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Taking advantage of geometry has been always a current base in Iranian traditional architecture for accommodate survey among form, stability and coordination. Recognition of components’ geometrical behavior along organic :union: making’s direction among skeleton, space and background systems causes integrated feedback formation among effective elements in collection’s stability. Based on existing geometrical limitations in their structures and coordination, Iranian girih as modular units are capable of developing in x and y axes by considering visual values and actionable efficiency. According to controlled process of Iranian girih s’ structure in mentioned axes, transferring this discipline in z axis for -3dimensional action’s maintenance of structure collection is also discussed. So, firstly current article has considered usage method of girih geometry productive parameters by Grasshopper graphical coding software, and then resulting collection of various forms from girih geometry is introduced as a population of analyzable genes by genetic algorithm method. Thereby, supports’ optimized location is developed by -3dimentional action among components for reaching an efficient form of girih’s geometry. Adapted to survey, prevalent population of introduced genes collections is selected after simultaneously analysis of form and mechanism by Karamba addition and the most optimized status of supports’ location is selected in circumstances that structure’s components has the minimum stress. Then, the optimized state and organized sample in supports’ location are considered to explore about resulting behavior in both states toward load transferring to case foundation. According to this study results, it can be concluded that by defining certain legislations, geographical mechanism of Iranian girih causes an integrated behavior’s controlling and multi-dimensional action among quality parameters such as cladding structures’ designing and quantity parameters such as proper behavior toward forces. This coordinating feedback between architecture and structure in supports’ optimized location which results from genetic algorithm method, decreases stress in structures’ components and also maximizes structure’s stability besides economic advantage in used materials. So, firstly current article has considered usage method of girih geometry productive parameters by Grasshopper graphical coding software, and then resulting collection of various forms from girih geometry is introduced as a population of analyzable genes by genetic algorithm method. Thereby, supports’ optimized location is developed by -3dimentional action among components for reaching an efficient form of girih’s geometry. Adapted to survey, prevalent population of introduced genes collections is selected after simultaneously analysis of form and mechanism by Karamba addition and the most optimized status of supports’ location is selected in circumstances that structure’s components has the minimum stress. Then, the optimized state and organized sample in supports’ location are considered to explore about resulting behavior in both states toward load transferring to case foundation. According to this study results, it can be concluded that by defining certain legislations, geographical mechanism of Iranian girih causes an integrated behavior’s controlling and multi-dimensional action among quality parameters such as cladding structures’ designing and quantity parameters such as proper behavior toward forces. Based on existing geometrical limitations in their structures and coordination, Iranian girih as modular units are capable of developing in x and y axes by considering visual values and actionable efficiency. According to controlled process of Iranian girih s’ structure in mentioned axes, transferring this discipline in z axis for -3dimensional action’s maintenance of structure collection is also discussed. So, firstly current article has considered usage method of girih geometry productive parameters by Grasshopper graphical coding software, and then resulting collection of various forms from girih geometry is introduced as a population of analyzable genes by genetic algorithm method. Thereby, supports’ optimized location is developed by -3dimentional action among components for reaching an efficient form of girih’sgeometry. Adapted to survey, prevalent population of introduced genes collections is selected after simultaneously analysis of form and mechanism by Karamba addition and the most optimized status of supports’ location is selected in circumstances that structure’s components has the minimum stress. Then, the optimized state and organized sample in supports’ location are considered to explore about resulting behavior in both states toward load transferring to case foundation. According to controlled process of Iranian girih s’ structure in mentioned axes, transferring this discipline in z axis for -3dimensional action’s maintenance of structure collection is also discussed. So, firstly current article has considered usage method of girih geometry productive parameters by Grasshopper graphical coding software, and then resulting collection of various forms from girih geometry is introduced as a population of analyzable genes by genetic algorithm method. Thereby, supports’ optimized location is developed by -3dimentional action among components for reaching an efficient form of girih’s geometry. Adapted to survey, prevalent population of introduced genes collections is selected after simultaneously analysis of form and mechanism by Karamba addition and the most optimized status of supports’ location is selected in circumstances that structure’s components has the minimum stress. Then, the optimized state and organized sample in supports’ location are considered to explore about resulting behavior in both states toward load transferring to case foundation. According to controlled process of Iranian girih s’ structure in mentioned axes, transferring this discipline in z axis for -3dimensional action’s maintenance of structure collection is also discussed. So, firstly current article has considered usage method of girih geometry productive parameters by Grasshopper graphical coding software, and then resulting collection of various forms from girih geometry is introduced as a population of analyzable genes by genetic algorithm method. Thereby, supports’ optimized location is developed by -3dimentional action among components.

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Conformational changes during protein -protein or ligand -protein docking play an important role in the biological processes. These changes involve low frequency collective motions, and normal mode analysis is generally used for finding the frequencies and mode shapes of the proteins. Many studies have been focused on the prediction of these transitions using different protein models. Among them, elastic network models are popular, as they are simple and do not require energy minimization. However, so far no systematic study has been done about considering the effect of different parameters in prediction of these conformational changes. In this study 20 proteins with pre-determined conformational changes were selected and the success and validation of each elastic network model in predicting the bound state were tested. According to the results, the first three modes play the major role in predicting the conformational changes. Moreover, choosing the proper cutoff radius is more effective than the potential function. Results also show that non-exponential models with 10 angestrom cutoff are more accurate in predicting conformational changes, in spite of their simplicity and being less time consuming.

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Many phenomena in molecular biophysics happen over time and length scales that are inaccessible by fully atomistic computer simulations. Therefore, coarse-graining has become a common strategy for bridging the gap in time and length scale between the atomistic simulation and biological processes. Furthermore, in many cases the system dynamics is better represented in terms of collective coordinates. This study is concerned with a rigorous coarse-graining method for dynamics of linear systems using collective coordinates of the resiudes rather than coordinates of individual atoms. In this method an invertible linear time-independent map is considered to relate the original displacements to the collective coordinates. Then, the conformational space of the transformed system is divided into master and slave degrees of freedom. Under the assumption that the masters are slower than the slaves and by expanding the masters’ displacements in Taylor series with respect to time variable, the method results in effective stiffness, friction and mass for the coarse-grained system in terms of collective coordinates of the residues. Center of mass and hydrodynamic center of reaction coordinates of the residues are considered as collective coordinates. Application of the method to finding the relaxation dynamics of various proteins shows that using center of mass coordinates significantly improves the results.