• Title/Summary/Keyword: MD simulations

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Molecular Modeling of Enantio-discrimination of α-Methoxy-α-trifluoromethylphenylacetic Acid (MTPA) by Cyclomaltoheptaose (β-Cyclodextrin) and 6-Amino-6-deoxy-cyclomaltoheptaose

  • Jung, Eun-Kyoung;Jeong, Karp-Joo;Lee, Sang-San;Kim, Jee-In;Jung, Seun-Ho
    • Bulletin of the Korean Chemical Society
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    • v.24 no.11
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    • pp.1627-1631
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    • 2003
  • Molecular modeling was performed to comprehend the chiral recognition of ${\alpha}$-methoxy-${\alpha}$-trifluoromethylphenylacetic acid (MTPA) enantiomers by cyclomaltoheptaose (${\beta}$-cyclodextrin,${\beta}$-CD) and 6-amino-6-deoxy-cyclomaltoheptaose (am-${\beta}$-CD). Monte Carlo (MC) docking coupled to constant temperature molecular dynamics (MD) simulations was applied to the investigation for the ${\alpha}$-methoxy-${\alpha}$-trifluoromethylphenylacetic acid complexation with two different CDs in terms of the relative distribution of the interaction energies. The calculated results are finely correlated with the experimental observations in chiral recognition thermodynamics. Am-${\beta}$-CD as a host showed the superior enantio-discrimination ability to the native ${\beta}$-CD where the amino group of am-${\beta}$-CD was critically involved in enhancing the ability of chiral discrimination via the Coulombic interaction with MTPA.

Processor Allocation Scheme on the Mesh-connected System with Faults (오류가 있는 메쉬 시스템에서의 프로세서 할당 기법)

  • Seo, Kyung-Hee
    • The KIPS Transactions:PartA
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    • v.12A no.4 s.94
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    • pp.281-288
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    • 2005
  • Efficient utilization of processing resources in a large multicomputer system with the possibility of fault occurrence depends on the reliable processor management scheme. This paper presents a dynamic and reliable processor allocation strategy to increase the performance of mesh-connected parallel systems with faulty processors The basic idea is to reconfigure a faulty mesh system into a maximum convex system using the fault-free upper or lower boundary nodes to compensate for the non-boundary faulty nodes. To utilize the non-rectangular shaped system parts, our strategy tries to allocate L-shaped submeshes instead of signaling the allocation failure. Extensive simulations show that the strategy performs more efficiently than other strategies in terms of the job response time md the system utilization.

Direct Instantaneous Torque Control of SRM using 4-level Converter (4-레벨 콘버터를 이용한 SRM의 순시 토오크 제어 기법)

  • Lee, Dong-Hee;Lee, Sang-Hun;Ahn, Jin-Woo
    • The Transactions of the Korean Institute of Power Electronics
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    • v.12 no.3
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    • pp.205-212
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    • 2007
  • This paper presents a direct instantaneous torque control (DITC) of Switched Reluctance Motor (SRM) with a novel 4-level converter to develop a uniform torque and to improve a dynamic performance. The DITC method can reduce a high torque ripple of SRM. Drive efficiency and dynamic performance with conventional drive are low due to a slow excitation current build-up. Since the 4-level converter can obtain an addition boosted voltage to have a fast excitation and demagnetization, it can Improve dynamic performance and efficiency easily. To apply the DITC technique to a 4-level converter, a novel control scheme is presented according to the operating modes. Additionally, selection of capacitances of boosted capacitor and efficiency improvement of 4-level converter are analyzed. At last, the validity of proposed method is verified by some computer simulations md comparative experiments.

Nanofluid flow and heat transfer from heated square cylinder in the presence of upstream rectangular cylinder under Couette-Poiseuille flow

  • Sharma, Swati;Maiti, Dilip K.;Alam, Md. Mahbub;Sharma, Bhupendra K.
    • Wind and Structures
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    • v.29 no.1
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    • pp.65-75
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    • 2019
  • A heated square cylinder (with height $A^*$) is kept parallel to the cold wall at a fixed gap height $0.5A^*$ from the wall. Another adiabatic rectangular cylinder (of same height $A^*$ and width $0.5A^*$) is placed upstream in an inline tandem arrangement. The spacing between the two cylinders is fixed at $3.0A^*$. The inlet flow is taken as Couette-Poiseuille flow based non-linear velocity profile. The conventional fluid (also known as base fluid) is chosen as water (W) whereas the nanoparticle material is selected as $Al_2O_3$. Numerical simulations are performed by using SIMPLE algorithm based Finite Volume approach with staggered grid arrangement. The dependencies of hydrodynamic and heat transfer characteristics of the cylinder on non-dimensional parameters governing the nanofluids and the fluid flow are explored here. A critical discussion is made on the mechanism of improvement/reduction (due to the presence of the upstream cylinder) of heat transfer and drag coefficient, in comparison to those of an isolated cylinder. It is observed that the heat transfer increases with the increase in the non-linearity in the incident velocity profile at the inlet. For the present range studied, particle concentration has a negligible effect on heat transfer.

