Non-descanned versus descanned epifluorescence collection in two-photon microscopy: Experiments and Monte Carlo simulations

We report on the design, test and Monte Carlo simulations of a non-descanned (NDS) collection port that we compare to a descanned (DS) port implemented on the same confocal microscope to carry out two-photon excitation fluorescence (TPEF) imaging. Our optical concept provides compactness, a wide field of view to the NDS port and allows the usage of small-area photosensors. The collection efficiency of the NDS port was measured with respect to those of the DS port as function of the imaging depth within a tissue-like optical phantom, for two high numerical aperture objectives. A NDS-to-DS collection ratio as high as about 30 was found for an imaging depth of 500 μm, corresponding to four mean scattering paths of the collected photons within the turbid medium. Measurements were fully interpreted by Monte Carlo simulations of light scattering through the turbid medium and collection by the spatio-angular apertured DS and NDS ports. Comparison of XZ cross-sectional views of mice liver samples imaged with the two ports emphasized the advantage of our NDS device for imaging deeply inside biological samples using TPEF microscopy.     

Analysis of light propagation in highly scattering media by path-length-assigned Monte Carlo simulations

Numerical analysis of optical propagation in highly scattering media is investigated when light is normally incident to the surface and re-emerges backward from the same point. This situation corresponds to practical light scattering setups, such as in optical coherence tomography. The simulation uses the path-length-assigned Monte Carlo method based on an ellipsoidal algorithm. The spatial distribution of the scattered light is determined and the dependence of its width and penetration depth on the path-length is found. The backscattered light is classified into three types, in which ballistic, snake, and diffuse photons are dominant.     

The influence of reverse excitation transfer on donor and acceptor fluorescence decay: Monte Carlo simulations

Department of Technical Physics and Applied Mathematics, Technical University of Gdańsk, Narutowicza 11/12, 80–952 Gdańsk, Poland. Published in Zhurnal Prikladnoi Spektroskopii, Vol. 62, No. 4, pp. 179–184, July–August, 1995.     

Out-of-focus fluorescence collection in two-photon microscopy of scattering media

Imaging depth in two-photon microscopy is ultimately limited by the out-of-focus fluorescence background which is collected indistinctly with the useful in-focus signal in scattering samples. We report on a complete Monte Carlo analysis of the collection process in two-photon imaging of turbid media. Epifluorescence collection efficiency of the microscope is shown to vary significantly from point to point inside the scattering medium, to the detriment of the in-focus signal and in favor to the background, lowering the signal-to-background ratio in the image. Moreover we found that this ratio is almost independent of the collecting path field of view for situations where the background overcomes the signal. Assuming that the out-of-focus background can be subtracted to the image, the signal-to-noise ratio in two-photon microscopy is forecast to benefit from enlarging the collection field of view, with a gain roughly proportional to this enlargement for deep imaging. Asymptotic behaviors of the Monte Carlo simulations are quantitatively interpreted from ballistic and diffusive approximations.     

Monte Carlo方法模拟非直视紫外光散射覆盖范围

针对大气中紫外光散射通信的特点, 用Monte Carlo方法对紫外光非直视(NLOS) 通信三种工作方式的覆盖范围进行分析, 建立了基于Monte Carlo方法的NLOS紫外光传输模型.利用Monte Carlo模拟方法对三种NLOS散射方式的单次和多次散射路径损耗及覆盖范围进行模拟研究, 结果表明, 多次散射和单次散射的路径损耗基本一致, NLOS(a) 类全向发送全向接收通信方式覆盖范围最小但全方位性好, NLOS(b) 类定向发送全向接收通信方式的覆盖范围较大但有一定方向性, NLOS(c) 类定向发送定向接收通信方式的覆盖范围最大但有很强的方向性.     

Supercooled superfluids in Monte Carlo simulations

We perform path integral Monte Carlo simulations to study the imaginary time dynamics of metastable supercooled superfluid states and nearly superglassy states of a one component fluid of spinless bosons square wells. Our study shows that the identity of the particles and the exchange symmetry is crucial for the frustration necessary to obtain metastable states in the quantum regime. Whereas the simulation time has to be chosen to determine whether we are in a metastable state or not, the imaginary time dynamics tells us if we are or not close to an arrested glassy state.     

