Integrating sequence information in microarray data analysis by free energy modeling

Microarray technology is a high-throughput method for genotyping and gene expression profiling. Limited sensitivity and specificity are one of the essential problems for this technology. Most of existing methods of microarray data analysis have an apparent limitation for they merely deal with the numerical part of microarray data and have made little use of gene sequence information. Because it's the gene sequences that precisely define the physical objects being measured by a microarray, it is natural to make the gene sequences an essential part of the data analysis. This dissertation focused on the development of free energy models to integrate sequence information in microarray data analysis. The models were used to characterize the mechanism of hybridization on microarrays and enhance sensitivity and specificity of microarray measurements. ^ Cross-hybridization is a major obstacle factor for the sensitivity and specificity of microarray measurements. In this dissertation, we evaluated the scope of cross-hybridization problem on short-oligo microarrays. The results showed that cross hybridization on arrays is mostly caused by oligo fragments with a run of 10 to 16 nucleotides complementary to the probes. Furthermore, a free-energy based model was proposed to quantify the amount of cross-hybridization signal on each probe. This model treats cross-hybridization as an integral effect of the interactions between a probe and various off-target oligo fragments. Using public spike-in datasets, the model showed high accuracy in predicting the cross-hybridization signals on those probes whose intended targets are absent in the sample. ^ Several prospective models were proposed to improve Positional Dependent Nearest-Neighbor (PDNN) model for better quantification of gene expression and cross-hybridization. ^ The problem addressed in this dissertation is fundamental to the microarray technology. We expect that this study will help us to understand the detailed mechanism that determines sensitivity and specificity on the microarrays. Consequently, this research will have a wide impact on how microarrays are designed and how the data are interpreted. ^

Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.

Collisional Formation and Modeling of Asteroid Families

In the last decade, thanks to the development of sophisticated numerical codes, major breakthroughs have been achieved in our understanding of the formation of asteroid families by catastrophic disruption of large parent bodies. In this review, we describe numerical simulations of asteroid collisions that reproduced the main properties of families, accounting for both the fragmentation of an asteroid at the time of impact and the subsequent gravitational interactions of the generated fragments. The simulations demonstrate that the catastrophic disruption of bodies larger than a few hundred meters in diameter leads to the formation of large aggregates due to gravitational reaccumulation of smaller fragments, which helps explain the presence of large members within asteroid families. Thus, for the first time, numerical simulations successfully reproduced the sizes and ejection velocities of members of representative families. Moreover, the simulations provide constraints on the family dynamical histories and on the possible internal structure of family members and their parent bodies.

3D Direct Simulation Monte Carlo Modelling of the Inner Gas Coma of Comet 67P/Churyumov-Gerasimenko: A Parameter Study

Direct Simulation Monte Carlo (DSMC) is a powerful numerical method to study rarefied gas flows such as cometary comae and has been used by several authors over the past decade to study cometary outflow. However, the investigation of the parameter space in simulations can be time consuming since 3D DSMC is computationally highly intensive. For the target of ESA's Rosetta mission, comet 67P/Churyumov-Gerasimenko, we have identified to what extent modification of several parameters influence the 3D flow and gas temperature fields and have attempted to establish the reliability of inferences about the initial conditions from in situ and remote sensing measurements. A large number of DSMC runs have been completed with varying input parameters. In this work, we present the simulation results and conclude on the sensitivity of solutions to certain inputs. It is found that among cases of water outgassing, the surface production rate distribution is the most influential variable to the flow field.

A multimodal tablet-based interface for designing and reviewing 3D engineering models

