Predicting protein protein interfaces as clusters of optimal docking area points
- Authors: Arafat, Yasir , Kamruzzaman, Joarder , Karmakar, Gour , Fernandez-Recio, Juan
- Date: 2009
- Type: Text , Journal article
- Relation: International Journal of data mining and bioinformatics Vol. 3, no. 1 (2009), p. 55-67
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- Description: Abstract: Desolvation property is used here to predict protein-protein binding sites exploiting the fact that lower-valued 'optimal docking area' ODA (Fernandez-Recio et al., 2005) points form cluster at the interface. The proposed method involves two steps; clustering the ODA points and representing ODA points by average ODA values. On 51 nonredundant proteins, results show the success rate improved considerably. Considering only significant ODA, the previous ODA method has obtained a success rate of 65% with overall success rate of 39%. The proposed method improved the overall success rate to 61%. Further, comparable results were found for X-ray and NMR structures.
New gene selection algorithm using hypeboxes to improve performance of classifiers
- Authors: Bagirov, Adil , Mardaneh, Karim
- Date: 2020
- Type: Text , Journal article
- Relation: International Journal of Bioinformatics Research and Applications Vol. 16, no. 3 (2020), p. 269-289
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- Description: The use of DNA microarray technology allows to measure the expression levels of thousands of genes in one single experiment which makes possible to apply classification techniques to classify tumours. However, the large number of genes and relatively small number of tumours in gene expression datasets may (and in some cases significantly) diminish the accuracy of many classifiers. Therefore, efficient gene selection algorithms are required to identify most informative genes or groups of genes to improve the performance of classifiers. In this paper, a new gene selection algorithm is developed using marginal hyberboxes of genes or groups of genes for each tumour type. Informative genes are defined using overlaps between hyberboxes. The results on six gene expression datasets demonstrate that the proposed algorithm is able to considerably reduce the number of genes and significantly improve the performance of classifiers. © 2020 Inderscience Enterprises Ltd.
Thermal and thermal damage responses during switching bipolar radiofrequency ablation employing bipolar needles : a computational study on the effects of different electrode configuration, input voltage and ablation duration
- Authors: Cheong, Jason , Ooi, Ean Hin , Ooi, Ean Tat
- Date: 2020
- Type: Text , Journal article
- Relation: International Journal for Numerical Methods in Biomedical Engineering Vol. 36, no. 9 (2020), p.
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- Description: Recent studies have demonstrated the effectiveness of switching bipolar radiofrequency ablation (bRFA) in treating liver cancer. Nevertheless, the clinical use of the treatment remains less common than conventional monopolar RFA – likely due to the lack of understanding of how the tissues respond thermally to the switching effect. The problem is exacerbated by the numerous possible switching combinations when bRFA is performed using bipolar needles, thus making theoretical deduction and experimental studies difficult. This article addresses this issue via computational modelling by examining if significant variation in the treatment outcome exists amongst six different electrode configurations defined by the X-, C-, U-, N-, Z- and O-models. Results indicated that the tissue thermal and thermal damage responses varied depending on the electrode configuration and the operating conditions (input voltage and ablation duration). For a spherical tumour, 30 mm in diameter, complete ablation could not be attained in all configurations with 70 V input voltage and 5 minutes ablation duration. Increasing the input voltage to 90 V enlarged the coagulation zone in the X-model only. With the other configurations, extending the ablation duration to 10 minutes was found to be the better at enlarging the coagulation zone. © 2020 John Wiley & Sons, Ltd.
