Search results for: homology modeling

Authors: Z. Altawallbeh

Abstract:

In this paper, an explicit homotopic function is constructed to compute the Hochschild homology of a finite dimensional free k-module V. Because the polynomial algebra is of course fundamental in the computation of the Hochschild homology HH and the cyclic homology CH of commutative algebras, we concentrate our work to compute HH of the polynomial algebra, by providing certain homotopic function.

Keywords: Exterior algebra, free resolution, free and projective modules, Hochschild homology, homotopic function, symmetric algebra.

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Authors: Jayashree Ramana

Abstract:

An alarming emergence of multidrug-resistant strains of the tuberculosis pathogen Mycobacterium tuberculosis and continuing high worldwide incidence of tuberculosis has invigorated the search for novel drug targets. The enzyme glutamate racemase (MurI) in bacteria catalyzes the stereoconversion of L-glutamate to D-glutamate which is a component of the peptidoglycan cell wall of the bacterium. The inhibitors targeted against MurI from several bacterial species have been patented and are advocated as promising antibacterial agents. However there are none available against MurI from Mycobacterium tuberculosis, due to the lack of its threedimensional structure. This work accomplished two major objectives. First, the tertiary structure of MtMurI was deduced computationally through homology modeling using the templates from bacterial homologues. It is speculated that like in other Gram-positive bacteria, MtMurI exists as a dimer and many of the protein interactions at the dimer interface are also conserved. Second, potent candidate inhibitors against MtMurI were identified through docking against already known inhibitors in other organisms.

Keywords: Glutamate racemase, homology modeling, docking, drug resistance.

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Authors: Nazar Zaki, Safaai Deris

Abstract:

The amount of the information being churned out by the field of biology has jumped manifold and now requires the extensive use of computer techniques for the management of this information. The predominance of biological information such as protein sequence similarity in the biological information sea is key information for detecting protein evolutionary relationship. Protein sequence similarity typically implies homology, which in turn may imply structural and functional similarities. In this work, we propose, a learning method for detecting remote protein homology. The proposed method uses a transformation that converts protein sequence into fixed-dimensional representative feature vectors. Each feature vector records the sensitivity of a protein sequence to a set of amino acids substrings generated from the protein sequences of interest. These features are then used in conjunction with support vector machines for the detection of the protein remote homology. The proposed method is tested and evaluated on two different benchmark protein datasets and it-s able to deliver improvements over most of the existing homology detection methods.

Keywords: Protein homology detection; support vectormachine; string kernel.

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Authors: Ewa Wywial, Shaneen M. Singh

Abstract:

The PRAF family of proteins is a plant specific family of proteins with distinct domain architecture and various unique sequence/structure traits. We have carried out an extensive search of the Arabidopsis genome using an automated pipeline and manual methods to verify previously known and identify unknown instances of PRAF proteins, characterize their sequence and build 3D structures of their individual domains. Integrating the sequence, structure and whatever little known experimental details for each of these proteins and their domains, we present a comprehensive characterization of the different domains in these proteins and their variant properties.

Keywords: PRAF proteins, homology modeling, Arabidopsisthaliana

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Authors: Chil-Chyuan Kuo, Chen-Hsuan Tsai

Abstract:

This study presents a cost-effective approach for rapid fabricating modeling platforms utilized in fused deposition modeling system. A small-batch production of modeling platforms about 20 pieces can be obtained economically through silicone rubber mold using vacuum casting without applying the plastic injection molding. The air venting systems is crucial for fabricating modeling platform using vacuum casting. Modeling platforms fabricated can be used for building rapid prototyping model after sandblasting. This study offers industrial value because it has both time-effectiveness and cost-effectiveness.

Keywords: Vacuum casting, fused deposition modeling, modeling platform, sandblasting, surface roughness.

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Authors: Pradip Peter Dey, Bhaskar Raj Sinha, Mohammad Amin, Hassan Badkoobehi

Abstract:

Mathematical, graphical and intuitive models are often constructed in the development process of computational systems. The Unified Modeling Language (UML) is one of the most popular modeling languages used by practicing software engineers. This paper critically examines UML models and suggests an augmented use case view with the addition of new constructs for modeling software. It also shows how a use case diagram can be enhanced. The improved modeling constructs are presented with examples for clarifying important design and implementation issues.

Keywords: Software architecture, software design, Unified Modeling Language (UML), user interface.

