Achieving a more realistic assessment of rockfall hazards by coupling three-dimensional process models and field-based tree-ring data

Sound knowledge of the spatial and temporal patterns of rockfalls is fundamental for the management of this very common hazard in mountain environments. Process-based, three-dimensional simulation models are nowadays capable of reproducing the spatial distribution of rockfall occurrences with reasonable accuracy through the simulation of numerous individual trajectories on highly-resolved digital terrain models. At the same time, however, simulation models typically fail to quantify the ‘real’ frequency of rockfalls (in terms of return intervals). The analysis of impact scars on trees, in contrast, yields real rockfall frequencies, but trees may not be present at the location of interest and rare trajectories may not necessarily be captured due to the limited age of forest stands. In this article, we demonstrate that the coupling of modeling with tree-ring techniques may overcome the limitations inherent to both approaches. Based on the analysis of 64 cells (40 m × 40 m) of a rockfall slope located above a 1631-m long road section in the Swiss Alps, we illustrate results from 488 rockfalls detected in 1260 trees. We illustrate that tree impact data cannot only be used (i) to reconstruct the real frequency of rockfalls for individual cells, but that they also serve (ii) the calibration of the rockfall model Rockyfor3D, as well as (iii) the transformation of simulated trajectories into real frequencies. Calibrated simulation results are in good agreement with real rockfall frequencies and exhibit significant differences in rockfall activity between the cells (zones) along the road section. Real frequencies, expressed as rock passages per meter road section, also enable quantification and direct comparison of the hazard potential between the zones. The contribution provides an approach for hazard zoning procedures that complements traditional methods with a quantification of rockfall frequencies in terms of return intervals through a systematic inclusion of impact records in trees.

Low-dimensional modeling of streaks in a wedge flow boundary layer

This paper is concerned with the low dimensional structure of optimal streaks in a wedge flow boundary layer, which have been recently shown to consist of a unique (up to a constant factor) three-dimensional streamwise evolving mode, known as the most unstable streaky mode. Optimal streaks exhibit a still unexplored/unexploited approximate self-similarity (not associated with the boundary layer self-similarity), namely the streamwise velocity re-scaled with their maximum remains almost independent of both the spanwise wavenumber and the streamwise coordinate; the remaining two velocity components instead do not satisfy this property. The approximate self-similar behavior is analyzed here and exploited to further simplify the description of optimal streaks. In particular, it is shown that streaks can be approximately described in terms of the streamwise evolution of the scalar amplitudes of just three one-dimensional modes, providing the wall normal profiles of the streamwise velocity and two combinations of the cross flow velocity components; the scalar amplitudes obey a singular system of three ordinary differential equations (involving only two degrees of freedom), which approximates well the streamwise evolution of the general streaks.

Computational adaptive optics for live three-dimensional biological imaging

Light microscopy of thick biological samples, such as tissues, is often limited by aberrations caused by refractive index variations within the sample itself. This problem is particularly severe for live imaging, a field of great current excitement due to the development of inherently fluorescent proteins. We describe a method of removing such aberrations computationally by mapping the refractive index of the sample using differential interference contrast microscopy, modeling the aberrations by ray tracing through this index map, and using space-variant deconvolution to remove aberrations. This approach will open possibilities to study weakly labeled molecules in difficult-to-image live specimens.

Photoactive yellow protein: A structural prototype for the three-dimensional fold of the PAS domain superfamily

