Parameter Recovery in Frequency-Domain Time-Resolved Fluorescence Spectroscopy; Resolution of the Prototropic Forms of 5-Carboxyfluorescein in the Physiological pH Range

In time-resolved fluorescence spectroscopy, the resolution of fluorescence species becomes increasingly difficult as their respective lifetimes get closer. For a biexponential decay, a factor of 1.4 between the two decay times is commonly accepted as the practical resolution limit. The goal of the present contribution is to characterize the fluorescence probe 5-carboxyfluorescein using frequency-domain time-resolved fluorescence spectroscopy (FD-TRFS). To resolve the different prototropic forms of this probe, the limit above had to be overcome. For this purpose, the standard global analysis method was used, and special emphasis was put on the errors associated with the recovered parameters. In particular, a Monte Carlo simulation was performed to estimate these errors and the results of this analysis were compared with those delivered by software packages widely used in the field. The lifetimes of the trianionic and dianionic forms of 5-carboxyfluorescein were 4.01 ± 0.06 and 3.03 ± 0.09 ns, respectively, and the pK _a for this acid–base equilibrium was determined to be 6.9 ± 0.3.     

Deriving Intrinsic Parameters of Photoinduced Electron Transfer Reaction from the Transient Effect Probed by Picosecond Time-Resolved Fluorescence Quenching

Fluorescence quenching of a pyrylium salt (PDP²⁺) by toluene in acetonitrile gives rise to a nonexponential decay. This behavior is ascribed to the so-called transient effect occurring at high quencher concentrations for diffusion-controlled reactions. First, the Kalman filter was used to deconvolute the original signal from the experimental decay curve and the response function of the apparatus. This treatment led to a calculated deconvoluted decay curve which enabled the transient effect analysis to be conducted. This real decay curve was then analyzed using two models. The Smoluchowski—Collins—Kimball (SCK) model, applied to diffusion-controlled reactions, yielded the reaction radius r _AD and the intrinsic rate constant k _act of the bimolecular electron transfer reaction. The Marcus electron transfer/diffusion (ETD) model, which provides a powerful method to evaluate the electronic coupling H _el associate with the reaction, was also used but is more difficult to handle due to extensive computational needs. Finally, the adequacy of the two models (SCK and ETD) for analysis of the transient effect was addressed, as well as the appropriateness of the Kalman filter for fluorescence signal deconvolution.     

A General Method for Constrained Analysis of Fluorescence Anisotropy Decay: Application of the Steady-State Anisotropy

Time-resolved fluorescence anisotropy is an invaluable method for investigating the internal and rotational dynamics of biomolecules. The range of rotational motions detectable by anisotropy decay is limited by the fluorescence lifetime; typically, a depolarizing motion may be resolved if the associated correlation time is between 0.1 and 10 times the intensity decay lifetime. To extend that range and to improve the recovery of anisotropy decay parameters, a general analytical method has been developed. This procedure utilizes a modification of Lagrange multiplier methods to constrain the values of the iterated kinetic parameters during nonlinear least-squares analysis of anisotropy decay data. The form of the constraint equation is derived from the classic relationship between the decay parameters and the steady-state anisotropy, which can be simply and accurately measured. Application of the constraint to analyses of synthetic data sets increased the accuracy of recovery by decreasing the uncertainty in the iterated parameters. The constraint also enabled the accurate recovery of correlation times that were a factor of 30 greater than the fluorescence lifetime, although it did not improve recovery of correlation times that were much shorter than the lifetime. Using this technique, it should now be possible to characterize the dynamics of larger macromolecules and assemblies than those that can currently be studied by fluorescence anisotropy decay.     

