Search results for: RNA folding

Authors: A. Niknejad, G. H. Liaghat, A. H. Behravesh, H. Moslemi Naeini

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In this paper, a theoretical formula is presented to predict the instantaneous folding force of the first fold creation in a square column under axial loading. Calculations are based on analysis of “Basic Folding Mechanism" introduced by Wierzbicki and Abramowicz. For this purpose, the sum of dissipated energy rate under bending around horizontal and inclined hinge lines and dissipated energy rate under extensional deformations are equated to the work rate of the external force on the structure. Final formula obtained in this research, reasonably predicts the instantaneous folding force of the first fold creation versus folding distance and folding angle and also predicts the instantaneous folding force instead of the average value. Finally, according to the calculated theoretical relation, instantaneous folding force of the first fold creation in a square column was sketched versus folding distance and was compared to the experimental results which showed a good correlation.

Keywords: Instantaneous force, Folding force, Honeycomb, Square column.

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Authors: A. Niknejad, G. H. Liaghat, A. H. Behravesh, H. Moslemi Naeini

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In this paper, a semi empirical formula is presented based on the experimental results to predict the first pick (maximum force) value in the instantaneous folding force- axial distance diagram of a square column. To achieve this purpose, the maximum value of the folding force was assumed to be a function of the average folding force. Using the experimental results, the maximum value of the force necessary to initiate the first fold in a square column was obtained with respect to the geometrical quantities and material properties. Finally, the results obtained from the semi empirical relation in this paper, were compared to the experimental results which showed a good correlation.

Keywords: Honeycomb, folding force, square column, aluminum, axial loading.

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Authors: Mohd A. Mezher, Maysam F. Abbod

Abstract:

Genetic Folding (GF) a new class of EA named as is introduced for the first time. It is based on chromosomes composed of floating genes structurally organized in a parent form and separated by dots. Although, the genotype/phenotype system of GF generates a kernel expression, which is the objective function of superior classifier. In this work the question of the satisfying mapping-s rules in evolving populations is addressed by analyzing populations undergoing either Mercer-s or none Mercer-s rule. The results presented here show that populations undergoing Mercer-s rules improve practically models selection of Support Vector Machine (SVM). The experiment is trained multi-classification problem and tested on nonlinear Ionosphere dataset. The target of this paper is to answer the question of evolving Mercer-s rule in SVM addressed using either genetic folding satisfied kernel-s rules or not applied to complicated domains and problems.

Keywords: Genetic Folding, GF, Evolutionary Algorithms, Support Vector Machine, Genetic Algorithm, Genetic Programming, Multi-Classification, Mercer's Rules

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Authors: Abd Elrahman Elgamala, N. Darwish, I. Bondouk, Sh. Hamada

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Available experimental angular distributions for ⁶Li elastically scattered from ¹⁶O nucleus in the energy range 13.0–50.0 MeV are investigated and reanalyzed using optical model of the conventional phenomenological potential and also using double folding optical model of different interaction models: DDM3Y1, CDM3Y1, CDM3Y2, and CDM3Y3. All the involved models of interaction are of M3Y Paris except DDM3Y1 which is of M3Y Reid and the main difference between them lies in the different values for the parameters of the incorporated density distribution function F(ρ). We have extracted the renormalization factor N_R for ⁶Li+¹⁶O nuclear system in the energy range 13.0–50.0 MeV using the aforementioned interaction models.

Keywords: Elastic scattering, optical model, folding potential, density distribution.

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Authors: Do-Jin Jang, Sung-Ah Kim

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In designing a kinetic façade, it is hard for the designer to make digital models due to its complex geometry with motion. This paper aims to present a methodology of converting a point cloud of a physical model into a single digital model with a certain topology and motion. The method uses a Microsoft Kinect sensor, and color markers were defined and applied to three paper folding-inspired designs. Although the resulted digital model cannot represent the whole folding range of the physical model, the method supports the designer to conduct a performance-oriented design process with the rough physical model in the reduced folding range.

Keywords: Design media, kinetic façades, tangible user interface, 3D scanning.

