• EDISON SW 활용 경진대회 논문집
• /
• 제4회(2015년)
• /
• pp.14-23
• /
• 2015

Alzheimer's disease is one of the most common types of degenerative dementia. As a considerable cause of Alzheimer's disease, neurotoxic plaques composed of 39 to 42 residue-long amyloid beta($A{\beta}$) fibrils have been found in the patient's brain in large quantity. A previous study found that erythrosine B (ER), a red color food dye approved by FDA, inhibits the formation of amyloid beta fibril structures. Here, in an attempt to elucidate the inhibition mechanism, we performed molecular dynamics simulations to demonstrate the conformational change of $A{\beta}40$ induced by 2 ERs in atomistic detail. During the simulation, the ERs bound to the surfaces of both N-terminus and C-terminus regions of $A{\beta}40$ rapidly. The observed stacking of the ERs and the aromatic side chains near the N-terminus region suggests a possible inhibition mechanism in which disturbing the inter-chain stacking of PHEs destabilizes beta-sheet enriched in amyloid beta fibrils. The bound ERs block water molecules and thereby help stabilizing alpha helical structure at the main chain of C-terminus and interrupt the formation of the salt-bridge ASP23-LYS28 at the same time. Our findings can help better understanding of the current and upcoming treatment studies for Alzheimer's disease by suggesting inhibition mechanism of ER on the conformational transition of $A{\beta}40$ at the molecular level.

• Journal of Ginseng Research
• /
• 제44권5호
• /
• pp.690-696
• /
• 2020

Background: As the main metabolites of ginsenosides, 20(S, R)-protopanaxadiol [PPD(S, R)] and 20(S, R)-protopanaxatriol [PPT(S, R)] are the structural basis response to a series of pharmacological effects of their parent components. Although the estrogenicity of several ginsenosides has been confirmed, however, the underlying mechanisms of their estrogenic effects are still largely unclear. In this work, PPD(S, R) and PPT(S, R) were assessed for their ability to bind and activate human estrogen receptor α (hERα) by a combination of in vitro and in silico analysis. Methods: The recombinant hERα ligand-binding domain (hERα-LBD) was expressed in E. coli strain. The direct binding interactions of ginsenosides with hERα-LBD and their ERα agonistic potency were investigated by fluorescence polarization and reporter gene assays, respectively. Then, molecular dynamics simulations were carried out to simulate the binding modes between ginsenosides and hERα-LBD to reveal the structural basis for their agonist activities toward receptor. Results: Fluorescence polarization assay revealed that PPD(S, R) and PPT(S, R) could bind to hERα-LBD with moderate affinities. In the dual luciferase reporter assay using transiently transfected MCF-7 cells, PPD(S, R) and PPT(S, R) acted as agonists of hERα. Molecular docking results showed that these ginsenosides adopted an agonist conformation in the flexible hydrophobic ligand-binding pocket. The stereostructure of C-20 hydroxyl group and the presence of C-6 hydroxyl group exerted significant influence on the hydrogen bond network and steric hindrance, respectively. Conclusion: This work may provide insight into the chemical and pharmacological screening of novel therapeutic agents from ginsenosides.

• Molecules and Cells
• /
• 제46권8호
• /
• pp.513-525
• /
• 2023

Orange carotenoid protein (OCP) of photosynthetic cyanobacteria binds to ketocarotenoids noncovalently and absorbs excess light to protect the host organism from light-induced oxidative damage. Herein, we found that mutating valine 40 in the α3 helix of Gloeocapsa sp. PCC 7513 (GlOCP1) resulted in blue- or red-shifts of 6-20 nm in the absorption maxima of the lit forms. We analyzed the origins of absorption maxima shifts by integrating X-ray crystallography, homology modeling, molecular dynamics simulations, and hybrid quantum mechanics/molecular mechanics calculations. Our analysis suggested that the single residue mutations alter the polar environment surrounding the bound canthaxanthin, thereby modulating the degree of charge transfer in the photoexcited state of the chromophore. Our integrated investigations reveal the mechanism of color adaptation specific to OCPs and suggest a design principle for color-specific photoswitches.

