Database technologies for l-system simulations in virtual plant applications on bioinformatics

One of the most important advantages of database systems is that the underlying mathematics is rich enough to specify very complex operations with a small number of statements in the database language. This research covers an aspect of biological informatics that is the marriage of information technology and biology, involving the study of real-world phenomena using virtual plants derived from L-systems simulation. L-systems were introduced by Aristid Lindenmayer as a mathematical model of multicellular organisms. Not much consideration has been given to the problem of persistent storage for these simulations. Current procedures for querying data generated by L-systems for scientific experiments, simulations and measurements are also inadequate. To address these problems the research in this paper presents a generic process for data-modeling tools (L-DBM) between L-systems and database systems. This paper shows how L-system productions can be generically and automatically represented in database schemas and how a database can be populated from the L-system strings. This paper further describes the idea of pre-computing recursive structures in the data into derived attributes using compiler generation. A method to allow a correspondence between biologists' terms and compiler-generated terms in a biologist computing environment is supplied. Once the L-DBM gets any specific L-systems productions and its declarations, it can generate the specific schema for both simple correspondence terminology and also complex recursive structure data attributes and relationships.

Numerical simulations of wind and temperature structure within an Alpine lake basin, Lake Tekapo, New Zealand

High-resolution numerical model simulations have been used to study the local and mesoscale thermal circulations in an Alpine lake basin. The lake (87 km(2)) is situated in the Southern Alps, New Zealand and is located in a glacially excavated rock basin surrounded by mountain ranges that reach 3000 m in height. The mesoscale model used (RAMS) is a three-dimensional non-hydrostatic model with a level 2.5 turbulence closure scheme. The model demonstrates that thermal forcing at local (within the basin) and regional (coast-to-basin inflow) scales drive the observed boundary-layer airflow in the lake basin during clear anticyclonic summertime conditions. The results show that the lake can modify (perturb) both the local and regional wind systems. Following sunrise, local thermal circulations dominate, including a lake breeze component that becomes embedded within the background valley wind system. This results in a more divergent flow in the basin extending across the lake shoreline. However, a closed lake breeze circulation is neither observed nor modelled. Modelling results indicate that in the latter part of the day when the mesoscale (coast-to-basin) inflow occurs, the relatively cold pool of lake air in the basin can cause the intrusion to decouple from the surface. Measured data provide qualitative and quantitative support for the model results.

SAR calculation using FDTD simulations

The main intend of this work, is to determinate the Specific Absorption Rate (SAR) on human head tissues exposed to radiation caused by sources of 900 and 1800MHz, since those are the typical frequencies for mobile communications systems nowadays. In order to determinate the SAR, has been used the FDTD (Finite Difference Time Domain), which is a numeric method in time domain, obtained from the Maxwell equations in differential mode. In order to do this, a computational model from the human head in two dimensions made with cells of the smallest possible size was implemented, respecting the limits from computational processing. It was possible to verify the very good efficiency of the FDTD method in the resolution of those types of problems.

The folding of knotted proteins: insights from lattice simulations

We carry out systematic Monte Carlo simulations of Go lattice proteins to investigate and compare the folding processes of two model proteins whose native structures differ from each other due to the presence of a trefoil knot located near the terminus of one of the protein chains. We show that the folding time of the knotted fold is larger than that of the unknotted protein and that this difference in folding time is particularly striking in the temperature region below the optimal folding temperature. Both proteins display similar folding transition temperatures, which is indicative of similar thermal stabilities. By using the folding probability reaction coordinate as an estimator of folding progression we have found out that the formation of the knot is mainly a late folding event in our shallow knot system.

Evaluation of the respiratory motion effect in small animal PET images with GATE Monte Carlo simulations

The rapid growth in genetics and molecular biology combined with the development of techniques for genetically engineering small animals has led to increased interest in in vivo small animal imaging. Small animal imaging has been applied frequently to the imaging of small animals (mice and rats), which are ubiquitous in modeling human diseases and testing treatments. The use of PET in small animals allows the use of subjects as their own control, reducing the interanimal variability. This allows performing longitudinal studies on the same animal and improves the accuracy of biological models. However, small animal PET still suffers from several limitations. The amounts of radiotracers needed, limited scanner sensitivity, image resolution and image quantification issues, all could clearly benefit from additional research. Because nuclear medicine imaging deals with radioactive decay, the emission of radiation energy through photons and particles alongside with the detection of these quanta and particles in different materials make Monte Carlo method an important simulation tool in both nuclear medicine research and clinical practice. In order to optimize the quantitative use of PET in clinical practice, data- and image-processing methods are also a field of intense interest and development. The evaluation of such methods often relies on the use of simulated data and images since these offer control of the ground truth. Monte Carlo simulations are widely used for PET simulation since they take into account all the random processes involved in PET imaging, from the emission of the positron to the detection of the photons by the detectors. Simulation techniques have become an importance and indispensable complement to a wide range of problems that could not be addressed by experimental or analytical approaches.