Incorporating time-delays in S-System model for reverse engineering genetic networks
- Authors: Chowdhury, Ahsan , Chetty, Madhu , Nguyen, Vinh
- Date: 2013
- Type: Text , Journal article
- Relation: BMC Bioinformatics Vol. 14, no. (2013), p. 1-22
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- Description: Background In any gene regulatory network (GRN), the complex interactions occurring amongst transcription factors and target genes can be either instantaneous or time-delayed. However, many existing modeling approaches currently applied for inferring GRNs are unable to represent both these interactions simultaneously. As a result, all these approaches cannot detect important interactions of the other type. S-System model, a differential equation based approach which has been increasingly applied for modeling GRNs, also suffers from this limitation. In fact, all S-System based existing modeling approaches have been designed to capture only instantaneous interactions, and are unable to infer time-delayed interactions. Results In this paper, we propose a novel Time-Delayed S-System (TDSS) model which uses a set of delay differential equations to represent the system dynamics. The ability to incorporate time-delay parameters in the proposed S-System model enables simultaneous modeling of both instantaneous and time-delayed interactions. Furthermore, the delay parameters are not limited to just positive integer values (corresponding to time stamps in the data), but can also take fractional values. Moreover, we also propose a new criterion for model evaluation exploiting the sparse and scale-free nature of GRNs to effectively narrow down the search space, which not only reduces the computation time significantly but also improves model accuracy. The evaluation criterion systematically adapts the max-min in-degrees and also systematically balances the effect of network accuracy and complexity during optimization. Conclusion The four well-known performance measures applied to the experimental studies on synthetic networks with various time-delayed regulations clearly demonstrate that the proposed method can capture both instantaneous and delayed interactions correctly with high precision. The experiments carried out on two well-known real-life networks, namely IRMA and SOS DNA repair network in Escherichia coli show a significant improvement compared with other state-of-the-art approaches for GRN modeling.
Chemical characterization of MEA degradation in PCC pilot plants operating in Australia
- Authors: Cruickshank, Alicia , Verheyen, Vincent , Adeloju, Samuel , Meuleman, Erik , Chaffee, Alan , Cottrell, Aaron , Feron, Paul
- Date: 2013
- Type: Text , Journal article
- Relation: Energy Procedia Vol. 37, no. (2013), p. 877-882
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- Description: An important step towards commercial scale post-combustion CO2 capture from coal-fired power stations is understanding solvent degradation. Laboratory scale trials have identified three main solvent degradation pathways for 30% MEA: oxidative degradation, carbamate polymerization and formation of heat stable salts. This paper probes the semi-volatile organic compounds produced from a single batch of 30% MEA which was used to capture CO2 from a black coal-fired power station (Tarong, Queensland, Australia) for approximately 700 hours, followed by 500 hours at the brown coal-fired power station (Loy Yang, Victoria, Australia). Comparisons are made between the compounds identified in this aged solvent system with MEA degradation reactions described in literature. Most of semi-volatile compounds tentatively identified by GC/MS have previously been reported in laboratory scale degradation trials. Our preliminary results show low levels of degradation products were present in samples after its use in the pilot plant at Tarong (black coal) and consequent 13 months storage, but much higher concentrations were later found in the same solvent during its at use in the pilot plant at Loy Yang Power (brown coal). Further work includes identifying the cause of poor GC/MS repeatability and investigating the relative rates of reactions described in literature. The impact of inorganic anions and dissolved metals on MEA degradation will also be explored.
Use of stochastic XFEM in the investigation of heterogeneity effects on the tensile strength of intermediate geotechnical materials
- Authors: Dyson, Ashley , Tang, Zhan , Tolooiyan, Ali
- Date: 2018
- Type: Text , Journal article
- Relation: Finite Elements in Analysis and Design Vol. 145, no. (2018), p. 1-9
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- Description: The numerical simulation of an Unconfined Expansion Test (UET) is presented with tensile strength fracture criteria assigned by stochastic methods to take into account material heterogeneity. Tests are performed by producing radial cavity expansion models of thinly sliced cylindrical specimens. The introduction of element-wise allocation of fracture parameters generates instances of specimen failure without the requirement of predefined fracture zones, permitting discontinuities to form naturally within zones containing weak strength parameters. The parallel application of an in-house Python scripts and eXtended Finite Element Method (XFEM) facilitates the investigation of heterogeneity effects on the tensile strength of intermediate geotechnical materials.