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Authors: Ahmed H. Amer, A. Amar, Sh. Hamada, I. I. Bondouk, F. A. El-Hussiny

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Elastic scattering of α-particles from 9Be and 11B nuclei at different alpha energies have been analyzed. Optical model parameters (OMPs) of α-particles elastic scattering by these nuclei at different energies have been obtained. In the present calculations, the real part of the optical potential are derived by folding of nucleonnucleon (NN) interaction into nuclear matter density distribution of the projectile and target nuclei using computer code FRESCO. A density-dependent version of the M3Y interaction (CDM3Y6), which is based on the G-matrix elements of the Paris NN potential, has been used. Volumetric integrals of the real and imaginary potential depth (JR, JW) have been calculated and found to be energy dependent. Good agreement between the experimental data and the theoretical predictions in the whole angular range. In double folding (DF) calculations, the obtained normalization coefficient Nr is in the range 0.70–1.32.

Keywords: Elastic scattering of α-particles, optical model parameters, double folding model, nucleon-nucleon interaction.

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Authors: Sh. Hamada

Abstract:

The current work aims to study the rainbow like-structure observed in the elastic scattering of alpha particles on both ¹²C and ¹⁶O nuclei. We reanalyzed the experimental elastic scattering angular distributions data for α+¹²C and α+¹⁶O nuclear systems at different energies using both optical model and double folding potential of different interaction models such as: CDM3Y1, DDM3Y1, CDM3Y6 and BDM3Y1. Potential created by BDM3Y1 interaction model has the shallowest depth which reflects the necessity to use higher renormalization factor (N_r). Both optical model and double folding potential of different interaction models fairly reproduce the experimental data.

Keywords: Nuclear rainbow, elastic scattering, optical model, double folding, density distribution.

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Authors: Ahmed H. Amer, A. Amar, Sh. Hamada, I. I. Bondouk

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Elastic scattering of Protons and deuterons from ¹¹B nuclei at different p, d energies have been analyzed within the framework of optical model code (ECIS88). The elastic scattering of ³He+¹¹B nuclear system at different ³He energies have been analyzed using double folding model code (FRESCO). The real potential obtained from the folding model was supplemented by a phenomenological imaginary potential, and during the fitting process the real potential was normalized and the imaginary potential optimized. Volumetric integrals of the real and imaginary potential depths (J_R, J_W) have been calculated for ³He+¹¹B system. The agreement between the experimental data and the theoretical calculations in the whole angular range is fairly good. Normalization factor N_r is calculated in the range between 0.70 and 1.236.

Keywords: Elastic scattering, optical model parameters, double folding model, nuclear density distribution.

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Authors: Pedro Pablo González Pérez, Hiram I. Beltrán, Arturo Rojo-Domínguez, Máximo EduardoSánchez Gutiérrez

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Multi-agent system approach has proven to be an effective and appropriate abstraction level to construct whole models of a diversity of biological problems, integrating aspects which can be found both in "micro" and "macro" approaches when modeling this type of phenomena. Taking into account these considerations, this paper presents the important computational characteristics to be gathered into a novel bioinformatics framework built upon a multiagent architecture. The version of the tool presented herein allows studying and exploring complex problems belonging principally to structural biology, such as protein folding. The bioinformatics framework is used as a virtual laboratory to explore a minimalist model of protein folding as a test case. In order to show the laboratory concept of the platform as well as its flexibility and adaptability, we studied the folding of two particular sequences, one of 45-mer and another of 64-mer, both described by an HP model (only hydrophobic and polar residues) and coarse grained 2D-square lattice. According to the discussion section of this piece of work, these two sequences were chosen as breaking points towards the platform, in order to determine the tools to be created or improved in such a way to overcome the needs of a particular computation and analysis of a given tough sequence. The backwards philosophy herein is that the continuous studying of sequences provides itself important points to be added into the platform, to any time improve its efficiency, as is demonstrated herein.

Keywords: multi-agent systems, blackboard-based agent architecture, bioinformatics framework, virtual laboratory, protein folding.

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Authors: A. E. El-Ahmady, M. Abu-Saleem

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The purpose of this paper is to give a combinatorial characterization and construct representations of the chaotic fundamental groups of the chaotic submanifolds of chaotic flat space by using some geometrical transformations. The chaotic homotopy groups of the limit folding for chaotic flat space are presented. The chaotic fundamental groups of some types of chaotic geodesics in chaotic flat space are deduced.

Keywords: Chaotic flat space, Chaotic folding, Chaotic retractions, Chaotic fundamental groups.