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Authors: Huaiyu Zhang

Abstract:

The method of modeling is the key technology for digital mockup (DMU). Based upon the developing for mechanical product DMU, the theory, method and approach for virtual environment (VE) and virtual object (VO) were studied. This paper has expounded the design goal and architecture of DMU system, analyzed the method of DMU application, and researched the general process of physics modeling and behavior modeling.

Keywords: DMU, VR, virtual environment, virtual object, physics modeling, behavior modeling

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Authors: M. J. Norashirene, Y. Zakiah, S. Nurdiana, I. Nur Hilwani, M. H. Siti Khairiyah, M. J. Muhamad Arif

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In this study, six bacterial isolates of a slightly thermophilic organism from the Sg. Klah hot spring, Malaysia were successfully isolated and designated as M7T55D1, M7T55D2, M7T55D3, M7T53D1, M7T53D2 and M7T53D3 respectively. The bacterial isolates were screened for their cellulose hydrolytic ability on Carboxymethlycellulose agar medium. The isolated bacterial strains were identified morphologically, biochemically and molecularly with the aid of 16S rDNA sequencing. All of the bacteria showed their optimum growth at a slightly alkaline pH of 7.5 with a temperature of 55°C. All strains were Gram-negative, non-spore forming type, strictly aerobic, catalase-positive and oxidase-positive with the ability to produce thermostable cellulase. Based on BLASTn results, bacterial isolates of M7T55D2 and M7T53D1 gave the highest homology (97%) with similarity to Tepidimonas ignava while isolates M7T55D1, M7T55D3, M7T53D2 and M7T53D3 showed their closest homology (97%-98%) with Tepidimonas thermarum. These cellulolytic thermophiles might have a commercial potential to produce valuable thermostable cellulase.

Keywords: Cellulase, Cellulolytic, Thermophiles, 16S rDNA Gene.

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Authors: Katalina Grigorova, Kaloyan Mironov

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The paper focuses on the benefits of business process modeling. Although this discipline is developing for many years, there is still necessity of creating new opportunities to meet the ever increasing users’ needs. Because one of these needs is related to the conversion of business process models from one standard to another, the authors have developed a converter between BPMN and EPC standards using workflow patterns as intermediate tool. Nowadays there are too many systems for business process modeling. The variety of output formats is almost the same as the systems themselves. This diversity additionally hampers the conversion of the models. The presented study is aimed at discussing problems due to differences in the output formats of various modeling environments.

Keywords: Business process modeling, business process modeling standards, workflow patterns, converting models.

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Authors: Ziaddin Daie Koozekanani, Mina Zolfy Lighvan

Abstract:

One of the most challengeable issues in ESL (Electronic System Level) design is the lack of a general modeling scheme for on chip communication architecture. In this paper some of the mostly used methodologies for modeling and representation of on chip communication are investigated. Our goal is studying the existing methods to extract the requirements of a general representation scheme for communication architecture synthesis. The next step, will be introducing a modeling and representation method for being used in automatically synthesis process of on chip communication architecture.

Keywords: Communication architecture, System on Chip, Communication Modeling and Representation

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Authors: Charles D. Otine, Samuel B. Kucel, Lena Trojer

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Selecting the data modeling technique for an information system is determined by the objective of the resultant data model. Dimensional modeling is the preferred modeling technique for data destined for data warehouses and data mining, presenting data models that ease analysis and queries which are in contrast with entity relationship modeling. The establishment of data warehouses as components of information system landscapes in many organizations has subsequently led to the development of dimensional modeling. This has been significantly more developed and reported for the commercial database management systems as compared to the open sources thereby making it less affordable for those in resource constrained settings. This paper presents dimensional modeling of HIV patient information using open source modeling tools. It aims to take advantage of the fact that the most affected regions by the HIV virus are also heavily resource constrained (sub-Saharan Africa) whereas having large quantities of HIV data. Two HIV data source systems were studied to identify appropriate dimensions and facts these were then modeled using two open source dimensional modeling tools. Use of open source would reduce the software costs for dimensional modeling and in turn make data warehousing and data mining more feasible even for those in resource constrained settings but with data available.

Keywords: About Database, Data Mining, Data warehouse, Dimensional Modeling, Open Source.

