• 한국지반환경공학회 논문집
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• 제25권4호
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• pp.13-20
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• 2024

본 논문에서는 유동체를 해석할 수 있는 수치해석기법 중 하나인 SPH(Smoothed Particle Hydrodynamics)의 병렬해석 알고리즘이 소개된다. 무요소법(meshless method)의 SPH는 연속체 거동을 입자기반으로 표현하기 때문에 컴퓨팅하는데 높은 자원을 요구한다. 그래서 병렬해석 알고리즘은 SPH 시뮬레이션에서 필수적으로 고려되어야 한다. 계산영역을 일정한 간격으로 분할시켜 독립적으로 해석하는 영역분할 알고리즘은 병렬해석 알고리즘 중에 가장 대표적인 방법이다. 그리고 그 중 Cartesian 좌표계의 영역분할 방법은 입자들의 좌표를 빠르고 편리하게 검색할 수 있는 장점이 있어, DEM(Discrete Element Method)이나 MD(Molecular Dynamics)에서 대중적으로 사용되고 있다. 그러나 SPH의 경우 입자들이 smoothing 길이 이내의 주위 입자 정보가 필요하기 때문에 분할 영역 간의 입자정보 공유가 중요하다. 그리고 이에 따른 CPU의 로드밸런스가 중요하다. 본 연구에서는 직교 영역분할의 크기를 동적으로 미소화 시켜 잉여 CPU가 발생하지 않도록 하는 높은 병렬효율성의 알고리즘이 제안되었다. 그리고 수치해석 모델을 통하여 효율성을 검증하였다. 유동체 모델에 대해 총 30 CPU까지 제안된 방법의 병렬효율성을 검토하였고, 28개의 물리적 코어 수까지 90%의 병렬효율성을 얻을 수 있었다.

• Journal of Ginseng Research
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• 제46권1호
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• pp.156-166
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• 2022

Background: Panax ginseng Meyer (P. ginseng), a herb distributed in Korea, China and Japan, exerts benefits on diverse inflammatory conditions. However, the underlying mechanism and active ingredients remains largely unclear. Herein, we aimed to explore the active ingredients of P. ginseng against inflammation and elucidate underlying mechanisms. Methods: Inflammation model was constructed by lipopolysaccharide (LPS) in C57BL/6 mice and RAW264.7 macrophages. Molecular docking, molecular dynamics, surface plasmon resonance imaging (SPRi) and immunofluorescence were utilized to predict active component. Results: P. ginseng significantly inhibited LPS-induced lung injury and the expression of proinflammatory factors, including TNF-α, IL-6 and IL-1β. Additionally, P. ginseng blocked fluorescencelabeled LPS (LPS488) binding to the membranes of RAW264.7 macrophages, the phosphorylation of nuclear factor-κB (NF-κB) and mitogen-activated protein kinases (MAPKs). Furthermore, molecular docking demonstrated that ginsenoside Ro (GRo) docked into the LPS binding site of toll like receptor 4 (TLR4)/myeloid differentiation factor 2 (MD2) complex. Molecular dynamic simulations showed that the MD2-GRo binding conformation was stable. SPRi demonstrated an excellent interaction between TLR4/ MD2 complex and GRo (K_D value of 1.16 × 10^-9 M). GRo significantly inhibited LPS488 binding to cell membranes. Further studies showed that GRo markedly suppressed LPS-triggered lung injury, the transcription and secretion levels of TNF-α, IL-6 and IL-1β. Moreover, the phosphorylation of NF-κB and MAPKs as well as the p65 subunit nuclear translocation were inhibited by GRo dose-dependently. Conclusion: Our results suggest that GRo exerts anti-inflammation actions by direct inhibition of TLR4 signaling pathway.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2011년도 제40회 동계학술대회 초록집
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• pp.407-408
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• 2011

Natural boron consists of two stable isotopes 10B and 11B with natural abundance of 18.8 atom percent of 10B and 81.2 atom percent of 11B. The thermal neutron absorption cross-section for 10B and 11B are 3837 barn and 0.005 barn respectively. 10B enriched specific compounds are used for control rods and as a reactor coolant additives. In this work 2 methods for boron enrichment were analysed: 1) Gas irradiation in static conditions. Dissociation occurs due to multiphoton absorption by specific isotopes in appropriately tuned laser field. IR shifted laser pulses are usually used in combination with increasing the laser intensity also improves selectivity up to some degree. In order to prevent recombination of dissociated molecules BCl3 is mixed with H2S 2) SILARC method. Advantages of this method: a) Gas cooling is helpful to split and shrink boron isotopes absorption bands. In order to achieve better selectivity BCl3 gas has to be substantially rarefied (~0.01%-5%) in mixture with carrier gas. b) Laser intensity is lower than in the first method. Some preliminary calculations of dissociation and recombination with carrier gas molecules energetics for both methods will be demonstrated Boron separation in SILARC method can be represented as multistage process: 1) Mixture of BCl3 with carrier gas is putted in reservoir 2) Gas overcooling due to expansion through Laval nozzle 3) IR multiphoton absorption by gas irradiated by specifically tuned laser field with subsequent gradual gas condensation in outlet chamber It is planned to develop software which includes these stages. This software will rely on the following available software based on quantum molecular dynamics in external quantized field: 1) WavePacket: Each particle is treated semiclassicaly based on Wigner transform method 2) Turbomole: It is based on local density methods like density of functional methods (DFT) and its improvement- coupled clusters approach (CC) to take into account quantum correlation. These models will be used to extract information concerning kinetic coefficients, and their dependence on applied external field. Information on radiative corrections to equation of state induced by laser field which take into account possible phase transition (or crossover?) can be also revealed. This mixed phase equation of state with quantum corrections will be further used in hydrodynamical simulations. Moreover results of these hydrodynamical simulations can be compared with results of CFD calculations. The first reasonable question to ask before starting the CFD simulations is whether turbulent effects are significant or not, and how to model turbulence? The questions of laser beam parameters and outlet chamber geometry which are most optimal to make all gas volume irradiated is also discussed. Relationship between enrichment factor and stagnation pressure and temperature based on experimental data is also reported.

