Monte Carlo modeling of the patient and treatment delivery complexities for high dose rate brachytherapy

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Bayesian Optimisation Algorithm for Nurse Scheduling, Scalable Optimization via Probabilistic Modeling

Our research has shown that schedules can be built mimicking a human scheduler by using a set of rules that involve domain knowledge. This chapter presents a Bayesian Optimization Algorithm (BOA) for the nurse scheduling problem that chooses such suitable scheduling rules from a set for each nurse’s assignment. Based on the idea of using probabilistic models, the BOA builds a Bayesian network for the set of promising solutions and samples these networks to generate new candidate solutions. Computational results from 52 real data instances demonstrate the success of this approach. It is also suggested that the learning mechanism in the proposed algorithm may be suitable for other scheduling problems.

Geological realism in hydrogeological and geophysical inverse modeling: A review

Scientific curiosity, exploration of georesources and environmental concerns are pushing the geoscientific research community toward subsurface investigations of ever-increasing complexity. This review explores various approaches to formulate and solve inverse problems in ways that effectively integrate geological concepts with geophysical and hydrogeological data. Modern geostatistical simulation algorithms can produce multiple subsurface realizations that are in agreement with conceptual geological models and statistical rock physics can be used to map these realizations into physical properties that are sensed by the geophysical or hydrogeological data. The inverse problem consists of finding one or an ensemble of such subsurface realizations that are in agreement with the data. The most general inversion frameworks are presently often computationally intractable when applied to large-scale problems and it is necessary to better understand the implications of simplifying (1) the conceptual geological model (e.g., using model compression); (2) the physical forward problem (e.g., using proxy models); and (3) the algorithm used to solve the inverse problem (e.g., Markov chain Monte Carlo or local optimization methods) to reach practical and robust solutions given today's computer resources and knowledge. We also highlight the need to not only use geophysical and hydrogeological data for parameter estimation purposes, but also to use them to falsify or corroborate alternative geological scenarios.

I. Quantal effects in biochemical cooperativity and a proposed mechanism for the differentiation of calcium signaling in synaptic plasticity. II. Evolutionary algorithms for the optimization of methods in computational chemistry

In Part 1 of this thesis, we propose that biochemical cooperativity is a fundamentally non-ideal process. We show quantal effects underlying biochemical cooperativity and highlight apparent ergodic breaking at small volumes. The apparent ergodic breaking manifests itself in a divergence of deterministic and stochastic models. We further predict that this divergence of deterministic and stochastic results is a failure of the deterministic methods rather than an issue of stochastic simulations.

Ergodic breaking at small volumes may allow these molecular complexes to function as switches to a greater degree than has previously been shown. We propose that this ergodic breaking is a phenomenon that the synapse might exploit to differentiate Ca$^{2+}$ signaling that would lead to either the strengthening or weakening of a synapse. Techniques such as lattice-based statistics and rule-based modeling are tools that allow us to directly confront this non-ideality. A natural next step to understanding the chemical physics that underlies these processes is to consider \textit{in silico} specifically atomistic simulation methods that might augment our modeling efforts.

In the second part of this thesis, we use evolutionary algorithms to optimize \textit{in silico} methods that might be used to describe biochemical processes at the subcellular and molecular levels. While we have applied evolutionary algorithms to several methods, this thesis will focus on the optimization of charge equilibration methods. Accurate charges are essential to understanding the electrostatic interactions that are involved in ligand binding, as frequently discussed in the first part of this thesis.

MULTISCALE MODELING OF LIQUID CRYSTALLINE/NANOTUBE COMPOSITES

The objective of this research is to synthesize structural composites designed with particular areas defined with custom modulus, strength and toughness values in order to improve the overall mechanical behavior of the composite. Such composites are defined and referred to as 3D-designer composites. These composites will be formed from liquid crystalline polymers and carbon nanotubes. The fabrication process is a variation of rapid prototyping process, which is a layered, additive-manufacturing approach. Composites formed using this process can be custom designed by apt modeling methods for superior performance in advanced applications. The focus of this research is on enhancement of Young's modulus in order to make the final composite stiffer. Strength and toughness of the final composite with respect to various applications is also discussed. We have taken into consideration the mechanical properties of final composite at different fiber volume content as well as at different orientations and lengths of the fibers. The orientation of the LC monomers is supposed to be carried out using electric or magnetic fields. A computer program is modeled incorporating the Mori-Tanaka modeling scheme to generate the stiffness matrix of the final composite. The final properties are then deduced from the stiffness matrix using composite micromechanics. Eshelby's tensor, required to calculate the stiffness tensor using Mori-Tanaka method, is calculated using a numerical scheme that determines the components of the Eshelby's tensor (Gavazzi and Lagoudas 1990). The numerical integration is solved using Gaussian Quadrature scheme and is worked out using MATLAB as well. . MATLAB provides a good deal of commands and algorithms that can be used efficiently to elaborate the continuum of the formula to its extents. Graphs are plotted using different combinations of results and parameters involved in finding these results