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Authors: Hiram I. Beltrán, Arturo Rojo-Domínguez, Máximo Eduardo Sánchez Gutiérrez, Pedro Pablo González Pérez

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A computational platform is presented in this contribution. It has been designed as a virtual laboratory to be used for exploring optimization algorithms in biological problems. This platform is built on a blackboard-based agent architecture. As a test case, the version of the platform presented here is devoted to the study of protein folding, initially with a bead-like description of the chain and with the widely used model of hydrophobic and polar residues (HP model). Some details of the platform design are presented along with its capabilities and also are revised some explorations of the protein folding problems with different types of discrete space. It is also shown the capability of the platform to incorporate specific tools for the structural analysis of the runs in order to understand and improve the optimization process. Accordingly, the results obtained demonstrate that the ensemble of computational tools into a single platform is worthwhile by itself, since experiments developed on it can be designed to fulfill different levels of information in a self-consistent fashion. By now, it is being explored how an experiment design can be useful to create a computational agent to be included within the platform. These inclusions of designed agents –or software pieces– are useful for the better accomplishment of the tasks to be developed by the platform. Clearly, while the number of agents increases the new version of the virtual laboratory thus enhances in robustness and functionality.

Keywords: genetic algorithms, multi-agent systems, bioinformatics, optimization, protein folding, structural biology.

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Authors: A. Breda, C. Cruz

Abstract:

The Japanese art of origami provides a rich context for designing exploratory mathematical activities for children and young people. By folding a simple sheet of paper, fascinating and surprising planar and spatial configurations emerge. Equally surprising is the unfolding process, which also produces striking patterns. The procedure of folding, unfolding, and folding again allows the exploration of interesting geometric patterns. When adequately and systematically done, we may deduce some of the mathematical rules ruling origami. As the child/youth folds the sheet of paper repeatedly, he can physically observe how the forms he obtains are transformed and how they relate to the pattern of the corresponding unfolding, creating space for the understanding/discovery of mathematical principles regulating the folding-unfolding process. As part of a 2023 Summer Academy organized by a Portuguese university, a session entitled “Folding, Thinking and Generalizing” took place. 23 students attended the session, all enrolled in the 2nd cycle of Portuguese Basic Education and aged between 10 and 12 years old. The main focus of this session was to foster the development of critical cognitive and socio-emotional skills among these young learners, using origami. These skills included creativity, critical analysis, mathematical reasoning, collaboration, and communication. Employing a qualitative, descriptive, and interpretative analysis of data, collected during the session through field notes and students’ written productions, our findings reveal that structured origami-based activities not only promote student engagement with mathematical concepts in a playful and interactive but also facilitate the development of socio-emotional skills, which include collaboration and effective communication between participants. This research highlights the value of integrating origami into educational practices, highlighting its role in supporting comprehensive cognitive and emotional learning experiences.

Keywords: Active learning, hands-on activities, origami, creativity, critical thinking.

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Authors: M. Zarei Mahmoudabadi, M. Sadighi

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In the study of honeycomb crushing under quasistatic loading, two parameters are important, the mean crushing stress and the wavelength of the folding mode. The previous theoretical models did not consider the true cylindrical curvature effects and the flow stress in the folding mode of honeycomb material. The present paper introduces a modification on Wierzbicki-s model based on considering two above mentioned parameters in estimating the mean crushing stress and the wavelength through implementation of the energy method. Comparison of the results obtained by the new model and Wierzbicki-s model with existing experimental data shows better prediction by the model presented in this paper.

Keywords: Crush strength, Flow stress, Honeycomb, Quasistatic load.

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Authors: A. Amar, N. Burtebayev, Sh. Hamada, Kerimkulov Zhambul, N. Amangieldy

Abstract:

Analysis of the elastic scattering of protons on 6,7Li nuclei has been done in the framework of the optical model at the beam energies up to 50 MeV. Differential cross sections for the 6,7Li + p scattering were measured over the proton laboratory–energy range from 400 to 1050 keV. The elastic scattering of 6,7Li+p data at different proton incident energies have been analyzed using singlefolding model. In each case the real potential obtained from the folding model was supplemented by a phenomenological imaginary potential, and during the fitting process the real potential was normalized and the imaginary potential optimized. Normalization factor NR is calculated in the range between 0.70 and 0.84.

Keywords: scattering of protons on 6, 7Li nuclei, Esis88 Codesingle-folding model, phenomenological.

