User-defined Patterns Research Articles

Using triangle-based cubic interpolation in generation of object-adaptive fringe pattern

The object-adaptive fringe projection technique employs user-defined uneven spaced fringe patterns, instead of the evenly spaced fringe patterns, to measure the deformation of the object surface. With this technique, the quality of the object-adaptive fringe patterns is very important for guaranteeing the measurement accuracy. In this paper, a simple and effective method to generate such fringe patterns based on the cubic Beziér interpolation is presented. It can realize the cubic Beziér interpolation through three nearest points and thereby the time required for generating the adaptive fringe patterns is significantly reduced without loss of accuracy. Numerical simulations and experiments have demonstrated the accuracy and effectiveness of the proposed method.

Real time dynamic fracture with volumetric approximate convex decompositions

We propose a new fast, robust and controllable method to simulate the dynamic destruction of large and complex objects in real time. The common method for fracture simulation in computer games is to pre-fracture models and replace objects by their pre-computed parts at run-time. This popular method is computationally cheap but has the disadvantages that the fracture pattern does not align with the impact location and that the number of hierarchical fracture levels is fixed. Our method allows dynamic fracturing of large objects into an unlimited number of pieces fast enough to be used in computer games. We represent visual meshes by volumetric approximate convex decompositions (VACD) and apply user-defined fracture patterns dependent on the impact location. The method supports partial fracturing meaning that fracture patterns can be applied locally at multiple locations of an object. We propose new methods for computing a VACD, for approximate convex hull construction and for detecting islands in the convex decomposition after partial destruction in order to determine support structures.

Fabricating Nanoscale Chemical Gradients with ThermoChemical NanoLithography

Production of chemical concentration gradients on the submicrometer scale remains a formidable challenge, despite the broad range of potential applications and their ubiquity throughout nature. We present a strategy to quantitatively prescribe spatial variations in functional group concentration using ThermoChemical NanoLithography (TCNL). The approach uses a heated cantilever to drive a localized nanoscale chemical reaction at an interface, where a reactant is transformed into a product. We show using friction force microscopy that localized gradients in the product concentration have a spatial resolution of ~20 nm where the entire concentration profile is confined to sub-180 nm. To gain quantitative control over the concentration, we introduce a chemical kinetics model of the thermally driven nanoreaction that shows excellent agreement with experiments. The comparison provides a calibration of the nonlinear dependence of product concentration versus temperature, which we use to design two-dimensional temperature maps encoding the prescription for linear and nonlinear gradients. The resultant chemical nanopatterns show high fidelity to the user-defined patterns, including the ability to realize complex chemical patterns with arbitrary variations in peak concentration with a spatial resolution of 180 nm or better. While this work focuses on producing chemical gradients of amine groups, other functionalities are a straightforward modification. We envision that using the basic scheme introduced here, quantitative TCNL will be capable of patterning gradients of other exploitable physical or chemical properties such as fluorescence in conjugated polymers and conductivity in graphene. The access to submicrometer chemical concentration and gradient patterning provides a new dimension of control for nanolithography.

Multiphoton polymerization using optical trap assisted nanopatterning

In this letter, we show the combination of multiphoton polymerization and optical trap assisted nanopatterning (OTAN) for the additive manufacturing of structures with nanometer resolution. User-defined patterns of polymer nanostructures are deposited on a glass substrate by a 3.5 μm polystyrene sphere focusing IR femtosecond laser pulses, showing minimum feature sizes of λ/10. Feature size depends on the applied laser fluence and the bead surface spacing. A finite element model describes the intensity enhancement in the microbead focus. The results presented suggest that OTAN in combination with multiphoton processing is a viable technique for additive nanomanufacturing with sub-diffraction-limited resolution.

Ontology Change Management and Identification of Change Patterns

Ontologies can support a variety of purposes, ranging from capturing the conceptual knowledge to the organisation of digital content and information. However, information systems are always subject to change and ontology change management can pose challenges. In this sense, the application and representation of ontology changes in terms of higher-level change operations can describe more meaningful semantics behind the applied change. In this paper, we propose a four-phase process that covers the operationalization, representation and detection of higher-level changes in ontology evolution life cycle. We present different levels of change operators based on the granularity and domain-specificity of changes. The first layer is based on generic atomic level change operators, whereas the next two layers are user-defined (generic/domain-specific) change patterns. We introduce layered change logs for the explicit operational representation of ontology changes. We formalised the change log using a graph-based approach. We introduce a technique to identify composite changes that not only assists in formulating ontology change log data in a more concise manner, but also helps in realizing the semantics and intent behind any applied change. Furthermore, we identify frequent change sequences that are applied as a reference to discover reusable, often domain-specific and usage-driven change patterns. We describe the pattern identification algorithms and evaluate their performance.

