Next Issue
Previous Issue

Table of Contents

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

  • Issues are regarded as officially published after their release is announced to the table of contents alert mailing list.
  • You may sign up for e-mail alerts to receive table of contents of newly released issues.
  • PDF is the official format for papers published in both, html and pdf forms. To view the papers in pdf format, click on the "PDF Full-text" link, and use the free Adobe Readerexternal link to open them.
View options order results:
result details:
Displaying articles 1-32
Export citation of selected articles as:
Open AccessArticle Mixed Variational Formulations for Micro-cracked Continua in the Multifield Framework
Algorithms 2009, 2(1), 606-622; https://doi.org/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)
Figures

Figure 1

Open AccessReview Recent Advances in the Computational Discovery of Transcription Factor Binding Sites
Algorithms 2009, 2(1), 582-605; https://doi.org/10.3390/a2010582
Received: 6 January 2009 / Accepted: 17 March 2009 / Published: 24 March 2009
Cited by 13 | 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
[...] Read more.
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)
Figures

Figure 1

Open AccessReview Mathematical Programming Techniques for Sensor Networks
Algorithms 2009, 2(1), 565-581; https://doi.org/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
[...] Read more.
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)
Figures

Figure 1

Open AccessArticle Multi-Band Spectral Subtraction Method for Electrolarynx Speech Enhancement
Algorithms 2009, 2(1), 550-564; https://doi.org/10.3390/a2010550
Received: 30 October 2008 / Revised: 6 February 2009 / Accepted: 25 February 2009 / Published: 13 March 2009
Cited by 6 | 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
[...] Read more.
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
Figures

Figure 1

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; https://doi.org/10.3390/a2010533
Received: 16 January 2009 / Revised: 17 February 2009 / Accepted: 3 March 2009 / Published: 12 March 2009
Cited by 3 | 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
[...] Read more.
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
Figures

Figure 1

Open AccessReview A Review of Closed-Loop Algorithms for Glycemic Control in the Treatment of Type 1 Diabetes
Algorithms 2009, 2(1), 518-532; https://doi.org/10.3390/a2010518
Received: 30 October 2008 / Revised: 23 January 2009 / Accepted: 25 February 2009 / Published: 12 March 2009
Cited by 33 | 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
[...] Read more.
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)
Figures

Figure 1

Open AccessArticle A Novel Algorithm for Macromolecular Epitope Matching
Algorithms 2009, 2(1), 498-517; https://doi.org/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
[...] Read more.
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)
Figures

Figure 1

Open AccessArticle Semi-empirical Algorithm for the Retrieval of Ecology-Relevant Water Constituents in Various Aquatic Environments
Algorithms 2009, 2(1), 470-497; https://doi.org/10.3390/a2010470
Received: 27 October 2008 / Revised: 11 January 2009 / Accepted: 25 February 2009 / Published: 10 March 2009
Cited by 19 | 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
[...] Read more.
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)
Figures

Figure 1

Open AccessArticle Structural Fingerprints of Transcription Factor Binding Site Regions
Algorithms 2009, 2(1), 448-469; https://doi.org/10.3390/a2010448
Received: 4 December 2008 / Revised: 2 February 2009 / Accepted: 5 March 2009 / Published: 10 March 2009
Cited by 1 | 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
[...] Read more.
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)
Figures

Figure 1

Open AccessArticle Resonance in Interacting Induced-Dipole Polarizing Force Fields: Application to Force-Field Derivatives
Algorithms 2009, 2(1), 437-447; https://doi.org/10.3390/a2010437
Received: 5 December 2008 / Revised: 15 January 2009 / Accepted: 27 February 2009 / Published: 10 March 2009
Cited by 1 | 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
[...] Read more.
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)
Figures

Figure 1

Open AccessArticle Protein-Protein Interaction Analysis by Docking
Algorithms 2009, 2(1), 429-436; https://doi.org/10.3390/a2010429
Received: 1 December 2008 / Revised: 19 January 2009 / Accepted: 27 February 2009 / Published: 10 March 2009
Cited by 1 | 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
[...] Read more.
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)
Figures

Figure 1

Open AccessReview Genetic Algorithms in Application to the Geometry Optimization of Nanoparticles
Algorithms 2009, 2(1), 410-428; https://doi.org/10.3390/a2010410
Received: 24 November 2008 / Revised: 6 January 2009 / Accepted: 26 February 2009 / Published: 4 March 2009
Cited by 13 | 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
[...] Read more.
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)
Figures

Figure 1

Open AccessArticle A Sensor-Based Learning Algorithm for the Self-Organization of Robot Behavior
Algorithms 2009, 2(1), 398-409; https://doi.org/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
[...] Read more.
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)
Figures

Figure 1

Open AccessArticle Algorithm for Active Suppression of Radiation and Acoustical Scattering Fields by Some Physical Bodies in Liquids
Algorithms 2009, 2(1), 361-397; https://doi.org/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
[...] Read more.
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)
Figures

Figure 1

Open AccessReview Radio-Isotope Identification Algorithms for NaI γ Spectra
Algorithms 2009, 2(1), 339-360; https://doi.org/10.3390/a2010339
Received: 26 November 2008 / Revised: 13 February 2009 / Accepted: 20 February 2009 / Published: 3 March 2009
Cited by 33 | 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,
[...] Read more.
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
Figures

Figure 1

Back to Top