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Algorithms, Volume 2, Issue 1 (March 2009), Pages 1-622

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Research

Jump to: Review

Open AccessArticle A Finite Element Flux-Corrected Transport Method for Wave Propagation in Heterogeneous Solids
Algorithms 2009, 2(1), 1-18; doi:10.3390/a2010001
Received: 29 October 2008 / Revised: 31 December 2008 / Accepted: 9 January 2009 / Published: 13 January 2009
Cited by 4 | PDF Full-text (2387 KB) | HTML Full-text | XML Full-text
Abstract
When moving discontinuities in solids need to be simulated, standard finite element (FE) procedures usually attain low accuracy because of spurious oscillations appearing behind the discontinuity fronts. To assure an accurate tracking of traveling stress waves in heterogeneous media, we propose here a
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When moving discontinuities in solids need to be simulated, standard finite element (FE) procedures usually attain low accuracy because of spurious oscillations appearing behind the discontinuity fronts. To assure an accurate tracking of traveling stress waves in heterogeneous media, we propose here a flux-corrected transport (FCT) technique for structured as well as unstructured space discretizations. The FCT technique consists of post-processing the FE velocity field via diffusive/antidiffusive fluxes, which rely upon an algorithmic length-scale parameter. To study the behavior of heterogeneous bodies featuring compliant interphases of any shape, a general scheme for computing diffusive/antidiffusive fluxes close to phase boundaries is proposed too. The performance of the new FE-FCT method is assessed through one-dimensional and two-dimensional simulations of dilatational stress waves propagating along homogeneous and composite rods. Full article
Open AccessArticle Comparison of Different Neural Network Approaches for the Tropospheric Profiling over the Inter-tropical lands Using GPS Radio Occultation Data
Algorithms 2009, 2(1), 31-45; doi:10.3390/a2010031
Received: 9 December 2008 / Revised: 12 January 2009 / Accepted: 14 January 2009 / Published: 20 January 2009
Cited by 3 | PDF Full-text (980 KB) | HTML Full-text | XML Full-text
Abstract
In this study different approaches based on multilayer perceptron neural networks are proposed and evaluated with the aim to retrieve tropospheric profiles by using GPS radio occultation data. We employed a data set of 445 occultations covering the land surface within the Tropics,
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In this study different approaches based on multilayer perceptron neural networks are proposed and evaluated with the aim to retrieve tropospheric profiles by using GPS radio occultation data. We employed a data set of 445 occultations covering the land surface within the Tropics, split into desert and vegetation zone. The neural networks were trained with refractivity profiles as input computed from geometrical occultation parameters provided by the FORMOSAT-3/COSMIC satellites, while the targets were the dry and wet refractivity profiles and the dry pressure profiles obtained from the contemporary European Centre for Medium-Range Weather Forecast data. Such a new retrieval algorithm was chosen to solve the atmospheric profiling problem without the constraint of an independent knowledge of one atmospheric parameter at each GPS occultation. Full article
Open AccessArticle A Novel Block-based Watermarking Scheme Using the SVD Transform
Algorithms 2009, 2(1), 46-75; doi:10.3390/a2010046
Received: 29 August 2008 / Revised: 11 December 2008 / Accepted: 14 January 2009 / Published: 22 January 2009
Cited by 22 | PDF Full-text (763 KB) | HTML Full-text | XML Full-text
Abstract
In this paper, a block-based watermarking scheme based on the Singular Value Decomposition (SVD) is proposed. Our watermark, a pseudo-random Gaussian sequence, is embedded by modifying the angles formed by the right singular vectors of each block of the original image. The orthogonality
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In this paper, a block-based watermarking scheme based on the Singular Value Decomposition (SVD) is proposed. Our watermark, a pseudo-random Gaussian sequence, is embedded by modifying the angles formed by the right singular vectors of each block of the original image. The orthogonality property of the right singular vector matrix is preserved during the embedding process. Several experiments have been carried out to test the performance of the proposed scheme against different attack scenarios. We conclude that the proposed scheme is resistant against common signal processing operations and attacks, while it preserves the quality of the original image. Full article
Open AccessArticle Algorithm for Nanotubes Computer Generation with Different Configurations
Algorithms 2009, 2(1), 108-120; doi:10.3390/a2010108
Received: 28 November 2008 / Revised: 20 January 2009 / Accepted: 26 January 2009 / Published: 2 February 2009
Cited by 3 | PDF Full-text (1056 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The algorithm here described concerns generation, visualization, and modification of molecular nanostructures of single-walled nanotubes (NTs) of particular configurations (armchair, zipper, multiple zipper, zigzag, or chiral) by means of a Graphical User Interface (GUI). NTs are made from a carbon graphene sheet created
[...] Read more.
