Atomic force microscopy of protein films and crystals

A customized atomic force microscopy (AFM) instrument optimized for imaging protein crystals in solution is described. The device was tested on crystals and Langmuir-Blodgett (LB) films of two proteins with quite different molecular weights. This approach enables the periodicity and morphology of crystals to be studied in their mother liquid, thereby preserving the native periodic protein crystal structure, which is typically destroyed by drying. Moreover, the instrument appears to distinguish protein crystals from salt crystals, which under the optical microscope are frequently quite similar, the difference between them often being revealed only during x-ray analysis. AFM estimates of the packing, order, and morphology of the given single proteins appear quite similar in the LB thin film and in the crystals, which means that routine crystal measurements can be performed at high resolution. The AFM consists of a custom-built measuring head and a homemade flexible SPM controller which can drive the head for contact, noncontact and spectroscopy modes, thus providing the user with a high degree of customization for crystal measurement.     

Querying and creating visualizations by analogy

While there have been advances in visualization systems, particularly in multi-view visualizations and visual exploration, the process of building visualizations remains a major bottleneck in data exploration. We show that provenance metadata collected during the creation of pipelines can be reused to suggest similar content in related visualizations and guide semi-automated changes. We introduce the idea of query-by-example in the context of an ensemble of visualizations, and the use of analogies as first-class operations in a system to guide scalable interactions. We describe an implementation of these techniques in VisTrails, a publicly-available, open-source system.     

Ambient occlusion and edge cueing to enhance real time molecular visualization

The paper presents a set of combined techniques to enhance the real-time visualization of simple or complex molecules (up to order of 106 atoms) space fill mode. The proposed approach includes an innovative technique for efficient computation and storage of ambient occlusion terms, a small set of GPU accelerated procedural impostors for space-fill and ball-and-stick rendering, and novel edge-cueing techniques. As a result, the user's understanding of the three-dimensional structure under inspection is strongly increased (even for still images), while the rendering still occurs in real time.     

Lower and upper bounds for the two-echelon capacitated location-routing problem

In this paper, we introduce two algorithms to address the two-echelon capacitated location-routing problem (2E-CLRP). We introduce a branch-and-cut algorithm based on the solution of a new two-index vehicle-flow formulation, which is strengthened with several families of valid inequalities. We also propose an adaptive large-neighbourhood search (ALNS) meta-heuristic with the objective of finding good-quality solutions quickly. The computational results on a large set of instances from the literature show that the ALNS outperforms existing heuristics. Furthermore, the branch-and-cut method provides tight lower bounds and is able to solve small- and medium-size instances to optimality within reasonable computing times.     

New insights on multi-state component criticality and importance

In this paper, new importance measures for multi-state systems with multi-state components are introduced and evaluated. These new measures complement and enhance current work done in the area of multi-state reliability. In general, importance measures are used to evaluate and rank the criticality of component or component states with respect to system reliability. The focus of the study is to provide intuitive and clear importance measures that can be used to enhance system reliability from two perspectives: (1) how a specific component affects multi-state system reliability and (2) how a particular component state or set of states affects multi-state system reliability. The first measure unsatisfied demand index, provides insight regarding a component or component state contribution to unsatisfied demand. The second measure multi-state failure frequency index, elaborates on an approach that quantifies the contribution of a particular component or component state to system failure. Finally, the multi-state redundancy importance identifies where to allocate component redundancy as to improve system reliability. The findings of this study indicate that both perspectives can be used to complement each other and as an effective tool to assess component criticality. Examples illustrate and compare the proposed measures with previous multi-state importance measures.     

D-Index: Distance Searching Index for Metric Data Sets

In order to speedup retrieval in large collections of data, index structures partition the data into subsets so that query requests can be evaluated without examining the entire collection. As the complexity of modern data types grows, metric spaces have become a popular paradigm for similarity retrieval. We propose a new index structure, called D-Index, that combines a novel clustering technique and the pivot-based distance searching strategy to speed up execution of similarity range and nearest neighbor queries for large files with objects stored in disk memories. We have qualitatively analyzed D-Index and verified its properties on actual implementation. We have also compared D-Index with other index structures and demonstrated its superiority on several real-life data sets. Contrary to tree organizations, the D-Index structure is suitable for dynamic environments with a high rate of delete/insert operations.     

Heuristic design of cancer chemotherapies

A methodology using heuristic search methods is proposed for optimizing cancer chemotherapies with drugs acting on a specific phase of the cell cycle. Specifically, two evolutionary algorithms, and a simulated annealing method are considered. The methodology relies on an underlying mathematical model for tumor growth that includes cycle phase specificity, and multiple applications of a single cytotoxic agent. The goal is to determine effective protocols for administering the agent, so that the tumor is eradicated, while the immune system remains above a given threshold. Results confirm that modern heuristic methods are a good choice for optimizing complex systems. The three algorithms considered produced effective solutions, and provided drug schedules suitable for practice, although some methods excelled others in performance. A discussion of comparative results is presented.     

Experimental and Numerical Analysis of Soil–Pipe Interaction

Cases of pipeline damage caused by landslides are common in coastal or mountainous regions, where a continuous monitoring/repair activity is planned in order to maintain their serviceability. The analysis of the soil–structure interaction phenomenon can be invoked to improve the planning and design of buried pipelines, to guide monitoring, and to reduce the risk of damage or failure. Two different approaches are considered in this paper: small scale laboratory tests and numerical simulations using the distinct element method (DEM). The experimental setup consists of a box filled with sand and water. Several experiments were performed, in which the diameter and the depth of the tube varied. The numerical simulations are divided in two separate series: in the first, the numerical model is calibrated and its reliability in reproducing the experimental tests is checked; in the second series, the direction of the relative displacement between the tube and the surrounding “numerical soil” varies over the range ±90° with respect to the horizontal. In the latter, both vertical and horizontal components of the drag force are measured and the corresponding interaction diagrams are constructed. The DEM simulations provide useful information about the shape of the failure mechanisms and the force transfer within the soil.