A heuristic model for the simulation of the deformation of elastic and spongy material for virtual reality applications

This paper presents a practical algorithm for the simulation of interactive deformation in a 3D polygonal mesh model. The algorithm combines the conventional simulation of deformation using a spring-mass-damping model, solved by explicit numerical integration, with a set of heuristics to describe certain features of the transient behaviour, to increase the speed and stability of solution. In particular, this algorithm was designed to be used in the simulation of synthetic environments where it is necessary to model realistically, in real time, the effect on non-rigid surfaces being touched, pushed, pulled or squashed. Such objects can be solid or hollow, and have plastic, elastic or fabric-like properties. The algorithm is presented in an integrated form including collision detection and adaptive refinement so that it may be used in a self-contained way as part of a simulation loop to include human interface devices that capture data and render a realistic stereoscopic image in real time. The algorithm is designed to be used with polygonal mesh models representing complex topology, such as the human anatomy in a virtual-surgery training simulator. The paper evaluates the model behaviour qualitatively and then concludes with some examples of the use of the algorithm.

On the derived category of a regular toric scheme

Let X be a quasi-compact scheme, equipped with an open covering by affine schemes U s = Spec A s . A quasi-coherent sheaf on X gives rise, by taking sections over the U s , to a diagram of modules over the coordinate rings A s , indexed by the intersection poset S of the covering. If X is a regular toric scheme over an arbitrary commutative ring, we prove that the unbounded derived category of quasi-coherent sheaves on X can be obtained from a category of Sop-diagrams of chain complexes of modules by inverting maps which induce homology isomorphisms on hyper-derived inverse limits. Moreover, we show that there is a finite set of weak generators, one for each cone in the fan S. The approach taken uses the machinery of Bousfield–Hirschhorn colocalisation of model categories. The first step is to characterise colocal objects; these turn out to be homotopy sheaves in the sense that chain complexes over different open sets U s agree on intersections up to quasi-isomorphism. In a second step it is shown that the homotopy category of homotopy sheaves is equivalent to the derived category of X.

Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life

Background. The assembly of the tree of life has seen significant progress in recent years but algae and protists have been largely overlooked in this effort. Many groups of algae and protists have ancient roots and it is unclear how much data will be required to resolve their phylogenetic relationships for incorporation in the tree of life. The red algae, a group of primary photosynthetic eukaryotes of more than a billion years old, provide the earliest fossil evidence for eukaryotic multicellularity and sexual reproduction. Despite this evolutionary significance, their phylogenetic relationships are understudied. This study aims to infer a comprehensive red algal tree of life at the family level from a supermatrix containing data mined from GenBank. We aim to locate remaining regions of low support in the topology, evaluate their causes and estimate the amount of data required to resolve them. Results. Phylogenetic analysis of a supermatrix of 14 loci and 98 red algal families yielded the most complete red algal tree of life to date. Visualization of statistical support showed the presence of five poorly supported regions. Causes for low support were identified with statistics about the age of the region, data availability and node density, showing that poor support has different origins in different parts of the tree. Parametric simulation experiments yielded optimistic estimates of how much data will be needed to resolve the poorly supported regions (ca. 103 to ca. 104 nucleotides for the different regions). Nonparametric simulations gave a markedly more pessimistic image, some regions requiring more than 2.8 105 nucleotides or not achieving the desired level of support at all. The discrepancies between parametric and nonparametric simulations are discussed in light of our dataset and known attributes of both approaches. Conclusions. Our study takes the red algae one step closer to meaningful inclusion in the tree of life. In addition to the recovery of stable relationships, the recognition of five regions in need of further study is a significant outcome of this work. Based on our analyses of current availability and future requirements of data, we make clear recommendations for forthcoming research.

Part-whole relations between food webs and the validity of local food-web descriptions

This work analyzes the relationship between large food webs describing potential feeding relations between species and smaller sub-webs thereof describing relations actually realized in local communities of various sizes. Special attention is given to the relationships between patterns of phylogenetic correlations encountered in large webs and sub-webs. Based on the current theory of food-web topology as implemented in the matching model, it is shown that food webs are scale invariant in the following sense: given a large web described by the model, a smaller, randomly sampled sub-web thereof is described by the model as well. A stochastic analysis of model steady states reveals that such a change in scale goes along with a re-normalization of model parameters. Explicit formulae for the renormalized parameters are derived. Thus, the topology of food webs at all scales follows the same patterns, and these can be revealed by data and models referring to the local scale alone. As a by-product of the theory, a fast algorithm is derived which yields sample food webs from the exact steady state of the matching model for a high-dimensional trophic niche space in finite time. (C) 2008 Elsevier B.V. All rights reserved.

