Simulation of insect movement with respect to plant architecture and morphogenesis

Developments in computer and three dimensional (3D) digitiser technologies have made it possible to keep track of the broad range of data required to simulate an insect moving around or over the highly heterogeneous habitat of a plant's surface. Properties of plant parts vary within a complex canopy architecture, and insect damage can induce further changes that affect an animal's movements, development and likelihood of survival. Models of plant architectural development based on Lindenmayer systems (L-systems) serve as dynamic platforms for simulation of insect movement, providing ail explicit model of the developing 3D structure of a plant as well as allowing physiological processes associated with plant growth and responses to damage to be described and Simulated. Simple examples of the use of the L-system formalism to model insect movement, operating Lit different spatial scales-from insects foraging on an individual plant to insects flying around plants in a field-are presented. Such models can be used to explore questions about the consequences of changes in environmental architecture and configuration on host finding, exploitation and its population consequences. In effect this model is a 'virtual ecosystem' laboratory to address local as well as landscape-level questions pertinent to plant-insect interactions, taking plant architecture into account. (C) 2002 Elsevier Science B.V. All rights reserved.

An atomistic simulation of solid state sintering using Monte Carlo methods

This paper presents results on the simulation of the solid state sintering of copper wires using Monte Carlo techniques based on elements of lattice theory and cellular automata. The initial structure is superimposed onto a triangular, two-dimensional lattice, where each lattice site corresponds to either an atom or vacancy. The number of vacancies varies with the simulation temperature, while a cluster of vacancies is a pore. To simulate sintering, lattice sites are picked at random and reoriented in terms of an atomistic model governing mass transport. The probability that an atom has sufficient energy to jump to a vacant lattice site is related to the jump frequency, and hence the diffusion coefficient, while the probability that an atomic jump will be accepted is related to the change in energy of the system as a result of the jump, as determined by the change in the number of nearest neighbours. The jump frequency is also used to relate model time, measured in Monte Carlo Steps, to the actual sintering time. The model incorporates bulk, grain boundary and surface diffusion terms and includes vacancy annihilation on the grain boundaries. The predictions of the model were found to be consistent with experimental data, both in terms of the microstructural evolution and in terms of the sintering time. (C) 2002 Elsevier Science B.V. All rights reserved.

Conditional simulation of random fields by successive residuals

This paper presents a new approach to the LU decomposition method for the simulation of stationary and ergodic random fields. The approach overcomes the size limitations of LU and is suitable for any size simulation. The proposed approach can facilitate fast updating of generated realizations with new data, when appropriate, without repeating the full simulation process. Based on a novel column partitioning of the L matrix, expressed in terms of successive conditional covariance matrices, the approach presented here demonstrates that LU simulation is equivalent to the successive solution of kriging residual estimates plus random terms. Consequently, it can be used for the LU decomposition of matrices of any size. The simulation approach is termed conditional simulation by successive residuals as at each step, a small set (group) of random variables is simulated with a LU decomposition of a matrix of updated conditional covariance of residuals. The simulated group is then used to estimate residuals without the need to solve large systems of equations.

Simulation of the load-unload response ratio and critical sensitivity in the lattice solid model

The Load-Unload Response Ratio (LURR) method is an intermediate-term earthquake prediction approach that has shown considerable promise. It involves calculating the ratio of a specified energy release measure during loading and unloading where loading and unloading periods are determined from the earth tide induced perturbations in the Coulomb Failure Stress on optimally oriented faults. In the lead-up to large earthquakes, high LURR values are frequently observed a few months or years prior to the event. These signals may have a similar origin to the observed accelerating seismic moment release (AMR) prior to many large earthquakes or may be due to critical sensitivity of the crust when a large earthquake is imminent. As a first step towards studying the underlying physical mechanism for the LURR observations, numerical studies are conducted using the particle based lattice solid model (LSM) to determine whether LURR observations can be reproduced. The model is initialized as a heterogeneous 2-D block made up of random-sized particles bonded by elastic-brittle links. The system is subjected to uniaxial compression from rigid driving plates on the upper and lower edges of the model. Experiments are conducted using both strain and stress control to load the plates. A sinusoidal stress perturbation is added to the gradual compressional loading to simulate loading and unloading cycles and LURR is calculated. The results reproduce signals similar to those observed in earthquake prediction practice with a high LURR value followed by a sudden drop prior to macroscopic failure of the sample. The results suggest that LURR provides a good predictor for catastrophic failure in elastic-brittle systems and motivate further research to study the underlying physical mechanisms and statistical properties of high LURR values. The results provide encouragement for earthquake prediction research and the use of advanced simulation models to probe the physics of earthquakes.

