Comparative studies of open qubit via Bloch equation and master equation of Redfield form

In this paper, we investigate the dynamics of an open qubit model by solving two sets of its reduced dynamical equations. One set of the equations is the well-known Bloch equations and the other is the widely investigated master equations of Redfield form. Both of them are obtained from the perturbation approximation which demands the system of interest weakly coupled to its environment. It is shown that the qubit has a longer decoherence and relaxiation time as the dynamics is described by the Redfield equantions.     

Low-temperature dynamics of amorphous polymers and evolution over time of spectra of single impurity molecules: II. Model calculations and analysis of results

The results of a statistical analysis of the spectra of single molecules of tetra-tert-butylterrylene in amorphous polyisobutylene at temperatures of 2, 4.5, and 7 K are presented. Model calculations of such spectra for this system are performed in the context of the stochastic theory of the spectra of single molecules in lowtemperature glasses. Analysis of the multiplet structure of the experimental and model spectra made it possible to obtain data about the minimal distance between impurity chromophore molecules and two-level systems and about the distribution parameters of their coupling constant. The interaction of a chromophore with quasilocal low-frequency vibrational modes of the matrix was found to influence the structure and parameters of the spectra observed. The model calculations performed showed that the specific structure of the spectra of single molecules at low temperatures is determined by the interactions with a small number of nearby two-level systems.     

光合作用体系捕光复合物线性和非线性光谱的理论研究：修正的Redfield方法的验证

使用数值精确的级联方程方法对其计算可靠性进行了验证．目前已知,修正的Redfield方法所用的微扰和马尔科夫近似,在中间耦合区对激发态能量转移会给出不正确的描述．因此研究其在计算各 种光谱信号时是否仍然有效有重要意义．利用不同参数下的二聚体模型和Fenna-Matthews-Olson复合物模型,使用级联方程方法和修正的Redfield方法,计算并比较了它们的吸收谱、发射谱和二维电子相干光谱．研究发现在较大的参数范围内两种方法给出一致的结果,这两种方法的对比也增进了对光合作用捕光复合物的2D光谱中量子拍频信号来源的认识．     

Molecular recognition of chromophore molecules to amine terminated surfaces

We report the design and characterization of quartz surfaces that can bind to three retinal based chromophores. The amine terminated surfaces were engineered in order to mimic the environment of the opsin protein that accommodates binding of chromophore molecules in the human eye. Each surface coupling step was characterized by water contact angle measurements, ellipsometry, atomic force microscopy, X-ray photoelectron spectroscopy, and transmission infrared spectroscopy. The spectroscopic techniques confirmed that the three chromophore molecules can bind to the surface using a Schiff base mode. Our data suggests that the availability of the amine groups on the surface is critical in the accommodation of the binding of different chromophores.     

On the theory of frequency-shifted secondary emission of light-harvesting molecular systems

The expressions are obtained for the intensity of the frequency-shifted secondary emission of a chromophore playing the role of a reaction center in the simplest model three-chromophore molecular “lightharvesting” antenna, which is constructed and oriented in space so that the incident photons coherently excite two of its chromophore pigments. The quantum-field formalism was used, which takes into account the generalized (quantum-electrodynamic) dipole-dipole, as well as radiative and nonradiative dissipative interactions between pigments and the reaction center of the antenna. The special features of the excitation spectrum of the Raman scattering line and the frequency-shifted fluorescence spectrum of the reaction center of the molecular antenna under study are discussed. A comparison of the expressions obtained for the excitation and fluorescence spectra and with the corresponding expressions obtained for a bichromophore molecular system, which differs from a three-chromophore antenna by the absence of one of the pigments, revealed the properties of the mechanism of action of light-harvesting molecular antennas that have not been found earlier. In particular, it is shown that “the light-harvesting” caused by the collective dissipative interactions of pigments with the reaction center of the antenna can substantially exceed a sum of contributions from separate pigments.     

