Inverse Monte Carlo Simulation Research Articles

Reconstruction of Optical Properties in Turbid Media: Omitting the Need of the Collimated Transmission for an Integrating Sphere Setup.

Currently, the most reliable approach to reconstruct optical properties, namely absorption coefficient, reduced scattering coefficient, scattering coefficient and asymmetry factor, of turbid media is through inverse Monte Carlo simulation. To determine these optical properties, three measurements are required: total transmission, total reflection and collimated transmission. However, the accurate determination of the collimated transmission is very difficult. To overcome the difficulty of measuring the collimated transmission, it is proposed to measure the total transmission and total reflection of the same sample with two different thicknesses instead. To prove this alternative solution, machine learning is used to prove that the repeated measurement for two different thicknesses carries all the necessary information. As a result, all four optical properties can be measured with high accuracy, particularly for interpolation problems where the test data fall within the range of the training data. For extrapolation problems, high accuracy can be achieved in the determination of at least the absorption coefficient, reduced scattering coefficient and scattering coefficient. Hence, these results allow that in the future, an easier and therefore more precise reconstruction of the optical properties is possible, potentially even with inverse Monte Carlo simulations as the current standard.

Designing a use-error robust machine learning model for quantitative analysis of diffuse reflectance spectra.

Machine learning (ML)-enabled diffuse reflectance spectroscopy (DRS) is increasingly used as an alternative to the computation-intensive inverse Monte Carlo (MCI) simulation to predict tissue's optical properties, including the absorption coefficient, and reduced scattering coefficient, . We aim to develop a use-error-robust ML algorithm for optical property prediction from DRS spectra. We developed a wavelength-independent regressor (WIR) to predict optical properties from DRS data. For validation, we generated 1520 simulated DRS spectra with the forward Monte Carlo model, where to , and to . We introduced common use-errors, such as wavelength miscalibrations and intensity fluctuations. Finally, we collected 882 experimental DRS images from 170 tissue-mimicking phantoms and compared performances of the WIR model, a dense neural network, and the MCI model. When compounding all use-errors on simulated data, the WIR model best balanced accuracy and speed, yielding errors of 1.75% for and 1.53% for , compared to the MCI's 50.9% for and 24.6% for . Regarding experimental data, WIR model had mean errors of 13.2% and 6.1% for and , respectively. The errors for MCI were about eight times higher. The WIR model presents reliable use-error-robust optical property predictions from DRS data.

Skin optical properties from 200 to 300 nm support far UV-C skin-safety in vivo

The growing threat of multi-drug resistant pathogens and airborne microbial diseases has highlighted the need to improve or develop novel disinfection methods for clinical environments. Conventional ultraviolet C (UV-C) lamps effectively inactivate microorganisms but are harmful to human skin and eyes upon exposure. The use of new 233 nm far UV-C LEDs as an antiseptic can overcome those limitations. In this research, the light penetration into the skin was elucidated for the UV-C region (<300 nm) by measuring the scattering and absorption of skin layers and inverse Monte Carlo simulation, and further confirmed by the first clinical pilot trial in which healthy volunteers were irradiated with a dose of 60 mJ/cm2 at 233 nm. The radiation is strongly absorbed in the stratum corneum, resulting in minimal skin damage without inducing inflammatory responses. The results suggest that 233 nm far UV-C light emitting diodes (LEDs) could effectively inactivate microorganisms, while being safe and soft for the skin.

Local atomic configurations in mechanically alloyed amorphous (FeCoNi)70Ti10B20 powders

The atomic structure of amorphous (FeCoNi)70Ti10B20 alloy synthesized by mechanical alloying was investigated using high energy synchrotron X-ray diffraction and inverse Monte Carlo simulations of pair distribution functions. Empirical potential structure refinement indicates a chemical short-range order at the length scales of 2.1–2.5 Å via local atomic arrangements forming deformed bcc-like clusters. The structural model obtained was described by bond lengths, coordination numbers, and bond angle distribution functions determined for the first neighbor atoms by x-ray scattering supplemented with 3D Monte Carlo simulations.

