• BMB Reports
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• 제31권5호
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• pp.459-467
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• 1998

A new set of functional group interaction energy descriptors relevant to the ACE (Angiotensin-Converting Enzyme) inhibitory peptide, QSAR (Quantitative Structure Activity Relationships), is presented. The functional group interaction energies approximate the charged interactions and distances between functional groups in molecules. The effective energies of the computationally derived geometries are useful parameters for deriving 3D-QSAR models, especially in the absence of experimentally known active site conformation. ACE is a regulatory zinc protease in the renin-angiotensin system. Therapeutic inhibition of this enzyme has proven to be a very effective treatment for the management of hypertension. The non bond interaction energy values among functional groups of six-feature of ACE inhibitory peptides were used as descriptor terms and analyzed for multivariate correlation with ACE inhibition activity. The functional group interaction energy descriptors used in the regression analysis were obtained by a series of inhibitor structures derived from molecular mechanics and semi-empirical calculations. The descriptors calculated using electrostatic and steric fields from the precisely defined functional group were sufficient to explain the biological activity of inhibitor. Application of the descriptors to the inhibition of ACE indicates that the derived QSAR has good predicting ability and provides insight into the mechanism of enzyme inhibition. The method, functional group interaction energy analysis, is expected to be applicable to predict enzyme inhibitory activity of the rationally designed inhibitors.

• Bulletin of the Korean Chemical Society
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• 제35권8호
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• pp.2494-2504
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• 2014

P38 mitogen activated protein (MAP) kinase is an important anti-inflammatory drug target, which can be activated by responding to various stimuli such as stress and immune response. Based on the conformation of the conserved DFG loop (in or out), binding inhibitors are termed as type-I and II. Type-I inhibitors are ATP competitive, whereas type-II inhibitors bind in DFG-out conformation of allosteric pocket. It remains unclear that how these allosteric inhibitors stabilize the DFG-out conformation and interact. Organosilicon compounds provide unusual opportunity to enhance potency and diversity of drug molecules due to their low toxicity. However, very few examples have been reported to utilize this property. In this regard, we performed docking of an inhibitor (BIRB) and its silicon analog (Si-BIRB) in an allosteric binding pocket of p38. Further, molecular dynamics (MD) simulations were performed to study the dynamic behavior of the simulated complexes. The difference in the biological activity and mechanism of action of the simulated inhibitors could be explained based on the molecular mechanics/generalized Born surface area (MM/GBSA) binding free energy per residue decomposition. MM/GBSA showed that biological activities were related with calculated binding free energy of inhibitors. Analyses of the per-residue decomposed energy indicated that van der Waals and non-polar interactions were predominant in the ligand-protein interactions. Further, crucial residues identified for hydrogen bond, salt bridge and hydrophobic interactions were Tyr35, Lys53, Glu71, Leu74, Leu75, Ile84, Met109, Leu167, Asp168 and Phe169. Our results indicate that stronger hydrophobic interaction of Si-BIRB with the binding site residues could be responsible for its greater binding affinity compared with BIRB.

• 터널과지하공간
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• 제25권3호
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• pp.293-302
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• 2015

박층 뿜칠 라이너(TSL)는 숏크리트와 철망을 대체하는 새로운 암반 지보재로서 고려되고 있다. 하지만 아직까지 TSL의 핵심 제작기술이 공개되지 않은 관계로 독자적인 TSL 개발이 요구되고 있다. 따라서 본 연구에는 TSL의 개발을 위한 첫 번째 단계로서, 2가지의 경제적인 분말형 TSL 시작품 배합조건들을 도출하였고 이들을 액상 및 분말 재료가 혼합되는 2성분 외국산 TSL의 역학적 성능들과 실험적으로 비교하였다. 실험결과, 1가지 TSL 시작품 배합조건은 파괴 시의 신장률이 낮게 나타나 지보재로서의 활용이 어려운 것으로 나타났으나, 나머지 TSL 시작품 배합조건은 기존 외국산 TSL보다 큰 인장강도와 부착강도를 발현하는 등 우수한 성능을 나타내었으며 유럽 EFNARC(2008)의 모든 성능기준을 만족하여 지보재로서 활용이 가능한 것으로 검증되었다. 단, 외국산 2성분 TSL과 비교할 때 TSL 시작품의 연성을 추가적으로 향상시키기 위한 보완이 필요한 것으로 나타났다.