• Journal of Photoscience
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• 제9권2호
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• pp.51-54
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• 2002

We propose a novel mechanism (Twist Sharing Mechanism) for the cis-trans photoisomerization of rhodopsin, based on the molecular dynamics (MD) simulation study. New things devised in our simulations are (1) the adoption of Mt. Fuji potentials in the excited state for twisting of the three bonds C9=C10, C11=C12 and C13=14 which are modeled using the detailed ab initio quantum chemical calculations and (2) to use the rhodopsin structure which was resolved recently by the X-ray crystallographic study. As a result, we found the followings: Due to the intramolecular steric hindrance between 20-methyl and 10-H in the retinal chromophore, the C12-C13 and C10-C11 bonds are considerably twisted counterclockwise in rhodopsin, allowing only counterclockwise rotation of the C11 =C12 in the excited state. The movement of 19-methyl in rhodopsin is blocked by the surrounding three amino acids, Thr 118, Met 207 and Tyr 268, prohibiting the rotation of C9=C10. As a result only all-trans form of the chromophore is obtainable as a photoproduct. At the 90$^{\circ}$ twisting of C11=C12 in the course of photoisomerization, twisting energies of the other bonds amount to about 20 kcal/mol. If the transition state for the thermal isomerization is assumed to be similar to this structure, the activation energy for the thermal isomerization around C11=C12'in rhodopsin is elevated by about 20 kcal/mol and the thermal isomerization rate is decelerated by 10$\^$-14/ times than that of the retinal chromophore in solution, protecting photosignal from the thermal noise.

• Advances in environmental research
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• 제7권2호
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• pp.139-159
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• 2018

Green Leaf Volatiles (GLVs) is a class of biogenically emitted oxygenated hydrocarbons that have been identified as a potential source of Secondary Organic Aerosols (SOA) via aqueous oxidation. The physico-chemical properties of GLVs are vital to understanding their fate and transport in the atmosphere via fog processing, but few experimental data are available. We studied the aqueous solubility, 1-octanol/water partition coefficient, and Henry's law constant ($K_H$) of five GLVs at $25^{\circ}C$: methyl jasmonate, methyl salicylate, 2-methyl-3-buten-2-ol, cis-3-hexen-1-ol, and cis-3-hexenyl acetate. Henry's law constant was also measured at temperatures and ionic strengths typical of fog. Experimental values are compared to scarcely-available literature values, as well as estimations using group and bond contribution methods, property-specific correlations and molecular dynamics simulations. From these values, the partition coefficients to the air-water interface were also calculated. The large Henry's law constant of methyl jasmonate ($8091{\pm}1121M{\cdot}atm^{-1}$) made it the most significant GLV for aqueous phase photochemistry. The HENRYWIN program's bond contribution method from the Estimation Programs Interface Suite (EPI Suite) produced the best estimate of the Henry's constant for GLVs. Estimations of 1-octanol/water partition coefficient and solubility are best when correlating an experimental value of one to find the other. Finally, the scavenging efficiency was calculated for each GLV indicating aqueous phase processing will be most important for methyl jasmonate.

• 한국컴퓨터정보학회논문지
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• 제15권12호
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• pp.175-180
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• 2010

본 논문에서는 고전적인 분자 동역학 시뮬레이션을 통해서 다양한 길이를 가진 이중벽 탄소나노 튜브로 만들어진 초고주파 나노 기계 공진기의 주파수 변동 특성을 분석한다. 분석의 목적은 이중벽 탄소나노 튜브 벽의 길이에 따라 변동하는 공진기의 주파수 분석이다. 실험 결과, 주파수 변동이 여러 가지 외벽 길이 값 L10에 대해서는 내벽/외벽 길이 비율 L5/L10의 함수로 최대 주파수로 정규화된 공진 주파수가 Pearson VII 함수에 잘 맞고, 여러 가지 내벽 길이 값에 대해서는 외벽/내벽 길이 비율의 함수로 최대 주파수로 정규화된 공진 주파수가 Gauss 분산 함수에 잘 맞는 것을 보여준다.