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Authors: Virupakshaiah DBM, Madiha Ahmed, Smita T. Patil, Chandrakanth Kelmani

Abstract:

Tuberculosis (TB) is a bacterial infectious disease caused by the obligate human pathogen, Mycobacterium tuberculosis. Multidrug-resistant tuberculosis (MDR-TB) is a global reality that threatens tuberculosis control. Resistance to antibiotic Rifampicin, occurs in 95% of cases through nucleotide substitutions in an 81-bp core region of the rpoB i.e; beta subunit of DNA dependant RNA polymerase. In this paper, we studied the Rifampicin-rpoB receptor interactions In silico. First, homology modeling was performed to obtain the three dimensional structure of Mycobacterium rpoB. Sixty analogs of Rifampicin were prepared using Marvin sketch software. Both original Rifampicin and the analogs were docked with rpoB and energy values were obtained. Out of sixty analogs, 43 analogs had lesser energy values than conventional Rifampicin and hence are predicted to have greater binding affinity to rpoB. Thus, this study offers a route for the development of Rifampicin analogs against multi drug resistant Mycobacterium rpoB.

Keywords: Marvin Sketch, Mycobacterium tuberculosis, Rifampicin, rpoB.

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Authors: Adla Bentellis, Zizette Boufaïda

Abstract:

Nowadays, the pace of business change is such that, increasingly, new functionality has to be realized and reliably installed in a matter of days, or even hours. Consequently, more and more business processes are prone to a continuous change. The objective of the research in progress is to use the MAP model, in a conceptual modeling method for flexible and adaptive business process. This method can be used to capture the flexibility dimensions of a business process; it takes inspiration from modularity concept in the object oriented paradigm to establish a hierarchical construction of the BP modeling. Its intent is to provide a flexible modeling that allows companies to quickly adapt their business processes.

Keywords: Business Process, Business process modeling, flexibility, MAP Model.

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Authors: Seong-Su Jeon, Seong-Jin Kim, Goon-Cherl Park

Abstract:

In this study, direct numerical simulation for the bubble condensation in the subcooled boiling flow was performed. The main goal was to develop the CFD modeling for the bubble condensation and to evaluate the accuracy of the VOF model with the developed CFD modeling. CFD modeling for the bubble condensation was developed by modeling the source terms in the governing equations of VOF model using UDF. In the modeling, the amount of condensation was determined using the interfacial heat transfer coefficient obtained from the bubble velocity, liquid temperature and bubble diameter every time step. To evaluate the VOF model using the CFD modeling for the bubble condensation, CFD simulation results were compared with SNU experimental results such as bubble volume and shape, interfacial area, bubble diameter and bubble velocity. Simulation results predicted well the behavior of the actual condensing bubble. Therefore, it can be concluded that the VOF model using the CFD modeling for the bubble condensation will be a useful computational fluid dynamics tool for analyzing the behavior of the condensing bubble in a wide range of the subcooled boiling flow.

Keywords: Bubble condensation, CFD modeling, Subcooled boiling flow, VOF model.

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Authors: Song Meng, Dianfu Ma, Yongwang Zhao, Jianxin Li

Abstract:

Cooperative visual modeling is more and more necessary in our complicated world. A collaborative environment which supports interactive operation and communication is required to increase work efficiency. We present a collaborative visual modeling framework which collaborative platform could be built on. On this platform, cooperation and communication is available for designers from different regions. This framework, which is different from other collaborative frameworks, contains a uniform message format, a message handling mechanism and other functions such as message pretreatment and Role-Communication-Token Access Control (RCTAC). We also show our implementation of this framework called Orchestra Designer, which support BPLE workflow modeling cooperatively online.

Keywords: colllaborative framework; visual modeling; message handling mechanism

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Authors: Zoltan Theisz, Gergely Mezei

Abstract:

Modern industrial automation relies on service oriented concepts of Internet of Things (IoT) device modeling in order to provide a flexible and extendable environment for service meta-repository. However, state-of-the-art meta-modeling techniques prefer design-time modeling, which results in a heavy usage of class sometimes unnecessary static subtyping. Although this approach benefits from clear-cut object-oriented design principles, it also seals the model repository for further dynamic extensions. In this paper, a dynamic multi-level modeling approach is introduced that enables dynamic subtyping through a more relaxed partial instantiation mechanism. The approach is demonstrated on a simple sensor network example.

Keywords: Meta-modeling, dynamic subtyping, DMLA, industrial automation, arrowhead.

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Authors: Hidetoshi Nonaka

Abstract:

This paper presents an interactive modeling system of uniform polyhedra using the isomorphic graphs. Especially, Kepler-Poinsot solids are formed by modifications of dodecahedron and icosahedron.