The ability to view and interact with 3D models has been happening for a long time. However, vision-based 3D modeling has only seen limited success in applications, as it faces many technical challenges. Hand-held mobile devices have changed the way we interact with virtual reality environments. Their high mobility and technical features, such as inertial sensors, cameras and fast processors, are especially attractive for advancing the state of the art in virtual reality systems. Also, their ubiquity and fast Internet connection open a path to distributed and collaborative development. However, such path has not been fully explored in many domains. VR systems for real world engineering contexts are still difficult to use, especially when geographically dispersed engineering teams need to collaboratively visualize and review 3D CAD models. Another challenge is the ability to rendering these environments at the required interactive rates and with high fidelity. In this document it is presented a virtual reality system mobile for visualization, navigation and reviewing large scale 3D CAD models, held under the CEDAR (Collaborative Engineering Design and Review) project. It’s focused on interaction using different navigation modes. The system uses the mobile device's inertial sensors and camera to allow users to navigate through large scale models. IT professionals, architects, civil engineers and oil industry experts were involved in a qualitative assessment of the CEDAR system, in the form of direct user interaction with the prototypes and audio-recorded interviews about the prototypes. The lessons learned are valuable and are presented on this document. Subsequently it was prepared a quantitative study on the different navigation modes to analyze the best mode to use it in a given situation.

Numerical simulation of the evolution of viscous rotating drops

In this contribution we simulate numerically the evolution of a viscous fluid drop rotating about a fixed axis at constant angular velocity ? or constant angular momentum L, surrounded by another viscous fluid. The problem is considered in the limit of large Ekman number and small Reynolds number. In the lecture we will describe the numerical method we have used to solve the PDE system that describes the evolution of the drop (3D boundary element method). We will also present the results we have obtained, paying special attention to the stability/instability of the equilibrium shapes.

Comparison of experimental and numerical sloshing loads in partially filled tanks

Sloshing describes the movement of liquids inside partially filled tanks, generating dynamic loads on the tank structure. The resulting impact pressures are of great importance in assessing structural strength, and their correct evaluation still represents a challenge for the designer due to the high level of nonlinearities involved, with complex free surface deformations, violent impact phenomena and influence of air trapping. In the present paper, a set of two-dimensional cases, for which experimental results are available, is considered to assess the merits and shortcomings of different numerical methods for sloshing evaluation, namely two commercial RANS solvers (FLOW-3D and LS-DYNA), and two academic software (Smoothed Particle Hydrodynamics and RANS). Impact pressures at various critical locations and global moment induced by water motion in a partially filled rectangular tank, subject to a simple harmonic rolling motion, are evaluated and predictions are compared with experimental measurements. 2012 Copyright Taylor and Francis Group, LLC.

A graph-based approach for latency modeling and optimization in multiview video encoding

We present a novel framework for encoding latency analysis of arbitrary multiview video coding prediction structures. This framework avoids the need to consider an specific encoder architecture for encoding latency analysis by assuming an unlimited processing capacity on the multiview encoder. Under this assumption, only the influence of the prediction structure and the processing times have to be considered, and the encoding latency is solved systematically by means of a graph model. The results obtained with this model are valid for a multiview encoder with sufficient processing capacity and serve as a lower bound otherwise. Furthermore, with the objective of low latency encoder design with low penalty on rate-distortion performance, the graph model allows us to identify the prediction relationships that add higher encoding latency to the encoder. Experimental results for JMVM prediction structures illustrate how low latency prediction structures with a low rate-distortion penalty can be derived in a systematic manner using the new model.

A parallel implementation of 3D Zernike moment analysis

Zernike polynomials are a well known set of functions that find many applications in image or pattern characterization because they allow to construct shape descriptors that are invariant against translations, rotations or scale changes. The concepts behind them can be extended to higher dimension spaces, making them also fit to describe volumetric data. They have been less used than their properties might suggest due to their high computational cost. We present a parallel implementation of 3D Zernike moments analysis, written in C with CUDA extensions, which makes it practical to employ Zernike descriptors in interactive applications, yielding a performance of several frames per second in voxel datasets about 2003 in size. In our contribution, we describe the challenges of implementing 3D Zernike analysis in a general-purpose GPU. These include how to deal with numerical inaccuracies, due to the high precision demands of the algorithm, or how to deal with the high volume of input data so that it does not become a bottleneck for the system.