Monte Carlo modeling and simulations of the High Definition (HD120) micro MLC and validation against measurements for a 6 MV beam

Purpose: The most recent Varian® micro multileaf collimator(MLC), the High Definition (HD120) MLC, was modeled using the BEAMNRCMonte Carlo code. This model was incorporated into a Varian medical linear accelerator, for a 6 MV beam, in static and dynamic mode. The model was validated by comparing simulated profiles with measurements. Methods: The Varian® Trilogy® (2300C/D) accelerator model was accurately implemented using the state-of-the-art Monte Carlo simulation program BEAMNRC and validated against off-axis and depth dose profiles measured using ionization chambers, by adjusting the energy and the full width at half maximum (FWHM) of the initial electron beam. The HD120 MLC was modeled by developing a new BEAMNRC component module (CM), designated HDMLC, adapting the available DYNVMLC CM and incorporating the specific characteristics of this new micro MLC. The leaf dimensions were provided by the manufacturer. The geometry was visualized by tracing particles through the CM and recording their position when a leaf boundary is crossed. The leaf material density and abutting air gap between leaves were adjusted in order to obtain a good agreement between the simulated leakage profiles and EBT2 film measurements performed in a solid water phantom. To validate the HDMLC implementation, additional MLC static patterns were also simulated and compared to additional measurements. Furthermore, the ability to simulate dynamic MLC fields was implemented in the HDMLC CM. The simulation results of these fields were compared with EBT2 film measurements performed in a solid water phantom. Results: Overall, the discrepancies, with and without MLC, between the opened field simulations and the measurements using ionization chambers in a water phantom, for the off-axis profiles are below 2% and in depth-dose profiles are below 2% after the maximum dose depth and below 4% in the build-up region. On the conditions of these simulations, this tungsten-based MLC has a density of 18.7 g cm− 3 and an overall leakage of about 1.1 ± 0.03%. The discrepancies between the film measured and simulated closed and blocked fields are below 2% and 8%, respectively. Other measurements were performed for alternated leaf patterns and the agreement is satisfactory (to within 4%). The dynamic mode for this MLC was implemented and the discrepancies between film measurements and simulations are within 4%. Conclusions: The Varian® Trilogy® (2300 C/D) linear accelerator including the HD120 MLC was successfully modeled and simulated using the Monte CarloBEAMNRC code by developing an independent CM, the HDMLC CM, either in static and dynamic modes.

Towards comparable simulations of cooperating objects and wireless sensor networks

Simulators are indispensable tools to support the development and testing of cooperating objects such as wireless sensor networks (WSN). However, it is often not possible to compare the results of different simulation tools. Thus, the goal of this paper is the specification of a generic simulation platform for cooperating objects. We propose a platform that consists of a set of simulators that together fulfill desired simulator properties. We show that to achieve comparable results the use of a common specification language for the software-under-test is not feasible. Instead, we argue that using common input formats for the simulated environment and common output formats for the results is useful. This again motivates that a simulation tool consisting of a set of existing simulators that are able to use common scenario-input and can produce common output which will bring us a step closer to the vision of achieving comparable simulation results.

Single side damage simulations and detection in beam-like structures

Beam-like structures are the most common components in real engineering, while single side damage is often encountered. In this study, a numerical analysis of single side damage in a free-free beam is analysed with three different finite element models; namely solid, shell and beam models for demonstrating their performance in simulating real structures. Similar to experiment, damage is introduced into one side of the beam, and natural frequencies are extracted from the simulations and compared with experimental and analytical results. Mode shapes are also analysed with modal assurance criterion. The results from simulations reveal a good performance of the three models in extracting natural frequencies, and solid model performs better than shell while shell model performs better than beam model under intact state. For damaged states, the natural frequencies captured from solid model show more sensitivity to damage severity than shell model and shell model performs similar to the beam model in distinguishing damage. The main contribution of this paper is to perform a comparison between three finite element models and experimental data as well as analytical solutions. The finite element results show a relatively well performance.

Automatic Electricity Markets Data Extraction for Realistic Multi-agent Simulations

Electricity markets worldwide suffered profound transformations. The privatization of previously nationally owned systems; the deregulation of privately owned systems that were regulated; and the strong interconnection of national systems, are some examples of such transformations [1, 2]. In general, competitive environments, as is the case of electricity markets, require good decision-support tools to assist players in their decisions. Relevant research is being undertaken in this field, namely concerning player modeling and simulation, strategic bidding and decision-support.

Monte Carlo simulations for dosimetric verification in photon and electron beam radiotherapy

Dissertação para obtenção do Grau de Doutor em Engenharia Biomédica

Lithium ion rechargeable batteries: State of the art and future needs of microscopic theoretical models and simulations

This review deals with the recent developments and present status of the theoretical models for the simulation of the performance of lithium ion batteries. Preceded by a description of the main materials used for each of the components of a battery -anode, cathode and separator- and how material characteristics affect battery performance, a description of the main theoretical models describing the operation and performance of a battery are presented. The influence of the most relevant parameters of the models, such as boundary conditions, geometry and material characteristics are discussed. Finally, suggestions for future work are proposed.

Numerical simulations of Lamb waves in plates using a semi-analytical finite element method

Magdeburg, Univ., Fak. für Maschinenbau, Diss., 2011

Simulations for modelling of population balance equations of particulate processes using the discrete particle model (DPM)

Magdeburg, Univ., Fak. für Mathematik, Diss., 2009