PAS domains are found in diverse proteins throughout all three kingdoms of life, where they apparently function in sensing and signal transduction. Although a wealth of useful sequence and functional information has become recently available, these data have not been integrated into a three-dimensional (3D) framework. The very early evolutionary development and diverse functions of PAS domains have made sequence analysis and modeling of this protein superfamily challenging. Limited sequence similarities between the ∼50-residue PAS repeats and one region of the bacterial blue-light photosensor photoactive yellow protein (PYP), for which ground-state and light-activated crystallographic structures have been determined to high resolution, originally were identified in sequence searches using consensus sequence probes from PAS-containing proteins. Here, we found that by changing a few residues particular to PYP function, the modified PYP sequence probe also could select PAS protein sequences. By mapping a typical ∼150-residue PAS domain sequence onto the entire crystallographic structure of PYP, we show that the PAS sequence similarities and differences are consistent with a shared 3D fold (the PAS/PYP module) with obvious potential for a ligand-binding cavity. Thus, PYP appears to prototypically exhibit all the major structural and functional features characteristic of the PAS domain superfamily: the shared PAS/PYP modular domain fold of ∼125–150 residues, a sensor function often linked to ligand or cofactor (chromophore) binding, and signal transduction capability governed by heterodimeric assembly (to the downstream partner of PYP). This 3D PAS/PYP module provides a structural model to guide experimental testing of hypotheses regarding ligand-binding, dimerization, and signal transduction.

Modelling continuum mechanics phenomena using three dimensional unstructured meshes on massively parallel processors

The difficulties encountered in implementing large scale CM codes on multiprocessor systems are now fairly well understood. Despite the claims of shared memory architecture manufacturers to provide effective parallelizing compilers, these have not proved to be adequate for large or complex programs. Significant programmer effort is usually required to achieve reasonable parallel efficiencies on significant numbers of processors. The paradigm of Single Program Multi Data (SPMD) domain decomposition with message passing, where each processor runs the same code on a subdomain of the problem, communicating through exchange of messages, has for some time been demonstrated to provide the required level of efficiency, scalability, and portability across both shared and distributed memory systems, without the need to re-author the code into a new language or even to support differing message passing implementations. Extension of the methods into three dimensions has been enabled through the engineering of PHYSICA, a framework for supporting 3D, unstructured mesh and continuum mechanics modeling. In PHYSICA, six inspectors are used. Part of the challenge for automation of parallelization is being able to prove the equivalence of inspectors so that they can be merged into as few as possible.

Three-dimensional, in-silico breast phantom for multimodality image simulations

We report on the construction of anatomically realistic three-dimensional in-silico breast phantoms with adjustable sizes, shapes and morphologic features. The concept of multiscale spatial resolution is implemented for generating breast tissue images from multiple modalities. Breast epidermal boundary and subcutaneous fat layer is generated by fitting an ellipsoid and 2nd degree polynomials to reconstructive surgical data and ultrasound imaging data. Intraglandular fat is simulated by randomly distributing and orienting adipose ellipsoids within a fibrous region immediately within the dermal layer. Cooper’s ligaments are simulated as fibrous ellipsoidal shells distributed within the subcutaneous fat layer. Individual ductal lobes are simulated following a random binary tree model which is generated based upon probabilistic branching conditions described by ramification matrices, as originally proposed by Bakic et al [3, 4]. The complete ductal structure of the breast is simulated from multiple lobes that extend from the base of the nipple and branch towards the chest wall. As lobe branching progresses, branches are reduced in height and radius and terminal branches are capped with spherical lobular clusters. Biophysical parameters are mapped onto the complete anatomical model and synthetic multimodal images (Mammography, Ultrasound, CT) are generated for phantoms of different adipose percentages (40%, 50%, 60%, and 70%) and are analytically compared with clinical examples. Results demonstrate that the in-silico breast phantom has applications in imaging performance evaluation and, specifically, great utility for solving image registration issues in multimodality imaging.

