Investigation of the influence on conformational transition of DNA induced by cationic lipid vesicles

Recent studies have focused on the structural features of DNA-lipid assemblies. In this paper we take nile blue A (NBA) as a probe molecule to study the influence of the conformational transition of DNA induced by didodecyldimethylammonium bromide (DDAB) cationic vesicles to the interaction between DNA and the probe molecules. We find that upon binding to DNA, a secondary conformational transition of DNA induced by the cationic liposome from the native B-form to the C-form resulted in the change of binding modes of NBA to DNA and different complexes are formed between DNA, DDAB and NBA.

Molecular dynamics study on the phase diagrams of linear and branched chain molecules

The particle transfer molecular dynamics is used to study the phase equilibria of linear and branched chain molecules. The scaling of the critical temperature versus chain length is obtained and the critical densities are found to decrease with increasing chain length, which are in agreement with the results of experiment and theory. The phase diagrams of the linear and the branched chain molecules nearly overlap with each other. Moreover, the radial distribution functions of linear and branched chain molecules in gas phase are very similar, but in the liquid phase, they are different for different kinds of chains.

Manipulations of atoms and molecules by scanning probe microscopyk

Scanning probe microscopy (SPM), including scanning tunneling microscopy (STM) and atomic force microscopy (AFM), has become a powerful tool in building nanoscale structures required by modern industry. In this article, the use of SPM for the manipulation of atoms and molecules for patterning nanostructures for opt-electronic and biomedical applications is reviewed. The principles and procedures of manipulation using STM and AFM-based technologies are presented with an emphasis on their ability to create a wide variety of nanostructures for different applications. The interaction among the atoms/molecules, surface, and tip are discussed. The approaches for positioning the atom/molecule from and to the desired locations and for precisely controlling its movement are elaborated for each specific manipulation technique. As an AFM-based technique, the dip-pen nanolithography is also included. Finally, concluding remarks on technological improvement and future research is provided.

Measuring Binding Kinetics Of Surface-Bound Molecules Using The Surface Plasmon Resonance Technique

Surface plasmon resonance (SPR) technology and the Biacore biosensor have been widely used to measure the kinetics of biomolecular interactions in the fluid phase. In the past decade, the assay was further extended to measure reaction kinetics when two counterpart molecules are anchored on apposed surfaces. However, the cell binding kinetics has not been well quantified. Here we report development of a cellular kinetic model, combined with experimental procedures for cell binding kinetic measurements, to predict kinetic rates per cell. Human red blood cells coated with bovine serum albumin and anti-BSA monoclonal antibodies (mAbs) immobilized on the chip were used to conduct the measurements. Sensor-grams for BSA-coated RBC binding onto and debinding from the anti-BSA mAb-immobilized chip were obtained using a commercial Biacore 3000 biosensor, and analyzed with the cellular kinetic model developed. Not only did the model fit the data well, but it also predicted cellular on and off-rates as well as binding affinities from curve fitting. The dependence of flow duration, flow rate, and site density of BSA on binding kinetics was tested systematically, which further validated the feasibility and reliability of the new approach. Crown copyright (c) 2008 Published by Elsevier Inc. All rights reserved.

Possibility of lifetime measurement in a flowing medium with phase fluorometry

The possibility of lifetime measurement in a flowing medium with phase fluorometry is investigated theoretically. A 3-D time dependent partial differential equation of the number density of atoms (or molecules) in the upper level of the fluorescence transition is solved analytically, taking flow, diffusion, optical excitation, decay, Doppler shift, and thickness of the excitation light sheet into account. An analytical expression of the intensity of the fluorescence signal in the flowing medium is deduced. Conditions are given, in which the principle of lifetime measurement with phase fluorometry in the static sample cell can be used in a flowing medium.

The kinetic-theory for dilute solid liquid 2-phase flow

On the basis of a brief review of the continuum theory for macroscopic descriptions and the kinetic theory for microscopic descriptions in solid/liquid two-phase flows, some suggestions are presented, i.e. the solid phase may be described by the Boltzmann equation and the liquid phase still be described by conservation laws in the continuum theory. Among them the action force on the particles by the liquid fluid is a coupling factor which connects the phases. For dilute steady solid/liquid two-phase flows, the particle velocity distribution function can be derived by analogy with the procedures in the kinetic theory of gas molecules for the equilibrium state instead of being assumed, as previous investigators did. This done, more detailed information, such as the velocity probability density distribution, mean velocity distribution and fluctuating intensity etc. can be obtained directly from the particle velocity distribution function or from its integration. Experiments have been performed for dilute solid/liquid two-phase flow in a 4 x 6 cm2 sized circulating square pipe system by means of laser Doppler anemometry so that the theories can be examined. The comparisons show that the theories agree very well with all the measured data.

Group velocity of probe light pulse in an open lambda system

The group velocity of the probe light pulse (GVPLP) propagating through an open Lambda-type atomic system with a spontaneously generated coherence is investigated when the weak probe and strong driving light fields have different frequencies. It is found that adjusting the detuning or Rabi frequency of the probe light field can realize switching of the GVPLP from subluminal to superluminal. Changing the relative phase between the probe and driving light. elds or atomic exit and injection rates can lead to GVPLP varying in a wider range, but cannot induce transformation of the property of the GVPLP. The absolute value of the GVPLP always increases with Rabi frequency of the driving light field increasing. For subluminal and superluminal propagation, the system always exhibits the probe absorption, and GVPLP is mainly determined by the slope of the steep dispersion.

