Simulation and experimental verification of the diffusion in an anisotropic fiber phantom

Diffusion weighted magnetic resonance imaging enables the visualization of fibrous tissues such as brain white matter. The validation of this non-invasive technique requires phantoms with a well-known structure and diffusion behavior. This paper presents anisotropic diffusion phantoms consisting of parallel fibers. The diffusion properties of the fiber phantoms are measured using diffusion weighted magnetic resonance imaging and bulk NMR measurements. To enable quantitative evaluation of the measurements, the diffusion in the interstitial space between fibers is modeled using Monte Carlo simulations of random walkers. The time-dependent apparent diffusion coefficient and kurtosis, quantifying the deviation from a Gaussian diffusion profile, are simulated in 3D geometries of parallel fibers with varying packing geometries and packing densities. The simulated diffusion coefficients are compared to the theory of diffusion in porous media, showing a good agreement. Based on the correspondence between simulations and experimental measurements, the fiber phantoms are shown to be useful for the quantitative validation of diffusion imaging on clinical MRI-scanners.     

Restricted diffusion in a model acinar labyrinth by NMR: theoretical and numerical results

A branched geometrical structure of the mammal lungs is known to be crucial for rapid access of oxygen to blood. But an important pulmonary disease like emphysema results in partial destruction of the alveolar tissue and enlargement of the distal airspaces, which may reduce the total oxygen transfer. This effect has been intensively studied during the last decade by MRI of hyperpolarized gases like helium-3. The relation between geometry and signal attenuation remained obscure due to a lack of realistic geometrical model of the acinar morphology. In this paper, we use Monte Carlo simulations of restricted diffusion in a realistic model acinus to compute the signal attenuation in a diffusion-weighted NMR experiment. We demonstrate that this technique should be sensitive to destruction of the branched structure: partial removal of the interalveolar tissue creates loops in the tree-like acinar architecture that enhance diffusive motion and the consequent signal attenuation. The role of the local geometry and related practical applications are discussed.     

NMR 中非线性梯度场下扩散行为的理论描述和蒙特卡罗模拟

利用传播子方法研究了在一般非线性场梯度下NMR信号的扩散衰减. 在自由扩散和平板间的限制扩散情况下获得了扩散衰减因子的理论表达式. 该表达式适用范围宽，且具有较简单的数学形式和明确的物理意义. 文中还将理论预测与蒙特卡罗模拟结果进行了比较. 结果表明：文中所采用的理论方法适合于表述自由扩散和短脉冲近似下的受限扩散；蒙特卡罗模拟提供了一种定性研究MRI和NMR中非均匀场梯度扩散衰减的方法.     

On the effects of dephasing due to local gradients in diffusion tensor imaging experiments: relevance for diffusion tensor imaging fiber phantoms

The effect of susceptibility differences between fluid and fibers on the properties of DTI fiber phantoms was investigated. Thereto, machine-made, easily producible and inexpensive DTI fiber phantoms were constructed by winding polyamide fibers of 15 microm diameter around a circular acrylic glass spindle. The achieved fractional anisotropy was 0.78+/-0.02. It is shown by phantom measurements and Monte Carlo simulations that the transversal relaxation time T(2) strongly depends on the angle between the fibers and the B(0) field if the susceptibilities of the fibers and fluid are not identical. In the phantoms, the measured T(2) time at 3 T decreased by 60% for fibers running perpendicular to B(0). Monte Carlo simulations confirmed this result and revealed that the exact relaxation time depends strongly on the exact packing of the fibers. In the phantoms, the measured diffusion was independent of fiber orientation. Monte Carlo simulations revealed that the measured diffusion strongly depends on the exact fiber packing and that field strength and -orientation dependencies of measured diffusion may be minimal for hexagonal packing while the diffusion can be underestimated by more than 50% for cubic packing at 3 T. To overcome these effects, the susceptibilities of fibers and fluid were matched using an aqueous sodium chloride solution (83 g NaCl per kilogram of water). This enables an orientation independent and reliable use of DTI phantoms for evaluation purposes.     