The algorithm here described concerns generation, visualization, and modification of molecular nanostructures of single-walled nanotubes (NTs) of particular configurations (armchair, zipper, multiple zipper, zigzag, or chiral) by means of a Graphical User Interface (GUI). NTs are made from a carbon graphene sheet created according to certain parameters defining required nanostructures. Generated NTs can easily be modified by replacing carbon atoms for nitrogen or boron, visualized and exported into a standard format useful as input to be analyzed and submitted to other applications in order to get optimized geometries and to carry out further calculations of molecular and electronic properties. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Figures

Open AccessArticle The Autonomous Stress Indicator for Remotely Monitoring Power System State and Watching for Potential Instability
Algorithms 2009, 2(1), 183-199; doi:10.3390/a2010183
Received: 9 October 2008 / Revised: 15 January 2009 / Accepted: 2 February 2009 / Published: 10 February 2009
PDF Full-text (722 KB) | HTML Full-text | XML Full-text
Abstract
The proposed Autonomous Stress Indicator (ASI) is a device that monitors the contents of the protection relays on a suspect weak power system bus and generates a performance level related to the degree of system performance degradation or instability. This gives the system
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The proposed Autonomous Stress Indicator (ASI) is a device that monitors the contents of the protection relays on a suspect weak power system bus and generates a performance level related to the degree of system performance degradation or instability. This gives the system operators some time (minutes) to take corrective action. In a given operating area there would not likely be a need for an ASI on every bus. Note that the ASI does not trip any breakers; it is an INFORMATION ONLY device. An important feature is that the system operator can subsequently interrogate the ASI to determine the factor(s) that led to the performance level that has been initially annunciated, thereby leading to a course of action. This paper traces the development of the ASI which is an ongoing project. The ASI could be also described as a stress-alert device whose function is to alert the System Operator of a stressful condition at its location. The characteristics (or essential qualities) of this device are autonomy, selectivity, accuracy and intelligence. These will fulfill the requirements of the recommendation of the Canada –US Task Force in the August 2003 system collapse. Preliminary tests on the IEEE 39-bus model indicate that the concept has merit and development work is in progress. While the ASI can be applied to all power system operating conditions, its principal application is to the degraded state of the system where the System Operator must act to restore the system to the secure state before it migrates to a stage of collapse. The work of ASI actually begins with the Areas of Vulnerability and ends with the Predictive Module as described in detail in this paper. An application example of a degraded system using the IEEE 39-bus system is included. Full article
(This article belongs to the Special Issue Neural Networks and Sensors)
Open AccessArticle Exhaustive Enumeration of Kinetic Model Topologies for the Analysis of Time-Resolved RNA Folding
Algorithms 2009, 2(1), 200-214; doi:10.3390/a2010200
Received: 1 December 2008 / Revised: 16 January 2009 / Accepted: 24 January 2009 / Published: 10 February 2009
Cited by 6 | PDF Full-text (1395 KB) | HTML Full-text | XML Full-text
Abstract
Unlike protein folding, the process by which a large RNA molecule adopts a functionally active conformation remains poorly understood. Chemical mapping techniques, such as Hydroxyl Radical (·OH) footprinting report on local structural changes in an RNA as it folds with single nucleotide resolution.
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Unlike protein folding, the process by which a large RNA molecule adopts a functionally active conformation remains poorly understood. Chemical mapping techniques, such as Hydroxyl Radical (·OH) footprinting report on local structural changes in an RNA as it folds with single nucleotide resolution. The analysis and interpretation of this kinetic data requires the identification and subsequent optimization of a kinetic model and its parameters. We detail our approach to this problem, specifically focusing on a novel strategy to overcome a factorial explosion in the number of possible models that need to be tested to identify the best fitting model. Previously, smaller systems (less than three intermediates) were computationally tractable using a distributed computing approach. However, for larger systems with three or more intermediates, the problem became computationally intractable. With our new enumeration strategy, we are able to significantly reduce the number of models that need to be tested using non-linear least squares optimization, allowing us to study systems with up to five intermediates. Furthermore, two intermediate systems can now be analyzed on a desktop computer, which eliminates the need for a distributed computing solution for most mediumsized data sets. Our new approach also allows us to study potential degeneracy in kinetic model selection, elucidating the limits of the method when working with large systems. This work establishes clear criteria for determining if experimental ·OH data is sufficient to determine the underlying kinetic model, or if other experimental modalities are required to resolve any degeneracy. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Open AccessArticle Automatic Determination of Stepsize Parameters in Monte Carlo Simulation Tested on a Bromodomain-Binding Octapeptide
Algorithms 2009, 2(1), 215-226; doi:10.3390/a2010215
Received: 30 October 2008 / Revised: 7 January 2009 / Accepted: 24 January 2009 / Published: 10 February 2009
Cited by 3 | PDF Full-text (170 KB) | HTML Full-text | XML Full-text
Abstract
The proportional integral controller, commonly used in engineering applications for process control, has been implemented for the tuning of the stepsizes in Metropolis Monte Carlo simulations. Similarly to the recent application for tuning the chemical potential parameter in grand-canonical ensemble simulation, the process-control
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The proportional integral controller, commonly used in engineering applications for process control, has been implemented for the tuning of the stepsizes in Metropolis Monte Carlo simulations. Similarly to the recent application for tuning the chemical potential parameter in grand-canonical ensemble simulation, the process-control approach was found to work well for the problem of selecting the stepsize for each torsion angle that results in a targeted acceptance rate during the simulation of an octapeptide in aqueous environment. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Open AccessArticle High Frequency Waves Propagating in Octagonal Bars: a Low Cost Computation Algorithm
