Search results for: ligand design

Authors: Ching-Wei Tsai, Chih-I Liu, Ruoh-Chyu Ruaana

Abstract:

A new strategy for oriented immobilization of proteins was proposed. The strategy contains two steps. The first step is to search for a docking site away from the active site on the protein surface. The second step is trying to find a ligand that is able to grasp the targeted site of the protein. To avoid ligand binding to the active site of protein, the targeted docking site is selected to own opposite charges to those near the active site. To enhance the ligand-protein binding, both hydrophobic and electrostatic interactions need to be included. The targeted docking site should therefore contain hydrophobic amino acids. The ligand is then selected through the help of molecular docking simulations. The enzyme α-amylase derived from Aspergillus oryzae (TAKA) was taken as an example for oriented immobilization. The active site of TAKA is surrounded by negatively charged amino acids. All the possible hydrophobic sites on the surface of TAKA were evaluated by the free energy estimation through benzene docking. A hydrophobic site on the opposite side of TAKA-s active site was found to be positive in net charges. A possible ligand, 3,3-,4,4- – Biphenyltetra- carboxylic acid (BPTA), was found to catch TAKA by the designated docking site. Then, the BPTA molecules were grafted onto silica gels and measured the affinity of TAKA adsorption and the specific activity of thereby immobilized enzymes. It was found that TAKA had a dissociation constant as low as 7.0×10-6 M toward the ligand BPTA on silica gel. The increase in ionic strength has little effect on the adsorption of TAKA, which indicated the existence of hydrophobic interaction between ligands and proteins. The specific activity of the immobilized TAKA was compared with the randomly adsorbed TAKA on primary amine containing silica gel. It was found that the orderly immobilized TAKA owns a specific activity twice as high as the one randomly adsorbed by ionic interaction.

Keywords: Protein Oriented immobilization, Molecular docking, ligand design, surface modification.

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Authors: Dije Dehari, Ahmed Jashari, Shefket Dehari, Agim Shabani

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New complexes of nickel (II) have been synthesized in the reaction mixture of nickel (II) acetate and 4-hydroxy-2-oxo-2H-chromene-3-carboxamide. Bis(4-hydroxy-2-oxo-2H-chromene-3-carboxamidato-O,O)nickel (II) and diaquabis(4-hydroxy-2-oxo-2H-chromene-3-carboxamidato-O,O)nickel (II) were characterized by elemental analysis, IR spectroscopy and ESI mass spectrometry. Elemental analysis and mass spectrometry data of the complexes suggests the stoichiometry of 1:2 (metal-ligand).

Keywords: Nickel complexes, 4-hydroxy-2-oxo-2H-chromene-3-carboxamide, IR spectroscopy, mass spectrometry.

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Authors: Baharak Khoshkholgh-Sima, Soroush Sardari, Jalal Izadi Mobarakeh, Ramezan Ali Khavari-Nejad

Abstract:

There is an urgent need to develop novel Mycobacterium tuberculosis (Mtb) drugs that are active against drug resistant bacteria but, more importantly, kill persistent bacteria. Our study structured based on integrated analysis of metabolic pathways, small molecule screening and similarity Search in PubChem Database. Metabolic analysis approaches based on Unified weighted used for potent target selection. Our results suggest that pantothenate synthetase (panC) and and 3-methyl-2-oxobutanoate hydroxymethyl transferase (panB) as a appropriate drug targets. In our study, we used pantothenate synthetase because of existence inhibitors. We have reported the discovery of new antitubercular compounds through ligand based approaches using computational tools.

Keywords: In Silico, Ligand-based Virtual Screening, Metabolic Pathways, Mycobacterium tuberculosis

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Authors: Fei Wang, Kaimin Shih

Abstract:

The persistent nature of perfluorochemicals (PFCs) has attracted global concern in recent years. Perfluorooctanesulfonate (PFOS) and perfluorooctanoate (PFOA) are the most commonly found PFC compounds, and thus their fate and transport play key roles in PFC distribution in the natural environment. The kinetic behavior of PFOS or PFOA on boehmite consists of a fast adsorption process followed by a slow adsorption process which may be attributed to the slow transport of PFOS or PFOA into the boehmite pore surface. The adsorption isotherms estimated the maximum adsorption capacities of PFOS and PFOA on boehmite as 0.877 μg/m2 and 0.633 μg/m2, with the difference primarily due to their different functional groups. The increase of solution pH led to a moderate decrease of PFOS and PFOA adsorption, owing to the increase of ligand exchange reactions and the decrease of electrostatic interactions. The presence of NaCl in solution demonstrated negative effects for PFOS and PFOA adsorption on boehmite surfaces, with potential mechanisms being electrical double layer compression, competitive adsorption of chloride.