Wildfire Assessment Using FARSITE Fire Modeling: A Case Study in the Chihuahua Desert of Mexico

The Chihuahua desert is one of the most biologically diverse ecosystems in the world, but suffers serious degradation because of changes in fire regimes resulting in large catastrophic fires. My study was conducted in the Sierra La Mojonera (SLM) natural protected area in Mexico. The purpose of this study was to implement the use of FARSITE fire modeling as a fire management tool to develop an integrated fire management plan at SLM. Firebreaks proved to detain 100% of wildfire outbreaks. The rosetophilous scrub experienced the fastest rate of fire spread and lowland creosote bush scrub experienced the slowest rate of fire spread. March experienced the fastest rate of fire spread, while September experienced the slowest rate of fire spread. The results of my study provide a tool for wildfire management through the use geospatial technologies and, in particular, FARSITE fire modeling in SLM and Mexico.

A general collaborative framework for modeling and perceiving distributed network behavior

Collaborative Anomaly Detection (CAD) is an emerging field of network security in both academia and industry. It has attracted a lot of attention, due to the limitations of traditional fortress-style defense modes. Even though a number of pioneer studies have been conducted in this area, few of them concern about the universality issue. This work focuses on two aspects of it. First, a unified collaborative detection framework is developed based on network virtualization technology. Its purpose is to provide a generic approach that can be applied to designing specific schemes for various application scenarios and objectives. Second, a general behavior perception model is proposed for the unified framework based on hidden Markov random field. Spatial Markovianity is introduced to model the spatial context of distributed network behavior and stochastic interaction among interconnected nodes. Algorithms are derived for parameter estimation, forward prediction, backward smooth, and the normality evaluation of both global network situation and local behavior. Numerical experiments using extensive simulations and several real datasets are presented to validate the proposed solution. Performance-related issues and comparison with related works are discussed.

Rainfall-runoff modeling using dynamic evolving neural fuzzy inference system with online learning

This is an open access article under the CC BY-NC-ND license.Neuro-Fuzzy Systems (NFS) are computational intelligence tools that have recently been employed in hydrological modeling. In many of the common NFS the learning algorithms used are based on batch learning where all the parameters of the fuzzy system are optimized off-line. Although these models have frequently been used, there is a criticism on such learning process as the number of rules are needed to be predefined by the user. This will reduce the flexibility of the NFS architecture while dealing with different data with different level of complexity. On the other hand, online or local learning evolves through local adjustments in the model as new data is introduced in sequence. In this study, dynamic evolving neural fuzzy inference system (DENFIS) is used in which an evolving, online clustering algorithm called the Evolving Clustering Method (ECM) is implemented. ECM is an online, maximum distance-based clustering method which is able to estimate the number of clusters in a data set and find their current centers in the input space through its fast, one-pass algorithm. The 10-minutes rainfall-runoff time series from a small (23.22 km2) tropical catchment named Sungai Kayu Ara in Selangor, Malaysia, was used in this study. Out of the 40 major events, 12 were used for training and 28 for testing. Results obtained by DENFIS were then compared with the ones obtained by physically-based rainfall-runoff model HEC-HMS and a regression model ARX. It was concluded that DENFIS results were comparable to HEC-HMS and superior to ARX model. This indicates a strong potential for DENFIS to be used in rainfall-runoff modeling.

Dynamical modeling of biogas production supported by an experimental anaerobic digestion process

This paper presents the development of a combined experimental and numerical approach to study the anaerobic digestion of both the wastes produced in a biorefinery using yeast for biodiesel production and the wastes generated in the preceding microbial biomass production. The experimental results show that it is possible to valorise through anaerobic digestion all the tested residues. In the implementation of the numerical model for anaerobic digestion, a procedure for the identification of its parameters needs to be developed. A hybrid search Genetic Algorithm was used, followed by a direct search method. In order to test the procedure for estimation of parameters, first noise-free data was considered and a critical analysis of the results obtain so far was undertaken. As a demonstration of its application, the procedure was applied to experimental data.