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Authors: N. Burtebayev, Sh. Hamada, Zh. Kerimkulov, D. K. Alimov, A. V. Yushkov, N. Amangeldi, A. N. Bakhtibaev

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The main aim of the current work is to examine if 14N  is candidate to be clusterized nuclei or not. In order to check this  attendance, we have measured the angular distributions for 14N ion  beam elastically scattered on 12C target nuclei at different low  energies; 17.5, 21, and 24.5MeV which are close to the Coulomb  barrier energy for 14N+12C nuclear system. Study of various transfer  reactions could provide us with useful information about the  attendance of nuclei to be in a composite form (core + valence). The  experimental data were analyzed using two approaches;  Phenomenological (Optical Potential) and semi-microscopic (Double  Folding Potential). The agreement between the experimental data and  the theoretical predictions is fairly good in the whole angular range.

 

Keywords: Deuteron Transfer, Elastic Scattering, Optical Model, Double Folding, Density Distribution.

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Authors: L. J. Fei, D. Sujan

Abstract:

This paper presents the fundamentals of Origami engineering and its application in nowadays as well as future industry. Several main cores of mathematical approaches such as Huzita- Hatori axioms, Maekawa and Kawasaki-s theorems are introduced briefly. Meanwhile flaps and circle packing by Robert Lang is explained to make understood the underlying principles in designing crease pattern. Rigid origami and its corrugation patterns which are potentially applicable for creating transformable or temporary spaces is discussed to show the transition of origami from paper to thick material. Moreover, some innovative applications of origami such as eyeglass, origami stent and high tech origami based on mentioned theories and principles are showcased in section III; while some updated origami technology such as Vacuumatics, self-folding of polymer sheets and programmable matter folding which could greatlyenhance origami structureare demonstrated in Section IV to offer more insight in future origami.

Keywords: Origami, origami application, origami engineering, origami technology, rigid origami.

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Authors: Nurul Bahiyah Ahmad Khairudin, Habibah A Wahab

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A new approach to predict the 3D structures of proteins by combining the knowledge-based method and Molecular Dynamics Simulation is presented on the chicken villin headpiece subdomain (HP-36). Comparative modeling is employed as the knowledge-based method to predict the core region (Ala9-Asn28) of the protein while the remaining residues are built as extended regions (Met1-Lys8; Leu29-Phe36) which then further refined using Molecular Dynamics Simulation for 120 ns. Since the core region is built based on a high sequence identity to the template (65%) resulting in RMSD of 1.39 Å from the native, it is believed that this well-developed core region can act as a 'nucleation center' for subsequent rapid downhill folding. Results also demonstrate that the formation of the non-native contact which tends to hamper folding rate can be avoided. The best 3D model that exhibits most of the native characteristics is identified using clustering method which then further ranked based on the conformational free energies. It is found that the backbone RMSD of the best model compared to the NMR-MDavg is 1.01 Å and 3.53 Å, for the core region and the complete protein, respectively. In addition to this, the conformational free energy of the best model is lower by 5.85 kcal/mol as compared to the NMR-MDavg. This structure prediction protocol is shown to be effective in predicting the 3D structure of small globular protein with a considerable accuracy in much shorter time compared to the conventional Molecular Dynamics simulation alone.

Keywords: 3D model, Chicken villin headpiece subdomain, Molecular dynamic simulation NMR-MDavg, RMSD.

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Authors: Jing Fang, Yao Cui, Mingming Wang, Shengli She, Jianping Yuan

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Wearable robotics is a potential solution in aiding gait rehabilitation of lower limbs dyskinesia patients, such as knee osteoarthritis or stroke afflicted patients. Many wearable robots have been developed in the form of rigid exoskeletons, but their bulk devices, high cost and control complexity hinder their popularity in the field of gait rehabilitation. Thus, the development of a portable, compliant and low-cost wearable robot for gait rehabilitation is necessary. Inspired by Chinese traditional folding fans and balloon inflators, the authors present an inflatable, foldable and variable stiffness knee exosuit (IFVSKE) in this paper. The pneumatic actuator of IFVSKE was fabricated in the shape of folding fans by using thermoplastic polyurethane (TPU) fabric materials. The geometric and mechanical properties of IFVSKE were characterized with experimental methods. To assist the knee joint smartly, an intelligent control profile for IFVSKE was proposed based on the concept of full-cycle energy management of the biomechanical energy during human movement. The biomechanical energy of knee joints in a walking gait cycle of patients could be collected and released to assist the joint motion just by adjusting the inner pressure of IFVSKE. Finally, a healthy subject was involved to walk with and without the IFVSKE to evaluate the assisting effects.