Simulation of the micro-physics of rocks using LSMearth

The particle-based Lattice Solid Model (LSM) was developed to provide a basis to study the physics of rocks and the nonlinear dynamics of earthquakes (MORA and PLACE, 1994; PLACE and MORA, 1999). A new modular and flexible LSM approach has been developed that allows different microphysics to be easily included in or removed from the model. The approach provides a virtual laboratory where numerical experiments can easily be set up and all measurable quantities visualised. The proposed approach provides a means to simulate complex phenomena such as fracturing or localisation processes, and enables the effect of different micro-physics on macroscopic behaviour to be studied. The initial 2-D model is extended to allow three-dimensional simulations to be performed and particles of different sizes to be specified. Numerical bi-axial compression experiments under different confining pressure are used to calibrate the model. By tuning the different microscopic parameters (such as coefficient of friction, microscopic strength and distribution of grain sizes), the macroscopic strength of the material and can be adjusted to be in agreement with laboratory experiments, and the orientation of fractures is consistent with the theoretical value predicted based on Mohr-Coulomb diagram. Simulations indicate that 3-D numerical models have different macroscopic properties than in 2-D and, hence, the model must be recalibrated for 3-D simulations. These numerical experiments illustrate that the new approach is capable of simulating typical rock fracture behaviour. The new model provides a basis to investigate nucleation, rupture and slip pulse propagation in complex fault zones without the previous model limitations of a regular low-level surface geometry and being restricted to two-dimensions.

Simulation of the influence of rate- and state-dependent friction on the macroscopic behavior of complex fault zones with the lattice solid model

In order to understand the earthquake nucleation process, we need to understand the effective frictional behavior of faults with complex geometry and fault gouge zones. One important aspect of this is the interaction between the friction law governing the behavior of the fault on the microscopic level and the resulting macroscopic behavior of the fault zone. Numerical simulations offer a possibility to investigate the behavior of faults on many different scales and thus provide a means to gain insight into fault zone dynamics on scales which are not accessible to laboratory experiments. Numerical experiments have been performed to investigate the influence of the geometric configuration of faults with a rate- and state-dependent friction at the particle contacts on the effective frictional behavior of these faults. The numerical experiments are designed to be similar to laboratory experiments by DIETERICH and KILGORE (1994) in which a slide-hold-slide cycle was performed between two blocks of material and the resulting peak friction was plotted vs. holding time. Simulations with a flat fault without a fault gouge have been performed to verify the implementation. These have shown close agreement with comparable laboratory experiments. The simulations performed with a fault containing fault gouge have demonstrated a strong dependence of the critical slip distance D-c on the roughness of the fault surfaces and are in qualitative agreement with laboratory experiments.

Molecular dynamics simulation of organic-inorganic nanocomposites: Layering behavior and interlayer structure of organoclays

Isothermal-isobaric (NPT) molecular dynamics simulation has been performed to investigate the layering behavior and structure of nanoconfined quaternary alkylammoniums in organoclays. This work is focused on systems consisting of two clay layers and a number of alkylammoniums, and involves the use of modified Dreiding force field. The simulated basal spacings of organoclays agree satisfactorily with the experimental results in the literature. The atomic density profiles in the direction normal to the clay surface indicate that the alkyl chains within the interlayer space of montmorillonite exhibit an obvious layering behavior. The headgroups of long alkyl chains are distributed within two layers close to the clay surface, whereas the distributions of methyl and methylene groups are strongly dependent on the alkyl chain length and clay layer charge. Monolayer, bilayer, and pseudo-trilayer structures are found in organoclays modified with single long alkyl chains, which are identical to the structural models based on the measured basal spacings. A pseudo-quadrilayer structure, for the first time to our knowledge, is also identified in organoclays with double long alkyl chains. In the mixture structure of paraffin-type and multilayer, alkyl chains do not lie flat within a single layer but interlace, and also jump to the next layer in pseudo-trilayer as well as next nearest layer in pseudo-quadrilayer.

Large-eddy simulation of heat transfer downstream of a backward-facing step

Large-eddy simulation is used to predict heat transfer in the separated and reattached flow regions downstream of a backward-facing step. Simulations were carried out at a Reynolds number of 28 000 (based on the step height and the upstream centreline velocity) with a channel expansion ratio of 1.25. The Prandtl number was 0.71. Two subgrid-scale models were tested, namely the dynamic eddy-viscosity, eddy-diffusivity model and the dynamic mixed model. Both models showed good overall agreement with available experimental data. The simulations indicated that the peak in heat-transfer coefficient occurs slightly upstream of the mean reattachment location, in agreement with experimental data. The results of these simulations have been analysed to discover the mechanisms that cause this phenomenon. The peak in heat-transfer coefficient shows a direct correlation with the peak in wall shear-stress fluctuations. It is conjectured that the peak in these fluctuations is caused by an impingement mechanism, in which large eddies, originating in the shear layer, impact the wall just upstream of the mean reattachment location. These eddies cause a 'downwash', which increases the local heat-transfer coefficient by bringing cold fluid from above the shear layer towards the wall.