Keywords: PFOS, PFOA, adsorption, electrostatic interaction, ligand exchange

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Authors: Hamza Simsir, Nurettin Eltugral, Selhan Karagoz

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Surface modification and functionalization has been an important tool for scientists in order to open new frontiers in nanoscience and nanotechnology. Desired surface characteristics for the intended applications can be achieved with surface functionalization. In this work, the effect of water soluble ligands on the adsorption capabilities of silver nanoparticles onto AC which was synthesized from German beech wood was investigated. Sodium borohydride (NaBH4) and polyvinyl alcohol (PVA) were used as the ligands. Silver nanoparticles with different surface coatings have average sizes range from 10 to 13 nm. They were synthesized in aqueous media by reducing Ag (I) ion in the presence of ligands. These particles displayed adsorption tendencies towards AC when they were mixed together and shaken in distilled water. Silver nanoparticles (NaBH4-AgNPs) reduced and stabilized by NaBH4 adsorbed onto AC with a homogenous dispersion of aggregates with sizes in the range of 100-400 nm. Beside, silver nanoparticles, which were prepared in the presence of both NaBH4 and PVA (NaBH4/PVA-Ag NPs), demonstrated that NaBH4/PVA-Ag NPs adsorbed and dispersed homogenously but, they aggregated with larger sizes on the AC surface (range from 300 to 600 nm). In addition, desorption resistance of Ag nanoparticles were investigated in distilled water. According to the results AgNPs were not desorbed on the AC surface in distilled water.

Keywords: Activated carbon, adsorption, ligand, silver nanoparticles.

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Authors: Yi-Zhong Weng, Chien-Kang Huang, Yu-Feng Huang, Chi-Yuan Yu, Darby Tien-Hao Chang

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Search for a tertiary substructure that geometrically matches the 3D pattern of the binding site of a well-studied protein provides a solution to predict protein functions. In our previous work, a web server has been built to predict protein-ligand binding sites based on automatically extracted templates. However, a drawback of such templates is that the web server was prone to resulting in many false positive matches. In this study, we present a sequence-order constraint to reduce the false positive matches of using automatically extracted templates to predict protein-ligand binding sites. The binding site predictor comprises i) an automatically constructed template library and ii) a local structure alignment algorithm for querying the library. The sequence-order constraint is employed to identify the inconsistency between the local regions of the query protein and the templates. Experimental results reveal that the sequence-order constraint can largely reduce the false positive matches and is effective for template-based binding site prediction.

Keywords: Protein structure, binding site, functional prediction

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Authors: G. V. Novikov, V. S. Sivozhelezov, S. S. Kolesnikov, K. V. Shaitan

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The study reports about the influence of binding of orthosteric ligands as well as point mutations on the conformational dynamics of β-2-adrenoreceptor. Using molecular dynamics simulation we found that there was a little fraction of active states of the receptor in its apo (ligand free) ensemble corresponded to its constitutive activity. Analysis of MD trajectories indicated that such spontaneous activation of the receptor is accompanied by the motion in intracellular part of its alpha-helices. Thus receptor’s constitutive activity directly results from its conformational dynamics. On the other hand the binding of a full agonist resulted in a significant shift of the initial equilibrium towards its active state. Finally, the binding of the inverse agonist stabilized the receptor in its inactive state. It is likely that the binding of inverse agonists might be a universal way of constitutive activity inhibition in vivo. Our results indicate that ligand binding redistribute pre-existing conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux-Model) of the receptor rather than cause induced fit in it. Therefore, the ensemble of biologically relevant receptor conformations is encoded in its spatial structure, and individual conformations from that ensemble might be used by the cell in conformity with the physiological behavior.

Keywords: Seven-transmembrane receptors, constitutive activity, activation, x-ray crystallography, principal component analysis, molecular dynamics simulation.