A new reliability analysis method based on the conjugate gradient direction
- Authors: Ezzati, Ghasem , Mammadov, Musa , Kulkarni, Siddhivinayak
- Date: 2015
- Type: Text , Journal article
- Relation: Structural and Multidisciplinary Optimization Vol. 51, no. 1 (2015), p. 89-98
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- Description: Reliability-based design optimization (RBDO) is an important area in structural optimization. A principal step of the RBDO process is to solve a reliability analysis problem. This problem has been considered in inner loop of double-loop RBDO approaches. Although many algorithms have been developed for solving this problem, there are still some challenges. Existing algorithms do not have good convergence rates and often diverge. There is a need to develop more efficient and stable algorithms that can be used for evaluating all performance functions sufficiently. In this paper, a new method, called “Conjugate Gradient Analysis (CGA) Method”, is proposed to apply in the reliability analysis problems. This method is based on the conjugate gradient method. Some mathematical problems are provided in order to demonstrate the advantages of the proposed method compared with the existing methods. © 2014, Springer-Verlag Berlin Heidelberg.
On topology optimization and canonical duality method
- Authors: Gao, David
- Date: 2018
- Type: Text , Journal article
- Relation: Computer Methods in Applied Mechanics and Engineering Vol. 341, no. (2018), p. 249-277
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- Description: Topology optimization for general materials is correctly formulated as a bi-level knapsack problem, which is considered to be NP-hard in global optimization and computer science. By using canonical duality theory (CDT) developed by the author, the linear knapsack problem can be solved analytically to obtain global optimal solution at each design iteration. Both uniqueness, existence, and NP-hardness are discussed. The novel CDT method for general topology optimization is refined and tested by both 2-D and 3-D benchmark problems. Numerical results show that without using filter and any other artificial technique, the CDT method can produce exactly 0-1 optimal density distribution with almost no checkerboard pattern. Its performance and novelty are compared with the popular SIMP and BESO approaches. Additionally, some mathematical and conceptual mistakes in literature are explicitly addressed. A brief review on the canonical duality theory for modeling multi-scale complex systems and for solving general nonconvex/discrete problems are given in Appendix. This paper demonstrates a simple truth: elegant designs come from correct model and theory. © 2018
Prediction of gold-bearing localised occurrences from limited exploration data
- Authors: Grigoryev, Igor , Bagirov, Adil , Tuck, Michael
- Date: 2020
- Type: Text , Journal article
- Relation: International Journal of Computational Science and Engineering Vol. 21, no. 4 (2020), p. 503-512
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- Description: Inaccurate drill-core assay interpretation in the exploration stage presents challenges to long-term profit of gold mining operations. Predicting the gold distribution within a deposit as precisely as possible is one of the most important aspects of the methodologies employed to avoid problems associated with financial expectations. The prediction of the variability of gold using a very limited number of drill-core samples is a very challenging problem. This is often intractable using traditional statistical tools where with less than complete spatial information certain assumptions are made about gold distribution and mineralisation. The decision-support predictive modelling methodology based on the unsupervised machine learning technique, presented in this paper avoids some of the restrictive limitations of traditional methods. It identifies promising exploration targets missed during exploration and recovers hidden spatial and physical characteristics of the explored deposit using information directly from drill hole database. Copyright © 2020 Inderscience Enterprises Ltd.