• 한국전산구조공학회논문집
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• 제27권2호
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• pp.87-94
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• 2014

페리다이나믹 이론은 재료파괴 및 균열진전 해석에 적합하다. 그러나 적분 방정식을 풀기위해 많은 비국부 상호작용을 해석해야만 하기 때문에 일반적으로 사용되는 국부 모델들에 비해 비효율적이다. 따라서 효율적이면서 정확한 해석 모델을 구성하기 위해 페리다이나믹 모델과 다른 국부 모델을 연성하는 연성 해석법의 개발이 필요하다. 연성 방법론 개발을 위해서는 불연속성 혹은 응력 집중이 발생될 것으로 예상되는 영역에는 페리다이나믹 모델을 구성하고 상대적으로 변형 거동이 복잡하지 않은 영역은 국부 모델을 구성하는 방법이 많이 사용된다. 본 연구에서는 최근에 개발된 힘-기반 연성 방법론을 소개한다. 이 방법론에서는 블랜딩 함수를 활용하여 연성 영역을 사이에 두고 페리다이나믹 모델과 탄성체 모델을 연성한다. 수치예제를 통해 연성 모델이 집중하중 해석 혹은 정적파괴 해석 문제를 효율적이고 엄밀하게 해석할 수 있음을 확인하였다. 이와 같은 문제들은 일반적인 탄성체 모델을 사용해서는 엄밀한 해석이 어렵다. 반면에 페리다이나믹 모델은 엄밀한 해석이 가능하지만 계산 시간과 비용이 매우 많이 요구된다는 문제점이 있다.

• Structural Engineering and Mechanics
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• 제75권6호
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• pp.643-657
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• 2020

This study presents experimental and numerical investigations on circular steel tube confined ultra high performance concrete (UHPC) columns under axial compression. The plain UHPC without fibers was designed to achieve a compressive strength ranged between 150 MPa and 200 MPa. Test results revealed that loading on only the UHPC core can generate a significant confinement effect for the UHPC core, thus leading to an increase in both strength and ductility of columns, and restricting the inherent brittleness of unconfined UHPC. All tested columns failed by shear plane failure of the UHPC core, this causes a softening stage in the axial load versus axial strain curves. In addition, an increase in the steel tube thickness or the confinement index was found to increase the strength and ductility enhancement and to reduce the magnitude of the loss of load capacity. Besides, steel tube with higher yield strength can improve the post-peak behavior. Based on the test results, the load contribution of the steel tube and the concrete core to the total load was examined. It was found that no significant confinement effect can be developed before the peak load, while the ductility of post-peak stage is mainly affected by the degree of the confinement effect. A finite element model (FEM) was also constructed in ABAQUS software to validate the test results. The effect of bond strength between the steel tube and the UHPC core was also investigated through the change of friction coefficient in FEM. Furthermore, the mechanism of circular steel tube confined UHPC columns was examined using the established FEM. Based on the results of FEM, the confining pressures along the height of each modeled column were shown. Furthermore, the interaction between the steel tube and the UHPC core was displayed through the slip length and shear stresses between two surfaces of two materials.

• Structural Engineering and Mechanics
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• 제78권3호
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• pp.231-253
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• 2021

Pure bending loading conditions are not frequently occurred in practical engineering, but the flexural researches are important since it's the basis of mechanical property researches under complex loading. Hence, the objective of this paper is to investigate the flexural behavior of concrete-filled rectangular steel tube (CFRT) through combined experimental and numerical studies. Flexural tests were conducted to investigate the mechanical performance of CFRT under bending. The load vs. deflection curves during the loading process was analyzed in detail. All the specimens behaved in a very ductile manner. Besides, based on the experimental result, the composite action between the steel tube and core concrete was studies and examined. Furthermore, the feasibility and accuracy of the numerical method was verified by comparing the computed results with experimental observations. The full curves analysis on the moment vs. curvature curves was further conducted, where the development of the stress and strain redistribution in the steel tube and core concrete was clarified comprehensively. It should be noted that there existed bond slip between the core concrete and steel tube during the loading process. And then, an extensive parametric study, including the steel strength, concrete strength, steel ratio and aspect ratio, was performed. Finally, design formula to calculate the ultimate moment and flexural stiffness of CFRTs were presented. The predicted results showed satisfactory agreement with the experimental and FE results. Additionally, the difference between the experimental/FE and predicted results using the related design codes were illustrated.

• Advances in nano research
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• 제7권1호
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• pp.39-49
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• 2019

This paper focuses on two main objectives. The first one is to exploit an energy equivalent model and finite element method to evaluate the equivalent Young's modulus of single walled carbon nanotubes (SWCNTs) at any orientation angle by using tensile test. The calculated Young's modulus is validated with published experimental results. The second target is to exploit the finite element simulation to investigate mechanical buckling and natural frequencies of SWCNTs. Energy equivalent model is presented to describe the atomic bonding interactions and their chemical energy with mechanical structural energies. A Program of Nanotube modeler is used to generate a geometry of SWCNTs structure by defining its chirality angle, overall length of nanotube and bond length between two adjacent nodes. SWCNTs are simulated as a frame like structure; the bonds between each two neighboring atoms are treated as isotropic beam members with a uniform circular cross section. Carbon bonds is simulated as a beam and the atoms as nodes. A finite element model using 3D beam elements is built under the environment of ANSYS MAPDL environment to simulate a tensile test and characterize equivalent Young's modulus of whole CNT structure. Numerical results are presented to show critical buckling loads, axial and transverse natural frequencies of SWCNTs with different orientation angles and lengths. The understanding of mechanical behaviors of CNTs are essential in developing such structures due to their great potential in wide range of engineering applications.