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Authors: M. K. Holst, P. H. Kirkegaard, L. D. Christoffersen

Abstract:

Present paper presents a parametric performancebased design model for optimizing hospital design. The design model operates with geometric input parameters defining the functional requirements of the hospital and input parameters in terms of performance objectives defining the design requirements and preferences of the hospital with respect to performances. The design model takes point of departure in the hospital functionalities as a set of defined parameters and rules describing the design requirements and preferences.

Keywords: Architectural Layout Design, Hospital Design, Parametric design, Performance-based models.

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Authors: Miyoun Won, Youngkyung Choi

Abstract:

In the meantime, there were lots of hardware solutions like products or urban facilities for crime prevention in the public design area. Meanwhile, people have growing interest in public design so by making a village; community design in public design is getting active by the society. The system for crime prevention is actively done by the citizens who created the community. Regarding the social situation, in this project, we saw it as a kind of community design practices and researched about 'how does community design influence Crime prevention?' The purpose of this study is to propose the community design as a way of preventing the crime in the city. First, we found out about the definition, elements and methods of community design by reviewing the theory. And then, this study analyzed the case that was enforced in Seoul and organize the elements and methods of community design. This study can be refer to Public Design based on civil participation and make the community design area contribute to expand the way of solving social problems.

Keywords: Public Design, Sustainable Community Design, Crime Prevention, Participatory Design.

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Authors: Niloofar Khedri, Masoud Rahgozar, MahmoudReza Hashemi

Abstract:

Design patterns describe good solutions to common and reoccurring problems in program design. Applying design patterns in software design and implementation have significant effects on software quality metrics such as flexibility, usability, reusability, scalability and robustness. There is no standard rule for using design patterns. There are some situations that a pattern is applied for a specific problem and this pattern uses another pattern. In this paper, we study the effect of using chain of patterns on software quality metrics.

Keywords: Design Patterns, Design patterns' Relationship, Software quality Metrics, Software Engineering.

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Authors: Ö. Şenyiğit, A. Çolak

Abstract:

It is of great importance for an architectural student to know the parameters through which he/she can conduct his/her design and makes his/her design effective in architectural education. Therefore; an empirical application study was carried out through the designing activity using the emulation model to support the design and design approaches of architectural students. During the investigation period, studies were done on the basic design elements and principles of the fall semester, and the emulation model, one of the designing methods that constitute the subject of the study, was fictionalized as three phased “recognition-interpretation-application”. As a result of the study, it was observed that when students were given a key method during the design process, their awareness increased and their aspects improved as well.

Keywords: Basic design, design education, design methods, emulation.

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Authors: R. Damaševičius

Abstract:

System-level design based on high-level abstractions is becoming increasingly important in hardware and embedded system design. This paper analyzes meta-design techniques oriented at developing meta-programs and meta-models for well-understood domains. Meta-design techniques include meta-programming and meta-modeling. At the programming level of design process, metadesign means developing generic components that are usable in a wider context of application than original domain components. At the modeling level, meta-design means developing design patterns that describe general solutions to the common recurring design problems, and meta-models that describe the relationship between different types of design models and abstractions. The paper describes and evaluates the implementation of meta-design in hardware design domain using object-oriented and meta-programming techniques. The presented ideas are illustrated with a case study.

Keywords: Design patterns, meta-design, meta-modeling, metaprogramming.

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Authors: S. Choodoung, U. Smutkupt

Abstract:

This study systemizes processes and methods in wooden furniture design that contains uniqueness in function and aesthetics. The study was done by research and analysis for designer-s consideration factors that affect function and production. Therefore, the study result indicates that such factors are design process (planning for design, product specifications, concept design, product architecture, industrial design, production), design evaluation as well as wooden furniture design dependent factors i.e. art (art style; furniture history, form), functionality (the strength and durability, area place, using), material (appropriate to function, wood mechanical properties), joints, cost, safety, and social responsibility. Specifically, all aforementioned factors affect good design. Resulting from direct experience gained through user-s usage, the designer must design the wooden furniture systemically and effectively. As a result, this study selected dinning armchair as a case study with all involving factors and all design process stated in this study.

Keywords: Furniture Design, Function Design, Aesthetic, Wooden Furniture.