Three dimensional circulation of water with variable wind in the Caspian Sea

This research is based on a numerical model for forecasting the three-dimensional behavior of (sea) water motion due to the effect of a variable wind velocity. The results obtained are then analyzed and compared with observation. This model is based on the equations that overcome the current and distribution of temperature by applying the method of finite difference with assuming Δx, Δy as constant and Δz, variable. The model is based on the momentum equation, continuity equation and thermodynamic energy equation and tension at the surface and middle layers and bottom stress. The horizontal and vertical eddy viscosity and thermal diffusivity coefficients we used in accordance with that of the Bennet on Outario Lake (1977). Considering the Caspian Sea dimension in numerical model the Coriolis parameter used with β effects and the approximation Boussines have been used. For the program controlling some simple experiment with boundary condition similar to that of the Caspian Sea have been done. For modeling the Caspian Sea the grid of the field was done as follows: At horizontal surface grid size is 10×10km extension and at vertical in 10 layers with varying thickness from surface to bed respectively as: 5, 10, 20, 3, 50, 100, 150, 200, 25, 500 and higher. The data of wind as velocity، direction and temperature of water related to 15th September 1995 at 6،12 and 18 o’clock were obtained from synoptic station at the Caspian Sea shore and the research marine of Haji Alief. The information concerning shore wind was measured and by the method of SPM (shore protection manual) was transferred to far shore winds through interpolation and by use of inverse square distance of position distribution of the wind velocity at the Caspian surface field was obtained. The model has been evaluated according to the reports and observations. Through studying the position of the current in different layers، the velocity in the cross section in the northern، southern and the middle layers، will be discussed. The results reveal the presence of the circulation cells in the three above mentioned areas. The circulation with depth is reduced too. The results obtained through the numerical solution of the temperature equation have been compared with the observation. The temperature change in different layers in cross section illustrates the relative accordance of the model mentioned.

Coupling of Chemical Kinetics with Computational Fluid Dynamics in a Three-Dimensional Engine Model

The role of computer modeling has grown recently to integrate itself as an inseparable tool to experimental studies for the optimization of automotive engines and the development of future fuels. Traditionally, computer models rely on simplified global reaction steps to simulate the combustion and pollutant formation inside the internal combustion engine. With the current interest in advanced combustion modes and injection strategies, this approach depends on arbitrary adjustment of model parameters that could reduce credibility of the predictions. The purpose of this study is to enhance the combustion model of KIVA, a computational fluid dynamics code, by coupling its fluid mechanics solution with detailed kinetic reactions solved by the chemistry solver, CHEMKIN. As a result, an engine-friendly reaction mechanism for n-heptane was selected to simulate diesel oxidation. Each cell in the computational domain is considered as a perfectly-stirred reactor which undergoes adiabatic constant- volume combustion. The model was applied to an ideally-prepared homogeneous- charge compression-ignition combustion (HCCI) and direct injection (DI) diesel combustion. Ignition and combustion results show that the code successfully simulates the premixed HCCI scenario when compared to traditional combustion models. Direct injection cases, on the other hand, do not offer a reliable prediction mainly due to the lack of turbulent-mixing model, inherent in the perfectly-stirred reactor formulation. In addition, the model is sensitive to intake conditions and experimental uncertainties which require implementation of enhanced predictive tools. It is recommended that future improvements consider turbulent-mixing effects as well as optimization techniques to accurately simulate actual in-cylinder process with reduced computational cost. Furthermore, the model requires the extension of existing fuel oxidation mechanisms to include pollutant formation kinetics for emission control studies.

Three dimensional numerical simulation of thermohaline currents of the Persian Gulf