Algorithms 2009, 2(1), 227-246; doi:10.3390/a2010227
Received: 3 December 2008 / Revised: 23 January 2009 / Accepted: 11 February 2009 / Published: 17 February 2009
Cited by 6 | PDF Full-text (462 KB) | HTML Full-text | XML Full-text
Abstract
In this paper a hybrid semi-analytical Finite Element formulation is proposed to efficiently calculate the time dependent response due to stress waves propagating in a slender solid with uniform cross-section when excited by impulsive forces. The formulation takes advantage of the direct and
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In this paper a hybrid semi-analytical Finite Element formulation is proposed to efficiently calculate the time dependent response due to stress waves propagating in a slender solid with uniform cross-section when excited by impulsive forces. The formulation takes advantage of the direct and inverse Fourier transform to formulate and solve the governing wave equation. The framework is applied to an octagonal viscoelastic isotropic steel bar. Full article
Open AccessArticle Self-organization of Dynamic Distributed Computational Systems Applying Principles of Integrative Activity of Brain Neuronal Assemblies
Algorithms 2009, 2(1), 247-258; doi:10.3390/a2010247
Received: 28 November 2008 / Revised: 26 January 2009 / Accepted: 16 February 2009 / Published: 17 February 2009
Cited by 1 | PDF Full-text (336 KB) | HTML Full-text | XML Full-text
Abstract
This paper presents a method for self-organization of the distributed systems operating in a dynamic context. We propose the use of a simple biologically (cognitive neuroscience) inspired method for system configuration that allows allocating most of the computational load to off-line in order
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This paper presents a method for self-organization of the distributed systems operating in a dynamic context. We propose the use of a simple biologically (cognitive neuroscience) inspired method for system configuration that allows allocating most of the computational load to off-line in order to improve the scalability property of the system. The method proposed has less computational burden at runtime than traditional system adaptation approaches. Full article
(This article belongs to the Special Issue Neural Networks and Sensors)
Open AccessArticle Design of Sensor Networks for Chemical Plants Based on Meta-Heuristics
Algorithms 2009, 2(1), 259-281; doi:10.3390/a2010259
Received: 3 November 2008 / Revised: 8 January 2009 / Accepted: 17 February 2009 / Published: 20 February 2009
Cited by 5 | PDF Full-text (244 KB)
Abstract
In this work the optimal design of sensor networks for chemical plants is addressed using stochastic optimization strategies. The problem consists in selecting the type, number and location of new sensors that provide the required quantity and quality of process information. Ad-hoc strategies
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In this work the optimal design of sensor networks for chemical plants is addressed using stochastic optimization strategies. The problem consists in selecting the type, number and location of new sensors that provide the required quantity and quality of process information. Ad-hoc strategies based on Tabu Search, Scatter Search and Population Based Incremental Learning Algorithms are proposed. Regarding Tabu Search, the intensification and diversification capabilities of the technique are enhanced using Path Relinking. The strategies are applied for solving minimum cost design problems subject to quality constraints on variable estimates, and their performances are compared. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Open AccessArticle Recognizing Human Activities from Sensors Using Hidden Markov Models Constructed by Feature Selection Techniques
Algorithms 2009, 2(1), 282-300; doi:10.3390/a2010282
Received: 28 November 2008 / Revised: 2 February 2009 / Accepted: 16 February 2009 / Published: 21 February 2009
Cited by 10 | PDF Full-text (422 KB) | HTML Full-text | XML Full-text
Abstract
In this paper a method for selecting features for Human Activity Recognition from sensors is presented. Using a large feature set that contains features that may describe the activities to recognize, Best First Search and Genetic Algorithms are employed to select the feature
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In this paper a method for selecting features for Human Activity Recognition from sensors is presented. Using a large feature set that contains features that may describe the activities to recognize, Best First Search and Genetic Algorithms are employed to select the feature subset that maximizes the accuracy of a Hidden Markov Model generated from the subset. A comparative of the proposed techniques is presented to demonstrate their performance building Hidden Markov Models to classify different human activities using video sensors. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Open AccessArticle Algorithm for Active Suppression of Radiation and Acoustical Scattering Fields by Some Physical Bodies in Liquids
Algorithms 2009, 2(1), 361-397; doi:10.3390/a2010361
Received: 27 October 2008 / Revised: 8 January 2009 / Accepted: 8 January 2009 / Published: 4 March 2009
PDF Full-text (903 KB) | HTML Full-text | XML Full-text
Abstract
An algorithm for the suppression of the radiation and scattering fields created by vibration of the smooth closed surface of a body of arbitrary shape placed in a liquid is designed and analytically explored. The frequency range of the suppression allows for both
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An algorithm for the suppression of the radiation and scattering fields created by vibration of the smooth closed surface of a body of arbitrary shape placed in a liquid is designed and analytically explored. The frequency range of the suppression allows for both large and small wave sizes on the protected surface. An active control system is designed that consists of: (a) a subsystem for fast formation of a desired distribution of normal oscillatory velocities or displacements (on the basis of pulsed Huygens' sources) and (b) a subsystem for catching and targeting of incident waves on the basis of a grid (one layer) of monopole microphones, surrounding the surface to be protected. The efficiency and stability of the control algorithm are considered. The algorithm forms the control signal during a time much smaller than the minimum time scale of the waves to be damped. The control algorithm includes logical and nonlinear operations, thus excluding interpretation of the control system as a traditional combination of linear electric circuits, where all parameters are constant (in time). This algorithm converts some physical body placed in a liquid into one that is transparent to a special class of incident waves. The active control system needs accurate information on its geometry, but does not need either prior or current information about the vibroacoustical characteristics of the protected surface, which in practical cases represents a vast amount of data. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Open AccessArticle A Sensor-Based Learning Algorithm for the Self-Organization of Robot Behavior