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Authors: Chiung-Hui Chen

Abstract:

With the approaching of digital era, various interactive service platforms and systems support human beings- needs in lives by different contents and measures. Design strategies have gradually turned from function-based to user-oriented, and are often customized. In other words, how designers include users- value reaction in creation becomes the goal. Creative design service of interior design requires positive interaction and communication to allow users to obtain full design information, recognize the style and process of personal needs, develop creative service design, lower communication time and cost and satisfy users- sense of achievement. Thus, by constructing a co-design method, based on the communication between interior designers and users, this study recognizes users- real needs and provides the measure of co-design for designers and users.

Keywords: Co-Design, Customized, Design Service, Interactive Genetic Algorithm, Interior Design.

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Authors: Nouf Saad Alnassar, Susan Grant, Ray Holland

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This research study examines cases of Saudi Arabian universities and female academics for work environment issues within the context of design management applications. The study proposes use of design research, ergonomics and systems design thinking to develop the university design which facilitates removal of physical and cognitive barriers for female academics. Review of literature demonstrates that macro and micro ergonomic combined with design management and system design strategies can significantly improve the workplace design for female academics. The university design model would be prepared based on the analyses of primary data obtained from archived documents, participants' observation logs, photo audits, focus groups and semi-structured interviews of currently employed female academics in the selected case universities.

Keywords: Design management, workplace design, university design, ergonomics.

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Authors: Pratap Sriram Sundar, Chandan Chowdhury, Sagar Kamarthi

Abstract:

Nature has perfected her designs over 3.5 billion years of evolution. Research fields such as biomimicry, biomimetics, bionics, bio-inspired computing, and nature-inspired designs have explored nature-made artifacts and systems to understand nature’s mechanisms and intelligence. Learning from nature, the researchers have generated sustainable designs and innovation in a variety of fields such as energy, architecture, agriculture, transportation, communication, and medicine. Axiomatic design offers a method to judge if a design is good. This paper analyzes design aspects of one of the nature’s amazing object: chicken egg. The functional requirements (FRs) of components of the object are tabulated and mapped on to nature-chosen design parameters (DPs). The ‘independence axiom’ of the axiomatic design methodology is applied to analyze couplings and to evaluate if eggs’ design is good (i.e., uncoupled design) or bad (i.e., coupled design). The analysis revealed that eggs design is a good design, i.e., uncoupled design. This approach can be applied to any nature’s artifacts to judge whether their design is a good or a bad. This methodology is valuable for biomimicry studies. This approach can also be a very useful teaching design consideration of biology and bio-inspired innovation.

Keywords: Uncoupled design, axiomatic design, nature design, design evaluation.

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Authors: Mohammad Rajabalinejad

Abstract:

Safety is often seen as a requirement or a performance indicator through the design process, and this does not always result in optimally safe products or systems. This paper suggests integrating the best safety practices with the design process to enrich the exploration experience for designers and add extra values for customers. For this purpose, the commonly practiced safety standards and design methods have been reviewed and their common blocks have been merged forming Safety Cube. Safety Cube combines common blocks for design, hazard identification, risk assessment and risk reduction through an integral approach. An example application presents the use of Safety Cube for design of machinery.

Keywords: Safety, safety cube, design, product, system, machinery.

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Authors: D. Barron, M. Zeegers

Abstract:

In this paper, we argue that Design research is basic to countries- national productivity and competition agendas at the same time that vagaries of research training presents as one of the barriers faced by Design Higher Degree by Research students in engaging those agendas. We argue that, given industry requirements for research-trained recruits, students have the right to expect that research training will provide the foundations of a successful career on an academic or research pathway or a professional pathway, but that universities have yet to address problems in their provision of research training for Design doctoral students. We suggest that to facilitate this, rigorous research conducted on the provision of Doctoral programs in Design would serve to inform future activities in Design research in productive ways.

Keywords: Design, Doctoral Design Education, Research Training

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Authors: Yue Hu, Xilu Zhao, Takao Yamaguchi, Manabu Sasajima, Yoshio Koike, Akira Hara

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This study optimized the design parameters of a cone loudspeaker as an example of high flexibility of the product design. We developed an acoustic analysis software program that considers the impact of damping caused by air viscosity. In sound reproduction, it is difficult to optimize each parameter of the loudspeaker design. To overcome the limitation of the design problem in practice, this study presents an acoustic analysis algorithm to optimize the design parameters of the loudspeaker. The material character of cone paper and the loudspeaker edge were the design parameters, and the vibration displacement of the cone paper was the objective function. The results of the analysis showed that the design had high accuracy as compared to the predicted value. These results suggested that although the parameter design is difficult, with experience and intuition, the design can be performed easily using the optimized design found with the acoustic analysis software.