Monte Carlo simulations of sexual reproduction

Modifying the Redfield model of sexual reproduction and the Penna model of biological aging, we compare reproduction with and without recombination in age-structured populations. In constrast to Redfield and in agreement with Bernardes we find sexual reproduction to be preferred to asexual one. In particular, the presence of old but still reproducing males helps the survival of younger females beyond their reproductive age.     

Statistical analysis of spectra of single impurity molecules and dynamics of disordered solids: II. Manifestation of interaction of two-level systems with impurity molecules at different distances

Manifestations in the spectra of impurity chromophore molecules in a disordered solid matrix of the interaction of these molecules with two-level systems (TLSs) of the matrix are analyzed. The characteristic distances within the limits of which the interaction between TLSs and an impurity molecule leads, in the main, to either splitting or broadening of the spectrum, as well as the distance beginning with which this interaction is practically undetectable, are determined. Information about the effective value of the minimal distance between impurity molecules and TLSs, which is caused by nonzero sizes of the molecules and the TLSs, is presented. The analysis is performed by a statistical processing of experimental and model spectra of single tetra-tert-butylterrylene molecules in amorphous polyisobutylene at a temperature of 2 K, when the contribution of quasi-local low-frequency vibrational modes of the matrix to these spectra can be neglected.     

Effect of a protein on the light energy conversion in dual fluorophore-nitroxide probes studied by ESR and fluorescence spectroscopy

Probing biological environment with dual fluorophore-nitroxide (FN) molecules in which fluorophore is tethered with nitroxide, a fluorescence quencher, opens unique opportunities to study molecular dynamics and micropolarity of the medium which affect intramolecular fluorescence quenching (IFQ), electron transfer, photoreduction and light energy conversion. In such molecules, the excited fragment of the chromophore can serve as an electron donor, and the nitroxide fragment as an electron acceptor. The same groups allow monitoring of molecular dynamics and also make it possible to measure micropolarity of the medium in the vicinity of the donor (by fluorescence technique) and acceptor (by electron spin resonance [ESR]) moieties. In the present work, two dual dansyl-nitroxide probes were incorporated in a binding site of bovine serum albumin. Their interactions with the protein, mobility, and photoreduction, as well as micropolarity of the media, have been studied by ESR and fluorescence methods. IFQ and spectral relaxation shift of the dansyl fragment have been monitored by time-resolved fluorescence technique. In parallel, computational studies on intramolecular dynamics of the FN probe were performed. On the basis of the Marcus model of the electron transfer between the excited dansyl fluorophore (donor) and nitroxide group (acceptor) and our experimental data, the mechanism of the electron transfer in the dual molecules incorporated into bovine serum albumin was established. It was shown that dual FN molecules in the protein meet main requirements for an efficient light energy conversion system.     

Polarization nonlinear optics of quadratically nonlinear azopolymers

The polarization properties of second harmonic and sum-frequency signals generated by femtosecond laser pulses in films of polymers containing covalent groups of an azobenzothiazole chromophore polarized by an external electric field are investigated. It is shown that the methods of polarization nonlinear optics make it possible to determine the structure of oriented molecular dipoles and reveal important properties of the motion of collectivized π electrons in organic molecules with strong optical nonlinearities. The polarization measurements show that the tensor of quadratic nonlinear optical susceptibility of chromophore fragments oriented by an external field in macromolecules of the noted azopolymers has a degenerate form. This is indicative of a predominantly one-dimensional character of motion of collectivized π electrons along an extended group of atoms in such molecules.     

Carrier-envelope phase measurement by all-optical poling with a polar side-chain polymer

Dependence of all-optical poling efficiency on carrier-envelope phase (CEP) could be measured using photoisomerization of dye molecules which are covalently bound to a polymer main chain and have large difference in static dipole moment between the ground state and excited state. Increased chromophore density leads to an order of magnitude reduction in signal-detection time from a dye doped polymer. Analysis of all-optical poling experiments with CEP changes clearly showed the presence of polarization restoring force to zero polarization. This enables resetting of SH activity in the all-optical poling process to be used for fast response loop of CEP stabilization. Phenomenological model could explain well the difference in the growth-and-decay dynamics of poling between sample of dye doped in polymer studied previously and that grafted to a polymer main chain used in the present paper.     