Molecular dynamics simulations of the oligonucleotide with the modified phosphate/phosphonate internucleotide linkage

Impact of the internucleotide linkage modification by inserting a methylene group to the P-O bond (—O—PO ₂ ^— —O— chain changed for —O—PO ₂ ^— —CH₂—O—), on the modified oligonucleotide binding ability to the natural DNA strand was studied by molecular dynamics simulation. Complex of (dT)₁₁ with a deoxyadenosine undecamer containing alternating modified and natural internucleotide linkage was studied as a model system. The Amber force field was completed by a set of new parameters needed to model the modified part of the nucleotide. The simulations confirmed existence of a double-helical complex the melting point of which is considerably higher than 300 K. While the thymidine (unmodified) strand possesses a B-type secondary structure, the conformation of the adenosine (modified) strand is not stable at 300 K. The -ggt conformation of the modified linkages is highly preferred, temporary jumps to the -g-gt and ggt conformations were, however, observed.     

Photoinduced Oxidation of Diphenylbisanthene and Its Spectral Manifestations

The absorption and fluorescence spectra of diphenylbisanthene (DPB) in n-octane and benzene at 300 and 77 K have been investigated. The appreciable Stokes shift of the fluorescence band (180 cm^–1 in n-octane and 440 cm^–1 in benzene) points to the nonplanar character of the aromatic skeleton of DPB, which has been confirmed by results of the optimization of the molecule geometry by the AMI quantum-mechanical method. It has been found that spectral manifestations of the products of photoinduced transformations of DPB molecules are observed in the UV region (200–350 nm), and it has been shown that the observed photochemical process is two orders of magnitude less effective than for diphenylhelianthrene. On the basis of the experimental data and the results of the quantum-chemical calculations of the electronic spectra of molecules of DPB and endoperoxides (ZINDO/S method), it has been concluded that the end products of DPB phototransformations are its endobiperoxides in which —O—O— groups are added to the phenyl-substituted benzene rings of the aromatic skeleton.     

Spin — lattice relaxation in chlorofluorocarbon liquids

We have used the spin — echo method to measure spin — lattice relaxation times in liquid chlorofluorocarbons over a wide range of temperatures, frequencies, and molecular weights. Analysis of the experimental data shows that to determine the kinetic parameters of viscous liquids it is necessary to use the theory of nuclear magnetic relaxation by translational diffusion. We describe a method for the computer calculation of these parameters and discuss the results.Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Fizika, No. 3, pp. 46–51, March, 1976.     

Modified Maximum Entropy Method and Estimating the AIF via DCE-MRI Data Analysis

Background: For the kinetic models used in contrast-based medical imaging, the assignment of the arterial input function named AIF is essential for the estimation of the physiological parameters of the tissue via solving an optimization problem. Objective: In the current study, we estimate the AIF relayed on the modified maximum entropy method. The effectiveness of several numerical methods to determine kinetic parameters and the AIF is evaluated—in situations where enough information about the AIF is not available. The purpose of this study is to identify an appropriate method for estimating this function. Materials and Methods: The modified algorithm is a mixture of the maximum entropy approach with an optimization method, named the teaching-learning method. In here, we applied this algorithm in a Bayesian framework to estimate the kinetic parameters when specifying the unique form of the AIF by the maximum entropy method. We assessed the proficiency of the proposed method for assigning the kinetic parameters in the dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), when determining AIF with some other parameter-estimation methods and a standard fixed AIF method. A previously analyzed dataset consisting of contrast agent concentrations in tissue and plasma was used. Results and Conclusions: We compared the accuracy of the results for the estimated parameters obtained from the MMEM with those of the empirical method, maximum likelihood method, moment matching (“method of moments”), the least-square method, the modified maximum likelihood approach, and our previous work. Since the current algorithm does not have the problem of starting point in the parameter estimation phase, it could find the best and nearest model to the empirical model of data, and therefore, the results indicated the Weibull distribution as an appropriate and robust AIF and also illustrated the power and effectiveness of the proposed method to estimate the kinetic parameters.     