Numerical simulation of stochastic ordinary differential equations in biomathematical modelling

In this work we discuss the effects of white and coloured noise perturbations on the parameters of a mathematical model of bacteriophage infection introduced by Beretta and Kuang in [Math. Biosc. 149 (1998) 57]. We numerically simulate the strong solutions of the resulting systems of stochastic ordinary differential equations (SDEs), with respect to the global error, by means of numerical methods of both Euler-Taylor expansion and stochastic Runge-Kutta type. (C) 2003 IMACS. Published by Elsevier B.V. All rights reserved.

Numerical simulation of abrupt contraction flows using the Double Convected Pom-Pom model

The Double Convected Pom-Pom model was recently introduced to circumvent some numerical and theological defects found in other formulations of the Pom-Pom concept. It is used here for the simulation of a benchmark problem: the flow in an abrupt planar contraction. The predictions are compared with birefringence measurements and show reasonable quantitative agreement with experimental data. A parametric study is also carried out with the aim of analysing the effect of the branching parameter on vortex dynamics and extrudate swell. The results show that the Double Convected Pom-Pom model (DCPP) model is able to discriminate between branched and linear macromolecular structures in accordance with experimental observations. In that respect, the role of the extensional properties in determining complex flow behaviour is stressed. Also, the ratio of the first normal stress difference to the shear stress appears to play a major role in die swell observation. For the time being, the role of the second normal stress difference appears to be less obvious to evaluate in this complex flow. (C) 2004 Elsevier B.V. All rights reserved.

Molecular dynamics simulation of the structural and dynamic properties of dioctadecyldimethyl ammoniums in organoclays

The structural and dynamic properties of dioctadecyldimethylammoniums (DODDMA) intercalated into 2:1 layered clays are investigated using isothermal-isobaric (NPT) molecular dynamics (MD) simulation. The simulated results are in reasonably good agreement with the available experimental measurements, such as X-ray diffraction (XRD), atom force microscopy (AFM), Fourier transform infrared (FTIR), and nuclear magnetic resonance (NMR) spectroscopies. The nitrogen atoms are found to be located mainly within two layers close to the clay surface whereas methylene groups form a pseudoquadrilayer structure. The results of tilt angle and order parameter show that interior two-bond segments of alkyl chains prefer an arrangement parallel to the clay surface, whereas the segments toward end groups adopt a random orientation. In addition, the alkyl chains within the layer structure lie almost parallel to the clay surface whereas those out of the layer structure are essentially perpendicular to the surface. The trans conformations are predominant in all cases although extensive gauche conformations are observed, which is in agreement with previous simulations on n-butane. Moreover, an odd-even effect in conformation distributions is observed mainly along the chains close to the head and tail groups. The diffusion constants of both nitrogen atoms and methylene groups in these nanoconfined alkyl chains increase with the temperature and methelene position toward the tail groups.

A parallel implementation of the lattice solid model for the simulation of rock mechanics and earthquake dynamics

The Lattice Solid Model has been used successfully as a virtual laboratory to simulate fracturing of rocks, the dynamics of faults, earthquakes and gouge processes. However, results from those simulations show that in order to make the next step towards more realistic experiments it will be necessary to use models containing a significantly larger number of particles than current models. Thus, those simulations will require a greatly increased amount of computational resources. Whereas the computing power provided by single processors can be expected to increase according to Moore's law, i.e., to double every 18-24 months, parallel computers can provide significantly larger computing power today. In order to make this computing power available for the simulation of the microphysics of earthquakes, a parallel version of the Lattice Solid Model has been implemented. Benchmarks using large models with several millions of particles have shown that the parallel implementation of the Lattice Solid Model can achieve a high parallel-efficiency of about 80% for large numbers of processors on different computer architectures.

Fast simulation of a quantum phase transition in an ion-trap realizable unitary map

We show that a specific implementation of a unitary map on multiple qubits in an ion trap is physically equivalent to a Hamiltonian evolution that belongs to the same universality class as the transverse Ising Hamiltonian. We suggest experimental signatures, and present numerical simulations for the case of four qubits.

Three-dimensional simulation of the rolling of a saturated fibro-porous media

This paper describes recent advances made in computational modelling of the sugar cane liquid extraction process. The saturated fibro-porous material is rolled between circumferentially grooved rolls, which enhance frictional grip and provide a low-resistance path for liquid flow during the extraction process. Previously reported two-dimensional (2D) computational models, account for the large deformation of the porous material by solving the fully coupled governing fibre stress and fluid-flow equations using finite element techniques. While the 2D simulations provide much insight into the overarching cause-effect relationships, predictions of mechanical quantities such as roll separating force and particularly torque as a function of roll speed and degree of compression are not satisfactory for industrial use. It is considered that the unsatisfactory response in roll torque prediction may be due to the stress levels that exist between the groove tips and roots which have been largely neglected in the geometrically simplified 2D model. This paper gives results for both two- and three-dimensional finite element models and highlights their strengths and weaknesses in predicting key milling parameters. (c) 2005 Elsevier B.V. All rights reserved.