Keywords: Biomechanical energy management, gait rehabilitation, knee exosuit, wearable robotics.

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Authors: Gökhan Silahtaroğlu

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Decision tree algorithms have very important place at classification model of data mining. In literature, algorithms use entropy concept or gini index to form the tree. The shape of the classes and their closeness to each other some of the factors that affect the performance of the algorithm. In this paper we introduce a new decision tree algorithm which employs data (attribute) folding method and variation of the class variables over the branches to be created. A comparative performance analysis has been held between the proposed algorithm and C4.5.

Keywords: Classification, decision tree, split, pruning, entropy, gini.

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Authors: Abhay Asthana, Gyati Shilakari Asthana

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It is the patient compliance and stability in combination with controlled drug delivery and biocompatibility that forms the core feature in present research and development of sustained biodegradable patch formulation intended for wound healing. The aim was to impart sustained degradation, sterile formulation, significant folding endurance, elasticity, biodegradability, bio-acceptability and strength. The optimized formulation comprised of polymers including Hydroxypropyl methyl cellulose, Ethylcellulose, and Gelatin, and Citric Acid PEG Citric acid (CPEGC) triblock dendrimers and active Curcumin. Polymeric mixture dissolved in geometric order in suitable medium through continuous stirring under ambient conditions. With continued stirring Curcumin was added with aid of DCM and Methanol in optimized ratio to get homogenous dispersion. The dispersion was sonicated with optimum frequency and for given time and later casted to form a patch form. All steps were carried out under strict aseptic conditions. The formulations obtained in the acceptable working range were decided based on thickness, uniformity of drug content, smooth texture and flexibility and brittleness. The patch kept on stability using butter paper in sterile pack displayed folding endurance in range of 20 to 23 times without any evidence of crack in an optimized formulation at room temperature (RT) (24 ± 2°C). The patch displayed acceptable parameters after stability study conducted in refrigerated conditions (8±0.2°C) and at RT (24 ± 2°C) up to 90 days. Further, no significant changes were observed in critical parameters such as elasticity, biodegradability, drug release and drug content during stability study conducted at RT 24±2°C for 45 and 90 days. The drug content was in range 95 to 102%, moisture content didn’t exceeded 19.2% and patch passed the content uniformity test. Percentage cumulative drug release was found to be 80% in 12h and matched the biodegradation rate as drug release with correlation factor R2>0.9. The biodegradable patch based formulation developed shows promising results in terms of stability and release profiles.

Keywords: Sustained biodegradation, wound healing, polymeric patch, stability.

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Authors: Mohamed A. Saleem

Abstract:

Using mostly seismic data, this study intends to show some examples of igneous intrusions found in some areas of the Sirt Basin and explore the period of their emplacement as well as the interrelationships between these sills. The study area is located in the south of the Zallah Trough, south-west Sirt basin, Libya. It is precisely between the longitudes 18.35ᵒ E and 19.35ᵒ E, and the latitudes 27.8ᵒ N and 28.0ᵒ N. Based on a variety of criteria that are usually used as marks on the igneous intrusions, 12 igneous intrusions (Sills), have been detected and analysed using 3D seismic data. One or more of the following were used as identification criteria: the high amplitude reflectors paired with abrupt reflector terminations, vertical offsets, or what is described as a dike-like connection, the violation, the saucer form, and the roughness. Because of their laying between the hosting layers, the majority of these intrusions are classified as sills. Another distinguishing feature is the intersection geometry link between some of these sills. Every single sill has given a name just to distinguish the sills from each other such as S-1, S-2, and … S-12. To avoid the repetition of description, the common characteristics and some statistics of these sills are shown in summary tables, while the specific characters that are not common and have been noticed for each sill are shown individually. The sills, S-1, S-2, and S-3, are approximately parallel to one other, with the shape of these sills being governed by the syncline structure of their host layers. The faults that dominated the strata (pre-upper Cretaceous strata) have a significant impact on the sills; they caused their discontinuity, while the upper layers have a shape of anticlines. S-1 and S-10 are the group's deepest and highest sills, respectively, with S-1 seated near the basement's top and S-10 extending into the sequence of the upper cretaceous. The dramatic escalation of sill S-4 can be seen in North-South profiles. The majority of the interpreted sills are influenced and impacted by a large number of normal faults that strike in various directions and propagate vertically from the surface to the basement's top. This indicates that the sediment sequences were existed before the sill’s intrusion, deposited, and that the younger faults occurred more recently. The pre-upper cretaceous unit is the current geological depth for the Sills S-1, S-2 … S-9, while Sills S-10, S-11, and S-12 are hosted by the Cretaceous unit. Over the sills S-1, S-2, and S-3, which are the deepest sills, the pre-upper cretaceous surface has a slightly forced folding, these forced folding is also noticed above the right and left tips of sill S-8 and S-6, respectively, while the absence of these marks on the above sequences of layers supports the idea that the aforementioned sills were emplaced during the early upper cretaceous period.