Some properties of the speciation model for food-web structure - Mechanisms for degree distributions and intervality

We present a mathematical analysis of the speciation model for food-web structure, which had in previous work been shown to yield a good description of empirical data of food-web topology. The degree distributions of the network are derived. Properties of the speciation model are compared to those of other models that successfully describe empirical data. It is argued that the speciation model unities the underlying ideas of previous theories. In particular, it offers a mechanistic explanation for the success of the niche model of Williams and Martinez and the frequent observation of intervality in empirical food webs. (c) 2005 Elsevier Ltd. All rights reserved.

An explanatory model for food-web structure and evolution

Food webs are networks describing who is eating whom in an ecological community. By now it is clear that many aspects of food-web structure are reproducible across diverse habitats, yet little is known about the driving force behind this structure. Evolutionary and population dynamical mechanisms have been considered. We propose a model for the evolutionary dynamics of food-web topology and show that it accurately reproduces observed food-web characteristics in the steady state. It is based on the observation that most consumers are larger than their resource species and the hypothesis that speciation and extinction rates decrease with increasing body mass. Results give strong support to the evolutionary hypothesis. (C) 2005 Elsevier B.V. All rights reserved.

NON-GAUSSIAN STATISTICS OF OIL PRICING TIME-SERIES: A CASE STUDY

The stochastic nature of oil price fluctuations is investigated over a twelve-year period, borrowing feedback from an existing database (USA Energy Information Administration database, available online). We evaluate the scaling exponents of the fluctuations by employing different statistical analysis methods, namely rescaled range analysis (R/S), scale windowed variance analysis (SWV) and the generalized Hurst exponent (GH) method. Relying on the scaling exponents obtained, we apply a rescaling procedure to investigate the complex characteristics of the probability density functions (PDFs) dominating oil price fluctuations. It is found that PDFs exhibit scale invariance, and in fact collapse onto a single curve when increments are measured over microscales (typically less than 30 days). The time evolution of the distributions is well fitted by a Levy-type stable distribution. The relevance of a Levy distribution is made plausible by a simple model of nonlinear transfer. Our results also exhibit a degree of multifractality as the PDFs change and converge toward to a Gaussian distribution at the macroscales.

Information theoretic measures of UHG graphs with low computational complexity

We introduce a novel graph class we call universal hierarchical graphs (UHG) whose topology can be found numerously in problems representing, e.g., temporal, spacial or general process structures of systems. For this graph class we show, that we can naturally assign two probability distributions, for nodes and for edges, which lead us directly to the definition of the entropy and joint entropy and, hence, mutual information establishing an information theory for this graph class. Furthermore, we provide some results under which conditions these constraint probability distributions maximize the corresponding entropy. Also, we demonstrate that these entropic measures can be computed efficiently which is a prerequisite for every large scale practical application and show some numerical examples. (c) 2007 Elsevier Inc. All rights reserved.

Closable multipliers

Let $(X,\mu)$ and $(Y,\nu)$ be standard measure spaces. A function $\nph\in L^\infty(X\times Y,\mu\times\nu)$ is called a (measurable) Schur multiplier if the map $S_\nph$, defined on the space of Hilbert-Schmidt operators from $L_2(X,\mu)$ to $L_2(Y,\nu)$ by multiplying their integral kernels by $\nph$, is bound-ed in the operator norm. The paper studies measurable functions $\nph$ for which $S_\nph$ is closable in the norm topology or in the weak* topology. We obtain a characterisation of w*-closable multipliers and relate the question about norm closability to the theory of operator synthesis. We also study multipliers of two special types: if $\nph$ is of Toeplitz type, that is, if $\nph(x,y)=f(x-y)$, $x,y\in G$, where $G$ is a locally compact abelian group, then the closability of $\nph$ is related to the local inclusion of $f$ in the Fourier algebra $A(G)$ of $G$. If $\nph$ is a divided difference, that is, a function of the form $(f(x)-f(y))/(x-y)$, then its closability is related to the ``operator smoothness'' of the function $f$. A number of examples of non closable, norm closable and w*-closable multipliers are presented.

On the set of hypercyclic vectors for the differentiation

Let D be the differentiation operator Df = f' acting on the Fréchet space H of all entire functions in one variable with the standard (compact-open) topology. It is known since the 1950’s that the set H(D) of hypercyclic vectors for the operator D is non-empty. We treat two questions raised by Aron, Conejero, Peris and Seoane-Sepúlveda whether the set H(D) contains (up to the zero function) a non-trivial subalgebra of H or an infinite-dimensional closed linear subspace of H. In the present article both questions are answered affirmatively.

Molecular dynamics and principal components analysis of human telomeric quadruplex multimers.