Inverse acoustical characterization of natural jute sound absorbing material by the particle swarm optimization method

For modeling of jute as acoustic material, knowledge of its non-acoustical parameters like porosity, tortuosity, air flow resistivity, thermal and viscous characteristic lengths is a prime requisite. Measurement of these non-acoustical parameters is not straightforward and involves a dedicated measurement setup. So in order to overcome this issue, the inverse acoustical characterization can be used. In this paper, the particle swarm optimization method (PSO) is used as an optimization method. This method estimates the non-acoustical parameters of jute material in felt form by minimizing the error between experimental and theoretical sound absorption data. In this work, the impedance prediction models for fibrous materials like Johnson–Champoux–Allard model with rigid and limp frame and Garai–Pompoli model is used for sound absorption coefficient calculation by the transfer matrix method along with the PSO. The inverse estimated non-acoustical parameters for jute material are then compared with estimated and experimentally measured parameters for jute felts. Using these inversely predicted parameters, sound absorption of multilayer sound absorbers is also studied.     

结合实际刻蚀数据的离子刻蚀产额优化建模方法

刻蚀表面仿真是研究等离子体刻蚀工艺过程机理的重要手段.在刻蚀表面仿真方法中,刻蚀表面演化模型和离子刻蚀产额模型直接决定了刻蚀表面演化结果.但现有的刻蚀表面演化模型不够精确,且目前离子刻蚀产额模型主要来自分子动力学仿真和物理实验,而实际加工过程十分复杂,等效的离子刻蚀产额包含很多因素.针对这些问题,首先对当前的刻蚀表面演化模型进行改进,同时重新定义了离子刻蚀产额模型的优化目标,并利用实际刻蚀加工数据来优化离子刻蚀产额模型.为缩短优化模型所用时间,采用并行方法来加速优化过程.最后,将得到的离子刻蚀产额模型参数应用于采用元胞自动机法的刻蚀工艺实际仿真过程中.实验结果表明,该优化建模方法确实提高了仿真的精确度,同时优化过程所用时间也大大减少.     

Simulation of the Double Proton Transfer Dynamics in the Benzoic Acid Dimer

A numerical simulation of the rate constants of the double proton transfer in the benzoic acid dimer at partial and complete deuteration of hydrogen bonds in the dimer as well as at different hydrostatic pressures applied to the sample has been carried out on the basis of the model of a multistage process activated by equilibrium radiation. It has been shown that this model, as opposed to the known approach based on the synthesis of two processes — activation (Boltzmann–Arrhenius model) and molecular tunneling (Goldanskii model) — can describe both low- and high-temperature rate constants of reactions using a single set of parameters characterizing the process of interaction of the transforming molecule with the thermal field.     

A model for the stabilization of atomic hydrogen centers in borate glasses

A previously proposed model describing the trapping site of the interstitial atomic hydrogen in borate glasses is analyzed. In this model the atomic hydrogen is stabilized at the centers of oxygen polygons belonging to B–O ring structures in the glass network by van der Waals forces. The previously reported atomic hydrogen isothermal decay experimental data are discussed in the light of this microscopic model. A coupled differential equation system of the observed decay kinetics was solved numerically using the Runge Kutta method. The experimental untrapping activation energy of 0.7×10⁻¹⁹ J is in good agreement with the calculated results of dispersion interaction between the stabilized atomic hydrogen and the neighboring oxygen atoms at the vertices of hexagonal ring structures.     

Scattering of electron stream waves on metal-dielectric periodic structures

The results of the theoretical and experimental research of the surface waves scattering of an electron stream and a planar dielectric waveguide on metal-dielectric structures of the dielectric prism — band diffraction grating-type are presented. Within the approximation of the given current there has been carried out a numerical analysis of energy characteristics of diffraction-Cerenkov radiation for a wide interval of the main system parameters change. The results of numerical analysis are confirmed by the data of experimental simulation.     

Fluorescence probes of viscosity: A comparative study of the fluorescence anisotropy decay of perylene and 3,9-dibromoperylene in glycerol

The authors compare the results of fluorescence anisotropy decay measurements for glycerol solutions of perylene with those of 3,9-dibromoperylene (DBP). For both molecules a good linear dependence is observed between the glycerol viscosity (varied by temperature) and the longer rotational correlation time obtained as a result of a global (using data obtained at 256- and 430-nm excitation wavelengths) biexponential analysis of the fluorescence anisotropy decay, at least in the range of 7–60 P for perylene and 4–60 P for DBP. This significantly extends the reported range of 0.5 to 150 cP investigated by Williams and Ben-Amotz [1] with the probe BTBP.     