Keywords: Kepler-Poinsot solid, Shape modeling, Polyhedralgraph, Graph drawing.

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Authors: A. Retbi, M. Khalidi Idrissi, S. Bennani

Abstract:

The success of an e-learning system is highly dependent on the quality of its educational content and how effective, complete, and simple the design tool can be for teachers. Educational modeling languages (EMLs) are proposed as design languages intended to teachers for modeling diverse teaching-learning experiences, independently of the pedagogical approach and in different contexts. However, most existing EMLs are criticized for being too abstract and too complex to be understood and manipulated by teachers. In this paper, we present a visual EML that simplifies the process of designing learning scenarios for teachers with no programming background. Based on the conceptual framework of the activity theory, our resulting visual EML focuses on using Domainspecific modeling techniques to provide a pedagogical level of abstraction in the design process.

Keywords: Educational modeling language, Domain Specific Modeling, authoring systems, learning scenario.

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Authors: Bassam Atieh Rajabi, Sai Peck Lee

Abstract:

Business Process Modeling (BPM) is the first and most important step in business process management lifecycle. Graph based formalism and rule based formalism are the two most predominant formalisms on which process modeling languages are developed. BPM technology continues to face challenges in coping with dynamic business environments where requirements and goals are constantly changing at the execution time. Graph based formalisms incur problems to react to dynamic changes in Business Process (BP) at the runtime instances. In this research, an adaptive and flexible framework based on the integration between Object Oriented diagramming technique and Petri Net modeling language is proposed in order to support change management techniques for BPM and increase the representation capability for Object Oriented modeling for the dynamic changes in the runtime instances. The proposed framework is applied in a higher education environment to achieve flexible, updatable and dynamic BP.

Keywords: Business Process Modeling, Change Management, Graph Based Modeling, Rule Based Modeling, Object Oriented PetriNet.

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Authors: Kyong-min Lee, Moon Soo Chang, PooGyeon Park

Abstract:

In this paper, we propose a geometric modeling of illumination on the patterned image containing etching transistor. This image is captured by a commercial camera during the inspection of a TFT-LCD panel. Inspection of defect is an important process in the production of LCD panel, but the regional difference in brightness, which has a negative effect on the inspection, is due to the uneven illumination environment. In order to solve this problem, we present a geometric modeling of illumination consisting of an interpolation using the least squares method and 3D modeling using bezier surface. Our computational time, by using the sampling method, is shorter than the previous methods. Moreover, it can be further used to correct brightness in every patterned image.

Keywords: Bezier, defect, geometric modeling, illumination, inspection, LCD, panel.

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Authors: K. M. Tan, A. Anvar, T.F. Lu

Abstract:

A sophisticated simulator provides a cost-effective measure to carry out preliminary mission testing and diagnostic while reducing potential failures for real life at sea trials. The presented simulation framework covers three key areas: AUV modeling, sensor modeling, and environment modeling. AUV modeling mainly covers the area of AUV dynamics. Sensor modeling deals with physics and mathematical models that govern each sensor installed onto the AUV. Environment model incorporates the hydrostatic, hydrodynamics, and ocean currents that will affect the AUV in a real-time mission. Based on this designed simulation framework, custom scenarios provided by the user can be modeled and its corresponding behaviors can be observed. This paper focuses on the accuracy of the simulated data from AUV model and environmental model derived from a developed AUV test-bed which was jointly upgraded by DSTO and the University of Adelaide. The main contribution of this paper is to experimentally verify the accuracy of the proposed simulation framework.

Keywords: Autonomous Underwater Vehicle (AUV), simulator, framework, robotics, maritime robot, modeling.

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Authors: Aouattou Nabila, Saighi Mohamed, Fekih Malika

Abstract:

The modeling of water transfer in the unsaturated zone uses techniques and methods of the soil physics to solve the Richards-s equation. However, there is a disaccord between the size of the measurements provided by the soil physics and the size of the fields of hydrological modeling problem, to which is added the strong spatial variability of soil hydraulic properties. The objective of this work was to develop a methodology to estimate the hydrodynamic parameters for modeling water transfers at different hydrological scales in the soil-plant atmosphere systems.

Keywords: Hydraulic properties, Modeling, Unsaturated zone, Transfer, Water

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Authors: Jacek Kuraś, Jacek Lembas, Marek Skomorowski

Abstract:

In this paper, we introduce GODYS-PC software package for modeling, simulating and analyzing dynamic systems. To illustrate the use of GODYS-PC we present a few examples which concern modeling and simulating of engineering systems. In order to compare GODYS-PC with widely used in academia and industry Simulink®, the same examples are provided both in GODYS-PC and Simulink®.