Analysis of the Fracture of Reinforced Concrete Flat Elements Subjected to Explosions. Experimental Procedure and Numerical Validation

Many of the material models most frequently used for the numerical simulation of the behavior of concrete when subjected to high strain rates have been originally developed for the simulation of ballistic impact. Therefore, they are plasticity-based models in which the compressive behavior is modeled in a complex way, while their tensile failure criterion is of a rather simpler nature. As concrete elements usually fail in tensión when subjected to blast loading, available concrete material models for high strain rates may not represent accurately their real behavior. In this research work an experimental program of reinforced concrete fíat elements subjected to blast load is presented. Altogether four detonation tests are conducted, in which 12 slabs of two different concrete types are subjected to the same blast load. The results of the experimental program are then used for the development and adjustment of numerical tools needed in the modeling of concrete elements subjected to blast.

The PSE-3D instability analysis methodology for flows depending strongly on two and weakly on the third spatial dimension

The present contribution discusses the development of a PSE-3D instability analysis algorithm, in which a matrix forming and storing approach is followed. Alternatively to the typically used in stability calculations spectral methods, new stable high-order finitedifference-based numerical schemes for spatial discretization 1 are employed. Attention is paid to the issue of efficiency, which is critical for the success of the overall algorithm. To this end, use is made of a parallelizable sparse matrix linear algebra package which takes advantage of the sparsity offered by the finite-difference scheme and, as expected, is shown to perform substantially more efficiently than when spectral collocation methods are used. The building blocks of the algorithm have been implemented and extensively validated, focusing on classic PSE analysis of instability on the flow-plate boundary layer, temporal and spatial BiGlobal EVP solutions (the latter necessary for the initialization of the PSE-3D), as well as standard PSE in a cylindrical coordinates using the nonparallel Batchelor vortex basic flow model, such that comparisons between PSE and PSE-3D be possible; excellent agreement is shown in all aforementioned comparisons. Finally, the linear PSE-3D instability analysis is applied to a fully three-dimensional flow composed of a counter-rotating pair of nonparallel Batchelor vortices.

Advances in the modeling, characterization and reliability of concentrator multijunction solar cells

