Husin Alatas

Anharmonic oscillation effect on the Davydov-Scott monomer in a thermal bath

The dynamics of Davydov-Scott monomer in a thermal bath with higher order amide-sites displacement leads to anharmonic oscillation effect is investigated using full-quantum approach and the Lindblad formulation of master equation. The specific heat is calculated based on the thermodynamic partition function using the path integral method. The temperature dependence of the specific heat is studied. In the model the specific heat anomaly as pointed out in recent works by Ingold [Phys. Rev. E 79, 061105 (2009)] is also observed. However, it is found that the anomaly occurs at high-temperature region, and the anharmonic oscillation restores the positivity of specific heat.

The thermal denaturation of the Peyrard?Bishop model with an external potential

The impact of various types of external potentials to the Peyrard-Bishop DNA denaturation is investigated through statistical mechanics approach. The partition function is obtained using transfer integral method, and further the stretching of hydrogen bond is calculated using time independent perturbation method. It is shown that all types of external potentials accelerate the denaturation processes at lower temperature. In particular, it is argued that the Gaussian potential with infinitesimal width reproduces a constant force at one end of DNA sequence as already done in some previous works.

Dynamics of DNA breathing in the Peyrard–Bishop model with damping and external force

Abstract The impact of the damping effect and external forces on DNA breathing is investigated within the Peyrard–Bishop model. In the continuum limit, the dynamics of the breathing of DNA is described by the forced-damped nonlinear Schrodinger equation and studied by means of the variational method. The analytical solutions are obtained for special cases. It is shown that the breather propagation is decelerated in the presence of a damping factor without the external force, while the envelope velocity and the amplitude increase significantly with the presence of external force. It is particularly found that the higher harmonic terms are enhanced when the periodic force is applied. It is finally argued that the external force accelerates the DNA breathing.

Single-Frequency Refractive Index Sensor Based on a Finite One-Dimensional Photonic Crystals with Two Defects

A numerical analysis by means of transfer matrix method has been performed on finite one-dimensional photonic crystals consisting of two-layer repeated cells and two non-identical defect cells for the normal incident transverse electric (TE) wave. The study reveals a remarkable new feature showing that the variation of a photonic pass-band transmittance can be induced by varying the refractive index of one of the defect layer at practically the same peak frequency, which offers the potential application for single frequency sensing. The result further demonstrates the flexibility of tailoring the system parameters for application in the desired range of refractive index at the required sensitivity. It is also shown that the photonic pass-band (PPB) peak transmittance is generally less than unity in the index range considered, except for the case with the grating segment lengths (M,N,L) satisfying the condition N=M+L. This peculiar feature is explained qualitatively in this work.

Real-time optical sensor based on one dimensional photonic crystals with defects

A previous theoretical study of a finite one-dimensional photonic crystal composed of 12 unit cells with two defects had shown the existence of Photonic Pass Band (PPB) inside the Stop Band, which was suggested as a useful refractive index sensor due to the sensitive variation of PPB with respect to the change of refractive index of defect layer material. We report in this presentation our successful fabrication of a prototype of this system by means of electron beam evaporation equipment in a sample chamber at pressure of 10−3 Pa with BK-7 glass substrate at temperature 573 K. Each of the photonic cells is composed of a high index layer of OS-5 with refractive index of n =3D2.10, and an equal thickness low index layer of MgF2 with n =3D 1.38. In the first defect cell, the high index layer has twice the thickness of the other layers with the low index layer left unchanged, while in the second, defect cell is separated by 6 unit cells, and the first layer is void to be filled with the sample solution. The device was used for measuring the refractive index of sugar solution with concentration range of 20–500 g/L in the real time mode. The result was found to achieve determination coefficient more than 90%. Further measurement performed has demonstrated a result in good agreement with theoretical prediction reported previously.

Analytic study of stationary solitons in deep nonlinear Bragg grating

A study of nonlinear Bragg grating has been carried out using a modified scheme of approximation originally proposed by Iizuka and de Sterke. A complete classification of the solitonic solutions in the system was given. We further demonstrated in this work the existence of in-gap dark and antidark soliton, in addition to the out-gap solutions reported previously. We also found at the boundaries in the bifurcation diagram, the large-amplitude out-gap antidark soliton and broad in-gap dark soliton.

Fabrication and characterization of NO 2 gas sensor based on one dimensional photonic crystal for measurement of air pollution index

We have fabricated the corresponding photonic crystal (PC) structure by means of electron beam evaporation in a sample chamber at a pressure of 10−3Pa with BK-7 glass substrate at temperatures of 573K. This PC device is applied as a sensor to detect the concentration of NO2 gas dissolved in specific reagent Griess Saltzmann. From spectroscopic measurement it is found that the absorption spectral of the NO2 gas to be in the range of light source wavelength 500–550 nm. Based on this fact, we set up the PCs to admit a photonic pass band (PPB) at a wavelength of 550 nm. To enhance the performance, the device is designed to work on the basis of both absorption and PPB variation phenomena. The experimental results show that the response of the device correlates linearly with the concentration of dissolved NO2 gas and exhibits high sensitivity with coefficient determination of 99%. This sensor is potential to apply in an air pollution index measurement system

Statistical mechanics of Davydov-Scott's protein model in thermal bath

The thermodynamic properties of Davydov-Scott monomer contacting with thermal bath is investigated using Lindblad open quantum system formalism. The Lindblad equation is investigated through path integral method. It is found that the environmental effects contribute destructively to the specific heat, and large interaction between amide-I and amide-site is not preferred for a stable Davydov-Scott monomer.

Performance changes of a grated waveguide at resonance wavelengths next to its band-edges due to modified edge sections

An efficient numerical scheme developed on the basis of Green’s function method is applied to the investigation of structural effects on the performance of planar grated waveguide at the first resonance wavelengths next to the band-edges. Restricting ourselves to the transverse-electric waves, this study is focused on the effects induced by variations of the grating cell number and the depths of its four outer grooves on both sides. The different patterns of groove depth gradation or apodization considered in this study are all characterized by decreasing depth toward the ends while retaining the longitudinal grating symmetry. The effects of the modifications are expressed in terms of changes in the modal transmittance, reflectance, and out-of-plane scattering loss as well as the group velocity and resonant field enhancement. The most favorable result characterized by 15% transmittance enhancement and 85% loss reduction is achieved for the case with the most gradual changes in the groove depth. It is further shown that, for the investigated range of parameters, both the group velocity and field enhancement can best be improved by increasing the length of the uniform grating, without introducing any modification.

OPTICAL SENSING AND SWITCHING DEVICE BASED ON A FINITE DEEP NONLINEAR BRAGG GRATING WITH A MIRROR

We investigate the detailed transition of the dark to antidark soliton-like states in a system of finite deep nonlinear Bragg grating equipped with a movable metallic mirror and illuminated by a continuous laser source. As reported previously, the transition can be induced mechanically by moving the mirror as well as optically by changing the light source intensity.