Keywords: Modeling, simulating and analyzing dynamicsystems.

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Authors: Himanshu Payal, Sachin Maheshwari, Pushpendra S. Bharti

Abstract:

Electrical discharge machining (EDM), a non-conventional machining process, finds wide applications for shaping difficult-to-cut alloys. Process modeling of EDM is required to exploit the process to the fullest. Process modeling of EDM is a challenging task owing to involvement of so many electrical and non-electrical parameters. This work is an attempt to model the EDM process using artificial neural network (ANN). Experiments were carried out on die-sinking EDM taking Inconel 825 as work material. ANN modeling has been performed using experimental data. The prediction ability of trained network has been verified experimentally. Results indicate that ANN can predict the values of performance measures of EDM satisfactorily.

Keywords: Artificial neural network, EDM, metal removal rate, modeling, surface roughness.

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Authors: Ahmad Habibizad Navin, Mehdi Naghian Fesharaki, Mirkamal Mirnia, Mohamad Teshnelab, Ehsan Shahamatnia

Abstract:

In this paper we introduce new data oriented modeling of uniform random variable well-matched with computing systems. Due to this conformity with current computers structure, this modeling will be efficiently used in statistical inference.

Keywords: Uniform random variable, Data oriented modeling, Statistical inference, Prodigraph, Statistically complete tree, Uniformdigital probability digraph, Uniform n-complete probability tree.

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Authors: Radek Němec

Abstract:

Today's business environment requires that companies have access to highly relevant information in a matter of seconds. Modern Business Intelligence tools rely on data structured mostly in traditional dimensional database schemas, typically represented by star schemas. Dimensional modeling is already recognized as a leading industry standard in the field of data warehousing although several drawbacks and pitfalls were reported. This paper focuses on the analysis of another data warehouse modeling technique - the anchor modeling, and its characteristics in context with the standardized dimensional modeling technique from a query performance perspective. The results of the analysis show information about performance of queries executed on database schemas structured according to principles of each database modeling technique.

Keywords: Data warehousing, anchor modeling, star schema, anchor schema, query performance.

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Authors: Kwa-Sur Tam

Abstract:

This paper reviews various approaches that have been used for the modeling and simulation of large-scale engineering systems and determines their appropriateness in the development of a RICS modeling and simulation tool. Bond graphs, linear graphs, block diagrams, differential and difference equations, modeling languages, cellular automata and agents are reviewed. This tool should be based on linear graph representation and supports symbolic programming, functional programming, the development of noncausal models and the incorporation of decentralized approaches.

Keywords: Interdisciplinary, dynamic, functional programming, object-oriented.

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Authors: Raman Paranjape

Abstract:

We present a new approach to evaluation of Cyber Security in Power Systems using the method of modeling the power systems Infrastructure using software agents. Interfaces between module and the home smart meter are recognized as the primary points of intrusion.

Keywords: Power Systems, Modeling and Simulation, Agent systems.

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Authors: Jihye Jeon

Abstract:

This paper analyzes the conceptual framework of three statistical methods, multiple regression, path analysis, and structural equation models. When establishing research model of the statistical modeling of complex social phenomenon, it is important to know the strengths and limitations of three statistical models. This study explored the character, strength, and limitation of each modeling and suggested some strategies for accurate explaining or predicting the causal relationships among variables. Especially, on the studying of depression or mental health, the common mistakes of research modeling were discussed.

Keywords: Multiple regression, path analysis, structural equation models, statistical modeling, social and psychological phenomenon.

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Authors: Stefanie Heinke, Carina Pereira, Jan Spillner, Steffen Leonhardt

Abstract:

Severe heart failure is a common problem that has a significant effect on health expenditures in industrialized countries; moreover it reduces patient-s quality of life. However, current research usually focuses either on detailed modeling of the heart or on detailed modeling of the cardiovascular system. Thus, this paper aims to present a sophisticated model of the heart enhanced with an extensive model of the cardiovascular system. Special interest is on the pressure and flow values close to the heart since these values are critical to accurately diagnose causes of heart failure. The model is implemented in Dymola an object-oriented, physical modeling language. Results achieved with the novel model show overall feasibility of the approach. Moreover, results are illustrated and compared to other models. The novel model shows significant improvements.

Keywords: Cardiovascular system, heart, modeling.

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