各向同性紊流能量衰减的大涡模拟

在多重网格驱动的,高效且得到充分验证的有限体积方法的基础上发展了可压缩流大涡模拟的方法.空间离散采用Jameson的中心格式附加二阶和四阶耗散的方法,时间推进则采用了双时间步长的方法.亚格子剪切应力张量和亚格子热通量用Smagorinsky模型进行模拟.通过对各向同性紊流能量衰减的模拟来验证本方法的准确性和高效性,模拟得到的能量谱和紊流动能衰减历程与过滤后的CBC实验数据吻合良好.     

Simple recursive implementation of fast multipole method

In this paper we present an implementation of the well known “fast multipole” method (FMM) for the efficient calculation of dipole fields. The main advantage of the present implementation is simplicity—we believe that a major reason for the lack of use of FMMs is their complexity. One of the simplifications is the use of polynomials in the Cartesian coordinates rather than spherical harmonics. We have implemented it in the context of an arbitrary hierarchical system of cells—no periodic mesh is required, as it is for FFT (fast Fourier transform) methods. The implementation is in terms of recursive functions. Results are given for application to micromagnetic simulation. Complete source code is provided for an open-source implementation of this method, as well as an installer for the resulting program.     

Lens Design: Global Optimization with Escape Function

The technique of using the ‘escape function’ for global optimization in lens design is described. This includes how to identify two solutions as independent; the threshold value for this criterion can be chosen to determine how to explore local solutions—rough or fine. Choice of appropriate values for two parameters in the escape function is most important, since this will affect the efficiency of the automatic global optimization process. There are two problems, i.e. giving default values at the beginning of the design, and determining a default rule to change them when the escape is unsuccessful. The latter was solved by assuming a ‘saddle path’ as the best route to escape. An exact solution for the former was not found, but a hint for finding a second best solution is shown based on the statistical study of local minima.     

On the transport of activated particles by flow and diffusion

It will be shown, how the spatial decay of active molecules — excited electronically or activated otherwise (e.g., chemical processes) is determined by diffusion and flow as well as by the intrinsic molecular constant. The exact analysis in cylindric geometry leads to a set of unique solutions, which in lowest order are characterized by a weak gradient of the particle concentration at the wall and a pronounced kernel in the center of the tube. In special cases there exists a simple but powerfull expansion of any distribution in the source, which are very similar to Fourier-Bessel series. The solutions in lowest order will be used to analyze the measured decay of activated oxygen in a steady stream of molecular oxygen. Since the decay constant is determined by volume deactivation and by the removal of particles at the wall, evaluation of experimental data, however, remains necessarily ambiguous.     

Ag/Si(111)-(7X7) Heteroepitaxy—STM Experiment and KMC Simulations

Heteroepitaxial growth of Ag on Si(111)-(7X7) surface at various conditions was experimentally studied by scanning tunneling microscopy. A growth model based on experiments was used for kinetic Monte Carlo (KMC) simulations. The simulations of nucleation and island growth at low coverage and fitting experimental data provided basic growth parameters. Further growth—formation of a discontinuous transition film (wetting layer)—was implemented into the basic model. The suggested growth mechanism was successfully tested using the KMC simulations. The choice of experiments, the role of minimizing processes and parameters in the model, and efficiency of the used approach is demonstrated and discussed.     

Epstein-layer and dielectric-slab electromagnetic models of semiconductor injection lasers

This paper is devoted to a comparison of two electromagnetic models of junction lasers — the dielectric slab and the Epstein layer. The main emphasis is on the discussion of possible methods of matching the parameters appearing in both models. The threshold condition for active layer thickness and mode frequency at a given gain and mode number is solved numerically. It is shown that the discrepancies between both models become reasonably small when a proper method, involving averaging of the dielectric constant over the active and passive regions, is applied. The cases of the three lowest order TE transverse modes of homojunction, single-, and double-heterojunction lasers are considered. The obtained results suggest that the Epstein-layer model can approximate experimental data as well as the dielectricslab model does.