Los sistemas de concentración fotovoltaica (CPV) parecen ser una de las vías más prometedoras para generar electricidad a gran escala a precios competitivos. La investigación actual se centra en aumentar la eficiencia y la concentración de los sistemas para abaratar costes. Al mismo tiempo se investiga sobre la fiabilidad de los diferentes componentes que integran un sistema de concentración, ya que para que los sistemas de concentración sean competitivos es necesario que tengan una fiabilidad al menos similar a los sistemas basados en células de silicio. En la presente tesis doctoral se ha llevado a cabo el estudio de aspectos avanzados de células solares multi-unión diseñadas para trabajar a concentraciones ultra-altas. Para ello, se ha desarrollado un modelo circuital tridimensional distribuido con el que simular el comportamiento de las células solares triple-unión bajo distintas condiciones de funcionamiento, así mismo se ha realizado una caracterización avanzada de este tipo de células para comprender mejor su modo de operación y así poder contribuir a mejorar su eficiencia. Finalmente, se han llevado a cabo ensayos de vida acelerados en células multiunión comerciales para conocer la fiabilidad de este tipo de células solares. Para la simulación de células solares triple-unión se ha desarrollado en la presente tesis doctoral un modelo circuital tridimensinal distribuido el cuál integra una descripción completa de la unión túnel. De este modo, con el modelo desarrollado, hemos podido simular perfiles de luz sobre la célula solar que hacen que la densidad de corriente fotogenerada sea mayor a la densidad de corriente pico de la unión túnel. El modelo desarrollado también contempla la distribución lateral de corriente en las capas semiconductoras que componen y rodean la unión túnel. Por tanto, se ha podido simular y analizar el efecto que tiene sobre el funcionamiento de la célula solar que los concentradores ópticos produzcan perfiles de luz desuniformes, tanto en nivel de irradiancia como en el contenido espectral de la luz (aberración cromática). Con el objetivo de determinar cuáles son los mecanismos de recombinación que están limitando el funcionamiento de cada subcélula que integra una triple-unión, y así intentar reducirlos, se ha llevado a cabo la caracterización eléctrica de células solares monouni ón idénticas a las subcelulas de una triple-unión. También se ha determinado la curva corriente-tensión en oscuridad de las subcélulas de GaInP y GaAs de una célula dobleunión mediante la utilización de un teorema de reciprocidad electro-óptico. Finalmente, se ha analizado el impacto de los diferentes mecanismos de recombinación en el funcionamiento de la célula solar triple-unión en concentración. Por último, para determinar la fiabilidad de este tipo de células, se ha llevado a cabo un ensayo de vida acelerada en temperatura en células solares triple-unión comerciales. En la presente tesis doctoral se describe el diseño del ensayo, el progreso del mismo y los datos obtenidos tras el análisis de los resultados preliminares. Abstract Concentrator photovoltaic systems (CPV) seem to be one of the most promising ways to generate electricity at competitive prices. Nowadays, the research is focused on increasing the efficiency and the concentration of the systems in order to reduce costs. At the same time, another important area of research is the study of the reliability of the different components which make up a CPV system. In fact, in order for a CPV to be cost-effective, it should have a warranty at least similar to that of the systems based on Si solar cells. In the present thesis, we will study in depth the behavior of multijunction solar cells under ultra-high concentration. With this purpose in mind, a three-dimensional circuital distributed model which is able to simulate the behavior of triple-junction solar cells under different working conditions has been developed. Also, an advanced characterization of these solar cells has been carried out in order to better understand their behavior and thus contribute to improving efficiency. Finally, accelerated life tests have been carried out on commercial lattice-matched triple-junction solar cells in order to determine their reliability. In order to simulate triple-junction solar cells, a 3D circuital distributed model which integrates a full description of the tunnel junction has been developed. We have analyzed the behavior of the multijunction solar cell under light profiles which cause the current density photo-generated in the solar cell to be higher than the tunnel junction’s peak current density. The advanced model developed also takes into account the lateral current spreading through the semiconductor layers which constitute and surround the tunnel junction. Therefore, the effects of non-uniform light profiles, in both irradiance and the spectral content produced by the concentrators on the solar cell, have been simulated and analyzed. In order to determine which recombination mechanisms are limiting the behavior of each subcell in a triple-junction stack, and to try to reduce them when possible, an electrical characterization of single-junction solar cells that resemble the subcells in a triplejunction stack has been carried out. Also, the dark I-V curves of the GaInP and GaAs subcells in a dual-junction solar cell have been determined by using an electro-optical reciprocity theorem. Finally, the impact of the different recombination mechanisms on the behavior of the triple-junction solar cell under concentration has been analyzed. In order to determine the reliability of these solar cells, a temperature accelerated life test has been carried out on commercial triple-junction solar cells. In the present thesis, the design and the evolution of the test, as well as the data obtained from the analysis of the preliminary results, are presented.

Intraply fracture of fiber-reinforced composites: microscopic mechanisms and modeling

The fracture behavior parallel to the fibers of an E-glass/epoxy unidirectional laminate was studied by means of three-point tests on notched beams. Selected tests were carried out within a scanning electron microscope to ascertain the damage and fracture micromechanisms upon loading. The mechanical behavior of the notched beam was simulated within the framework of the embedded cell model, in which the actual composite microstructure was resolved in front of the notch tip. In addition, matrix and interface properties were independently measured in situ using a nanoindentor. The numerical simulations very accurately predicted the macroscopic response of the composite as well as the damage development and crack growth in front of the notch tip, demonstrating the ability of the embedded cell approach to simulate the fracture behavior of heterogeneous materials. Finally, this methodology was exploited to ascertain the influence of matrix and interface properties on the intraply toughness.

A Novel Method for Radio Propagation Simulation Based on Automatic 3D Environment Reconstruction

In this paper, a novel method to simulate radio propagation is presented. The method consists of two steps: automatic 3D scenario reconstruction and propagation modeling. For 3D reconstruction, a machine learning algorithm is adopted and improved to automatically recognize objects in pictures taken from target regions, and 3D models are generated based on the recognized objects. The propagation model employs a ray tracing algorithm to compute signal strength for each point on the constructed 3D map. Our proposition reduces, or even eliminates, infrastructure cost and human efforts during the construction of realistic 3D scenes used in radio propagation modeling. In addition, the results obtained from our propagation model proves to be both accurate and efficient