The evolution of radiation-induced point defects near symmetrical tilt Σ5 (310) <001> grain boundary in pure δ-plutonium: A molecular dynamics study

  • Wang, Yangzhong;Liu, Wenbo;Zhang, Jiahui;Yun, Di;Chen, Piheng
    • Nuclear Engineering and Technology
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    • v.53 no.5
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    • pp.1587-1592
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    • 2021
  • The effects of the symmetrical tilt Σ5 (310) <001> grain boundary (GB) on the evolution of radiation-induced point defects in pure δ-plutonium (Pu) were studied by Molecular dynamics (MD) simulations. The evolution of radiation-induced point defects was obtained when primary knock-on atom (PKA) was respectively set as -15 Å and 15 Å far from the GB and the number of residual defects was obtained as the distance from PKA to GB was changed. According to the results, compared with vacancies, interstitial atoms were more easily absorbed by GB. In addition, the formation energy of point defects was also calculated. The results showed that there was almost no difference for the formation energy of vacancies in the all matrix. However, the formation energy of interstitial atoms close to the GB was lower than that in the other bulk regions.

A Novel Approach for Optimizing Data Distribution in Cloud Computing (클라우드 컴퓨팅에서 데이터 분산 최적화를 위한 방법에 대한 연구)

  • Hung, Pham Phuoc;Islam, Md. Motaharul;Morales, Mauricio A.G.;Aazam, Mohammad;Huh, Eui-Nam
    • Proceedings of the Korea Information Processing Society Conference
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    • 2013.05a
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    • pp.183-186
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    • 2013
  • Modern day despite technology advancements that manufacture a new generation of mobile devices with generous resources, the fact that they can offer only limited processing capacity still remains a painful experience. So far, a number of research studies have been carried out, trying to eliminate problems arising from shortcomings in the connection between thin clients and cloud networks, yet little have been found efficient. In this paper, we present a novel approach, taking advantage of collaboration of thin and thick clients, particularly aiming at optimizing data distribution by splitting data and utilizing cloud computing (CC) resources so that expected Quality-of-Service (QoS) requirements can be met. Moreover, we conduct simulations to evaluate our approach. Our results evaluation shows that our approach has better performance than existing approaches.

TSCH-Based Scheduling of IEEE 802.15.4e in Coexistence with Interference Network Cluster: A DNN Approach

  • Haque, Md. Niaz Morshedul;Koo, Insoo
    • International Journal of Internet, Broadcasting and Communication
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    • v.14 no.1
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    • pp.53-63
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    • 2022
  • In the paper, we propose a TSCH-based scheduling scheme for IEEE 802.15.4e, which is able to perform the scheduling of its own network by avoiding collision from interference network cluster (INC). Firstly, we model a bipartite graph structure for presenting the slot-frame (channel-slot assignment) of TSCH. Then, based on the bipartite graph edge weight, we utilize the Hungarian assignment algorithm to implement a scheduling scheme. We have employed two features (maximization and minimization) of the Hungarian-based assignment algorithm, which can perform the assignment in terms of minimizing the throughput of INC and maximizing the throughput of own network. Further, in this work, we called the scheme "dual-stage Hungarian-based assignment algorithm". Furthermore, we also propose deep learning (DL) based deep neural network (DNN)scheme, where the data were generated by the dual-stage Hungarian-based assignment algorithm. The performance of the DNN scheme is evaluated by simulations. The simulation results prove that the proposed DNN scheme providessimilar performance to the dual-stage Hungarian-based assignment algorithm while providing a low execution time.

A Study on the Prediction of Elastoplastic Behavior of Carbon Nanotube/Polymer Composites (계면 결합력과 나노튜브의 응집에 따른 나노튜브/고분자 복합재의 탄소성 거동 예측에 대한 연구)