Modified processing conditions for optimized organic solar cells with inkjet printed P3HT:PC61BM active layers

Abstract Inkjet printing can be used to deposit the functional layers of organic solar cells and it offers advantages over spin coating such as the possibility to print films with user-defined patterns. In this study, inkjet printing was utilized to deposit polymer:fullerene solar cell active layers and different drying and annealing conditions were examined in order to optimize device performance. Low fill factors of approximately 30% were found for devices with printed active layers that were dried at 100 °C and a considerable shift in the fill factor of up to 60% was seen after post-annealing at 150 °C. Changes in the fill factor corresponded to an increase in device efficiency from ∼1.3% to ∼2.4% after post-annealing. An alternative active layer drying procedure was used based on solvent annealing which resulted in high fill factors of 60% and efficiencies of ∼2.4% without post-annealing. Blend films were examined with atomic force microscopy, ultra-violet visible spectroscopy and X-ray photoelectron spectroscopy. It was determined that solvent annealed, inkjet printed active layers are considerably rougher and show enhanced organization with respect to films that were dried at 100 °C. Two preparation routes are provided for devices with printed active layers with acceptable efficiencies based on quick drying and post-annealing or slow drying (solvent annealing).

Moving towards Positive Security Model for Web Application Firewall

The proliferation of web application and the pervasiveness of mobile technology make web-based attacks even more attractive and even easier to launch. Web Application Firewall (WAF) is an intermediate tool between web server and users that provides comprehensive protection for web application. WAF is a negative security model where the detection and prevention mechanisms are based on predefined or user-defined attack signatures and patterns. However, WAF alone is not adequate to offer best defensive system against web vulnerabilities that are increasing in number and complexity daily. This paper presents a methodology to automatically design a positive security based model which identifies and allows only legitimate web queries. The paper shows a true positive rate of more than 90% can be achieved.

Recognizing patterns in streams with imprecise timestamps

Large-scale event systems are becoming increasingly popular in a variety of domains. Event pattern evaluation plays a key role in monitoring applications in these domains. identifies matches of user-defined patterns on high-volume event streams. Existing work on pattern evaluation, however, assumes that the occurrence time of each event is known precisely and the events from various sources can be merged into a single stream with a total or partial order. We observe that in real-world applications event occurrence times are often unknown or imprecise. Therefore, we propose a temporal model that assigns a time interval to each event to represent all of its possible occurrence times and revisit pattern evaluation under this model. In particular, we propose the formal semantics of such pattern evaluation, two evaluation frameworks, and algorithms and optimizations in these frameworks. Our evaluation results using both real traces and synthetic systems show that the event-based framework always outperforms the point-based framework and with optimizations, it achieves high efficiency for a wide range of workloads tested.

Mirroring of Knowledge Practices based on User-defined Patterns

Mirroring of Knowledge Practices based on User-defined Patterns

PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment.

BackgroundThe Monte Carlo simulation of sequence evolution is routinely used to assess the performance of phylogenetic inference methods and sequence alignment algorithms. Progress in the field of molecular evolution fuels the need for more realistic and hence more complex simulations, adapted to particular situations, yet current software makes unreasonable assumptions such as homogeneous substitution dynamics or a uniform distribution of indels across the simulated sequences. This calls for an extensible simulation framework written in a high-level functional language, offering new functionality and making it easy to incorporate further complexity.ResultsPhyloSim is an extensible framework for the Monte Carlo simulation of sequence evolution, written in R, using the Gillespie algorithm to integrate the actions of many concurrent processes such as substitutions, insertions and deletions. Uniquely among sequence simulation tools, PhyloSim can simulate arbitrarily complex patterns of rate variation and multiple indel processes, and allows for the incorporation of selective constraints on indel events. User-defined complex patterns of mutation and selection can be easily integrated into simulations, allowing PhyloSim to be adapted to specific needs.ConclusionsClose integration with R and the wide range of features implemented offer unmatched flexibility, making it possible to simulate sequence evolution under a wide range of realistic settings. We believe that PhyloSim will be useful to future studies involving simulated alignments.

Impact of Local versus Global Ligand Density on Cellular Adhesion

α(v)β(3) integrin-mediated cell adhesion is crucially influenced by how far ligands are spaced apart. To evaluate the impact of local ligand density versus global ligand density of a given surface, we used synthetic micronanostructured cell environments with user-defined ligand spacing and patterns to investigate cellular adhesion. The development of stable focal adhesions, their number, and size as well as the cellular adhesion strength proved to be influenced by local more than global ligand density.