Keywords: Sirt Basin, Zallah Trough, igneous intrusions, seismic data.

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Authors: A. Amar, N. Burtebayev, Kerimkulov Zhambul, Sh. Hamada, N. Amangeldi

Abstract:

the elastic scattering of protons, deuterons and 3He on 6Li at different incident energies have been analyzed in the framework of the optical model using ECIS88 as well as SPI GENOA codes. The potential parameters were extracted in the phenomenological treatment of measured by us angular distributions and literature data. A good agreement between theoretical and experimental differential cross sections was obtained in whole angular range. Parameters for real part of potential have been also calculated microscopically with singleand double-folding model for the p and d, 3He scattering, respectively, using DFPOT code. For best agreement with experiment the normalization factor N for the potential depth is obtained in the range of 0.7-0.9.

Keywords: Elastic scattering, Esis88 Code single and doublefolding model, phenomenological, DWBA.

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Authors: Ran-Zan Wang, Yao-Ting Lee

Abstract:

This paper proposes a visual cryptography by random grids scheme with identifiable shares. The method encodes an image O in two shares that exhibits the following features: (1) each generated share has the same scale as O, (2) any share singly has noise-like appearance that reveals no secret information on O, (3) the secrets can be revealed by superimposing the two shares, (4) folding a share up can disclose some identification patterns, and (5) both of the secret information and the designated identification patterns are recognized by naked eye without any computation. The property to show up identification patterns on folded shares establishes a simple and friendly interface for users to manage the numerous shares created by VC schemes.

Keywords: Image Encryption, Image Sharing, Secret Sharing, Visual Cryptography.

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Authors: Yuan Zhang

Abstract:

Along with large population and great demands for urban development, Hong Kong serves as a typical high-density city with multiple altitudes, advanced three-dimensional traffic system, rich city open space, etc. This paper contributes to analyzing its complex urban form and evolution mechanism from three aspects of view, separately as time, space and buildings. Taking both horizontal and vertical dimension into consideration, this paper provides a perspective to explore the fascinating process of growing and space folding in the urban form of high-density city, also as a research reference for related high-density urban design.

Keywords: Evolution mechanism, high-density city, Hong Kong, urban form.

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Authors: A. Amar

Abstract:

Analysis of the elastic scattering of protons on ¹⁰B nuclei has been done in the framework of the optical model and single folding model at the beam energies up to 17 MeV. We could enhance the optical potential parameters using Esis88 Code, as well as SPI GENOA Code. Linear relationship between volume real potential (V₀) and proton energy (E_p) has been obtained. Also, surface imaginary potential W_D is proportional to the proton energy (E_p) in the range 0.400 and 17 MeV. The radiative reaction ¹⁰B(p,γ)¹¹C has been analyzed using potential model. A comparison between ¹⁰B(p,γ)¹¹C and ⁶Li(p,γ)⁷Be has been made. Good agreement has been found between theoretical and experimental results in the whole range of energy. The radiative resonance reaction ⁷Li(p,γ)⁸Be has been studied.

Keywords: Elastic scattering of protons on 10B nuclei, optical potential parameters, potential model, radiative reaction.