Reliability analysis of shuffle-exchange network systems
- Authors: Gunawan, Indra
- Date: 2012
- Type: Text , Journal article
- Relation: Reliability Engineering and System Safety Vol. 93, no. (2012), p. 271-276
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- Description: Shuffle-exchange networks (SENs) have been widely considered as practical interconnection systems due to their size of its switching elements (SEs) and uncomplicated configuration. SEN is a network among a large class of topologically equivalent multistage interconnection networks (MINs) that includes omega, indirect binary n-cube, baseline, and generalized cube. In this paper, SEN with additional stages that provide more redundant paths are analyzed. A common network topology with a 2×2 basic building block in a SEN and its variants in terms of extra-stages is investigated. As an illustration, three types of SENs are compared: SEN, SEN with an additional stage (SEN+), and SEN with two additional stages (SEN+2). Finally, three measures of reliability: terminal, broadcast, and network reliability for the three SEN systems are analyzed.
Fuzzy logic and gradient descent-based optimal adaptive robust controller with inverted pendulum verification
- Authors: Hadipour Lakmesari, S. , Mahmoodabadi, M. , Ibrahim, Yousef
- Date: 2021
- Type: Text , Journal article
- Relation: Chaos, Solitons and Fractals Vol. 151, no. (2021), p.
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- Description: This paper develops an adaptive robust combination of feedback linearization (FL) and sliding mode controller (SMC) based on fuzzy rules and gradient descent laws. The new suggested control algorithm is tested to stabilize a fourth-order under-actuated nonlinear inverted pendulum system. More precisely, the reliable feedback linearization approach and the robust SMC controller are combined to design a stable control effort. In order to enhance the performance of the suggested controller, an adaptation technique as long as fuzzy rules are applied to update the control gains and the boundary layer parameter. Then, a novel evolutionary algorithm termed multi-objective ant lion optimizer (MOALO) is implemented to determine the control coefficients. The analysis and results conducted on the inverted pendulum system demonstrate the desired performance of the proposed control scheme by providing an optimal smooth control input, suitable tracking performance, and proper time responses. © 2021 Elsevier Ltd
Characterizations of minimal elements of topical functions on semimodules with applications
- Authors: Hassani, Sara , Mohebi, Hossein
- Date: 2017
- Type: Text , Journal article
- Relation: Linear Algebra and Its Applications Vol. 520, no. (2017), p. 104-124
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- Description: In this paper, we first give characterizations of the superdifferential of extended valued topical functions defined on a semimodule with values in a semifield. Next, we characterize minimal elements of the upper support set of extended valued topical functions. Finally, as an application, we present a necessary and sufficient condition for global maximum of the difference of two strictly topical functions defined on a semimodule. (C) 2017 Elsevier Inc. All rights reserved.
Where is the rate in the rule?
- Authors: Herbert, Elizabeth
- Date: 2008
- Type: Text , Journal article
- Relation: Australian Senior Mathematics Journal Vol. 22, no. 2 (2008), p. 28-26
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- Description: The article reports on additional data collected during interviews for a project investigating the different ways rate may be experience by pre-calculus students. It evaluates the participants' understanding in a specific rate context. Insights into perceptions of rate in several different representations were provided by detailed analysis of the video record of each participant's interview. The article also presents the Victorian Essential Learning Standards (VELS) expectations with respect to the concept of rate.
- Description: C1
Adaptive phase-field modeling of brittle fracture using the scaled boundary finite element method
- Authors: Hirshikesh , Pramod, Aladurthi , Annabattula, Ratna , Ooi, Ean Tat , Song, Chongmin , Natarajan, Sundararajan
- Date: 2019
- Type: Text , Journal article
- Relation: Computer Methods in Applied Mechanics and Engineering Vol. 355, no. (2019), p. 284-307
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- Description: In this work, we propose an adaptive phase field method (PFM) to simulate quasi-static brittle fracture problems. The phase field equations are solved using the scaled boundary finite element method (SBFEM). The adaptive refinement strategy is based on an error indicator evaluated directly from the solutions of the SBFEM without any need for stress recovery techniques. Quadtree meshes are adapted to perform mesh refinement. The polygons with hanging nodes in the quadtree decomposition are treated as n−sided polygons within the framework of the SBFEM and do not require any special treatment in contrast to the conventional finite element method. Several benchmark problems are used to demonstrate the robustness and the efficacy of the proposed technique. The adaptive refinement strategy reduces the mesh burden when adopting the PFM to model fracture. Numerical results show an improvement in the computational efficiency in terms of the number of elements required in the standard PFM without compromising the accuracy of the solution.