Keywords: Air viscosity, design parameters, loudspeaker, optimization.

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Authors: Samrand Rashahmadi, Morteza Abbaszadeh, Sana Hoseyni, Raziyeh Alizadeh

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Design of a constant chord propeller is presented in this paper in order to reduce propeller-s design procedure-s costs. The design process was based on Lock and Goldstein-s techniques of propeller design and analysis. In order to calculate optimum chord of propeller, chord of a referential element is generalized as whole blades chord. The design outcome which named CS-X-1 is modeled & analyzed by CFD methods using K-ε: R.N.G turbulence model. Convergence of results of two codes proved that outcome results of design process are reliable. Design result is a two-blade propeller with a total diameter of 1.1 meter, radial velocity of 3000 R.P.M, efficiency above .75 and power coefficient near 1.05.

Keywords: Single rotating propeller, Design, C.F.D. test, constant chord

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Authors: Lisa M. Weltzer-Ward, Abbie Brown

Abstract:

The sequence Analyze, Design, Develop, Implement, and Evaluate (ADDIE) provides a powerful methodology for designing computer-based educational materials. Helping students to understand this design process sequence may be achieved by providing them with direct, guided experience. This article examines such help and guidance and the overall learning process from a student-s personal experience.

Keywords: ADDIE, education, instructional design, web design.

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Authors: Su Thet Mon Than, Khin Aung Lin, Mi Sandar Mon

Abstract:

This paper is intended to assist anyone with some general technical experience, but perhaps limited specific knowledge of heat transfer equipment. A characteristic of heat exchanger design is the procedure of specifying a design, heat transfer area and pressure drops and checking whether the assumed design satisfies all requirements or not. The purpose of this paper is how to design the oil cooler (heat exchanger) especially for shell-and-tube heat exchanger which is the majority type of liquid-to-liquid heat exchanger. General design considerations and design procedure are also illustrated in this paper and a flow diagram is provided as an aid of design procedure. In design calculation, the MatLAB and AutoCAD software are used. Fundamental heat transfer concepts and complex relationships involved in such exchanger are also presented in this paper. The primary aim of this design is to obtain a high heat transfer rate without exceeding the allowable pressure drop. This computer program is highly useful to design the shell-and-tube type heat exchanger and to modify existing deign.

Keywords: Shell-and-Tube Heat Exchanger, MatLAB and AutoCAD

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Authors: Shian Wan, Yi-Chang Wang, Yu-Chien Lin

Abstract:

This research discussed the various theories of service design, the importance of service design methodology, and the development of transformative service design framework. In this study, transformative service design is applied while building a new brand community service for women, children and infants retailing business. The goal is to enhance the brand recognition and customer loyalty, effectively increase the brand community engagement by embedding the brand community in social network and ultimately, strengthen the impact and the value of the company brand.

Keywords: Service design, transformative service design, brand community.

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Authors: Didier Casner, Jean Renaud, Remy Houssin, Dominique Knittel

Abstract:

In this paper, a novel approach for the multidisciplinary design optimization (MDO) of complex mechatronic systems. This approach, which is a part of a global project aiming to include the MDO aspect inside an innovative design process. As a first step, the paper considers the MDO as a redesign approach which is limited to the parametric optimization. After defining and introducing the different keywords, the proposed method which is based on the V-Model which is commonly used in mechatronics.

Keywords: mechatronics, Multidisciplinary Design Optimization (MDO), multiobjective optimization, engineering design.

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Authors: Ivayla Trifonova, Naoum Jamous, Holger Schrödl

Abstract:

A good web design is a prerequisite for a successful business nowadays, especially since the internet is the most common way for people to inform themselves. Web design includes the optical composition, the structure, and the user guidance of websites. The importance of each website leads to the question if there is a way to measure its usefulness. The aim of this paper is to suggest a methodology for the evaluation of web design. The desired outcome is to have an evaluation that is concentrated on a specific website and its target group.

