Review of the Synergies Between Computational Modeling and Experimental Characterization of Materials Across Length Scales

With the increasing interplay between experimental and computational approaches at multiple length scales, new research directions are emerging in materials science and computational mechanics. Such cooperative interactions find many applications in the development, characterization and design of complex material systems. This manuscript provides a broad and comprehensive overview of recent trends where predictive modeling capabilities are developed in conjunction with experiments and advanced characterization to gain a greater insight into structure-properties relationships and study various physical phenomena and mechanisms. The focus of this review is on the intersections of multiscale materials experiments and modeling relevant to the materials mechanics community. After a general discussion on the perspective from various communities, the article focuses on the latest experimental and theoretical opportunities. Emphasis is given to the role of experiments in multiscale models, including insights into how computations can be used as discovery tools for materials engineering, rather than to "simply" support experimental work. This is illustrated by examples from several application areas on structural materials. This manuscript ends with a discussion on some problems and open scientific questions that are being explored in order to advance this relatively new field of research.Comment: 25 pages, 11 figures, review article accepted for publication in J. Mater. Sc

Scribble based interactive 3D reconstruction via scene co-segmentation

In this paper, we present a novel interactive 3D reconstruction algorithm which renders a planar reconstruction of the scene. We consider a scenario where the user has taken a few images of a scene from multiple poses. The goal is to obtain a dense and visually pleasing reconstruction of the scene, including non-planar objects. Using simple user interactions in the form of scribbles indicating the surfaces in the scene, we develop an idea of 3D scribbles to propagate scene geometry across multiple views and perform co-segmentation of all the images into the different surfaces and non-planar objects in the scene. We show that this allows us to render a complete and pleasing reconstruction of the scene along with a volumetric rendering of the non-planar objects. We demonstrate the effectiveness of our algorithm on both outdoor and indoor scenes including the ability to handle featureless surfaces. Index Terms — image based modeling, interactive 3D re-construction 1

Video Depth-From-Defocus

Many compelling video post-processing effects, in particular aesthetic focus editing and refocusing effects, are feasible if per-frame depth information is available. Existing computational methods to capture RGB and depth either purposefully modify the optics (coded aperture, light-field imaging), or employ active RGB-D cameras. Since these methods are less practical for users with normal cameras, we present an algorithm to capture all-in-focus RGB-D video of dynamic scenes with an unmodified commodity video camera. Our algorithm turns the often unwanted defocus blur into a valuable signal. The input to our method is a video in which the focus plane is continuously moving back and forth during capture, and thus defocus blur is provoked and strongly visible. This can be achieved by manually turning the focus ring of the lens during recording. The core algorithmic ingredient is a new video-based depth-from-defocus algorithm that computes space-time-coherent depth maps, deblurred all-in-focus video, and the focus distance for each frame. We extensively evaluate our approach, and show that it enables compelling video post-processing effects, such as different types of refocusing

Modélisation du comportement mécanique de la neige à partir d'images microtomographiques

Characterizing the complex microstructure of snow and its mechanics is a major challenge for avalanche forecasting and hazard mapping. While the effect of environmental conditions on the snow metamorphism, which leads to numerous snow types, is fairly known, the relation between snow microstructure and mechanical properties is poorly understood because of the very fragile nature of snow. In order to decipher this relation for dry snow, this thesis presents a modeling approach of snow mechanics based on the three-dimensional microstructure of snow captured by X-ray microtomography and the properties of ice. First, in order to automatically process the microtomographic data, we take advantage of the minimization of the snow surface energy through metamorphism to efficiently binary segment grayscale images. Second, assuming an elastic brittle behavior of the ice matrix, the tensile strength of snow is modeled via a finite element approach. The model reveals an apparent pseudo-plastic behavior caused by damage, and the highly heterogenous stress distribution in the ice matrix. Third, we develop a discrete element model, accounting for grain-rearrangements and the creation/failure of inter-granular contacts. The grains, geometric input of the model, are detected in the microstructure with mechanically-relevant criteria and described as rigid clumps of spheres. The model evidences that the compression behavior of snow is mainly controlled by density but that the first stage of deformation is also sensible to the snow type. Last, the inter-granular bonds, recognized to be critical for the mechanical properties, are characterized through a new microstructural indicator, which effectively highly correlates with the simulated mechanical and physical properties.Caractériser les propriétés mécaniques de la neige est un défi majeur pour la prévision et la prédétermination du risque d’avalanche. Du fait du grand nombre de types de neige et de la difficulté à effectuer des mesures sur ce matériau très fragile, la compréhension de la relation entre la microstructure de la neige et ses propriétés mécaniques est encore incomplète. Cette thèse aborde ce problème par le biais d’une approche de modélisation mécanique basée sur la microstructure tridimensionnelle de neige obtenue par microtomographie aux rayons X. Tout d’abord, afin d’automatiser et améliorer la segmentation des images microtomographiques, un nouvel algorithme tirant profit de la minimisation de l’énergie de surface de la neige a été développé et évalué. L’image air-glace est ensuite utilisée comme entrée géométrique d’un modèle éléments finis où la glace est supposée élastique fragile. Ce modèle permet de reproduire le comportement fragile en traction et révèle le comportement pseudoplastique apparent causé par l’endommagement microscopique, ainsi que la forte hétérogénéité des contraintes dans la matrice de glace. Pour reproduire les grandes déformations impliquant le ré-arrangement de grains, un modèle par éléments discrets a ensuite été développé. Les grains sont identifiés dans la microstructure en utilisant des critères géométriques dont la pertinence mécanique a été démontrée, et décrits dans le modèle par des blocs rigides de sphères. Le comportement simulé en compression est dominé par le rôle de la densité mais révèle également des différences liées au type de neige. Enfin, pour distinguer le degré de cohésion entre les types de neige, un indicateur microstructurel a été développé et s’est avéré être fortement corrélé aux propriétés mécaniques et physiques du matériau