DRfit : A Java tool for the analysis of discrete data from multi-well plate assays
- Authors: Hofmann, Andreas , Preston, Sarah , Cross, Megan , Herath, Dilrukshi , Simon, Anne , Gasser, Robin
- Date: 2019
- Type: Text , Journal article
- Relation: BMC Bioinformatics Vol. 20, no. (2019), p. 1-6
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- Description: Background: Analyses of replicates in sets of discrete data, typically acquired in multi-well plate formats, is a recurring task in many contemporary areas in the Life Sciences. The availability of accessible cross-platform data analysis tools for such fundamental tasks in varied projects and environments is an important prerequisite to ensuring a reliable and timely turnaround as well as to provide practical analytical tools for student training. Results: We have developed an easy-to-use, interactive software tool for the analysis of multiple data sets comprising replicates of discrete bivariate data points. For each dataset, the software identifies the replicate data points from a defined matrix layout and calculates their means and standard errors. The averaged values are then automatically fitted using either a linear or a logistic dose response function. Conclusions: DRfit is a practical and convenient tool for the analysis of one or multiple sets of discrete data points acquired as replicates from multi-well plate assays. The design of the graphical user interface and the built-in analysis features make it a flexible and useful tool for a wide range of different assays.
Advances in the theory of compact groups and pro-lie groups in the last quarter century
- Authors: Hofmann, Karl , Morris, Sidney
- Date: 2021
- Type: Text , Journal article , Review
- Relation: Axioms Vol. 10, no. 3 (2021), p.
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- Description: This article surveys the development of the theory of compact groups and pro-Lie groups, contextualizing the major achievements over 125 years and focusing on some progress in the last quarter century. It begins with developments in the 18th and 19th centuries. Next is from Hilbert’s Fifth Problem in 1900 to its solution in 1952 by Montgomery, Zippin, and Gleason and Yamabe’s important structure theorem on almost connected locally compact groups. This half century included profound contributions by Weyl and Peter, Haar, Pontryagin, van Kampen, Weil, and Iwasawa. The focus in the last quarter century has been structure theory, largely resulting from extending Lie Theory to compact groups and then to pro-Lie groups, which are projective limits of finite-dimensional Lie groups. The category of pro-Lie groups is the smallest complete category containing Lie groups and includes all compact groups, locally compact abelian groups, and connected locally compact groups. Amongst the structure theorems is that each almost connected pro-Lie group G is homeomorphic to RI × C for a suitable set I and some compact subgroup C. Finally, there is a perfect generalization to compact groups G of the age-old natural duality of the group algebra R[G] of a finite group G to its representation algebra R(G, R), via the natural duality of the topological vector space RI to the vector space R(I), for any set I, thus opening a new approach to the Hochschild-Tannaka duality of compact groups. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.
Extended HP model for protein structure prediction
- Authors: Hoque, Md Tamjidul , Chetty, Madhu , Sattar, Abdul
- Date: 2009
- Type: Text , Journal article
- Relation: Computational Biology and Bioinformatics Vol. Jan-Feb 2011, no. (2009 ), p. 234-245
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- Description: This paper presents the impact of twins and the measures for their removal from the population of genetic algorithm (GA) when applied to effective conformational searching. It is conclusively shown that a twin removal strategy for a GA provides considerably enhanced performance when investigating solutions to complex ab initio protein structure prediction (PSP) problems in low-resolution model. Without twin removal, GA crossover and mutation operations can become ineffectual as generations lose their ability to produce significant differences, which can lead to the solution stalling. The paper relaxes the definition of chromosomal twins in the removal strategy to not only encompass identical, but also highly correlated chromosomes within the GA population, with empirical results consistently exhibiting significant improvements solving PSP problems.