Keywords: Evaluation methodology, factor analysis, target group, web design.

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Authors: Yuan-Jye Tseng, Yi-Shiuan Chen

Abstract:

The paper presented a sustainable design model for integrated evaluation of the design and supply chain of a product for the sustainable objectives. To design a product, there can be alternative ways to assign the detailed specifications to fulfill the same design objectives. In the design alternative cases, different material and manufacturing processes with various supply chain activities may be required for the production. Therefore, it is required to evaluate the different design cases based on the sustainable objectives. In this research, a closed-loop design model is developed by integrating the forward design model and reverse design model. From the supply chain point of view, the decisions in the forward design model are connected with the forward supply chain. The decisions in the reverse design model are connected with the reverse supply chain considering the sustainable objectives. The purpose of this research is to develop a mathematical model for analyzing the design cases by integrated evaluating the criteria in the closed-loop design and the closed-loop supply chain. The decision variables are built to represent the design cases of the forward design and reverse design. The cost parameters in a forward design include the costs of material and manufacturing processes. The cost parameters in a reverse design include the costs of recycling, disassembly, reusing, remanufacturing, and disposing. The mathematical model is formulated to minimize the total cost under the design constraints. In practical applications, the decisions of the mathematical model can be used for selecting a design case for the purpose of sustainable design of a product. An example product is demonstrated in the paper. The test result shows that the sustainable design model is useful for integrated evaluation of the design and the supply chain to achieve the sustainable objectives.

Keywords: Closed-loop design, closed-loop supply chain, design evaluation, mathematical model, supply chain management, sustainable design model.

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Authors: Arun Kumar V.A., Keshav Mohan

Abstract:

Adenylate kinase (AK) catalyse the phosphotransferase reaction plays an important role in cellular energy homeostasis. The inhibitors of bacterial AK are useful in the treatment of several bacterial infections. To the novel inhibitors of AK, docking studies performed by using the 3D structure of Bacillus stearothermophilus adenylate kinase from protein data bank (IZIP). 46 Quinoxaline analogues were docked in 1ZIP and selected the highly interacting compounds based on their binding energies, for further studies

Keywords: Kinase, quinoxaline, homeostasis, inhibitor, nucleotide.

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Authors: Petri Solanti, Russell Klein

Abstract:

Many designers are asking for an automated path from an abstract mathematical MATLAB model to a high-quality Register-Transfer Level (RTL) hardware description. Manual transformations of MATLAB or intermediate code are needed, when the design abstraction is changed. Design conversion is problematic as it is multidimensional and it requires many different design steps to translate the mathematical representation of the desired functionality to an efficient hardware description with the same behavior and configurability. Yet, a manual model conversion is not an insurmountable task. Using currently available design tools and an appropriate design methodology, converting a MATLAB model to efficient hardware is a reasonable effort. This paper describes a simple and flexible design methodology that was developed together with several design teams.

Keywords: Design methodology, high-level synthesis, MATLAB, verification.

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Authors: Melike Taşcıoğlu

Abstract:

This paper aims to combine film-editing principles with basic design principles to explore what graphic designers do in terms of storytelling. The sequential aspect of film is designed and examined through the art of editing. Examining the rules, principles and formulas of film editing can be a used as a method by graphic designers to further practice the art of storytelling. There are many publications and extensive research on design basics; however, time, pace, dramatic structure and choreography are not very well defined in the area of graphic design. In this era of creative storytelling and interdisciplinary collaboration, not only film editors, but also graphic designers and students of art and design should understand the theory and practice of editing to be able to create a strong mise-en-scène and not only a mise-en-page.

Keywords: Design principles, editing principles, editorial design, film editing, graphic design, storytelling.

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Authors: Kazuhide Sugiyama, Hiroshi Osada

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Lately management strategy that put Industrial Design (ID) in its core is recognized more important, as technology and price alone cannot differentiate a product. The needs to shorten the time to develop a product also shorten the development period of ID, and it necessitates the ID process management. This research analyzes the status of integration process of ID and Engineering Design (ED) of office equipment that requires the collaboration of ID and ED to clarify the issues for the efficiency of the development and to propose solutions.

Keywords: Industrial Design (ID), Engineering Design (ED), Integration process, Office equipment

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