Benchmarking and validation of a Geant4–SHADOW Monte Carlo simulation for dose calculations in microbeam radiation therapy

Microbeam radiation therapy (MRT) is a synchrotron‐based radiotherapy modality that uses high‐intensity beams of spatially fractionated radiation to treat tumours. The rapid evolution of MRT towards clinical trials demands accurate treatment planning systems (TPS), as well as independent tools for the verification of TPS calculated dose distributions in order to ensure patient safety and treatment efficacy. Monte Carlo computer simulation represents the most accurate method of dose calculation in patient geometries and is best suited for the purpose of TPS verification. A Monte Carlo model of the ID17 biomedical beamline at the European Synchrotron Radiation Facility has been developed, including recent modifications, using the Geant4 Monte Carlo toolkit interfaced with the SHADOW X‐ray optics and ray‐tracing libraries. The code was benchmarked by simulating dose profiles in water‐equivalent phantoms subject to irradiation by broad‐beam (without spatial fractionation) and microbeam (with spatial fractionation) fields, and comparing against those calculated with a previous model of the beamline developed using the PENELOPE code. Validation against additional experimental dose profiles in water‐equivalent phantoms subject to broad‐beam irradiation was also performed. Good agreement between codes was observed, with the exception of out‐of‐field doses and toward the field edge for larger field sizes. Microbeam results showed good agreement between both codes and experimental results within uncertainties. Results of the experimental validation showed agreement for different beamline configurations. The asymmetry in the out‐of‐field dose profiles due to polarization effects was also investigated, yielding important information for the treatment planning process in MRT. This work represents an important step in the development of a Monte Carlo‐based independent verification tool for treatment planning in MRT.     

Simulation of small molecule diffusion using continuous space disordered networks

Disordered networks were created and kinetic Monte Carlo simulations were conducted in order to assess the effects of jump network connectivity on the diffusion coefficient. Off-lattice jump networks were created using reverse Monte Carlo, with an objective function defined by agreement to specified inter-site connectivity, inter-site (jump path) distance and consecutive jump angle distributions. Both Gaussian and Poisson distributions of connectivity were applied, with average connectivities spanning a range appropriate for small molecules within a variety of polymers. Distance and angle distributions were taken from earlier work on jump networks in polypropylene. At short times, anomalous diffusion with a range of exponents n ≥ 0.4 was found over the domain of average connectivities. At longer times, diffusion was normal for connectivities above the percolation threshold, while particles were trapped for lower connectivities. The percolation threshold was slightly higher for Gaussian distributions of connectivity than for Poisson distributions. The diffusion coefficient increased linearly for connectivities well above the threshold, with slightly faster diffusion occurring for Gaussian distributions of connectivity.     

Measurements of restricted diffusion using an oscillating gradient spin-echo sequence

An oscillating gradient spin-echo (OGSE) pulse sequence was used to measure the apparent diffusion coefficient (D(app)) of water in the short diffusion time regime in the presence of restrictions. The diffusion coefficients of water in a simple water sample and a water and oil mixture were measured to be the same for different periods of the gradient oscillation, as expected when there are no restriction effects. The D(app) of water in the spaces between closely packed beads was also measured as a function of the gradient oscillation periods in the range 11 to 80 ms. The D(app) of water in restricted systems varies with the period of the gradient oscillation and the dispersion depends on the scale of the restriction. For a sample of packed beads of diameter 9.1 +/- 0.7 microm, the pore surface-to-volume ratio was estimated experimentally by this method to be 1.3 +/- 0.1 microm(-1), corresponding to a mean pore diameter of 6.4 +/- 0.7 microm. A Monte Carlo computer simulation of the NMR OGSE signal from the spins diffusing in a system of compartments was also implemented and the D(app) demonstrated similar behavior with gradient oscillation periods.     

Continuum model for low temperature relaxation of crystal steps

High and low temperature relaxation of crystal steps are described in a unified picture, using a continuum model based on a modified expression of the step-free energy. Results are in agreement with experiments and Monte Carlo simulations of step fluctuations and monolayer cluster diffusion and relaxation. In an extended model where mass exchange with neighboring terraces is allowed, step transparency and a low temperature regime for unstable step meandering are found.     