Algorithms 2009, 2(1), 398-409; doi:10.3390/a2010398
Received: 30 November 2008 / Accepted: 26 February 2009 / Published: 4 March 2009
Cited by 8 | PDF Full-text (2618 KB) | HTML Full-text | XML Full-text
Abstract
Ideally, sensory information forms the only source of information to a robot. We consider an algorithm for the self-organization of a controller. At short time scales the controller is merely reactive but the parameter dynamics and the acquisition of knowledge by an internal
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Ideally, sensory information forms the only source of information to a robot. We consider an algorithm for the self-organization of a controller. At short time scales the controller is merely reactive but the parameter dynamics and the acquisition of knowledge by an internal model lead to seemingly purposeful behavior on longer time scales. As a paradigmatic example, we study the simulation of an underactuated snake-like robot. By interacting with the real physical system formed by the robotic hardware and the environment, the controller achieves a sensitive and body-specific actuation of the robot. Full article
(This article belongs to the Special Issue Neural Networks and Sensors)
Open AccessArticle Protein-Protein Interaction Analysis by Docking
Algorithms 2009, 2(1), 429-436; doi:10.3390/a2010429
Received: 1 December 2008 / Revised: 19 January 2009 / Accepted: 27 February 2009 / Published: 10 March 2009
PDF Full-text (122 KB) | HTML Full-text | XML Full-text
Abstract
Based on a protein-protein docking approach we have developed a procedure to verify or falsify protein-protein interactions that were proposed by other methods such as yeast-2-hybrid assays. Our method currently utilizes intermolecular energies but can be expanded to incorporate additional terms such as
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Based on a protein-protein docking approach we have developed a procedure to verify or falsify protein-protein interactions that were proposed by other methods such as yeast-2-hybrid assays. Our method currently utilizes intermolecular energies but can be expanded to incorporate additional terms such as amino acid based pair-potentials. We show some early results that demonstrate the general applicability of our approach. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Open AccessArticle Resonance in Interacting Induced-Dipole Polarizing Force Fields: Application to Force-Field Derivatives
Algorithms 2009, 2(1), 437-447; doi:10.3390/a2010437
Received: 5 December 2008 / Revised: 15 January 2009 / Accepted: 27 February 2009 / Published: 10 March 2009
PDF Full-text (198 KB) | HTML Full-text | XML Full-text
Abstract
The Silberstein model of the molecular polarizability of diatomic molecules, generalized by Applequist et al. for polyatomic molecules, is analyzed. The atoms are regarded as isotropically polarizable points located at their nuclei, interacting via the fields of their induced dipoles. The use
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The Silberstein model of the molecular polarizability of diatomic molecules, generalized by Applequist et al. for polyatomic molecules, is analyzed. The atoms are regarded as isotropically polarizable points located at their nuclei, interacting via the fields of their induced dipoles. The use of additive values for atom polarizabilities gives poor results, in some cases leading to artificial predictions of absorption bands. The molecular polarizability of methane and its derivative are computed. The agreement with experimental mean molecular polarizabilities is within 1–5%. A hypothesis is indispensable for a suitable representation of polarizability derivative. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Open AccessArticle Structural Fingerprints of Transcription Factor Binding Site Regions
Algorithms 2009, 2(1), 448-469; doi:10.3390/a2010448
Received: 4 December 2008 / Revised: 2 February 2009 / Accepted: 5 March 2009 / Published: 10 March 2009
PDF Full-text (1258 KB) | HTML Full-text | XML Full-text
Abstract
Fourier transforms are a powerful tool in the prediction of DNA sequence properties, such as the presence/absence of codons. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers. In this work we apply Fourier techniques to
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Fourier transforms are a powerful tool in the prediction of DNA sequence properties, such as the presence/absence of codons. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers. In this work we apply Fourier techniques to the analysis of the structural properties of human chromosomes 21 and 22 and also to three sets of transcription factor binding sites within these chromosomes. We find that, for a given structural property, the structural property power spectra of chromosomes 21 and 22 are strikingly similar. We find common peaks in their power spectra for both Sp1 and p53 transcription factor binding sites. We use the power spectra as a structural fingerprint and perform similarity searching in order to find transcription factor binding site regions. This approach provides a new strategy for searching the genome data for information. Although it is difficult to understand the relationship between specific functional properties and the set of structural parameters in our database, our structural fingerprints nevertheless provide a useful tool for searching for function information in sequence data. The power spectrum fingerprints provide a simple, fast method for comparing a set of functional sequences, in this case transcription factor binding site regions, with the sequences of whole chromosomes. On its own, the power spectrum fingerprint does not find all transcription factor binding sites in a chromosome, but the results presented here show that in combination with other approaches, this technique will improve the chances of identifying functional sequences hidden in genomic data. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Open AccessArticle Semi-empirical Algorithm for the Retrieval of Ecology-Relevant Water Constituents in Various Aquatic Environments
Algorithms 2009, 2(1), 470-497; doi:10.3390/a2010470
Received: 27 October 2008 / Revised: 11 January 2009 / Accepted: 25 February 2009 / Published: 10 March 2009
Cited by 17 | PDF Full-text (809 KB) | HTML Full-text | XML Full-text