A boundary-based net-exchange Monte Carlo method for absorbing and scattering thick media

A boundary-based net-exchange Monte Carlo method was introduced (JQSRT 74 (2001) 563) that allows to bypass the difficulties encountered by standard Monte Carlo algorithms in the limit of optically thick absorption (and/or for quasi-isothermal configurations). With the present paper, this method is extended to scattering media. Developments are fully 3D, but illustrations are presented for plane parallel configuration. Compared to standard Monte Carlo algorithms, convergence qualities have been improved over a wide range of absorption and scattering optical thicknesses. The proposed algorithm still encounters a convergence difficulty in the case of optically thick, highly scattering media.     

Intervalley scattering in GaAs: ab initio calculation of the effective parameters for Monte Carlo simulations

Interactions between excited electrons and short-wavelength (intervalley) phonons in GaAs are studied using density functional theory for the conduction bands, and density functional perturbation theory for phonon frequencies and matrix elements of the electron–phonon interaction. We have calculated the deformation potentials (DPs) and the average intervalley scattering time 〈τ〉. The integration of the scattering probabilities over all possible final states in the Brillouin zone has been performed without any ad hoc assumption about the behavior of the electron–phonon matrix elements nor the topology of the conduction band. For transitions from the L point to Γ valley (within the first conduction band), we find 〈τ〉_L to be 1.5 ps at 300 K, in good agreement with time-resolved photoluminescence experiment. We discuss the difference between our calculated DPs, and effective parameters used in Monte Carlo simulations of optical and transport properties of semiconductors. The latter are based on Conwell’s model, in which electron–phonon interaction is described by one single constant and a parabolic model is used for conduction bands. We deduce the effective DP from our 〈τ〉, and compare it to our calculated DPs. We conclude that only effective DPs obtained from a full calculation of 〈τ〉 are relevant parameters for Monte Carlo simulations. PACS 71.10-w; 72.10.Di; 71.55.Eq     

Electrodeposition in highly viscous media: Experiments and simulations

Electrolyte viscosity plays an important role in ion transport. Here we study the effects of high viscosity variations in thin-layer electrochemical deposition (ECD) under constant-current conditions through experimental measurements and theoretical modelling. The viscosity was varied through glycerol and polymer additions and the tracking of convective fronts was performed through the use of optical and particle image velocimetry techniques with micron sized particles. The theoretical model, written in terms of dimensionless quantities, describes diffusive, migratory and convective ion transport in a fluid under constant-current conditions. Experiments reveal that as viscosity increases, convection decreases, while concentration gradients increase. These effects are more pronounced when the current increases. Theory and simulations predict that as viscosity increases, the Poisson and Reynolds numbers decrease whereas the Peclet and electric Grashof numbers increase. Therefore, electroconvection becomes more relevant.     

Cavity-bias sampling in reaction ensemble Monte Carlo simulations

A methodology is presented to sample efficiently configurations of reacting mixtures in the reaction ensemble Monte Carlo simulation technique. A cavity-biasing scheme is used, which more effectively samples configurations than conventional random sampling. Akin to other biasing schemes that are implemented into insertion-based Monte Carlo methods such as Gibbs ensemble Monte Carlo, the method presented here searches for space in the reacting mixture whereby the insertion of a product molecule is energetically favoured. This sampling bias is then corrected in the acceptance criteria. The approach allows for the study of reacting mixtures at high density as well as for polyatomic molecular species. For some cases, the method is shown to increase the efficiency of the reaction steps by a factor greater than 20. The approach is shown to be readily generalized to other biasing schemes such as orientational-biasing of polar molecules and configurational-biasing of chain-like molecules.     

Strong coupling in macrocyclic thiophene investigated by time-resolved two-photon excited fluorescence

We report the femtosecond dynamics of fluorescence anisotropy excited through the two-photon absorption (TPA), which provides direct signatures of delocalized electronic excitations for symmetrical macromolecular architectures. Two-photon excited fluorescence anisotropy is strongly correlated with the orientation and value of the transition moment from the excited state to the second and higher lying states. For macromolecular systems it leads to a relatively low initial fluorescence anisotropy and specific femtosecond anisotropy dynamics. We have experimentally demonstrated qualitatively different anisotropy dynamics for two- and one-photon absorption excitations for strongly coupled ring architecture prospective for artificial-light-harvesting applications and possessing an enhanced TPA-absorption cross section.     

