A similarity measure for graphs with low computational complexity

We present and analyze an algorithm to measure the structural similarity of generalized trees, a new graph class which includes rooted trees. For this, we represent structural properties of graphs as strings and define the similarity of two Graphs as optimal alignments of the corresponding property stings. We prove that the obtained graph similarity measures are so called Backward similarity measures. From this we find that the time complexity of our algorithm is polynomial and, hence, significantly better than the time complexity of classical graph similarity methods based on isomorphic relations. (c) 2006 Elsevier Inc. All rights reserved.

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.

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.

Framework for Establishing Limits of Tabular Aerodynamic Models for Flight Dynamics Analysis

This paper describes the use of the Euler equations for the generation and testing of tabular aerodynamic models for flight dynamics analysis. Maneuvers for the AGARD Standard Dynamics Model sharp leading-edge wind-tunnel geometry are considered as a test case. Wind-tunnel data is first used to validate the prediction of static and dynamic coefficients at both low and high angles, featuring complex vortical flow, with good agreement obtained at low to moderate angles of attack. Then the generation of aerodynamic tables is described based on a data fusion approach. Time-optimal maneuvers are generated based on these tables, including level flight trim, pull-ups at constant and varying incidence, and level and 90 degrees turns. The maneuver definition includes the aircraft states and also the control deflections to achieve the motion. The main point of the paper is then to assess the validity of the aerodynamic tables which were used to define the maneuvers. This is done by replaying them, including the control surface motions, through the time accurate computational fluid dynamics code. The resulting forces and moments are compared with the tabular values to assess the presence of inadequately modeled dynamic or unsteady effects. The agreement between the tables and the replay is demonstrated for slow maneuvers. Increasing rate maneuvers show discrepancies which are ascribed to vortical flow hysteresis at the higher rate motions. The framework is suitable for application to more complex viscous flow models, and is powerful for the assessment of the validity of aerodynamics models of the type currently used for studies of flight dynamics.

Transonic Aeroelastic Stability Analysis Using a Kriging-Based Schur Complement Formulation

A method is described to allow searches for transonic aeroelastic instability of realistically sized aircraft models in multidimensional parameter spaces when computational fluid dynamics are used to model the aerodynamics. Aeroelastic instability is predicted from a small nonlinear eigenvalue problem. The approximation of the computationally expensive interaction term modeling the fluid response is formulated to allow the automated and blind search for aeroelastic instability. The approximation uses a kriging interpolation of exact numerical samples covering the parameter space. The approach, demonstrated for the Goland wing and the multidisciplinary optimization transport wing, results in stability analyses over whole flight envelopes at an equivalent cost of several steady-state simulations.

Transonic aeroelastic simulation for instability searches and uncertainty analysis

In this paper the use of eigenvalue stability analysis of very large dimension aeroelastic numerical models arising from the exploitation of computational fluid dynamics is reviewed. A formulation based on a block reduction of the system Jacobian proves powerful to allow various numerical algorithms to be exploited, including frequency domain solvers, reconstruction of a term describing the fluid–structure interaction from the sparse data which incurs the main computational cost, and sampling to place the expensive samples where they are most needed. The stability formulation also allows non-deterministic analysis to be carried out very efficiently through the use of an approximate Newton solver. Finally, the system eigenvectors are exploited to produce nonlinear and parameterised reduced order models for computing limit cycle responses. The performance of the methods is illustrated with results from a number of academic and large dimension aircraft test cases.

Structural similarity of directed universal hierarchical graphs: A low computational complexity approach

In the present paper we mainly introduce an efficient approach to measure the structural similarity of so called directed universal hierarchical graphs. We want to underline that directed universal hierarchical graphs can be obtained from generalized trees which are already introduced. In order to classify these graphs, we state our novel graph similarity method. As a main result we notice that our novel algorithm has low computational complexity. (c) 2007 Elsevier Inc. All rights reserved.

A comparative analysis of multidimensional features of objects resembling sets of graphs

In the present paper, we introduce a notion of a style representing abstract, complex objects having characteristics that can be represented as structured objects. Furthermore, we provide some mathematical properties of such styles. As a main result, we present a novel approach to perform a meaningful comparative analysis of such styles by defining and using graph-theoretic measures. We compare two styles by comparing the underlying feature sets representing sets of graph structurally. To determine the structural similarity between the underlying graphs, we use graph similarity measures that are computationally efficient. More precisely, in order to compare styles, we map each feature set to a so-called median graph and compare the resulting median graphs. As an application, we perform an experimental study to compare special styles representing sets of undirected graphs and present numerical results thereof. (C) 2007 Elsevier Inc. All rights reserved.

How can cells sense the elasticity of a substrate? An analysis using a cell tensegrity model

A eukaryotic cell attaches and spreads on substrates, whether it is the extracellular matrix naturally produced by the cell itself, or artificial materials, such as tissue-engineered scaffolds. Attachment and spreading require the cell to apply forces in the nN range to the substrate via adhesion sites, and these forces are balanced by the elastic response of the substrate. This mechanical interaction is one determinant of cell morphology and, ultimately, cell phenotype. In this paper we use a finite element model of a cell, with a tensegrity structure to model the cytoskeleton of actin filaments and microtubules, to explore the way cells sense the stiffness of the substrate and thereby adapt to it. To support the computational results, an analytical 1D model is developed for comparison. We find that (i) the tensegrity hypothesis of the cytoskeleton is sufficient to explain the matrix-elasticity sensing, (ii) cell sensitivity is not constant but has a bell-shaped distribution over the physiological matrix-elasticity range, and (iii) the position of the sensitivity peak over the matrix-elasticity range depends on the cytoskeletal structure and in particular on the F-actin organisation. Our model suggests that F-actin reorganisation observed in mesenchymal stem cells (MSCs) in response to change of matrix elasticity is a structural-remodelling process that shifts the sensitivity peak towards the new value of matrix elasticity. This finding discloses a potential regulatory role of scaffold stiffness for cell differentiation.