Abstract
An advanced operational semi-empirical algorithm for processing satellite remote sensing data in the visible region is described. Based on the Levenberg-Marquardt multivariate optimization procedure, the algorithm is developed for retrieving major water colour producing agents: chlorophyll-a, suspended minerals and dissolved organics. Two assurance
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An advanced operational semi-empirical algorithm for processing satellite remote sensing data in the visible region is described. Based on the Levenberg-Marquardt multivariate optimization procedure, the algorithm is developed for retrieving major water colour producing agents: chlorophyll-a, suspended minerals and dissolved organics. Two assurance units incorporated by the algorithm are intended to flag pixels with inaccurate atmospheric correction and specific hydro-optical properties not covered by the applied hydro-optical model. The hydro-optical model is a set of spectral cross-sections of absorption and backscattering of the colour producing agents. The combination of the optimization procedure and a replaceable hydro-optical model makes the developed algorithm not specific to a particular satellite sensor or a water body. The algorithm performance efficiency is amply illustrated for SeaWiFS, MODIS and MERIS images over a variety of water bodies. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Open AccessArticle A Novel Algorithm for Macromolecular Epitope Matching
Algorithms 2009, 2(1), 498-517; doi:10.3390/a2010498
Received: 27 October 2008 / Revised: 11 January 2009 / Accepted: 25 February 2009 / Published: 11 March 2009
Cited by 3 | PDF Full-text (1685 KB) | HTML Full-text | XML Full-text
Abstract
Many macromolecules, namely proteins, show functional substructures or epitopes defined by characteristic spatial arrangements of groups of specific atoms or residues. The identification of such substructures in a set of macromolecular 3D-structures solves an important problem in molecular biology as it allows the
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Many macromolecules, namely proteins, show functional substructures or epitopes defined by characteristic spatial arrangements of groups of specific atoms or residues. The identification of such substructures in a set of macromolecular 3D-structures solves an important problem in molecular biology as it allows the assignment of functions to molecular moieties and thus opens the possibility of a mechanistic understanding of molecular function. We have devised an algorithm that models a functional epitope formed by a group of atoms or residues as set of points in cartesian space with associated functional properties. The algorithm searches for similar epitopes in a database of structures by an efficient multistage comparison of distance sets in the epitope and in the structures from the database. The search results in a list of optimal matches and corresponding optimal superpositions of query epitope and matching epitopes from the database. The algorithm is discussed against the background of related approaches, and it is successfully tested in three application scenarios: global match of two homologous proteins, search for an epitope on a homologous protein, and finding matching epitopes in a protein database. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Open AccessArticle An Image Pattern Tracking Algorithm for Time-resolved Measurement of Mini- and Micro-scale Motion of Complex Object
Algorithms 2009, 2(1), 533-549; doi:10.3390/a2010533
Received: 16 January 2009 / Revised: 17 February 2009 / Accepted: 3 March 2009 / Published: 12 March 2009
Cited by 2 | PDF Full-text (370 KB) | HTML Full-text | XML Full-text
Abstract
An image pattern tracking algorithm is described in this paper for time-resolved measurements of mini- and micro-scale movements of complex objects. This algorithm works with a high-speed digital imaging system, which records thousands of successive image frames in a short time period. The
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An image pattern tracking algorithm is described in this paper for time-resolved measurements of mini- and micro-scale movements of complex objects. This algorithm works with a high-speed digital imaging system, which records thousands of successive image frames in a short time period. The image pattern of the observed object is tracked among successively recorded image frames with a correlation-based algorithm, so that the time histories of the position and displacement of the investigated object in the camera focus plane are determined with high accuracy. The speed, acceleration and harmonic content of the investigated motion are obtained by post processing the position and displacement time histories. The described image pattern tracking algorithm is tested with synthetic image patterns and verified with tests on live insects. Full article
Open AccessArticle Multi-Band Spectral Subtraction Method for Electrolarynx Speech Enhancement
Algorithms 2009, 2(1), 550-564; doi:10.3390/a2010550
Received: 30 October 2008 / Revised: 6 February 2009 / Accepted: 25 February 2009 / Published: 13 March 2009
Cited by 4 | PDF Full-text (1207 KB) | HTML Full-text | XML Full-text
Abstract
Although the electrolarynx (EL) provides an important means of voice reconstruction for patients who lose their vocal cords by laryngectomies, the radiated noise and additive environment noise reduce the intelligibility of the resulting EL speech. This paper proposes an improved spectrum subtract algorithm
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Although the electrolarynx (EL) provides an important means of voice reconstruction for patients who lose their vocal cords by laryngectomies, the radiated noise and additive environment noise reduce the intelligibility of the resulting EL speech. This paper proposes an improved spectrum subtract algorithm by taking into account the non-uniform effect of colored noise on the spectrum of EL speech. Since the over-subtraction factor of each frequency band can be adjusted in the enhancement process, a better noise reduction effect was obtained and the perceptually annoying musical noise was efficiently reduced, as compared to other standard speech enhancement algorithms. Full article
Open AccessArticle Mixed Variational Formulations for Micro-cracked Continua in the Multifield Framework
Algorithms 2009, 2(1), 606-622; doi:10.3390/a2010606
Received: 9 March 2009 / Accepted: 24 March 2009 / Published: 27 March 2009
PDF Full-text (417 KB) | HTML Full-text | XML Full-text
Abstract
Within the framework of multifield continua, we move from the model of elastic microcracked body introduced in (Mariano, P.M. and Stazi, F.L., Strain localization in elastic microcracked bodies, Comp. Methods Appl. Mech. Engrg. 2001, 190, 5657–5677) and propose a few novel variational formulations
[...] Read more.