  • Yang, Seunghwa;Yu, Suyoung;Ryu, Junghyun;Cho, Maenghyo
    • Journal of the Computational Structural Engineering Institute of Korea
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    • v.26 no.6
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    • pp.423-430
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    • 2013
  • In this research, a paramteric study to account for the effect of interfacial strength and nanotube agglomeration on the elastoplastic behavior of carbon nanotube reinforced polypropylene composites is performed. At first, the elastoplastic behavior of nanocomposites is predicted from molecular dynamics(MD) simulations. By combining the MD simulation results with the nonlinear micromechanics model based on the Mori-Tanaka model, a two-step domain decomposition method is applied to inversely identify the elastoplastic behavior of adsorption interphase zone inside nanocomposites. In nonlinear micromechanics model, the secant moduli method combined with field fluctuation method is used to predict the elastoplastic behavior of nanocomposites. To account for the imperfect material interface between nanotube and matrix polymer, displacement discontinuity condition is applied to the micromechanics model. Using the elastoplastic behavior of the adsorption interphase zone obtained from the present study, stress-strain relation of nanocomposites at various interfacial bonding condition and local nanotube agglomeration is predicted from nonlinear micromechanics model with and without the adsorption interphase zone. As a result, it has been found that local nanotube agglomeration is the most important design factor to maximize reinforcing effect of nanotube in elastic and plastic behavior.

Chain Length Effect on the Configurational Properties of an n-Alkane Chain in Solution

  • Jeon, Seung-Ho;Ree, Tai-Kyue;Oh, In-Joon
    • Bulletin of the Korean Chemical Society
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    • v.7 no.5
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    • pp.367-371
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    • 1986
  • Dynamic and equilibrium properties of n-alkane chains immersed in solvent molecules have been investigated by a molecular dynamics method. The n-alkane chain is assumed to be a chain of elements (CH$_2$) interconnected by bonds having a fixed bond length and bond angle, but each bond of the chain is allowed to execute hindered internal rotation. We studied the effect of the number of the chain elements (N$_c$ = 10, 15 and 20) on the equilibrium properties of the system, e.g., the pair correlation functions between a chain element and solvent molecules, g$_{cs}$(r), and between the chain elements, g$_{cc}$(r), and the configurational properties such as the mean-square end-to-end distance < R$^2$ >, the mean-square radius of gyration < S$^2$ >, and the eigenvalues of the moment-of-inertia tensor < S$_i^2$ > / < S$^2$ > (i = 1, 2 and 3). We also studied the dynamic properties of the system, e.g., the autocorrelation function C(A;t) where A = R$^2$(t), = S$^2$(t), or = ${\vec{V}}(t)({\vec{V}}$ = velocity of the center of mass), and the diffusion coefficient D. The g$_{cs}$(r)'s are almost equal irrespective of the change of Nc while g$_{cc}$(r) becomes larger as N$_c$ increases; The MD computed configurational properties < R$^2$2 > and < S$^2$ > were found to be a little different from the values calculated from the statistical equations of < R$^2$ > and < S$^2$ >, it may be due to the fact that our model for the MD simulations includes a long-range volume effect. From the < S$_i^2$ > / < S$^2$ >, it is found that the chain molecule has a nearly spherical shape irrespective of the variation of N$_c$. For the dynamic properties we found that the C(R$^2$;t) and C(S$^2$;t) of lower N$_c$ decay faster than those of higher N$_c$, while the C($\vec V$;t) of the center of mass in the chain is weakly dependent on the N$_c$. The center of mass diffusion coefficient D$_c$ decreases as N$_c$ increases while the end point diffusion coefficient D$_e$ is nearly equal irrespective of the change of N$_c$.

The Contact and Parallel Analysis of SPH Using Cartesian Coordinate Based Domain Decomposition Method (Cartesian 좌표기반 동적영역분할을 고려한 SPH의 충돌 및 병렬해석)

  • Moonho Tak
    • Journal of the Korean GEO-environmental Society
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    • v.25 no.4
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    • pp.13-20
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    • 2024
  • In this paper, a parallel analysis algorithm for Smoothed Particle Hydrodynamics (SPH), one of the numerical methods for fluidic materials, is introduced. SPH, which is a meshless method, can represent the behavior of a continuum using a particle-based approach, but it demands substantial computational resources. Therefore, parallel analysis algorithms are essential for SPH simulations. The domain decomposition algorithm, which divides the computational domain into partitions to be independently analyzed, is the most representative method among parallel analysis algorithms. In Discrete Element Method (DEM) and Molecular Dynamics (MD), the Cartesian coordinate-based domain decomposition method is popularly used because it offers advantages in quickly and conveniently accessing particle positions. However, in SPH, it is important to share particle information among partitioned domains because SPH particles are defined based on information from nearby particles within the smoothing length. Additionally, maintaining CPU load balance is crucial. In this study, a highly parallel efficient algorithm is proposed to dynamically minimize the size of orthogonal domain partitions to prevent excess CPU utilization. The efficiency of the proposed method was validated through numerical analysis models. The parallel efficiency of the proposed method is evaluated for up to 30 CPUs for fluidic models, achieving 90% parallel efficiency for up to 28 physical cores.