Observational data and a three dimensional numerical model (POM) are used to investigate the Persian Gulf outflow structure and its spreading pathway into the Oman Sea. The model is based on orthogonal curvilinear coordinate system in horizontal and train following coordinate (sigma coordinate) system in vertical. In the simulation, the horizontal diffusivity coefficients are calculated form Smogorinsky diffusivity formula and the eddy vertical diffusivities are obtained from a second turbulence closure model (namely Mellor-Yamada level 2.5 model of turbulence). The modeling area includes the east of the Persian Gulf, the Oman Sea and a part of the north-east of the Indian Ocean. In the model, the horizontal grid spacing was assumed to be about 3.5 km and the number of vertical levels was set to 32. The simulations show that the mean salinity of the PG outflow does not change substantially during the year and is about 39 psu, while its temperature exhibits seasonal variations. These lead to variations in outflow density in a way that is has its maximum density in late winter (March) and its minimum in mid-summer (August). At the entrance to the Oman Sea, the PG outflow turns to the right due to Coriolis Effect and falls down on the continental slope until it gains its equilibrium depth. The highest density of the outflow during March causes it to sink more into the deeper depths in contrast to that of August which the density is the lowest one. Hence, the neutral buoyancy depths of the outflow are about 500 m and 250 m for March and August respectively. Then, the outflow spreads in its equilibrium depths in the Oman Sea in vicinity of western and southern boundaries until it approach the Ras al Hamra Cape where the water depth suddenly begins to increase. Therefore, during March, the outflow that is deeper and wider relative to August, is more affected by the steep slope topography and as a result of vortex stretching mechanism and conservation of potential vorticity it separates from the lateral boundaries and finally forms an anti-cyclonic eddy in the Oman Sea. But during August the outflow moves as before in vicinity of lateral boundaries. In addition, the interaction of the PG outflow with tide in the Strait of Hormuz leads to intermittency in outflow movement into the Oman Sea and it could be the major reason for generations of Peddy (Peddies) in the Oman Sea.

Fully Anisotropic Solution of the Three Dimensional Boltzmann Transport Equation

The development of accurate modeling techniques for nanoscale thermal transport is an active area of research. Modern day nanoscale devices have length scales of tens of nanometers and are prone to overheating, which reduces device performance and lifetime. Therefore, accurate temperature profiles are needed to predict the reliability of nanoscale devices. The majority of models that appear in the literature obtain temperature profiles through the solution of the Boltzmann transport equation (BTE). These models often make simplifying assumptions about the nature of the quantized energy carriers (phonons). Additionally, most previous work has focused on simulation of planar two dimensional structures. This thesis presents a method which captures the full anisotropy of the Brillouin zone within a three dimensional solution to the BTE. The anisotropy of the Brillouin zone is captured by solving the BTE for all vibrational modes allowed by the Born Von-Karman boundary conditions.

Effects Of High Pressure Homogenization On The Activity, Stability, Kinetics And Three-dimensional Conformation Of A Glucose Oxidase Produced By Aspergillus Niger.

High pressure homogenization (HPH) is a non-thermal method, which has been employed to change the activity and stability of biotechnologically relevant enzymes. This work investigated how HPH affects the structural and functional characteristics of a glucose oxidase (GO) from Aspergillus niger. The enzyme was homogenized at 75 and 150 MPa and the effects were evaluated with respect to the enzyme activity, stability, kinetic parameters and molecular structure. The enzyme showed a pH-dependent response to the HPH treatment, with reduction or maintenance of activity at pH 4.5-6.0 and a remarkable activity increase (30-300%) at pH 6.5 in all tested temperatures (15, 50 and 75°C). The enzyme thermal tolerance was reduced due to HPH treatment and the storage for 24 h at high temperatures (50 and 75°C) also caused a reduction of activity. Interestingly, at lower temperatures (15°C) the activity levels were slightly higher than that observed for native enzyme or at least maintained. These effects of HPH treatment on function and stability of GO were further investigated by spectroscopic methods. Both fluorescence and circular dichroism revealed conformational changes in the molecular structure of the enzyme that might be associated with the distinct functional and stability behavior of GO.

Low-density Three-dimensional Foam Using Self-reinforced Hybrid Two-dimensional Atomic Layers.