Within the framework of multifield continua, we move from the model of elastic microcracked body introduced in (Mariano, P.M. and Stazi, F.L., Strain localization in elastic microcracked bodies, Comp. Methods Appl. Mech. Engrg. 2001, 190, 5657–5677) and propose a few novel variational formulations of mixed type along with relevant mixed FEM discretizations. To this goal, suitably extended Hellinger-Reissner principles of primal and dual type are derived. A few numerical studies are presented that include an investigation on the interaction between a single cohesive macrocrack and diffuse microcracks (Mariano, P.M. and Stazi, F.L., Strain localization due to crack–microcrack interactions: X–FEM for a multifield approach, Comp. Methods Appl. Mech. Engrg. 2004, 193, 5035–5062). Full article
(This article belongs to the Special Issue Numerical Simulation of Discontinuities in Mechanics)

Review

Jump to: Research

Open AccessReview Neural Network Analysis and Evaluation of the Fetal Heart Rate
Algorithms 2009, 2(1), 19-30; doi:10.3390/a2010019
Received: 21 November 2008 / Revised: 4 January 2009 / Accepted: 8 January 2009 / Published: 16 January 2009
Cited by 12 | PDF Full-text (344 KB) | HTML Full-text | XML Full-text
Abstract
The aim of the present study is to obtain a highly objective automatic fetal heart rate (FHR) diagnosis. The neural network software was composed of three layers with the back propagation, to which 8 FHR data, including sinusoidal FHR, were input and the
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The aim of the present study is to obtain a highly objective automatic fetal heart rate (FHR) diagnosis. The neural network software was composed of three layers with the back propagation, to which 8 FHR data, including sinusoidal FHR, were input and the system was educated by the data of 20 cases with a known outcome. The output was the probability of a normal, intermediate, or pathologic outcome. The neural index studied prolonged monitoring. The neonatal states and the FHR score strongly correlated with the outcome probability. The neural index diagnosis was correct. The completed software was transferred to other computers, where the system function was correct. Full article
(This article belongs to the Special Issue Neural Networks and Sensors)
Open AccessReview On the Reconstruction of Three-dimensional Protein Structures from Contact Maps
Algorithms 2009, 2(1), 76-92; doi:10.3390/a2010076
Received: 30 November 2008 / Revised: 8 January 2009 / Accepted: 20 January 2009 / Published: 22 January 2009
Cited by 5 | PDF Full-text (240 KB) | HTML Full-text | XML Full-text
Abstract
The problem of protein structure prediction is one of the long-standing goals of Computational Biology. Although we are still not able to provide first principle solutions, several shortcuts have been discovered to compute the protein three-dimensional structure when similar protein sequences are available
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The problem of protein structure prediction is one of the long-standing goals of Computational Biology. Although we are still not able to provide first principle solutions, several shortcuts have been discovered to compute the protein three-dimensional structure when similar protein sequences are available (by means of comparative modeling and remote homology detection). Nonetheless, these approaches can assign structures only to a fraction of proteins in genomes and ab-initio methods are still needed. One relevant step of ab-initio prediction methods is the reconstruction of the protein structures starting from inter-protein residue contacts. In this paper we review the methods developed so far to accomplish the reconstruction task in order to highlight their differences and similarities. The different approaches are fully described and their reported performances, together with their computational complexity, are also discussed. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Open AccessReview A Survey on Star Identification Algorithms
Algorithms 2009, 2(1), 93-107; doi:10.3390/a2010093
Received: 30 October 2008 / Revised: 13 January 2009 / Accepted: 16 January 2009 / Published: 29 January 2009
Cited by 60 | PDF Full-text (370 KB) | HTML Full-text | XML Full-text
Abstract
The author surveys algorithms used in star identification, commonly used in star trackers to determine the attitude of a spacecraft. Star trackers are a staple of attitude determination systems for most types of satellites. The paper covers: (a) lost-in-space algorithms (when no a
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The author surveys algorithms used in star identification, commonly used in star trackers to determine the attitude of a spacecraft. Star trackers are a staple of attitude determination systems for most types of satellites. The paper covers: (a) lost-in-space algorithms (when no a priori attitude information is available), (b) recursive algorithms (when some a priori attitude information is available), and (c) non-dimensional algorithms (when the star tracker calibration is not well-known). The performance of selected algorithms and supporting algorithms are compared. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Open AccessReview Probabilistic Distributed Algorithms for Energy Efficient Routing and Tracking in Wireless Sensor Networks
Algorithms 2009, 2(1), 121-157; doi:10.3390/a2010121
Received: 24 October 2008 / Revised: 30 December 2008 / Accepted: 20 January 2009 / Published: 3 February 2009
Cited by 9 | PDF Full-text (413 KB) | HTML Full-text | XML Full-text
Abstract
In this work we focus on the energy efficiency challenge in wireless sensor networks, from both an on-line perspective (related to routing), as well as a network design perspective (related to tracking). We investigate a few representative, important aspects of energy efficiency: a)
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In this work we focus on the energy efficiency challenge in wireless sensor networks, from both an on-line perspective (related to routing), as well as a network design perspective (related to tracking). We investigate a few representative, important aspects of energy efficiency: a) the robust and fast data propagation b) the problem of balancing the energy dissipation among all sensors in the network and c) the problem of efficiently tracking moving entities in sensor networks. Our work here is a methodological survey of selected results that have already appeared in the related literature. In particular, we investigate important issues of energy optimization, like minimizing the total energy dissipation, minimizing the number of transmissions as well as balancing the energy load to prolong the system’s lifetime. We review characteristic protocols and techniques in the recent literature, including probabilistic forwarding and local optimization methods. We study the problem of localizing and tracking multiple moving targets from a network design perspective i.e. towards estimating the least possible number of sensors, their positions and operation characteristics needed to efficiently perform the tracking task. To avoid an expensive massive deployment, we try to take advantage of possible coverage overlaps over space and time, by introducing a novel combinatorial model that captures such overlaps. Under this model, we abstract the tracking network design problem by a covering combinatorial problem and then design and analyze an efficient approximate method for sensor placement and operation. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Open AccessReview A Survey on Position-Based Routing Algorithms in Wireless Sensor Networks