Finite Element Application to Analysis, Testing, and Manufacturing of Satellite Structures

Designing satellite structures poses an ongoing challenge as the interaction between analysis, experimental testing, and manufacturing phases is underdeveloped. Finite Element Analysis for Satellite Structures: Applications to Their Design, Manufacture and Testing explains the theoretical and practical knowledge needed to perform design of satellite structures. By layering detailed practical discussions with fully developed examples, Finite Element Analysis for Satellite Structures: Applications to Their Design, Manufacture and Testing provides the missing link between theory and implementation.
Computational examples cover all the major aspects of advanced analysis; including modal analysis, harmonic analysis, mechanical and thermal fatigue analysis using finite element method. Test cases are included to support explanations an a range of different manufacturing simulation techniques are described from riveting to shot peening to material cutting. Mechanical design of a satellites structures are covered in three steps: analysis step under design loads, experimental testing to verify design, and manufacturing.
Stress engineers, lecturers, researchers and students will find Finite Element Analysis for Satellite Structures: Applications to Their Design, Manufacture and Testing a key guide on with practical instruction on applying manufacturing simulations to improve their design and reduce project cost, how to prepare static and dynamic test specifications, and how to use finite element method to investigate in more details any component that may fail during testing.

Differential power analysis resistance of Camellia and countermeasure strategy on FPGAs

Security devices are vulnerable to Differential Power Analysis (DPA) that reveals the key by monitoring the power consumption of the circuits. In this paper, we present the first DPA attack against an FPGA implementation of the Camellia encryption algorithm with all key sizes and evaluate the DPA resistance of the algorithm. The Camellia cryptographic algorithm involves several different key-dependent intermediate operations including S-Box operations. In previous research, it was believed that the Camellia is stronger than AES due to the additional Whitening phase protecting the S-Box operation. However, we propose an attack that bypasses the Whitening phase and targets the S-Box. In this paper, we also discuss a lowcost countermeasure strategy to protect the Pre-whitening / Post-whitening and FL function of Camellia using Dual-rail Precharged Logic and to protect against attacks of the S-Box using Random Delay Insertion. © 2009 IEEE.

A pseudo-transient solution strategy for the analysis of delamination by means of interface elements

Recent efforts in the finite element modelling of delamination have concentrated on the development of cohesive interface elements. These are characterised by a bilinear constitutive law, where there is an initial high positive stiffness until a threshold stress level is reached, followed by a negative tangent stiffness representing softening (or damage evolution). Complete decohesion occurs when the amount of work done per unit area of crack surface is equal to a critical strain energy release rate. It is difficult to achieve a stable, oscillation-free solution beyond the onset of damage, using standard implicit quasi-static methods, unless a very refined mesh is used. In the present paper, a new solution strategy is proposed based on a pseudo-transient formulation and demonstrated through the modelling of a double cantilever beam undergoing Mode I delamination. A detailed analysis into the sensitivity of the user-defined parameters is also presented. Comparisons with other published solutions using a quasi-static formulation show that the pseudo-transient formulation gives improved accuracy and oscillation-free results with coarser meshes

Formal Analysis of MPI-based Parallel Programs

Most parallel computing applications in highperformance computing use the Message Passing Interface (MPI) API. Given the fundamental importance of parallel computing to science and engineering research, application correctness is paramount. MPI was originally developed around 1993 by the MPI Forum, a group of vendors, parallel programming researchers, and computational scientists. However, the document defining the standard is not issued by an official standards organization but has become a de facto standard © 2011 ACM.

Effect of membrane stiffness and cytoskeletal element density on mechanical stimuli within cells: an analysis of the consequences of ageing in cells

A finite element model of a single cell was created and used to investigate the effects of ageing on biophysical stimuli generated within a cell. Major cellular components were incorporated in the model: the membrane, cytoplasm, nucleus, microtubules, actin filaments, intermediate filaments, nuclear lamina, and chromatin. The model used multiple sets of tensegrity structures. Viscoelastic properties were assigned to the continuum components. To corroborate the model, a simulation of Atomic Force Microscopy (AFM) indentation was performed and results showed a force/indentation simulation with the range of experimental results.

Ageing was simulated by both increasing membrane stiffness (thereby modelling membrane peroxidation with age) and decreasing density of cytoskeletal elements (thereby modelling reduced actin density with age). Comparing normal and aged cells under indentation predicts that aged cells have a lower membrane area subjected to high strain compared to young cells, but the difference, surprisingly, is very small and would not be measurable experimentally. Ageing is predicted to have more significant effect on strain deep in the nucleus. These results show that computation of biophysical stimuli within cells are achievable with single-cell computational models whose force/displacement behaviour is within experimentally observed ranges. the models suggest only small, though possibly physiologically-significant, differences in internal biophysical stimuli between normal and aged cells.