Artificial carrier heating due to the introduction of ab initio Coulomb scattering in Monte Carlo simulations

Accurately treating ionised impurity scattering in a way suitable to describe the influence of random dopant fluctuations on device characteristics is important in next generation MOSFETs. Statistical variations are unobservable using a continuous treatment of the doping, requiring a discrete representation of impurities. In particle-based simulations the P³M method, which resolves the Coulomb interaction into long- and short-range components, is in principle capable of describing Coulomb scattering through propagation in this accurately resolved potential. However, numerically the integration of the equations of motion is inaccurate and controlling the errors in practical simulations is vital. In this paper we investigate the effect of the choice of short-range correction strategy and integration time step on accuracy in a 3D self-consistent ensemble Monte Carlo simulations featuring random discrete dopants. We illustrate the importance of the ‘ab initio’ Coulomb scattering comparing the effect of a single trapped charge in drift-diffusion and Monte Carlo simulations.     

Coherent multiple scattering effects and Monte Carlo method

Based on the comparison of the iteration procedure of solving the Bethe-Salpeter equation and the Monte Carlo method, we developed a method for simulating coherent multiple-scattering effects within the framework of a unified stochastic approach. The time correlation function and the interference component were calculated for the coherent backscattering from a multiply scattering medium.     

Evanescent-field-induced two-photon fluorescence: excitation of macroscopic areas of planar waveguides

Two-photon excitation (TPE) of fluorescence is a powerful tool for separating a faintly emitted fluorescence signal from background excitation noise. Until now TPE has only been accomplished for very small excitation areas of a few square micrometre dimensions since they are readily available in the focal zone of high-power lasers. In this paper we demonstrate, to our knowledge for the first time, two-photon excited fluorescence with planar thin-film waveguide structures of macroscopic excitation areas of the order of square millimetres to square centimetres. Based upon our results, it can be envisaged that the new combination of planar waveguide technology with TPE will become a powerful tool for macroscopic surface-interaction studies. It can also open the way for further improving the sensitivity of biosensing platforms like genomic and proteomic microarrays based upon planar waveguides. Received: 7 November 2001 / Published online: 23 November 2001     

Components of detector response function: Monte Carlo simulations and experiment

Components of the response function of an HPGe detector for 32 keV incident photons (Ba Kα x‐rays) were studied using a Monte Carlo program. Physical mechanisms and the role of incident photons, detector x‐rays, photoelectrons and Compton recoil and Auger electrons for each component were investigated. The position, intensity and shape of the components, particularly of the photoelectrons, were studied in detail. Two distinct components for photoelectron escape were identified by considering the fate of photoelectrons, Ge x‐rays and Auger electrons produced in the same interaction. In contrast to the often‐cited shelflike structure, it was found that both components have a slope. The contribution of recoil electrons to the spectrum for single, double and multiple Compton scattering followed by photoelectric absorption of the scattered photon was investigated. The results of the Monte Carlo simulations are presented along with the measured Ba x‐ray spectrum. Copyright © 2006 John Wiley & Sons, Ltd.     

Background study and Monte Carlo simulations for large-mass bolometers

Large-mass bolometers are today extensively used for dark matter and double beta decay searches, in both cases the ultimate experimental sensitivity is defined by the background level reached in such devices. The most common background sources and the techniques used for their identification and reduction are here reviewed, with a particular focus on double beta decay searches. The relevant role played by Monte Carlo simulations in this field is discussed. As a real case, the background optimization in the MiDBD experiment is described.     

Guaranteeing total balance in Metropolis algorithm Monte Carlo simulations

The condition of detailed balance has long been used as a proxy for the more difficult-to-prove condition of total balance, which along with ergodicity is required to guarantee convergence of a Markov Chain Monte Carlo (MCMC) simulation to the correct probability distribution. However, some simple-to-program update schemes such as the sequential and checkerboard Metropolis algorithms are known not to satisfy detailed balance for such common systems as the Ising model.