Entropy of electrolytes with off-centre charge cations. Monte Carlo studies

Monte Carlo techniques including Inverse Grand Canonical Monte Carlo simulations are utilized to calculate the entropy of a restricted primitive model electrolyte with the caveat that the cation charge centre is displaced from the geographical centre of the cation sphere towards the surface of the sphere. Calculations have been performed for symmetric valency (1:1) and asymmetric valency (2:1) electrolytes at 298.15 K for a range of electrolyte concentrations. The cation charge centre displacement accompanied by an increase of temperature leads to an increase of entropy. For the 2:1 valency system the entropy as a function of the square root of concentration reveals a broad inflexion region that separates the domains of deformation due to the electrostatic and steric interactions. When the central ion is an anion, and the charge centres of the surrounding cations are oriented towards the anion then the electrostatic interactions are stronger than in the standard restricted primitive model and the entropy decreases, while a central cation deforms the ionic atmosphere surrounding it and the entropy increases. In the low concentration regime good agreement is seen between the results from the Debye-Hückel limiting law and the corresponding simulations.

High-pressure phase transitions and melt structure of PbO2 : An analog for silica

In situ x-ray diffraction measurements and inverse Monte Carlo simulations of pair distribution functions were used to study the structural response of $\mathrm{Pb}{\mathrm{O}}_{2}$ under pressure and to characterize the local structure of liquid $\mathrm{Pb}{\mathrm{O}}_{2}$. Two phase transitions are observed upon room-temperature compression of crystalline $\mathrm{Pb}{\mathrm{O}}_{2}$ up to \ensuremath{\sim}65 GPa. The starting mixture of rutile structured $\ensuremath{\beta}\text{\ensuremath{-}}\mathrm{Pb}{\mathrm{O}}_{2}$ and orthorhombic $\ensuremath{\alpha}\text{\ensuremath{-}}\mathrm{Pb}{\mathrm{O}}_{2}$ undergoes a transition to a ${\mathrm{ZrO}}_{2}$-type orthorhombic phase with space group $Pbca$ at \ensuremath{\sim}21 GPa. Above 42 GPa, the $Pbca$ phase transforms to a cotunnite-type phase with space group $Pnam$. In this paper, we also report short-range order in liquid $\mathrm{Pb}{\mathrm{O}}_{2}$, showing \ensuremath{\sim}8--9-fold and 4--5-fold coordination around Pb and O atoms, respectively.

Environmental wave contours by inverse FORM and Monte Carlo Simulation with variance reduction techniques

Environmental contours of significant wave height and wave period are established for 10, 25 and 100 year-return periods by different approaches. The environmental contours are first derived by Direct sampling and by the Inverse First Order Reliability method (IFORM) using the Rosenblatt transformation. Then, the importance sampling technique is applied at different locations along the environmental contours to reduce the variance of the estimates and, consequently, to increase the accuracy and efficiency of the prediction method. The different environmental contours are derived from a large collection of hindcast wave data from offshore of Canary Islands, which is used as a case study to compare the different approaches.

From a proximal-deposition-dominated basin sink to a significant sediment source to the Chinese Loess Plateau: Insight from the quantitative provenance analysis on the Cenozoic sediments in the Qaidam basin, northern Tibetan Plateau

A better understanding of the Cenozoic source to sink relationship between the Qaidam Basin and the surrounding regions allows us to reveal the topographic evolution of the northern edge of Tibetan Plateau in response to the India-Asian collision and the Asian aridification process. However, the depositional history and provenance of Paleogene strata in the southwestern/northeastern Qaidam Basin and the genetic linkage between the Qaidam Basin and Cenozoic Chinese Loess Plateau is still debated. Here we compile ca. 12,000 U-Pb zircon analyses from the Qaidam Basin, Chinese Loess Plateau and the surrounding regions, and conduct quantitative provenance analysis using a MATLAB-based Inverse Monte Carlo simulation technique. When integrated with variations in stratigraphic thickness and lithology across the basin, our analysis suggests the minor topographic relief separating the Qaidam Basin from the Hoh Xil Basin to the south, served as the major source for the sediments deposited in the SW Qaidam Basin since the Paleogene. The Qilian Shan to the north, the underlying Mesozoic strata and the local paleo-reliefs to the southwest within the basin shed materials into the NE Qaidam Basin during the Paleogene. This finding exemplifies the fact that detrital zircon geochronology alone would lead to an incorrect interpretation if independent sedimentary evidence is not considered. Based on U-Pb detrital zircon geochronology data from Pliocene-Quaternary and loess samples collected from various locations in both the Qaidam Basin and Chinese Loess Plateau, our quantitative estimate shows that approximately 30% of materials in the Chinese Loess Plateau are derived from the sediments in the Qaidam Basin, twice the previous estimate. This higher proportion of the Qaidam Basin source for the Chinese Loess Plateau highlights that using a spatially limited sample set from the Qaidam Basin would result in underrating its contribution to the sediments preserved in the Chinese Loess Plateau.