Retinal in bacteriorhodopsin and related molecular models investigated with Raman spectroscopy and density functional theory calculations

A first‐principles assisted study of the Raman spectrum associated with the photoactive chromophore in bacteriorhodopsin (bR) allowed the elucidation of the effective coupling existing between the π electrons of the retinylidene chromophore and the local environment of the Schiff base. The role of the counter‐ion on the electronic and vibrational structure of the chromophore is investigated by means of density functional theory (DFT) calculations. Several molecular models of the retinylidene chromophore interacting with different counter‐ions facing the Schiff base have been considered. The counter‐ion induces a strong modulation of the position of both the UV–vis absorption maximum and the strong Raman active collective CC stretching mode, related to the effective conjugation coordinate (ECC). Experimental Raman and UV–vis absorption data are interpreted in the light of these theoretical findings. The data collected in this paper provide an interesting accumulation of points along the optical gap versus ECC wavenumber relationship. Copyright © 2011 John Wiley & Sons, Ltd.     

Influences of microscopic parameters of chiral molecules on the zero-frequency first hyperpolarizabilities

Based on one-electron-on-a-helix model and two-coupled-oscillator model, zero-frequency first hyperpolarizabilities of chiral molecules are investigated. Their expressions and the relations between them and microscopic parameters of chiral molecules are obtained by theoretical derivation. Furthermore, the relations of zero-frequency first hyperpolarizabilities with the wavelength of incident light and microscopic parameters of chiral molecules are simulated numerically. We find the fact that influences of microscopic parameters of chiral molecules on zero-frequency first hyperpolarizabilities are different by using different chiral molecular microscopic parameters such as the helix radius and the helix pitch for one-electron-on-a-helix model and α for two-coupled-oscillator model. Furthermore, the influence of microscopic molecular parameter to the zero-frequency first hyperpolarizabilities can also help to comprehend nonlinear optical mechanism of chiral molecules.     

一种共轭聚合物单分子发色团吸收和发射特性动态演变过程的实时测量

利用频域信息重构的散焦宽场成像测量了Poly[2,7-(9,9-dioctylfluorene)-alt-4,7-bis(thiophen-2-yl)benzo-2,1,3-thiadiazole](PFO-DBT)共轭聚合物单分子发色团的吸收与发射特性及其动态演变过程.通过调制用于激发共轭聚合物单分子的超短脉冲对的相对相位,对单分子荧光进行傅里叶变换的频域测量,跟踪发色团吸收偶极取向变化;通过测量散焦荧光成像光斑探测发色团发射偶极取向变化.研究发现, PFO-DBT共轭聚合物单分子发色团存在吸收和发射偶极取向均保持不变、其中之一变化以及两者同时变化三种情况.这种对共轭聚合物单分子发色团吸收和发射偶极取向演化过程的实时测量可用于分析共轭聚合物构象变化及其对能量转移过程的影响.     

Field Effects in Condensed Media on Polarized Absorption

The existence of anisotropic local field perturbation on electronic absorption is proved by non-zero linear dichroism of isotropic chromophores (Mo(CO)₆) in anisotropic environment. Two sources of such effects are possible: a) perturbation of the electronic energy levels in the chromophore by the static electric solvent field (= Stark effect) or, in case of anisotropic polarizable or dipolar molecules, similar effects involving molecular orientation, and b) dielectric effects on the effective radiation field. The latter effect was considered by various models: The Lorentz field model predicts an effect with wrong sign, it also yields too large a magitude if the anisotropy of the field is considered. If no local field correction is made and the anisotropy only operates in the radiation intensity a result more in agreement with experiment is obtained. By using the Onsager-Böttcher model one may take into account specific properties of the absorbing molecule, like anisotropy in α/r³ where α is its polarizability and r its Onsager radius.     