Comparison between fixed and Gaussian steplength in Monte Carlo simulations for diffusion processes

We analyze the different degrees of accuracy of two Monte Carlo methods for the simulation of one-dimensional diffusion processes with homogeneous or spatial dependent diffusion coefficient that we assume correctly described by a differential equation. The methods analyzed correspond to fixed and Gaussian steplengths. For a homogeneous diffusion coefficient it is known that the Gaussian steplength generates exact results at fixed time steps Δt. For spatial dependent diffusion coefficients the symmetric character of the Gaussian distribution introduces an error that increases with time. As an example, we consider a diffusion coefficient with constant gradient and show that the error is not present for fixed steplength with appropriate asymmetric jump probabilities.     

Density dependence of the transition temperature in a homogeneous bose-einstein condensate

Transition temperature data obtained as a function of particle density in the 4He-Vycor system are compared with recent theoretical calculations for 3D Bose-condensed systems. In the low density dilute Bose gas regime we find, in agreement with theory, a positive shift in the transition temperature of the form DeltaT/T0 = gamma(na(3))(1/3). At higher densities a maximum is found in the ratio of T(c)/T0 for a value of the interaction parameter, na(3), that is in agreement with path-integral Monte Carlo calculations.     

An efficient diffusion approximation for 3D radiative transfer parameterization: application to cloudy atmospheres

The three-dimensional (3D) diffusion radiative transfer equation, which utilizes a four-term spherical harmonics expansion for the scattering phase function and intensity, has been efficiently solved by using the full multigrid numerical method. This approach can simulate the transfer of solar and thermal infrared radiation in inhomogeneous cloudy conditions with different boundary conditions and sharp boundary discontinuity. The correlated k-distribution method is used in this model for incorporation of the gaseous absorption in multiple-scattering atmospheres for the calculation of broadband fluxes and heating rates in the solar and infrared spectra. Comparison of the results computed from this approach with those computed from plane-parallel and 3D Monte Carlo models shows excellent agreement. This 3D radiative transfer approach is well suited for radiation parameterization involving 3D and inhomogeneous clouds in climate models.     

Growth kinetics of metastable (3 3 1) nanofacet on Au and Pt(1 1 0) surfaces

A theoretical epitaxial growth model with realistic barriers for surface diffusion is investigated by means of kinetic Monte Carlo simulations to study the growth modes of metastable (3 3 1) nanofacets on Au and Pt(1 1 0) surfaces. The results show that under experimental atomic fluxes, the (3 3 1) nanofacets grow by 2D nucleation at low temperature in the submonolayer regime. A metastable growth phase diagram that can be useful to experimentalists is presented and looks similar to the one found for the stationary growth of the bcc(0 0 1) surface in the kinetic 6-vertex model.     

Beyond the Tonks-Girardeau gas: strongly correlated regime in quasi-one-dimensional Bose gases

We consider a homogeneous 1D Bose gas with contact interactions and a large attractive coupling constant. This system can be realized in tight waveguides by exploiting a confinement induced resonance of the effective 1D scattering amplitude. By using the diffusion Monte Carlo method we show that, for small densities, the gaslike state is well described by a gas of hard rods. The critical density for cluster formation is estimated using the variational Monte Carlo method. The behavior of the correlation functions and of the frequency of the lowest breathing mode for harmonically trapped systems shows that the gas is more strongly correlated than in the Tonks-Girardeau regime.     

Experimental and numerical study on simultaneous effects of scattering and absorption on fluorescence spectroscopy of a breast phantom

Detection of dysplastic lesions can decrease morbidity and mortality caused by cancer. The fluorescence spectroscopy is a noninvasive method of detecting dysplasia in several organs. During dysplastic progression, fluorescence intensity of spectrum is changed due to variation in absorption and scattering coefficients of tissue. In this work we have experimentally verified simultaneous effects of scattering and absorption coefficients on fluorescence intensity of different tissue like phantoms with the same optical properties as the human breast ductal carcinoma. The results are compared with those obtained by Monte Carlo simulation and good agreement between them is observed. This provides an important detecting method to discriminate dysplastic tissue from normal tissue.     