• 한국지구과학회:학술대회논문집
• /
• 한국지구과학회 2010년도 춘계학술발표회 논문집
• /
• pp.118-119
• /
• 2010

별탄생에 관한 연구는 최근 천문학 영역에서 활발히 진행되고 있으며, 별이 실제로 동역학적 과정을 거쳐 형성되고 분자운의 난류적 특성에 강하게 영향을 받는다는 것을 보여주고 있다. 별탄생 과정에 관한 관측적 영역에서 상당한 진전이 있음에도 불구하고, 별탄생의 초기단계는 여전히 해결되고 있지 않다. 따라서, 별 탄생의 복잡한 역학적 특성으로 인해 컴퓨터 시뮬레이션은 별탄생 연구의 중요한 도구로 사용된다. 우리는 SPH 시뮬레이션을 활용하여 낮은 질량의 별 탄생 과정을 제시하였고, 가장 진보된 dragon code를 사용하였다. 질량과 난류, 중심 밀도 등의 값을 변화시키면서 내부 특성의 변화를 살펴보고, 어떻게 진화하는지에 대해 알아보고자 한다. (질량범위는 0.1$5\;M{\odot}$) 이 결과에 근거하여 그들의 환경조건과 특성 그리고 성간운에서 낮은 질량의 별이 탄생하는 동안 어떻게 진화하는지에 대해 논의하고자 한다.

• 한국세라믹학회지
• /
• 제54권6호
• /
• pp.506-510
• /
• 2017

One of the characteristics of polycrystalline graphene that determines its material properties is grain size. Mechanical properties such as Young's modulus, yield strain and tensile strength depend on the grain size and show a reverse Hall-Petch effect at small grain size limit for some properties under certain conditions. While there is agreement on the grain size effect for Young's modulus and yield strain, certain MD simulations have led to disagreement for tensile strength. Song et al. showed a decreasing behavior for tensile strength, that is, a pseudo Hall-Petch effect for the small grain size domain up to 5 nm. On the other hand, Sha et al. showed an increasing behavior, a reverse Hall-Petch effect, for grain size domain up to 10 nm. Mortazavi et al. also showed results similar to those of Sha et al. We suspect that the main difference of these two inconsistent results is due to the different modeling. The modeling of polycrystalline graphene with regular size and (hexagonal) shape shows the pseudo Hall-Petch effect, while the modeling with random size and shape shows the reverse Hall-Petch effect. Therefore, this study is conducted to confirm that different modeling is the main reason for the different behavior of tensile strength of the polycrystalline structures. We conducted MD simulations with models derived from the Voronoi tessellation for two types of grain size distributions. One type is grains of relatively similar sizes; the other is grains of random sizes. We found that the pseudo Hall-Petch effect and the reverse Hall-Petch effect of tensile strength were consistently shown for the two different models. We suspect that this result comes from the different crack paths, which are related to the grain patterns in the models.

• 한국진공학회:학술대회논문집
• /
• 한국진공학회 2009년도 제38회 동계학술대회 초록집
• /
• pp.358-358
• /
• 2010

Ion beam bombardment at low energy forms nanosize patterns such as ripples, dots or wrinkles on the surface of polymers in ambient temperature and pressure. It has been known that the ion beam can alter the polymer surface that induces skins stiffer or the density higher by higher compressive stress or strain energies associated with chain scissions and crosslinks of the polymer. Atomic scale structure evolution in polymers is essential to understand a stress generation mechanism during the ion beam bombardment, which governs the nanoscale surface structure evolution. In this work, Molecular Dynamics (MD) simulations are employed to characterize the phenomenon occurred in bombardment between the ion beam and polymers that forms nanosize patterns. We investigate the structure evolution of Low Density Polyethylene (LDPE) at 300 K as the polymer is bombarded with Argon ions having various kinetic energies ranging from 100 eV to 1 KeV with 50 eV intervals having the fluence of $1.45\;{\times}\;1014 #/cm2$. These simulations use the Reactive Force Field (ReaxFF), which can mimic chemical covalent bonds and includes van der Waals potentials for describing the intermolecular interactions. The results show the details of the structural evolution of LDPE by the low energy Ar ion bombardment. Analyses through kinetic and potential energy, number of crosslinks and chain scissions, level of local densification and motions of atoms support that the residual strain energies on the surface is strongly associated with the number of crosslinks or scissored chains. Also, we could find an optimal Ar ion beam energy to make crosslinks well.