Algorithms 2009, 2(1), 158-182; doi:10.3390/a2010158
Received: 29 October 2008 / Revised: 17 December 2008 / Accepted: 29 January 2009 / Published: 9 February 2009
Cited by 24 | PDF Full-text (568 KB) | HTML Full-text | XML Full-text
Abstract
Wireless sensor networks (WSN) have attracted much attention in recent years for its unique characteristics and wide use in many different applications. Routing protocol is one of key technologies in WSN. In this paper, the position-based routing protocols are surveyed and classified into
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Wireless sensor networks (WSN) have attracted much attention in recent years for its unique characteristics and wide use in many different applications. Routing protocol is one of key technologies in WSN. In this paper, the position-based routing protocols are surveyed and classified into four categories: flooding-based, curve-based, grid-based and ant algorithm-based intelligent. To each category, the main contribution of related routing protocols is shown including the relationship among the routing protocols. The different routing algorithms in the same category and the different categories are compared based on popular metrics. Moreover, some open research directions in WSN are also discussed. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Open AccessReview Actual Pathogen Detection: Sensors and Algorithms - a Review
Algorithms 2009, 2(1), 301-338; doi:10.3390/a2010301
Received: 10 December 2008 / Revised: 13 February 2009 / Accepted: 24 February 2009 / Published: 3 March 2009
Cited by 12 | PDF Full-text (304 KB) | HTML Full-text | XML Full-text
Abstract
Pathogens feed on fruits and vegetables causing great food losses or at least reduction of their shelf life. These pathogens can cause losses of the final product or in the farms were the products are grown, attacking leaves, stems and trees. This review
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Pathogens feed on fruits and vegetables causing great food losses or at least reduction of their shelf life. These pathogens can cause losses of the final product or in the farms were the products are grown, attacking leaves, stems and trees. This review analyses disease detection sensors and algorithms for both the farm and postharvest management of fruit and vegetable quality. Mango, avocado, apple, tomato, potato, citrus and grapes were selected as the fruits and vegetables for study due to their world-wide consumption. Disease warning systems for predicting pathogens and insects on farms during fruit and vegetable production are commonly used for all the crops and are available where meteorological stations are present. It can be seen that these disease risk systems are being slowly replaced by remote sensing monitoring in developed countries. Satellite images have reduced their temporal resolution, but are expensive and must become cheaper for their use world-wide. In the last 30 years, a lot of research has been carried out in non-destructive sensors for food quality. Actually, non-destructive technology has been applied for sorting high quality fruit which is desired by the consumer. The sensors require algorithms to work properly; the most used being discriminant analysis and training neural networks. New algorithms will be required due to the high quantity of data acquired and its processing, and for disease warning strategies for disease detection. Full article
(This article belongs to the Special Issue Neural Networks and Sensors)
Open AccessReview Radio-Isotope Identification Algorithms for NaI γ Spectra
Algorithms 2009, 2(1), 339-360; doi:10.3390/a2010339
Received: 26 November 2008 / Revised: 13 February 2009 / Accepted: 20 February 2009 / Published: 3 March 2009
Cited by 29 | PDF Full-text (424 KB) | HTML Full-text | XML Full-text
Abstract
The performance of Radio-Isotope Identification (RIID) algorithms using NaI-based γ spectroscopy is increasingly important. For example, sensors at locations that screen for illicit nuclear material rely on isotope identification using NaI detectors to distinguish innocent nuisance alarms, arising from naturally occurring radioactive material,
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The performance of Radio-Isotope Identification (RIID) algorithms using NaI-based γ spectroscopy is increasingly important. For example, sensors at locations that screen for illicit nuclear material rely on isotope identification using NaI detectors to distinguish innocent nuisance alarms, arising from naturally occurring radioactive material, from alarms arising from threat isotopes. Recent data collections for RIID testing consist of repeat measurements for each of several measurement scenarios to test RIID algorithms. It is anticipated that vendors can modify their algorithms on the basis of performance on chosen measurement scenarios and then test modified algorithms on data for other measurement scenarios. It is therefore timely to review the current status of RIID algorithms on NaI detectors. This review describes γ spectra from NaI detectors, measurement issues and challenges, current RIID algorithms, data preprocessing steps, the role and current quality of synthetic spectra, and opportunities for improvements. Full article
Open AccessReview Genetic Algorithms in Application to the Geometry Optimization of Nanoparticles
Algorithms 2009, 2(1), 410-428; doi:10.3390/a2010410
Received: 24 November 2008 / Revised: 6 January 2009 / Accepted: 26 February 2009 / Published: 4 March 2009
Cited by 10 | PDF Full-text (597 KB) | HTML Full-text | XML Full-text
Abstract
Applications of genetic algorithms to the global geometry optimization problem of nanoparticles are reviewed. Genetic operations are investigated and importance of phenotype genetic operations, considering the geometry of nanoparticles, are mentioned. Other efficiency improving developments such as floating point representation and local relaxation
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Applications of genetic algorithms to the global geometry optimization problem of nanoparticles are reviewed. Genetic operations are investigated and importance of phenotype genetic operations, considering the geometry of nanoparticles, are mentioned. Other efficiency improving developments such as floating point representation and local relaxation are described broadly. Parallelization issues are also considered and a recent parallel working single parent Lamarckian genetic algorithm is reviewed with applications on carbon clusters and SiGe core-shell structures. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)
Open AccessReview A Review of Closed-Loop Algorithms for Glycemic Control in the Treatment of Type 1 Diabetes
Algorithms 2009, 2(1), 518-532; doi:10.3390/a2010518
Received: 30 October 2008 / Revised: 23 January 2009 / Accepted: 25 February 2009 / Published: 12 March 2009
Cited by 29 | PDF Full-text (204 KB) | HTML Full-text | XML Full-text
Abstract
With the discovery of insulin came a deeper understanding of therapeutic options for one of the most devastating chronic diseases of the modern era, diabetes mellitus. The use of insulin in the treatment of diabetes, especially in those with severe insulin deficiency (type