Guanine-rich DNA repeat sequences located at the terminal ends of chromosomal DNA can fold in a sequence-dependent manner into G-quadruplex structures, notably the terminal 150–200 nucleotides at the 3' end, which occur as a single-stranded DNA overhang. The crystal structures of quadruplexes with two and four human telomeric repeats show an all-parallel-stranded topology that is readily capable of forming extended stacks of such quadruplex structures, with external TTA loops positioned to potentially interact with other macromolecules. This study reports on possible arrangements for these quadruplex dimers and tetramers, which can be formed from 8 or 16 telomeric DNA repeats, and on a methodology for modeling their interactions with small molecules. A series of computational methods including molecular dynamics, free energy calculations, and principal components analysis have been used to characterize the properties of these higher-order G-quadruplex dimers and tetramers with parallel-stranded topology. The results confirm the stability of the central G-tetrads, the individual quadruplexes, and the resulting multimers. Principal components analysis has been carried out to highlight the dominant motions in these G-quadruplex dimer and multimer structures. The TTA loop is the most flexible part of the model and the overall multimer quadruplex becoming more stable with the addition of further G-tetrads. The addition of a ligand to the model confirms the hypothesis that flat planar chromophores stabilize G-quadruplex structures by making them less flexible.

Computational Investigation of Inlet Distortion at High Angles of Attack

Lip separation is one of the primary sources of inlet distortion, which can result in a loss in fan stability. High angles of incidence are one of several critical causes of lip separation. There have been many studies into inlet performance at high incidence, including the resulting distortion levels when lip separation occurs. However, the vast majority of these investigations have been carried out experimentally, with little in the way of computational results for inlet performance at high incidence. The flow topology within an inlet when lip separation has occurred is also not well understood. This work aims to demonstrate a suitable model for the prediction of inlet flows at high incidence using ANSYS CFX, looking at both the performance of the inlet and the separated flow topology within the inlet. The attenuating effect of the fan is also investigated, with particular emphasis on the flow redistribution ahead of the fan. The results show that the model used is suitable for predicting inlet performance in adverse operating conditions, showing good agreement with experimental results. In addition, the attenuation of the distortion by the fan is also captured by the numerical model.

Workspace evaluation of manipulators through finite-partition of SE(3)

Workspace analysis and optimization are important in a manipulator design. As the complete workspace of a 6-DOF manipulator is embedded into a 6-imensional space, it is difficult to quantify and qualify it. Most literatures only considered the 3-D sub workspaces of the complete 6-D workspace. In this paper, a finite-partition approach of the Special Euclidean group SE(3) is proposed based on the topology properties of SE(3), which is the product of Special Orthogonal group SO(3) and R^3. It is known that the SO(3) is homeomorphic to a solid ball D^3 with antipodal points identified while the geometry of R^3 can be regarded as a cuboid. The complete 6-D workspace SE(3) is at the first time parametrically and proportionally partitioned into a number of elements with uniform convergence based on its geometry. As a result, a basis volume element of SE(3) is formed by the product of a basis volume element of R^3 and a basis volume element of SO(3), which is the product of a basis volume element of D^3 and its associated integration measure. By this way, the integration of the complete 6-D workspace volume becomes the simple summation of the basis volume elements of SE(3). Two new global performance indices, i.e., workspace volume ratio Wr and global condition index GCI, are defined over the complete 6-D workspace. A newly proposed 3 RPPS parallel manipulator is optimized based on this finite-partition approach. As a result, the optimal dimensions for maximal workspace are obtained, and the optimal performance points in the workspace are identified.

Far field subwavelength source resolution using Phase Conjugating Lens Assisted With Evanescent-to-Propagating Spectrum Conversion

The imaging properties of a phase conjugating lens operating in the far field zone of the imaged source and augmented with scatterers positioned in the source near field region are theoretically studied in this paper. The phase conjugating lens consists of a double sided 2D assembly of straight wire elements, individually interconnected through phase conjugation operators. The scattering elements are straight wire segments which are loaded with lumped impedance loads at their centers. We analytically and numerically analyze all stages of the imaging process; i) evanescent-to-propagating spectrum conversion; ii) focusing properties of infinite or finite sized phase conjugating lens; iii) source reconstruction upon propagating-to-evanescent spectrum conversion. We show that the resolution that can be achieved depends critically on the separation distance between the imaged source and scattering arrangement, as well as on the topology of the scatterers used. Imaged focal widths of up to one-seventh wavelength are demonstrated. The results obtained indicate the possibility of such an arrangement as a potential practical means for realising using conventional materials devices for fine feature extraction by electromagnetic lensing at distances remotely located from the source objects under investigation