• Structural Engineering and Mechanics
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• 제78권2호
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• pp.163-174
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• 2021

Track-bridge interaction has become an essential part in the design of bridges and rails in terms of modern railways. As a unique ballastless slab track, the longitudinal continuous slab track (LCST) or referred to as the China railway track system Type-II (CRTS II) slab track, demonstrates a complex force mechanism. Therefore, a comprehensive track-bridge interaction study between multi-span simply supported beam bridges and the LCST is presented in this work. In specific, we have developed an integrated finite element model to investigate the overall interaction effects of the LCST-bridge system subjected to the actions of temperature changes, traffic loads, and braking forces. In that place, the deformation patterns of the track and bridge, and the distributions of longitudinal forces and the interfacial shear stress are studied. Our results show that the additional rail stress has been reduced under various loads and the rail's deformation has become much smoother after the transition of the two continuous structural layers of the LCST. However, the influence of the temperature difference of bridges is significant and cannot be ignored as this action can bend the bridge like the traffic load. The uniform temperature change causes the tensile stress of the concrete track structure and further induce cracks in them. Additionally, the influences of the friction coefficient of the sliding layer and the interfacial bond characteristics on the LCST's performance are discussed. The systematic study presented in this work may have some potential impacts on the understanding of the overall mechanical behavior of the LCST-bridge system.

• Structural Engineering and Mechanics
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• 제85권3호
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• pp.337-351
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• 2023

In this paper, the shear behavior of soft filling in rectangular-hollow concrete specimens was simulated using the 2D particle flow code (PFC2D). The laboratory-measured properties were used to calibrate some PFC2D micro-properties for modeling the behavior of geo-materials. The dimensions of prepared and modeled samples were 100 mm×100 mm. Some disc type narrow bands were removed from the central part of the model and different lengths of bridge areas (i.e., the distance between internal tips of two joints) with lengths of 30 mm, 50 mm, and 70 mm were produced. Then, the middle of the rectangular hollow was filled with cement material. Three filling sizes with dimensions of 5 mm×5 mm, 10 mm×5 mm, and 15 mm×5 mm were provided for different modeled samples. The parallel bond model was used to calibrate and re-produce these modeled specimens. Therefore, totally, 9 different types of samples were designed for the shear tests in PFC2D. The shear load was gradually applied to the model under a constant loading condition of 3 MPa (σc/3). The loading was continued till shear failure occur in the modeled concrete specimens. It has been shown that both tensile and shear cracks may occur in the fillings. The shear cracks mainly initiated from the crack (joint) tips and coalesced with another one. The shear displacements and shear strengths were both increased as the filling dimensions increased (for the case of a bridge area with a particular fixed length).

• Structural Engineering and Mechanics
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• 제82권1호
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• pp.121-131
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• 2022

The main goal of this study is to prepare a program for analyzing High Strength Steel Fibrous Reinforced Concrete (HSSFRC) slabs and predict the response and strength of the slab instead of preparing a prototype and testing it in the laboratory. For this purpose, new equations are proposed to represent the material properties of High Strength Steel Fibrous Reinforced Concrete. The proposed equations obtained from performing regression analysis on many experimental results using statistical programs. The finite element method is adopted for non-linear analysis of the slabs. The eight-node "Serendipity element" (3 DoF) is chosen to represent the concrete. The layered approach is adopted for concrete elements and the steel reinforcement is represented by a smeared layer. The compression properties of the concrete are modeled by a work hardening plasticity approach and the yield condition is determined depending on the first two stress invariants. A tensile strength criterion is adopted in order to estimate the cracks propagation. many experimental results for testing slabs are compared with the numerical results of the present study and a good agreement is achieved regarding load-deflection curves and crack pattern. The response of the load deflection curve is slightly stiff at the beginning because the creep effect is not considered in this study and for assuming perfect bond between the steel reinforcement and the concrete, however, a great agreement is achieved between the ultimate load from the present study and experimental results. For the models of the tension stiffening and cracked shear modulus, the value of Bg and Bt (Where Bg and Bt are the curvature factor for the cracked shear modulus and tension stiffening models respectively) equal to 0.005 give good results compared with experimental result.