Phase-type quantum-dot-array diffraction grating

A novel phase-type quantum-dot-array diffraction grating (QDADG) is reported. In contrast to an earlier amplitude-type QDADG [C. Wang , Rev. Sci. Instrum. 78, 053503 (2007)], the new phase-type QDADG would remove the zeroth order diffraction at some certain wavelength, as well as suppressing the higher-order diffractions. In this paper, the basic concept, the fabrication, the calibration techniques, and the calibration results are presented. Such a grating can be applied in the research fields of beam splitting, laser probe diagnostics, and so on.

Phase control of switching from positive to negative index material in a four-level atomic system

Electric and magnetic responses of the medium to the probe field are analysed in a four-level loop atomic system by taking into account the relative phase of the applied fields. An interesting phenomenon is found: under suitable conditions, a change of the refractive index from positive to negative can occur by modulating the relative phase of the applied fields. Then the medium can be switched from a positive index material to a negative index material in our scheme. In addition, a negative index material can be realized in different frequency regions by adjusting the relative phase. It may give us a convenient way to obtain the desired material with positive or negative index.

Photoelectron angular distributions of molecules in bichromatic laser fields of circular polarization

Photoelectron angular distributions (PADs) from above-threshold ionization of O-2 and N-2 molecules irradiated by a bichromatic laser field of circular polarization are Studied. The bichromatic laser field is specially modulated such that it can be used to mimic a sequence of one-cycle laser pulses. The PADs are greatly affected by the molecular alignment, the symmetry of the initial electronic distribution, and the carrier-envelope phase of the laser pulses. Generally, the PADs do not show any symmetry, and become symmetric about an axis only when the symmetric axis of laser field coincides with the symmetric axis of molecules. This study shows that the few-cycle laser pulses call be used to steer the photoelectrons and perform the selective ionization of molecules. (C) 2008 Elsevier B.V. All rights reserved.

Phase control of gain and dispersion in an open lambda-type inversionless lasing system

The control role of the relative phase between the probe and driving fields on the gain and dispersion in an open Lambda-type inversionless lasing system with spontaneously generated coherence (SGC) is investigated. It is shown that the inversionless gain and dispersion are quite sensitive to variation in the relative phase; by adjusting the value of the relative phase, electromagnetically induced transparency (EIT), a high refractive index with zero absorption and a larger inversionless gain can be realized. It is also shown that, in the contributions to the inversionless gain ( absorption) and dispersion, the contribution from SGC is always much larger than that from the dynamically induced coherence for any value of the relative phase. Our analysis shows that variation in the SGC effect will cause the spectrum regions and values of the inversionless gain and dispersion to vary evidently. We also found that, under the same conditions, the values of the inversionless gain and dispersion in the open system are evidently larger than those in the corresponding closed system; EIT occurs in the open system but cannot occur in the closed system.

Phase-sensitive atom localization in a loop Lambda-system

The behaviour of the Lambda-system has been studied theoretically in the context of atom localization. In addition to the probe field and the standing wave driving field, a microwave field is introduced to couple the two lower states, and as a result our Lambda-system forms a closed loop. Therefore phase-sensitive atom localization is expected. Indeed by appropriate choice of the relative phase between three fields, an improvement by a factor of 2 has been found in the detection probability of atoms within the sub-wavelength domain of the standing wave. The effect of other parameters is also investigated.

Coherent population accumulations of multiphoton transitions induced by an ultrashort pulse train in polar molecules

Coherent population accumulations of multiphoton transitions induced by an ultrashort pulse train in a two-level polar molecule are investigated theoretically by solving the density-matrix equations without invoking any of the standard approximations. It is shown due to the effects of permanent dipole moments, that the population accumulation of multiphoton transitions can be obtained in the polar molecule. Moreover, the population accumulations depend crucially on the relative phase between two sequential pulses, and the period in which the maximum population accumulation occurs is 2 pi/N in N-photon transitions.

Phase control of gain and dispersion in an open V-type system

The control role of the relative phase between the probe and driving fields on gain, dispersion and populations in an open V-type three-level system with spontaneously generated coherence is studied. The result shows that by adjusting the value of the relative phase, the transformation between lasing with inversion and lasing without inversion (LWI) can be realized and high dispersion (refractive index) without absorption can be obtained. The shape and value range of the dispersion curve are similar to those of the gain curve, and this similarity is closely related to the relative phase. The effects of the atomic exit and injection rates and the incoherent pump rate on the control role of the relative phase are also analysed. It is found easier to get LWI by adjusting the value of the relative phase using the open system rather than the closed system, and using an incoherent pump rather than without using the incoherent pump. Moreover the open system can give a larger LWI gain than the closed system.

Effects of relative phase in an open ladder system without incoherent pumping

We studied effects of the relative phase between the probe and driving fields on the absorption and dispersion properties in an open three-level ladder system with spontaneously generated coherence but without incoherent pumping. It is shown that by the phase controlling, switching from absorption to lasing without inversion (LWI) and enhancing remarkablely LWI gain can be realized; large index of refraction with zero absorption and the electromagnetically induced transparency can be obtained. We also find that varying the atomic injection and exit rates has a considerable influence on the phase dependent-absorption property of the probe field, existent of the atomic injection and exit rates gives the necessary condition of the realization of LWI, getting LWI is impossible in the corresponding closed system without incoherent pumping. We studied effects of the relative phase between the probe and driving fields on the absorption and dispersion properties in an open three-level ladder system with spontaneously generated coherence but without incoherent pumping. It is shown that by the phase controlling, switching from absorption to lasing without inversion (LWI) and enhancing remarkablely LWI gain can be realized; large index of refraction with zero absorption and the electromagnetically induced transparency can be obtained. We also find that varying the atomic injection and exit rates has a considerable influence on the phase dependent-absorption property of the probe field, existent of the atomic injection and exit rates gives the necessary condition of the realization of LWI, getting LWI is impossible in the corresponding closed system without incoherent pumping.