• Nuclear Engineering and Technology
• /
• 제42권6호
• /
• pp.620-635
• /
• 2010

In this paper we describe current activities on the project Multi-Scale Modeling and Analysis of convective boiling (MSMA), conducted jointly by the Paul Scherrer Institute (PSI) and the Swiss Nuclear Utilities (Swissnuclear). The long-term aim of the MSMA project is to formulate improved closure laws for Computational Fluid Dynamics (CFD) simulations for prediction of convective boiling and eventually of the Critical Heat Flux (CHF). As boiling is controlled by the competition of numerous phenomena at various length and time scales, a multi-scale approach is employed to tackle the problem at different scales. In the MSMA project, the scales on which we focus range from the CFD scale (macro-scale), bubble size scale (meso-scale), liquid micro-layer and triple interline scale (micro-scale), and molecular scale (nano-scale). The current focus of the project is on micro- and meso-scales modeling. The numerical framework comprises a highly efficient, parallel DNS solver, the PSI-BOIL code. The code has incorporated an Immersed Boundary Method (IBM) to tackle complex geometries. For simulation of meso-scales (bubbles), we use the Constrained Interpolation Profile method: Conservative Semi-Lagrangian $2^{nd}$ order (CIP-CSL2). The phase change is described either by applying conventional jump conditions at the interface, or by using the Phase Field (PF) approach. In this work, we present selected results for flows in complex geometry using the IBM, selected bubbly flow simulations using the CIP-CSL2 method and results for phase change using the PF approach. In the subsequent stage of the project, the importance of effects of nano-scale processes on the global boiling heat transfer will be evaluated. To validate the models, more experimental information will be needed in the future, so it is expected that the MSMA project will become the seed for a long-term, combined theoretical and experimental program.

• 한국전산유체공학회:학술대회논문집
• /
• 한국전산유체공학회 2005년도 추계 학술대회논문집
• /
• pp.11-19
• /
• 2005

First, methods of numerical analysis of gas-particle flows is classified into micro, meso and macro scale approaches based on the concept of multi-scale mechanics. Next, the explanation moves on to discrete particle simulation where motion of individual particles is calculated numerically using the Newtonian equations of motion. The author focuses on the cases where particle-to-particle interaction has significant effects on the phenomena. Concerning the particle-to-particle interaction, two cases are considered: the one is collision-dominated flows and the other is the contact-dominated flows. To treat this interaction mathematically, techniques named DEM(Distinct Element Method) or DSMC (Direct Simulation Monte Carlo) have been developed DEM, which has been developed in the field of soil mechanics, is useful for the contact -dominated flows and DSMC method, developed in molecular gas flows, is for the collision-dominated flows. Combining DEM or DSMC with CFD (computer fluid dynamics), the discrete particle simulation becomes a more practical tool for industrial flows because not only the particle-particle interaction but particle-fluid interaction can be handled. As examples of simulations, various results are shown, such as hopper flows, particle segregation phenomena, particle mixing in a rotating drum, dense phase pneumatic conveying, spouted bed, dense phase fluidized bed, fast circulating fluidized bed and so on.

• Steel and Composite Structures
• /
• 제14권4호
• /
• pp.335-347
• /
• 2013

In this paper, the nonlinear cylindrical bending behavior of functionally graded nanocomposite plates reinforced by single-walled carbon nanotubes (SWCNTs) is studied using an efficient and simple refined theory. This theory is based on assumption that the in-plane and transverse displacements consist of bending and shear components in which the bending components do not contribute toward shear forces and, likewise, the shear components do not contribute toward bending moments. 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 assumed to be graded in the thickness direction, and are estimated through a micromechanical model. The fundamental equations for functionally graded nanocomposite plates are obtained using the Von-Karman theory for large deflections 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 comparators.

• Bulletin of the Korean Chemical Society
• /
• 제34권12호
• /
• pp.3703-3708
• /
• 2013

The scaling relationship of the longest relaxation time of a single chain of semiflexible biological polyelectrolyte has been investigated by performing well-established coarse-grained Brownian dynamics simulations. Two kinds of longest relaxation times were estimated from time-sequences of chain trajectories, and their behaviors were interpreted by applying the scaling law for different molecular weights of polyelectrolyte and Debye lengths. The scaling exponents for longest stress relaxation and rotational relaxation are found in the ranges of 1.67-1.79 and 1.65-1.81, respectively, depending on the physicochemical interaction of electrostatic Debye screening. The scaling exponent increases with decreasing screening effect, which is a special feature of polyelectrolytes differing from neutral polymers. It revealed that the weak screening allows a polyelectrolyte chain to follow the behavior in good solvent due to the strong electrostatic repulsion between beads.