Twin removal in genetic algorithms for protein structure prediction using low-resolution model
- Authors: Hoque, Md Tamjidul , Chetty, Madhu , Lewis, Andrew , Sattar, Abdul
- Date: 2011
- Type: Text , Journal article
- Relation: IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 8, no. 1 (2011), p. 234-245
- Full Text: false
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- Description: This paper presents the impact of twins and the measures for their removal from the population of genetic algorithm (GA) when applied to effective conformational searching. It is conclusively shown that a twin removal strategy for a GA provides considerably enhanced performance when investigating solutions to complex ab initio protein structure prediction (PSP) problems in low-resolution model. Without twin removal, GA crossover and mutation operations can become ineffectual as generations lose their ability to produce significant differences, which can lead to the solution stalling. The paper relaxes the definition of chromosomal twins in the removal strategy to not only encompass identical, but also highly correlated chromosomes within the GA population, with empirical results consistently exhibiting significant improvements solving PSP problems.
Development of the scaled boundary finite element method for crack propagation modeling of elastic solids subjected to coupled thermo-mechanical loads
- Authors: Iqbal, M. D. , Birk, C. , Ooi, Ean Tat , Gravenkamp, H.
- Date: 2021
- Type: Text , Journal article
- Relation: Computer Methods in Applied Mechanics and Engineering Vol. 387, no. (2021), p.
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- Description: This study presents the development of the scaled boundary finite element method to model discrete crack propagation induced by thermal loads. The SBFEM excels in modeling stress singularities at sharp crack tips with high accuracy. Polygon meshes are used so that a robust local re-meshing algorithm can be utilized to propagate the crack. The scaled boundary finite element formulation for steady-state thermal stress analysis is presented. Following a scaled boundary finite element analysis of a given thermal problem, the effect of initial strains due to temperature is taken into account semi-analytically in a subsequent stress analysis. Several numerical examples are presented to validate the technique and illustrate its salient features. © 2021
Micro-scale heat transfer modelling of the contact line region of a boiling-sodium bubble
- Authors: Iyer, Siddharth , Kumar, Apurv , Coventry, Joe , Pye, John , Lipiński, Wojciech
- Date: 2020
- Type: Text , Journal article
- Relation: International Journal of Heat and Mass Transfer Vol. 160, no. (2020), p.
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- Description: The use of boiling liquid metals such as sodium is attractive for providing a near-isothermal heat source for engineering applications. However, previous use of boiling sodium as a coolant in nuclear reactors and as a heat transfer fluid in solar thermal applications has shown that the boiling process is unstable. To stabilise the flow, it is imperative to gain a better understanding of the boiling phenomena. An integral part of the boiling process is the evaporation of the region where the liquid-vapour interface meets the heater wall, referred to as the contact line region. The heat transfer modelling of this region formed below a single bubble in nucleate pool boiling of sodium is considered in this study. A contact line model previously developed for high Prandtl number flows is extended by including the effect of an electron pressure component which is unique to liquid metals. The assumptions made in the model are critically assessed to determine their validity for modelling micro-scale evaporation in sodium. The model was used to show that the evaporative heat flux from the contact line region in sodium can be up to six times larger compared to a high Prandtl number fluid FC-72 for a superheat of 15 K, owing to the high thermal conductivity of sodium. Furthermore, a study on the influence of specific characteristics of sodium — high boiling superheat and presence of an electron pressure — showed that the evaporative heat flux increases with increasing superheat and decreases with increasing electron pressure. © 2020 Elsevier Ltd
- Description: We gratefully acknowledge the financial support from the Australian Research Council (grant no. LP150101189 ). We thank our project partner Vast Solar Pty Ltd for their support and contributions.