Direct writing of micro/nano-scale patterns by means of particle lens arrays scanned by a focused diode pumped Nd:YVO4 laser

A practical approach to a well-known technique of laser micro/nano-patterning by optical near fields is presented. It is based on surface patterning by scanning a Gaussian laser beam through a self-assembled monolayer of silica micro-spheres on a single-crystalline silicon (Si) substrate. So far, the outcome of this kind of near-field patterning has been related to the simultaneous, parallel surface-structuring of large areas either by top hat or Gaussian laser intensity distributions. We attempt to explore the possibility of using the same technique in order to produce single, direct writing of features. This could be of advantage for applications in which only some areas need to be patterned (i.e. local area selective patterning) or single lines are required (e.g. a particular micro/nano-fluidic channel). A diode pumped Nd:YVO4 laser system (wavelength of 532 nm, pulse duration of 8 ns, repetition rate of 30 kHz) with a computer-controlled 3 axis galvanometer beam scanner was employed to write user-defined patterns through the particle lens array on the Si substrate. After laser irradiation, the obtained patterns which are in the micro-scale were composed of sub-micro/micro-holes or bumps. The micro-pattern resolution depends on the dimension of both the micro-sphere’s diameter and the beam’s spot size. The developed technique could potentially be employed to fabricate photonic crystal structures mimicking nature’s butterfly wings and anti-reflective “moth eye” arrays for photovoltaic cells.

Multibeam Antenna Arrays With Common Subarray Layouts

In this letter, an approach for the synthesis of multiple beam patterns sharing the same antenna array is numerically validated and enhanced. The approach is aimed at generating an optimal (principal) pattern with an independent set of excitations and K compromise patterns at the subarray level. The problem is mathematically formulated as the definition of a common subarray architecture and K independent sets of subarray weights such that the compromise patterns are close as much as possible to the K user-defined reference patterns. To reduce the level of the secondary lobes of the multiple patterns, a hybrid approach based on a deterministic procedure is applied.

Generation of Micropatterned Substrates Using Micro Photopatterning

Micro photopatterning (microPP) has been developed to rapidly test and generate different patterns for extracellular matrix adsorption without being hindered by the process of making physical stamps through nanolithography techniques. It uses two-photon excitation guided through a point-scanning confocal microscope to locally photoablate poly(vinyl) alcohol (PVA) thin films in user-defined computer-controlled patterns. PVA thin films are ideal for surface blocking, being hydrophilic substrates that deter protein adsorption and cell attachment. Because gold substrates are not used during microPP, all live-cell fluorescent-imaging techniques including total internal reflection fluorescence microscopy of GFP-linked proteins can be performed with minimal loss of fluorescence signal. Furthermore, because microPP does not require physical stamps for pattern generation, multiple ECMs or other proteins can be localized within microns of each other. This unit details the setup of microPP. It also provides troubleshooting techniques.

PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees

BackgroundTo effectively apply evolutionary concepts in genome-scale studies, large numbers of phylogenetic trees have to be automatically analysed, at a level approaching human expertise. Complex architectures must be recognized within the trees, so that associated information can be extracted.ResultsHere, we present a new software library, PhyloPattern, for automating tree manipulations and analysis. PhyloPattern includes three main modules, which address essential tasks in high-throughput phylogenetic tree analysis: node annotation, pattern matching, and tree comparison. PhyloPattern thus allows the programmer to focus on: i) the use of predefined or user defined annotation functions to perform immediate or deferred evaluation of node properties, ii) the search for user-defined patterns in large phylogenetic trees, iii) the pairwise comparison of trees by dynamically generating patterns from one tree and applying them to the other.ConclusionPhyloPattern greatly simplifies and accelerates the work of the computer scientist in the evolutionary biology field. The library has been used to automatically identify phylogenetic evidence for domain shuffling or gene loss events in the evolutionary histories of protein sequences. However any workflow that relies on phylogenetic tree analysis, could be automated with PhyloPattern.

Large-area laser nano-texturing with user-defined patterns

Writing nano-sized features less than the diffraction limit of the lasers efficiently over a large area requires special technology development. This paper reports the use of a self-assembled particle lens array with near-field enhancement effect to write millions of nano-sized user-defined features, e.g. English letters, lines, curves, simultaneously by angular beam scanning. About a 5 mm × 5 mm area can be written with a single shot of a laser beam or few scans for up to 100 million identical features of nano or sub-micro scales. With the help of certain environmental conditions, such as the use of a suitable chemical solution in conjunction with the particle lens array, the characteristic of the features produced can be further controlled, including the generation of reversed (e.g. pits become hills and grooves become walls) features of laser-written patterns. The technical challenges, experimental findings and theoretical analysis/simulation are presented.