Low-density nanostructured foams are often limited in applications due to their low mechanical and thermal stabilities. Here we report an approach of building the structural units of three-dimensional (3D) foams using hybrid two-dimensional (2D) atomic layers made of stacked graphene oxide layers reinforced with conformal hexagonal boron nitride (h-BN) platelets. The ultra-low density (1/400 times density of graphite) 3D porous structures are scalably synthesized using solution processing method. A layered 3D foam structure forms due to presence of h-BN and significant improvements in the mechanical properties are observed for the hybrid foam structures, over a range of temperatures, compared with pristine graphene oxide or reduced graphene oxide foams. It is found that domains of h-BN layers on the graphene oxide framework help to reinforce the 2D structural units, providing the observed improvement in mechanical integrity of the 3D foam structure.

Numerical investigation of the three-dimensional secondary instabilities in the time-developing compressible mixing layer

Mixing layers are present in very different types of physical situations such as atmospheric flows, aerodynamics and combustion. It is, therefore, a well researched subject, but there are aspects that require further studies. Here the instability of two-and three-dimensional perturbations in the compressible mixing layer was investigated by numerical simulations. In the numerical code, the derivatives were discretized using high-order compact finite-difference schemes. A stretching in the normal direction was implemented with both the objective of reducing the sound waves generated by the shear region and improving the resolution near the center. The compact schemes were modified to work with non-uniform grids. Numerical tests started with an analysis of the growth rate in the linear regime to verify the code implementation. Tests were also performed in the non-linear regime and it was possible to reproduce the vortex roll-up and pairing, both in two-and three-dimensional situations. Amplification rate analysis was also performed for the secondary instability of this flow. It was found that, for essentially incompressible flow, maximum growth rates occurred for a spanwise wavelength of approximately 2/3 of the streamwise spacing of the vortices. The result demonstrated the applicability of the theory developed by Pierrehumbet and Widnall. Compressibility effects were then considered and the maximum growth rates obtained for relatively high Mach numbers (typically under 0.8) were also presented.

Determination of Three-Dimensional Left Ventricle Motion to Analyze Ventricular Dyssyncrony in SPECT Images

A method to compute three-dimension (3D) left ventricle (LV) motion and its color coded visualization scheme for the qualitative analysis in SPECT images is proposed. It is used to investigate some aspects of Cardiac Resynchronization Therapy (CRT). The method was applied to 3D gated-SPECT images sets from normal subjects and patients with severe Idiopathic Heart Failure, before and after CRT. Color coded visualization maps representing the LV regional motion showed significant difference between patients and normal subjects. Moreover, they indicated a difference between the two groups. Numerical results of regional mean values representing the intensity and direction of movement in radial direction are presented. A difference of one order of magnitude in the intensity of the movement on patients in relation to the normal subjects was observed. Quantitative and qualitative parameters gave good indications of potential application of the technique to diagnosis and follow up of patients submitted to CRT.

Three-dimensional finite element thermal analysis of dental tissues irradiated with Er,Cr:YSGG laser

In the present study, a finite element model of a half-sectioned molar tooth was developed in order to understand the thermal behavior of dental hard tissues (both enamel and dentin) under laser irradiation. The model was validated by comparing it with an in vitro experiment where a sound molar tooth was irradiated by an Er,Cr:YSGG pulsed laser. The numerical tooth model was conceived to simulate the in vitro experiment, reproducing the dimensions and physical conditions of the typical molar sound tooth, considering laser energy absorption and calculating the heat transfer through the dental tissues in three dimensions. The numerical assay considered the same three laser energy densities at the same wavelength (2.79 mu m) used in the experiment. A thermographic camera was used to perform the in vitro experiment, in which an Er, Cr: YSGG laser (2.79 mu m) was used to irradiate tooth samples and the infrared images obtained were stored and analyzed. The temperature increments in both the finite element model and the in vitro experiment were compared. The distribution of temperature inside the tooth versus time plotted for two critical points showed a relatively good agreement between the results of the experiment and model. The three dimensional model allows one to understand how the heat propagates through the dentin and enamel and to relate the amount of energy applied, width of the laser pulses, and temperature inside the tooth. (C) 2008 American Institute of Physics. [DOI: 10.1063/1.2953526]