Surface structure and composition determination by low-energy electron scattering and Monte Carlo simulations

This thesis reports on surface and surface alloy structural and compositional determination with low-energy electron scattering and Monte Carlo simulations. Low-energy electron diffraction (LEED) technique and the newly developed low-energy electron microscopy (LEEM) IV technique are used to measure the electron scattering intensity spectra and dynamical multiple scattering analysis is performed to optimize the surface structural and non-structural parameters via comparison between the experimental spectra and calculated ones. My work focuses on the following four surface systems. (111), (110) and (001) surface structures of the semimetal bismuth are determined with LEED. The unreconstructed (1x1) structure is revealed for all three surfaces. The interlayer spacings for several outermost layers are resolved. All results agree with those obtained by first-principles calculations. The Debye temperatures for the Bi(111) and Bi(110) surface are found to be lower than that of the Bi bulk. In conjunction with the LEED technique, scanning tunneling microscopy (STM) observation is performed on the Bi(001) surface. Surface topology images show dominant bilayer steps and no single layer step. The newly developed LEEM-IV technique is used to investigate the PdCu surface alloy on the substrate Cu(001). Studies include quantifying the temporal evolution of Pd concentration on the Cu(001) terrace, mapping the 3D heterogeneous surface chemical composition, and identifying a step-overgrowth thin film growth mechanism. It is found that, at the initial deposition stages, Pd atoms reside in the second layer at the sample temperature of 473 K, and the Pd concentration increases exponentially with time. The heterogeneous structure and composition near the steps are found to be a result of the step-overgrowth. We highlight the LEEM-IV technique which provides a high lateral resolution at surfaces. We demonstrate a 3D profile of Pd concentration in the surface region by using the LEEM-IV technique. The reconstructed Si(001)-2x1 surface has been intriguing due to its great scientific and technical significance. Unfortunately, no satisfactory agreement between the LEED experimental and theoretical data have been achieved. Some controversies over this surface, such as the flip-flop dimer dynamics and the ground-state structure, still require further study. Utilizing LEEM to get electron scattering spectra from a single domain, we get a refined asymmetric tilted dimer structure. We investigate the 6H-SiC(0001) surface phase transition in order to ultimately understand the formation of graphene on it. LEEM diffraction data from a large single domain are analyzed for 3x3, 1x1 and 3x3 phases. All the surface structures turn out to have an A bi-layer bulk termination. It is found that the amount of Si at the surface decreases with increased temperature. Adatom-trimer-adlayer model for the 3x3 surface does not give a satisfactory result and more work needs to be done to resolve this structure. A mixed Si-vacancy top-site overlayer on the 1x1 surface is found. A 3x3 overlayer at the T4 registry on the substrate surface generates a best fit between experimental and calculated data

The Mechanism and Regulation of Bacteriophage DNA Packaging Motors

Many double-stranded DNA viruses use a packaging motor during maturation to recognize and transport genetic material into the capsid. In terminase motors, the TerS complex recognizes DNA, while the TerL motor packages the DNA into the capsid shell. Although there are several models for DNA recognition and translocation, how the motor components assemble and power DNA translocation is unknown. Using the thermophilic P74-26 bacteriophage model system, we discover that TerL uses a trans-activated ATP hydrolysis mechanism. Additionally, we identify critical residues for TerL ATP hydrolysis and DNA binding. With a combination of x-ray crystallography, SAXS, and molecular docking, we build a structural model for TerL pentamer assembly. Apo and ATP analog-bound TerL ATPase domain crystal structures show ligand-dependent conformational changes, which we propose power DNA translocation. Together, we assimilate these findings to build models for both motor assembly and DNA translocation. Additionally, with the P76-26 system, we identify the TerS protein as gp83. I find that P74-26 TerS is a nonameric ring that stimulates TerL ATPase activity while inhibiting TerL nuclease activity. Using cryoEM, I solve 3.8 Å and 4.8 Å resolution symmetric and asymmetric reconstructions of the TerS ring. I observe in P74-26 TerS, the conserved C-terminal beta-barrel is absent, and instead the region is flexible or unstructured. Furthermore, the helix-turn-helix motifs of P74-26 TerS are positioned differently than those of known TerS structures, suggesting P74-26 uses an alternative mechanism to recognize DNA