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Authors: Chyn Liaw, Chun-Wei Tung, Shinn-Jang Ho, Shinn-Ying Ho

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The γ-turns play important roles in protein folding and molecular recognition. The prediction and analysis of γ-turn types are important for both protein structure predictions and better understanding the characteristics of different γ-turn types. This study proposed a physicochemical property-based decision tree (PPDT) method to interpretably predict γ-turn types. In addition to the good prediction performance of PPDT, three simple and human interpretable IF-THEN rules are extracted from the decision tree constructed by PPDT. The identified informative physicochemical properties and concise rules provide a simple way for discriminating and understanding γ-turn types.

Keywords: Classification and regression tree (CART), γ-turn, Physicochemical properties, Protein secondary structure.

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Authors: Musammat F. Nahar, Anna Roujeinikova

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Bacterial molecular chaperone DnaK plays an essential role in protein folding, stress response and transmembrane targeting of proteins. DnaKs from many bacterial species, including Escherichia coli, Salmonella typhimurium and Haemophilus infleunzae are the molecular targets for the insect-derived antimicrobial peptide pyrrhocoricin. Pyrrhocoricin-like peptides bind in the substrate recognition tunnel. Despite the high degree of crossspecies sequence conservation in the substrate-binding tunnel, some bacteria are not sensitive to pyrrhocoricin. This work addresses the molecular mechanism of resistance of Helicobacter pylori DnaK to pyrrhocoricin. Homology modelling, structural and sequence analysis identify a single aminoacid substitution at the interface between the lid and the β-sandwich subdomains of the DnaK substrate-binding domain as the major determinant for its resistance.

Keywords: Helicobacter pylori, molecular chaperone DnaK, pyrrhocoricin, structural biology.

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Authors: T.A. Adegbola, IEA Aghachi, E.R. Sadiku

Abstract:

To investigates the effect of fiberglass clamping process improvement on drape simulation prediction. This has great effect on the mould and the fiber during manufacturing process. This also, improves the fiber strain, the quality of the fiber orientation in the area of folding and wrinkles formation during the press-forming process. Drape simulation software tool was used to digitalize the process, noting the formation problems on the contour sensitive part. This was compared with the real life clamping processes using single and double frame set-ups to observe the effects. Also, restrains are introduced by using clips, and the G-clamps with predetermine revolution to; restrain the fabric deformation during the forming process.The incorporation of clamping and fabric restrain deformation improved on the prediction of the simulation tool. Therefore, for effective forming process, incorporation of clamping process into the drape simulation process will assist in the development of fiberglass application in manufacturing process.

Keywords: clamping, fiberglass, drape simulation, pressforming.

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Authors: M. Michael Gromiha, Kiyonobu Yokota, Kazuhiko Fukui

Abstract:

We have developed an energy based approach for identifying the binding sites and important residues for binding in protein-protein complexes. We found that the residues and residuepairs with charged and aromatic side chains are important for binding. These residues influence to form cation-¤Ç, electrostatic and aromatic interactions. Our observation has been verified with the experimental binding specificity of protein-protein complexes and found good agreement with experiments. The analysis on surrounding hydrophobicity reveals that the binding residues are less hydrophobic than non-binding sites, which suggests that the hydrophobic core are important for folding and stability whereas the surface seeking residues play a critical role in binding. Further, the propensity of residues in the binding sites of receptors and ligands, number of medium and long-range contacts, and influence of neighboring residues will be discussed.

Keywords: Protein-protein interactions, energy based approach;binding sites, propensity, long-range contacts, hydrophobicity

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Authors: Abdulqader M. Mohsen, Ahamad Tajudin Khader, Dhanesh Ramachandram, Abdullatif Ghallab

Abstract:

The physical methods for RNA secondary structure prediction are time consuming and expensive, thus methods for computational prediction will be a proper alternative. Various algorithms have been used for RNA structure prediction including dynamic programming and metaheuristic algorithms. Musician's behaviorinspired harmony search is a recently developed metaheuristic algorithm which has been successful in a wide variety of complex optimization problems. This paper proposes a harmony search algorithm (HSRNAFold) to find RNA secondary structure with minimum free energy and similar to the native structure. HSRNAFold is compared with dynamic programming benchmark mfold and metaheuristic algorithms (RnaPredict, SetPSO and HelixPSO). The results showed that HSRNAFold is comparable to mfold and better than metaheuristics in finding the minimum free energies and the number of correct base pairs.

Keywords: Metaheuristic algorithms, dynamic programming algorithms, harmony search optimization, RNA folding, Minimum free energy.

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