• 한국해양공학회지
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• 제27권5호
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• pp.105-114
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• 2013

Lots of orders of special vessels and offshore plants for developing the resources in deepwater have been increased in recent. Because the most of accidents on those structures are caused by fire and explosion, many researchers have been investigated quantitatively to predict the cause and effect of fire and explosion based on both experiments and numerical simulations. The first step of the evaluation procedures leading to fire and explosion is to predict the dispersion of flammable or toxic material, in which the released material mixes with surrounding air and be diluted. In particular turbulent mixing, but density differences due to molecular weight or temperature as well as diffusion will contribute to the mixing. In the present paper, the numerical simulation of hydrogen dispersion inside a simple-shaped offshore structure was performed using a commercial CFD program, ANSYS-CFX. The simulated results for concentration of released hydrogen are compared to those of experiment and other simulation in Jordan et al.(2007). As a result, it is seen that the present simulation results are closer to the experiments than other simulation ones. Also it seems that the hydrogen dispersion is closely related to turbulent mixing and the selection of the turbulence model properly is significantly of importance to the reproduction of dispersion phenomena.

• Steel and Composite Structures
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• 제42권6호
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• pp.779-789
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• 2022

This work presents a non-linear cylindrical bending analysis of functionally graded plate reinforced by single-walled carbon nanotubes (SWCNTs) in thermal environment using a simple integral higher-order shear deformation theory (HSDT). This theory does not require shear correction factors and the transverse shear stresses vary parabolically through the thickness. The material properties of SWCNTs are assumed to be temperature-dependent and are obtained from molecular dynamics simulations. The material properties of functionally graded carbon nanotube-reinforced composites (FG-CNTCRs) are considered to be graded in the thickness direction, and are estimated through a micromechanical model. The non-linear strain-displacement relations in the Von Karman sense are used to study the effect of geometric non-linearity and the solution is obtained by minimization of the total potential energy. The numerical illustrations concern the nonlinear bending response of FG-CNTRC plates under different sets of thermal environmental conditions, from which results for uniformly distributed CNTRC plates are obtained as benchmarks.

• Advances in nano research
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• 제14권3호
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• pp.211-224
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• 2023

This work presents a modified analytical model for the bending behavior of axially functionally graded (AFG) carbon nanotubes reinforced composite (CNTRC) nanobeams. New higher order shear deformation beam theory is exploited to satisfy parabolic variation of shear through thickness direction and zero shears at the bottom and top surfaces.A Modified continuum nonlocal strain gradient theoryis employed to include the microstructure and the geometrical nano-size length scales. The extended rule of the mixture and the molecular dynamics simulations are exploited to evaluate the equivalent mechanical properties of FG-CNTRC beams. Carbon nanotubes reinforcements are distributed axially through the beam length direction with a new power graded function with two parameters. The equilibrium equations are derived with associated nonclassical boundary conditions, and Navier's procedure are used to solve the obtained differential equation and get the response of nanobeam under uniform, linear, or sinusoidal mechanical loadings. Numerical results are carried out to investigate the impact of inhomogeneity parameters, geometrical parameters, loadings type, nonlocal and length scale parameters on deflections and stresses of the AFG CNTRC nanobeams. The proposed model can be used in the design and analysis of MEMS and NEMS systems fabricated from carbon nanotubes reinforced composite nanobeam.

• Advances in nano research
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• 제16권3호
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• pp.289-301
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• 2024

In this work, an analytical model employing a new higher-order shear deformation beam theory is utilized to investigate the bending behavior of axially randomly oriented functionally graded carbon nanotubes reinforced composite nanobeams. A modified continuum nonlocal strain gradient theory is employed to incorporate both microstructural effects and geometric nano-scale length scales. The extended rule of mixture, along with molecular dynamics simulations, is used to assess the equivalent mechanical properties of functionally graded carbon nanotubes reinforced composite (FG-CNTRC) beams. Carbon nanotube reinforcements are randomly distributed axially along the length of the beam. The equilibrium equations, accompanied by nonclassical boundary conditions, are formulated, and Navier's procedure is used to solve the resulting differential equation, yielding the response of the nanobeam under various mechanical loadings, including uniform, linear, and sinusoidal loads. Numerical analysis is conducted to examine the influence of inhomogeneity parameters, geometric parameters, types of loading, as well as nonlocal and length scale parameters on the deflections and stresses of axially functionally graded carbon nanotubes reinforced composite (AFG CNTRC) nanobeams. The results indicate that, in contrast to the nonlocal parameter, the beam stiffness is increased by both the CNTs volume fraction and the length-scale parameter. The presented model is applicable for designing and analyzing microelectromechanical systems (MEMS) and nanoelectromechanical systems (NEMS) constructed from carbon nanotubes reinforced composite nanobeams.