Determination of the optical properties of cholesteatoma in the spectral range of 250 to 800 nm.

Cholesteatoma of the ear can lead to life-threatening complications and its only treatment is surgery. The smallest remnants of cholesteatoma can lead to recurrence of this disease. Therefore, the optical properties of this tissue are of high importance to identify and remove all cholesteatoma during therapy. In this paper, we determine the absorption coefficient µ a and scattering coefficient µ s ' of cholesteatoma and bone samples in the wavelength range of 250 nm to 800 nm obtained during five surgeries. These values are determined by high precision integrating sphere measurements in combination with an optimized inverse Monte Carlo simulation (iMCS). To conserve the optical behavior of living tissues, the optical spectroscopy measurements are performed immediately after tissue removal and preparation. It is shown that in the near-UV and visible spectrum clear differences exist between cholesteatoma and bone tissue. While µ a is decreasing homogeneously for cholesteatoma, it retains at the high level for bone in the region of 350 nm to 580 nm. Further, the results for the cholesteatoma measurements correspond to published healthy epidermis data. These differences in the optical parameters reveal the future possibility to detect and identify, automatically or semi-automatically, cholesteatoma tissue for active treatment decisions during image-guided surgery leading to a better surgical outcome.

Three-dimensional rendering of trabecular bone microarchitecture using a probabilistic approach

In the past, researchers have attempted to model trabecular bone using computational techniques. However, only a few of these models are visually similar, but not representative of the microstructural characteristics of real trabecular bones. In this study, we hypothesized that probabilistic modeling approaches could be used to generate representative digital models that capture the microstructural features of real trabecular bones. To test this hypothesis, we proposed a novel mathematical framework to build the digital models and compared the digital models to real bone specimens. First, an initial three-dimensional cellular structure was generated using Voronoi tessellation, with the faces and edges of the Voronoi cells considered as a pool of potential trabecular plates and rods, respectively. Then, inverse Monte Carlo simulations were performed to select, delete, or reassign plates and rods until the underlying size, orientation, and spatial distributions of the plates and rods converged to the target distributions obtained from real trabecular bone microstructures. Next, digital graphics techniques were used to define the thickness of trabecular plates and the diameter of trabecular rods, followed by writing the model into a Standard Tessellation Language file and then smoothing the model surfaces for a more natural appearance. To verify the efficacy of the digital model in capturing the microstructural features of real trabecular bones, forty-six digital models with a large variation in microstructural features were generated based on the target distributions obtained from trabecular bone specimens of twelve human cadaveric femurs. Then, the histomorphological parameters of the digital models were compared with those of the real trabecular bone specimens. The results indicate that the digital models are capable of capturing major microstructural features of the trabecular bone samples, thus proving the hypothesis that the proposed probabilistic modeling approach could render real trabecular bone microstructures.

Determination of optical properties of human tissues obtained from parotidectomy in the spectral range of 250 to 800nm.

.The optical properties of human tissues are an important parameter in medical diagnostics and therapy. The knowledge of these parameters can encourage the development of automated, computer-driven optical tissue analysis methods. We determine the absorption coefficient and scattering coefficient of different tissue types obtained during parotidectomy in the wavelength range of 250 to 800 nm. These values are determined by high precision integrating sphere measurements in combination with an optimized inverse Monte Carlo simulation. To conserve the optical behavior of living tissues, the optical spectroscopy measurements are performed immediately after tissue removal. Our study includes fresh samples of the ear, nose, and throat (ENT) region, as muscle tissue, nervous tissue, white adipose tissue, stromal tissue, parotid gland, and tumorous tissue of five patients. The measured behavior of adipose corresponds well with the literature, which sustains the applied method. It is shown that muscle is well supplied with blood as it features the same characteristic peaks at 430 and 555 nm in the absorption curve. The parameter decreases for all tissue types above 570 nm. The accuracy is adequate for the purposes of providing and of different human tissue types as muscle, fat, nerve, or gland tissue, which are embedded in large complex structures such as in the ENT area. It becomes possible for the first time to present reasonable results for the optical behavior of human soft tissue located in the ENT area and in the near-UV, visual, and near-infrared areas.