Inverse problems in cancellous bone: estimation of the ultrasonic properties of fast and slow waves using Bayesian probability theory

Quantitative ultrasonic characterization of cancellous bone can be complicated by artifacts introduced by analyzing acquired data consisting of two propagating waves (a fast wave and a slow wave) as if only one wave were present. Recovering the ultrasonic properties of overlapping fast and slow waves could therefore lead to enhancement of bone quality assessment. The current study uses Bayesian probability theory to estimate phase velocity and normalized broadband ultrasonic attenuation (nBUA) parameters in a model of fast and slow wave propagation. Calculations are carried out using Markov chain Monte Carlo with simulated annealing to approximate the marginal posterior probability densities for parameters in the model. The technique is applied to simulated data, to data acquired on two phantoms capable of generating two waves in acquired signals, and to data acquired on a human femur condyle specimen. The models are in good agreement with both the simulated and experimental data, and the values of the estimated ultrasonic parameters fall within expected ranges.     

蒙特卡罗剂量分布去噪中三维高斯和Savitzky-Golay滤波器的改进与混合

对模拟粒子轨迹数较少模拟时间较短的蒙特卡罗粗糙剂量分布进行三维滤波,可以加速其收敛速度.结合蒙特卡罗剂量分布特征,改进三维高斯和Savitzky-Golay滤波器,建立三维混合滤波方法,并比较并联和级联两种基本混合方式.根据卷积性质,提出用等效卷积核简化混合滤波器结构的方法.结果表明,改进后的高斯和Savitzky-Golay滤波器的整体去噪效果得以增强,混合滤波器进一步降低滤波结果的局部误差,两种混合滤波器都能够大幅度抑制MC粗糙剂量分布中的噪声,级联混合滤波器降噪效果略优于并联混合滤波器.     

Validation of the Ability of Full Configuration Interaction Quantum Monte Carlo for Studying the 2D Hubbard Model

To validate the ability of full configuration interaction quantum Monte Carlo(FCIQMC) for studying the 2 D Hubbard model near half-filling regime, the ground state energies of a 4 x 4 square lattice system with various interaction strengths are calculated. It is found that the calculated results are in good agreement with those obtained by exact diagonalization(i.e., the exact values for a given basis set) when the population of psi particles(psips) is higher than the critical population required to correctly sample the ground state wave function. In addition, the variations of the average computational time per 20 Monte Carlo cycles with the coupling strength and the number of processors are also analyzed. The calculated results show that the computational efficiency of an FCIQMC calculation is mainly affected by the total population of psips and the communication between processors. These results can provide useful references for understanding the FCIQMC algorithm, studying the ground state properties of the 2 D Hubbard model for the larger system size by the FCIQMC method and using a computational budget as effectively as possible.     

A Modified Monte Carlo Model of Speckle Tracking of Shear Wave Induced by Acoustic Radiation Force for Acousto-Optic Elasticity Imaging

A modified Monte Carlo model of speckle tracking of shear wave propagation in scattering media is proposed.The established Monte Carlo model mainly concerns the variations of optical electric field and speckle.The twodimensional intensity distribution and the time evolution of speckles in different probe locations are obtained.The fluctuation of speckle intensity tracks the acoustic-radiation-force shear wave propagation,and especially the reduction of speckle intensity implies attenuation of shear wave.Then,the shear wave velocity is estimated quantitatively on the basis of the time-to-peak algorithm and linear regression processing.The results reveal that a smaller sampling interval yields higher estimation precision and the shear wave velocity is estimated more efficiently by using speckle intensity difference than by using speckle contrast difference according to the estimation error.Hence,the shear wave velocity is estimated to be 2.25 m/s with relatively high accuracy for the estimation error reaches the minimum(0.071).     

Bulk mediated surface diffusion: the infinite system case

An analytical soluble model based on a Continuous Time Random Walk (CTRW) scheme for the adsorption-desorption processes at interfaces, called bulk-mediated surface diffusion, is presented. The time evolution of the effective probability distribution width on the surface is calculated and analyzed within an anomalous diffusion framework. The asymptotic behavior for large times shows a sub-diffusive regime for the effective surface diffusion but, depending on the observed range of time, other regimes may be obtained. Monte Carlo simulations show excellent agreement with analytical results. As an important byproduct of the indicated approach, we present the evaluation of the time for the first visit to the surface.Received: 2 September 2003, Published online: 8 December 2003PACS: 05.40.Fb Random walks and Levy flights - 02.50.Ey Stochastic processes - 46.65. + g Random phenomena and media