共轭聚合物单分子构象和能量转移特性研究

利用基于宽场显微光学系统的单分子散焦成像技术测量了不同构象poly[2,7-(9,9-dioctylfluorene)-alt-4,7-bis(thiophen-2-yl)benzo-2,1,3-thiadiazole](PFO-DBT)共轭聚合物单分子的光物理与动力学特性.通过分析共轭聚合物单分子的荧光轨迹和对应的发射偶极取向变化识别共轭聚合物单分子发光单元,发现延伸构象下的单分子呈现多发色团发光特性,而折叠构象下的单分子保持高效链间能量转移,呈现单个发色团发光特性.共轭聚合物单分子构象对能量转移效率的影响可用于研究基于共轭聚合物的光电器件和分子器件.     

A single-molecule study of polycrystalline microstructure by fluorescence polarization spectroscopy

The structure of n-hexadecane polycrystalline matrices is examined with single molecule fluorescence spectroscopy at a temperature of 1.7 K. Some single chromophores exhibit spectral dynamics during experiments: their resonances either jump between two frequencies or split into two components. By means of polarization measurements, we investigate the molecular spectra in order to distinguish between the case of two spatially unresolved molecules and the case of chromophore — two level system (TLS) pair. For closely spaced molecules two-dimensional Gaussian function fitting is applied to extract the spatial coordinates of the molecules. For TLS-chromophore systems, parameters of the TLSs are estimated.     

Specific features of the time dependence of intensity of differently polarized fluorescence components of bichromophore molecules caused by radiative dissipative interaction between their chromophores

Specific features of the time dependence of the intensity of differently polarized fluorescence components of a single bichromophore molecule and a monomolecular layer of such molecules are found. These features are related to the radiative dissipative interaction between chromophores of the molecule. The most prominent feature is the fall to zero of the intensity of fluorescence polarized perpendicular to polarization of the exciting light pulse at certain orientations of molecules with respect to the propagation direction of the light pulse. The complete quenching of this fluorescence component occurs when the excited-state population of an initially unexcited chromophore in molecules where only one of the two chromophores was excited reaches a maximum. As a result, the time dependence of the anisotropy of fluorescence of such molecular layers is described by hyperbolic secant with a maximum equal to unity at the quenching moment.     

Influence of solvent on the chiral resolution of organic molecules on Au(111): EC-STM study of biphenyl dicarboxylic acid on Au(111) in an aqueous environment

Adsorption-induced chiral resolution of organic molecules is important due to its potential applications in stereo-selective catalysis. We studied the adsorption-induced chiral resolution using a model achiral molecule of 4,4′ biphenyl dicarboxylic acid (BPDA) on Au(111) in 0.1 M perchloric acid (HClO₄) by electrochemical scanning tunneling microscopy (EC-STM). Our experimental data showed that the BPDA molecules formed island structures with distinctive preferred orientations at the length scale of the molecular size. The molecules did not show any orientational ordering above the length scale, indicating that chiral resolution was absent in the aqueous environment. Previously, the molecules were found to have chiral resolution on Au(111) in ultra-high vacuum conditions (UHV). We calculated angle-dependent binding energy between the substrate and a BPDA molecule, the intermolecular interactions between the BPDA molecules, and their interactions with water molecules. The calculations suggest that the absence of chiral resolution in the aqueous environment originated from the decrease in the intermolecular energy of the BPDA molecules due to their hydrogen bonds with the surrounding water molecules. The strength of the hydrogen bonding between BPDA molecules was sufficient to overcome the energy barrier for chiral resolution through rotational motion in UHV, but not in an aqueous environment.     

A Theory of Luminescence of Light‐Collecting Molecular Systems

Expressions are obtained for the intensity and the quantum yield of the sensitized luminescence of the chromophore that plays the role of a reaction center in the simplest model trichromophore molecular [lightcollecting] antenna which is so constructed and so oriented in space that the irradiation photons coherently excite its other two chromophorespigments. The quantum electrodynamics formalism which takes into account the radiative dissipative interaction between the pigments and the reaction center of the antenna was used. The comparative analysis of the obtained expressions with the corresponding expressions for the luminescence of a bichromophore molecular system, differing from the trichromophore antenna by the absence of one of the pigments, has shown that the collective dissipative interaction of the pigments with the reaction center of the antenna can be considered as a highly efficient mechanism of [light collection] in molecular antennas.