Técnicas de reconstrucción en tres dimensiones y realización de un programa informático para el trabajo con los modelos

En este proyecto se realiza la puesta en marcha de dos sistemas de reconstrucción de modelos en tres dimensiones: el primero basado en fotografías convencionales y el segundo realizado mediante un escáner de superficie. La motivación original del trabajo se encontraba en la aplicación de estas tecnologías para la reconstrucción de mamas para fines médicos, fin que fue descartado una vez analizadas las características y limitaciones de la tecnología disponible en la actualidad al alcance del mundo universitario. El proyecto se divide en dos partes principales. La primera trata de una revisión del estado del arte de las técnicas disponibles para la reconstrucción de objetos en tres dimensiones mediante fotografías convencionales, sin referencias numéricas de la localización de la cámara. Se presentan los métodos analizados y se exponen el conocimiento y tecnologías aprendidas, eligiendo una de ellas para su análisis. Posteriormente se explica el método de reconstrucción 3D a partir de un escáner de superficie, paradigma completamente diferente al anterior pero de gran repercusión y uso en la actualidad. En la segunda parte se ha realizado un programa que permite analizar modelos genéricos de reconstrucciones en tres dimensiones en un formato concreto. En este programa original creado para este trabajo se pone en práctica todo lo aprendido en las secciones anteriores. Con él se pueden realizar numerosas operaciones de tratamiento de modelos en 3D. Se termina el documento con las conclusiones aprendidas.Universidad de Sevilla. Máster en Ingeniería de Telecomunicació

Combining Network Modeling and Experimental Approaches to Predict Drug Combination Responses

Cancer is a lethal disease and complex at multiple levels of cell biology. Despite many advances in treatments, many patients do not respond to therapy. This is owing to the complexity of cancer-genetic variability due to mutations, the multi-variate biochemical networks within which drug targets reside and existence and plasticity of multiple cell states. It is generally understood that a combination of drugs is a way to address the multi-faceted drivers of cancer and drug resistance. However, the sheer number of testable combinations and challenges in matching patients to appropriate combination treatments are major issues. Here, we first present a general method of network inference which can be applied to infer biological networks. We apply this method to infer different kinds of networks in biological levels where cancer complexity resides-a biochemical network, gene expression and cell state transitions. Next, we focus our attention on glioblastoma and with pharmacological and biological considerations, obtain a ranked list of important drug targets in glioblastoms. We perform drug dose response experiments for 22 blood brain barrier penetrant drugs against 3 glioblastoma cell lines. These methods and experimental results inform a construction of a temporal cell state model to predict and experimentally validate combination treatments for certain drugs. We improve an experimental method to perform high throughput western blots and apply the method to discover biochemical interactions among some important proteins involved in temporal cell state transitions. Lastly, we illustrate a method to investigate potential resistance mechanisms in genome scale proteomic data. We hope that methods and results presented here can be adapted and improved upon to help in the discovery of biochemical interactions, capturing cell state transitions and ultimately help predict effective combination therapies for cancer

Large-scale 3D environmental modelling and visualisation for flood hazard warning.

3D environment reconstruction has received great interest in recent years in areas such as city planning, virtual tourism and flood hazard warning. With the rapid development of computer technologies, it has become possible and necessary to develop new methodologies and techniques for real time simulation for virtual environments applications. This thesis proposes a novel dynamic simulation scheme for flood hazard warning. The work consists of three main parts: digital terrain modelling; 3D environmental reconstruction and system development; flood simulation models. The digital terrain model is constructed using real world measurement data of GIS, in terms of digital elevation data and satellite image data. An NTSP algorithm is proposed for very large data assessing, terrain modelling and visualisation. A pyramidal data arrangement structure is used for dealing with the requirements of terrain details with different resolutions. The 3D environmental reconstruction system is made up of environmental image segmentation for object identification, a new shape match method and an intelligent reconstruction system. The active contours-based multi-resolution vector-valued framework and the multi-seed region growing method are both used for extracting necessary objects from images. The shape match method is used with a template in the spatial domain for a 3D detailed small scale urban environment reconstruction. The intelligent reconstruction system is designed to recreate the whole model based on specific features of objects for large scale environment reconstruction. This study then proposes a new flood simulation scheme which is an important application of the 3D environmental reconstruction system. Two new flooding models have been developed. The first one is flood spreading model which is useful for large scale flood simulation. It consists of flooding image spatial segmentation, a water level calculation process, a standard gradient descent method for energy minimization, a flood region search and a merge process. The finite volume hydrodynamic model is built from shallow water equations which is useful for urban area flood simulation. The proposed 3D urban environment reconstruction system was tested on our simulation platform. The experiment results indicate that this method is capable of dealing with complicated and high resolution region reconstruction which is useful for many applications. When testing the 3D flood simulation system, the simulation results are very close to the real flood situation, and this method has faster speed and greater accuracy of simulating the inundation area in comparison to the conventional flood simulation model