated, resulting in a large reduction of the longitudinal spatial holeburning effect.

A dynamic small-signal model is then developed by including the optical intensity and electron density distribution, as well as the dependence of the grating coupling coefficients on the electron density. Expressions are derived for the intensity and frequency noise spectrum, the spontaneous emission rate into the lasing mode, the linewidth enhancement factor, and the AM and FM modulation response. Different chirp components are identified in the FM response, and a new adiabatic chirp component is discovered. This new adiabatic chirp component is caused by the nonuniform longitudinal distributions, and is found to dominate at low frequencies. Distributed feedback lasers with partial gain coupling are analyzed, and it is shown how the dependence of the grating coupling coefficients on the electron density can result in an enhancement of the differential gain with an associated enhancement in modulation bandwidth and a reduction in chirp.

In the second part, spectral characteristics of passively mode-locked two-section multiple quantum well laser coupled to an external cavity are studied. Broad-band wavelength tuning using an external grating is demonstrated for the first time in passively mode-locked semiconductor lasers. A record tuning range of 26 nm is measured, with pulse widths of typically a few picosecond and time-bandwidth products of more than 10 times the transform limit. It is then demonstrated that these large time-bandwidth products are due to a strong linear upchirp, by performing pulse compression by a factor of 15 to a record pulse widths as low 320 fs.

A model for pulse propagation through a saturable medium with self-phase-modulation, due to the a-parameter, is developed for quantum well material, including the frequency dependence of the gain medium. This model is used to simulate two-section devices coupled to an external cavity. When no self-phase-modulation is present, it is found that the pulses are asymmetric with a sharper rising edge, that the pulse tails have an exponential behavior, and that the transform limit is 0.3. Inclusion of self-phase-modulation results in a linear upchirp imprinted on the pulse after each round-trip. This linear upchirp is due to a combination of self-phase-modulation in a gain section and absorption of the leading edge of the pulse in the saturable absorber.

Enhancing Kerr nonlinearity in an asymmetric double quantum well via Fano interference

We investigate the enhancement of Kerr nonlinearity in an asymmetric GaAs double quantum well via Fano interference, which is caused by tunneling from the excited subband to the continuum. In our structure, owing to Fano interference, the Kerr nonlinearity can be enhanced by appropriately choosing the values of the detunings and the intensity of the pump field, while cancel the linear and nonlinear absorptions.

Third harmonic enhancement due to Fano interference in semiconductor quantum well

We investigate the emission spectra of the semiconductor quantum well for few-cycle and sub-cycle pulse exciting. We find that Fano interference may induce third harmonic enhancement. Third harmonic enhancement varies with the magnitude and duration of the incident pulse, and may be enhanced by approximately one order of magnitude for the low intensity region of the sub-cycle incident pulse exciting.

Carrier-envelope phase control of carrier-wave Rabi flopping in asymmetric semiparabolic quantum well

We investigate the carrier-wave Rabi flopping effects in an asymmetric semiparabolic semiconductor quantum well (QW) with few-cycle pulse. It is found that higher spectral components of few-cycle ultrashort pulses in the semiparabolic QW depend crucially on the carrier-envelope phase (CEP) of the few-cycle ultrashort pulses: continuum and distinct peaks can be achieved by controlling the CEP. Our results demonstrate that by adjusting the CEP of few-cycle ultrashort pulses, the intersubband dynamics in the asymmetric semiparabolic QW can be controlled in an ultrashort timescale with moderate laser intensity. (c) 2008 Optical Society of America.

Tunneling-induced large cross-phase modulation in an asymmetric quantum well

We propose an asymmetric double AlGaAs/GaAs quantum well structure with a common continuum to generate a large cross-phase modulation (XPM). It is found, owing to resonant tunneling, that a large XPM can be achieved with vanishing linear and two-photon absorptions. (c) 2007 Optical Society of America.

Metallic thin fi lms on stepped surfaces: lateral scattering of quantum well states

Quantum well states of Ag films grown on stepped Au(111) surfaces are shown to undergo lateral scattering, in analogy with surface states of vicinal Ag(111). Applying angle resolved photoemission spectroscopy we observe quantum well bands with zone-folding and gap openings driven by surface/interface step lattice scattering. Experiments performed on a curved Au(111) substrate allow us to determine a subtle terrace-size effect, i.e., a fine step-density-dependent upward shift of quantum well bands. This energy shift is explained as mainly due to the periodically stepped crystal potential offset at the interface side of the film. Finally, the surface state of the stepped Ag film is analyzed with both photoemission and scanning tunneling microscopy. We observe that the stepped film interface also affects the surface state energy, which exhibits a larger terrace-size effect compared to surface states of bulk vicinal Ag(111) crystals

Air Quality and Europeans' Subjective Well-being

[EN]Happiness economics deals with self-reported subjective well-being, or life satisfaction, and its relationship to a wide variety of other variables. On the study of these other factors, this line of research has helped demonstrate that higher levels of environmental quality increase people’s subjective well-being. This paper focuses on analyzing the relationship between subjective well-being and air quality. On the one hand, the life satisfaction approach to environmental valuation is cautiously described, and on the other hand, the method is implemented in an empirical analysis that seeks to assess how an increase in the level of air pollution at a regional level affects individual-level subjective well-being in Europe. We use a dataset that merges the third wave of the European Social Survey (ESS) with a dataset that includes regional air pollution (including CO, PM10, NO2, SO2 and Benzene) and other regional variables. We find a robust negative impact for CO, a positive impact for SO2, and no conclusive evidence of any effect on subjective well-being for the remaining three pollutants.

Self-reported sitting time and physical activity: interactive associations with mental well-being and productivity in office employees

Background: Little is known about how sitting time, alone or in combination with markers of physical activity (PA), influences mental well-being and work productivity. Given the need to develop workplace PA interventions that target employees' health related efficiency outcomes; this study examined the associations between self-reported sitting time, PA, mental well-being and work productivity in office employees. Methods: Descriptive cross-sectional study. Spanish university office employees (n = 557) completed a survey measuring socio-demographics, total and domain specific (work and travel) self-reported sitting time, PA (International Physical Activity Questionnaire short version), mental well-being (Warwick-Edinburg Mental Well-Being Scale) and work productivity (Work Limitations Questionnaire). Multivariate linear regression analyses determined associations between the main variables adjusted for gender, age, body mass index and occupation. PA levels (low, moderate and high) were introduced into the model to examine interactive associations. Results: Higher volumes of PA were related to higher mental well-being, work productivity and spending less time sitting at work, throughout the working day and travelling during the week, including the weekends (p < 0.05). Greater levels of sitting during weekends was associated with lower mental well-being (p < 0.05). Similarly, more sitting while travelling at weekends was linked to lower work productivity (p < 0.05). In highly active employees, higher sitting times on work days and occupational sitting were associated with decreased mental well-being (p < 0.05). Higher sitting times while travelling on weekend days was also linked to lower work productivity in the highly active (p < 0.05). No significant associations were observed in low active employees. Conclusions: Employees' PA levels exerts different influences on the associations between sitting time, mental well-being and work productivity. The specific associations and the broad sweep of evidence in the current study suggest that workplace PA strategies to improve the mental well-being and productivity of all employees should focus on reducing sitting time alongside efforts to increase PA.