Agarose-based Tissue Mimicking Optical Phantoms for Diffuse Reflectance Spectroscopy.

This protocol describes how to make agarose-based tissue-mimicking phantoms and demonstrates how to determine their optical properties using a conventional optical system with an integrating sphere. Measuring systems for the acquisition of the diffuse reflectance and total transmittance spectra are constructed with a broadband white light source, a light guide, an achromatic lens, an integrating sphere, a sample holder, an optical fiber probe, and a multi-channel spectrometer. An acrylic mold consisting of two rectangular acrylic pieces and a U-shaped acrylic piece is constructed to create an epidermal phantom and a dermal phantom with whole blood. The application of a sodium dithionite (Na2S2O4) solution to the dermal phantom enables the researcher to deoxygenate hemoglobin in red blood cells distributed in the dermal phantom. The inverse Monte Carlo simulation with the diffuse reflectance and total transmittance spectra measured by a spectrometer with an integrating sphere is performed to determine the absorption coefficient spectrum µa(λ) and the reduced scattering coefficient spectrum µs'(λ) of each layer phantom. A two-layered phantom mimicking the diffuse reflectance of human skin tissue is also demonstrated by piling up the epidermal phantom on the dermal phantom.

Local structure of molten AuGa2 under pressure: Evidence for coordination change and planetary implications

In situ x-ray diffraction measurements and inverse Monte Carlo simulations of pair distribution functions were used to characterize the local structure of molten AuGa2 up to 16 GPa and 940 K. Our results document systematic changes in liquid structure due to a combination of bond compression and coordination increase. Empirical potential structure refinement shows the first-neighbor coordination of Ga around Au and of Au around Ga to increase from about 8 to 10 and 4 to 5, respectively between 0 and 16 GPa, and the inferred changes in liquid structure can explain the observed melting-point depression of AuGa2 up to 5 GPa. As intermetallic AuGa2 is an analogue for metallic SiO2 at much higher pressures, our results imply that structural changes documented for non-metallic silicate melts below 100 GPa are followed by additional coordination changes in the metallic state at pressures in the 0.2–1 TPa range achieved inside large planets.

Measurement of optical properties of pig esophagus by using a modified spectrometer set-up.

Optical properties (μa , μs and g) of certain human tissue types such as skin and blood have been very well investigated. However until today, for internal body organs such as the esophagus they are not well characterized. For ex-vivo measurements "Inverse Adding Doubling" (IAD) and Inverse Monte-Carlo-Simulation (IMCS) are state of the art. Both methods need the measurement of the collimated transmission. Current methods lack a proper way of measuring the collimated transmission. Hence, this measurement of the g-factor has a systematic error. Therefore, for the measurement of the collimated transmission, a new approach has been developed and evaluated with intralipid. Finally, the optical properties of mucosa, sub mucosa, muscularis and adventitia of pig esophagus tissue are calculated with IAD. The results are promising and in agreement with published literature.

Optical properties of peritoneal biological tissues in the spectral range of 350–2500 nm

The optical characteristics of biological tissues sampled from the anterior abdominal wall of laboratory rats are for the first time experimentally studied in a wide wavelength range (350-2500 nm). The experiments have been performed in vitro using a LAMBDA 950 (PerkinElmer, United States) spectrophotometer. Inverse Monte Carlo simulation is used to restore the spectral dependences for scattering and absorption coefficients, as well as the scattering anisotropy factor for biological tissue based on the recorded spectra of diffuse reflection and total and collimated transmissions.

Determination of the scattering coefficient of biological tissue considering the wavelength and absorption dependence of the anisotropy factor

The anisotropy factor g, one of the optical properties of biological tissues, has a strong influence on the calculation of the scattering coefficient μ s in inverse Monte Carlo (iMC) simulations. It has been reported that g has the wavelength and absorption dependence; however, few attempts have been made to calculate μ s using g values by taking the wavelength and absorption dependence into account. In this study, the angular distributions of scattered light for biological tissue phantoms containing hemoglobin as a light absorber were measured by a goniometric optical setup at strongly (405 nm) and weakly (664 nm) absorbing wavelengths to obtain g. Subsequently, the optical properties were calculated with the measured values of g by integrating sphere measurements and an iMC simulation, and compared with the results obtained with a conventional g value of 0.9. The μ s values with measured g were overestimated at the strongly absorbing wavelength, but underestimated at the weakly absorbing wavelength if 0.9 was used in the iMC simulation.