A Method for Generating Natural and User-Defined Sniffing Patterns in Anesthetized or Reduced Preparations

Sniffing has long been thought to play a critical role in shaping neural responses to odorants at multiple levels of the nervous system. However, it has been difficult to systematically examine how particular parameters of sniffing behavior shape odorant-evoked activity, in large part because of the complexity of sniffing behavior and the difficulty in reproducing this behavior in an anesthetized or reduced preparation. Here we present a method for generating naturalistic sniffing patterns in such preparations. The method involves a nasal ventilator whose movement is controlled by an analog command voltage. The command signal may consist of intranasal pressure transients recorded from awake rats and mice or user-defined waveforms. This "sniff playback" device generates intranasal pressure and airflow transients in anesthetized animals that approximate those recorded from the awake animal and are reproducible across trials and across preparations. The device accurately reproduces command waveforms over an amplitude range of approximately 1 log unit and up to frequencies of approximately 12 Hz. Further, odorant-evoked neural activity imaged during sniff playback appears similar to that seen in awake animals. This method should prove useful in investigating how the parameters of odorant sampling shape neural responses in a variety of experimental settings.

Propagation-prediction and site-planning software for wireless communication systems

Propagation-prediction and site-planning software for wireless communication networks has been developed. The software has a user-friendly graphical user interface (GUI), and provides calculations for large-scale and small-scale propagation parameters, including path loss (or received power) and delay profiles. Angles of arrival/departure, which are useful for the design of wireless systems employing multiple antennas, are also provided in the simulation. Some of the main features of the software include the use of a computationally efficient ray-tracing approach for simulating propagation in wireless environments, and the fact that users can upload AutoCAD .dxf files for indoor or outdoor environments. Both a single-building floor plan or an entire city layout can be simulated, and the user is provided with the ability to assign wall geometries and electrical parameters. User-defined realistic antenna radiation patterns for both the transmitting and receiving antennas are incorporated in the simulation. Broadband as well as polarization-dependent simulations are also included in the software.

MUSKEL: an expandable skeleton environment

Programming models based on algorithmic skeletons promise to raise the level of abstraction perceived by programmers when implementing parallel applications, while guaranteeing good performance figures. At the same time, however, they restrict the freedom of programmers to implement arbitrary parallelism exploitation patterns. In fact, efficiency is achieved by restricting the parallelism exploitation patterns provided to the programmer to the useful ones for which efficient implementations, as well as useful and efficient compositions, are known. In this work we introduce muskel , a full Java library targeting workstation clusters, networks and grids and providing the programmers with a skeleton based parallel programming environment. muskel is implemented exploiting (macro) data flow technology, rather than the more usual skeleton technology relying on the use of implementation templates. Using data flow, muskel easily and efficiently implements both classical, predefined skeletons, and user-defined parallelism exploitation patterns. This provides a means to overcome some of the problems that Cole identified in his skeleton manifesto as the issues impairing skeleton success in the parallel programming arena. We discuss fully how user-defined skeletons are supported by exploiting a data flow implementation, experimental results and we also discuss extensions supporting the further characterization of skeletons with non-functional properties, such as security, through the use of Aspect Oriented Programming and annotations.

Shear-Aligned Block Copolymer Thin Films as Nanofabrication Templates

Block copolymers spontaneously self-assemble into highly regular nanostructures; in bulk, these structures include spheres packed on a body-centered cubic lattice and cylinders arranged on a hexagonal lattice, where the diameter of the spheres or cylinders (typically 10-100 nm) is readily tunable through the polymer's molecular weight. In ultrathin films containing a monolayer of these nanostructures, similar morphologies are adopted: two-dimensional hexagonally-packed sphere arrays, and striped patterns formed by in-plane cylinders. By exploiting the chemical differences between the two blocks, such films can be used as masks, where the patterns formed by the spheres or cylinders are ultimately replicated in another material (perhaps inorganic), such as semiconductor dots (spheres) or metal wires (cylinders). But while self-assembly can produce highly-regular local structures, it does not provide any global order or orientation; for example, the coherence length for a block copolymer cylinder is typically less than a micron. This limits the application of the arrays formed by block copolymer templating. Recently, we have developed methods to shear-align the spheres or cylinders in block copolymer thin films, where the nanodomains are oriented in a common direction over centimeter lengths and square-centimeter areas. Shear-aligned films of cylinder-formers, when converted to arrays of metal nanowires, provide broadband optical polarizers which function down into the ultraviolet. By directing the path of a nonsolvent fluid flowing over the block copolymer film, we can shape the direction of the nanodomains, creating complex user-defined patterns of cylinder orientation on the millimeter length scale.