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With the discovery of insulin came a deeper understanding of therapeutic options for one of the most devastating chronic diseases of the modern era, diabetes mellitus. The use of insulin in the treatment of diabetes, especially in those with severe insulin deficiency (type 1 diabetes), with multiple injections or continuous subcutaneous infusion, has been largely successful, but the risk for short term and long term complications remains substantial. Insulin treatment decisions are based on the patient’s knowledge of meal size, exercise plans and the intermittent knowledge of blood glucose values. As such, these are open loop methods that require human input. The idea of closed loop control of diabetes treatment is quite different: automated control of a device that delivers insulin (and possibly glucagon or other medications) and is based on continuous or very frequent glucose measurements. Closed loop insulin control for type 1 diabetes is not new but is far from optimized. The goal of such a system is to avoid short-term complications (hypoglycemia) and long-term complications (diseases of the eyes, kidneys, nerves and cardiovascular system) by mimicking the normal insulin secretion pattern of the pancreatic beta cell. A control system for automated diabetes treatment consists of three major components, (1) a glucose sensing device that serves as the afferent limb of the system; (2) an automated control unit that uses algorithms which acquires sensor input and generates treatment outputs; and (3) a drug delivery device (primarily for delivery of insulin), which serves as the system’s efferent limb. There are several major issues that highlight the difficulty of interacting with the complex unknowns of the biological world. For example, development of accurate continuous glucose monitors is crucial; the state of the art in 2009 is that such devices sometimes experience drift and are intended only to supplement information received from standard intermittent blood glucose data. In addition, it is important to acknowledge that an “automated” closed loop pancreas cannot approach the complexity of the normal human endocrine pancreas, which takes continuous data from substrates, hormones, paracrine compounds and autonomic neural inputs, and in response, secretes four hormones. Another major issue is the substantial absorption/action delay of insulin given by the subcutaneous route. Because of this delay, some researchers have recently given a portion of the meal-related insulin in an open loop manner before the meal and found this hybrid approach to be superior to closed loop control. Proportional-Integral-Derivative (PID) systems adapted from the industrial sector utilize control algorithms that alter output based on proportional (difference between actual and target levels), derivative (rate of change) and integral (time-related summative) errors in glucose. These algorithms have proven to be very promising in limited clinical trials. Related algorithms include a “fading memory” system that combines the proportional-derivative components of a classic PID system with time-relating decay of input signals that allow greater emphasis on more recent glucose values, a characteristic noted in mammalian beta-cells. Model Predictive Control (MPC) systems are highly adaptive methods that utilize mathematical models based on observations of biological behavior patterns using system identification and are now undergoing testing in humans. The application of further mathematical models, such as fuzzy control and artificial neural networks, are also promising, but are largely clinically untested. In summary, the prospects for closed loop control of glycemia in persons with diabetes have improved considerably. Major limitations include the delayed absorption/action of subcutaneous insulin and the imperfect stability of currently-available continuous glucose sensors. The potential for improved glycemic control in persons with diabetes brings with it the potential for reduction in the frequency of acute and chronic complications of diabetes. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Open AccessReview Mathematical Programming Techniques for Sensor Networks
Algorithms 2009, 2(1), 565-581; doi:10.3390/a2010565
Received: 31 October 2008 / Revised: 2 March 2009 / Accepted: 2 March 2009 / Published: 17 March 2009
Cited by 14 | PDF Full-text (365 KB) | HTML Full-text | XML Full-text
Abstract
This paper presents a survey describing recent developments in the area of mathematical programming techniques for various types of sensor network applications. We discuss mathematical programming formulations associated with these applications, as well as methods for solving the corresponding problems. We also address
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This paper presents a survey describing recent developments in the area of mathematical programming techniques for various types of sensor network applications. We discuss mathematical programming formulations associated with these applications, as well as methods for solving the corresponding problems. We also address some of the challenges arising in this area, including both conceptual and computational aspects. Full article
(This article belongs to the Special Issue Sensor Algorithms)
Open AccessReview Recent Advances in the Computational Discovery of Transcription Factor Binding Sites
Algorithms 2009, 2(1), 582-605; doi:10.3390/a2010582
Received: 6 January 2009 / Accepted: 17 March 2009 / Published: 24 March 2009
Cited by 11 | PDF Full-text (241 KB) | HTML Full-text | XML Full-text
Abstract
The discovery of gene regulatory elements requires the synergism between computational and experimental techniques in order to reveal the underlying regulatory mechanisms that drive gene expression in response to external cues and signals. Utilizing the large amount of high-throughput experimental data, constantly growing
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The discovery of gene regulatory elements requires the synergism between computational and experimental techniques in order to reveal the underlying regulatory mechanisms that drive gene expression in response to external cues and signals. Utilizing the large amount of high-throughput experimental data, constantly growing in recent years, researchers have attempted to decipher the patterns which are hidden in the genomic sequences. These patterns, called motifs, are potential binding sites to transcription factors which are hypothesized to be the main regulators of the transcription process. Consequently, precise detection of these elements is required and thus a large number of computational approaches have been developed to support the de novo identification of TFBSs. Even though novel approaches are continuously proposed and almost all have reported some success in yeast and other lower organisms, in higher organisms the problem still remains a challenge. In this paper, we therefore review the recent developments in computational methods for transcription factor binding site prediction. We start with a brief review of the basic approaches for binding site representation and promoter identification, then discuss the techniques to locate physical TFBSs, identify functional binding sites using orthologous information, and infer functional TFBSs within some context defined by additional prior knowledge. Finally, we briefly explore the opportunities for expanding these approaches towards the computational identification of transcriptional regulatory networks. Full article
(This article belongs to the Special Issue Algorithms and Molecular Sciences)

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