Influence of diffuse reflectance measurement accuracy on the scattering coefficient in determination of optical properties with integrating sphere optics (a secondary publication).

An estimation error of the scattering coefficient of hemoglobin in the high absorption wavelength range has been observed in optical property calculations of blood-rich tissues. In this study, the relationship between the accuracy of diffuse reflectance measurement in the integrating sphere and calculated scattering coefficient was evaluated with a system to calculate optical properties combined with an integrating sphere setup and the inverse Monte Carlo simulation. Diffuse reflectance was measured with the integrating sphere using a small incident port diameter and optical properties were calculated. As a result, the estimation error of the scattering coefficient was improved by accurate measurement of diffuse reflectance. In the high absorption wavelength range, the accuracy of diffuse reflectance measurement has an effect on the calculated scattering coefficient.

OPTICAL MEASUREMENTS OF RAT MUSCLE SAMPLES UNDER TREATMENT WITH ETHYLENE GLYCOL AND GLUCOSE

With the objective to study the variation of optical properties of rat muscle during optical clearing, we have performed a set of optical measurements from that kind of tissue. The measurements performed were total transmittance, collimated transmittance, specular reflectance and total reflectance. This set of measurements is sufficient to determine diffuse reflectance and absorbance of the sample, also necessary to estimate the optical properties. All the performed measurements and calculated quantities will be used later in inverse Monte Carlo (IMC) simulations to determine the evolution of the optical properties of muscle during treatments with ethylene glycol and glucose. The results obtained with the measurements already provide some information about the optical clearing treatments applied to the muscle and translate the mechanisms of turning the tissue more transparent and sequence of regimes of optical clearing.

Activity coefficient of the dipolar Yukawa and Stockmayer fluids from the inverse grand-canonical Monte Carlo simulation

The inverse grand-canonical Monte Carlo (IGCMC) simulation is applied to calculate the activity coefficient of the dipolar Yukawa and Stockmayer fluids. The dependence of the activity coefficient and its dipolar contribution on the number density of a fluid at the reduced temperature T*=3.0 and reduced electric dipole moment (μ*)2=1.0, 3.0, and 5.0 is presented. The results are compared with predictions of: (i) the perturbation theory (PT), (ii) the free energy and virial routes of the mean spherical approximation (MSA), and (iii) Kronome–Liszi–Szalai (KLS) approach (J. Chem. Soc., Faraday Trans. 93 (1997), 3053–3059). Comparison shows that at (μ*)2=5.0 the PT results are in a very good agreement with the IGCMC data. The KLS approach yields the results convergent with the simulation one for low number densities of the fluid while the MSA free energy and virial routes underestimate and overestimate the dipolar interactions, respectively.

Simulation of color perception of layered dental composites using optical properties to evaluate the benefit of esthetic layer preparation technique

ObjectivesEsthetic restorations require that dental restorative materials have similar optical properties to teeth. To improve the color perception, the inhomogeneous morphology of the native tooth can be imitated by layering two optically different restorative materials. However until now the benefit of this method has not been satisfactorily demonstrated. MethodsThe optical parameters, absorption coefficient μa, scattering coefficient μs, anisotropy factor g and effective scattering coefficient μ′s, were determined for the enamel and dentin material of the restorative material systems Artemis® and Herculite XRV®. This was carried out for each material system in the wavelength range between 400 and 700nm using integrating sphere measurements followed by inverse Monte Carlo simulations. ResultsUsing the optical parameters and a forward Monte Carlo simulation, the color perception of layered samples could be predicted with a sufficient degree of accuracy. The total color impression was shown to be dependent on the sample thickness and the transparency/translucency of the single layers of enamel and dentin materials. ConclusionThe study demonstrated that the use of two materials is well-suited for the restoration of front teeth with their relatively high proportion of enamel. This study will continue further with the compilation of a data pool of optical parameters which will enable the application of calculation models to optimize the optical approximation of the natural tooth.