• Nuclear Engineering and Technology
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• 제47권6호
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• pp.662-668
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• 2015

A suspension of titanium nanoparticles (Ti NPs) in liquid sodium (Na) has been proposed as a method to mitigate the violent sodium-water reaction (SWR). The interparticle potential between Ti NPs in liquid Na may play a significant role in the agglomeration of NPs on the reaction surface and in the bulk liquid Na, since the potential contributes to a reduction in the long-term dispersion stability. For the effective control of the SWR with NPs, a physical understanding of the molecular dynamics of NPs in liquid Na is key. Therefore in this study, the nonretarded Van der Waals model and the solvation potential model are employed to analyze the interparticle potential. The ab initio calculation reveals that a strong repulsive force driven by the solvation potential exceeds the interparticle attraction and predicts the agglomeration energy required for two 10-nm Ti NPs to be $4{\times}10^{-17}J$. The collision theory suggests that Ti NPs can be effective suppressors of the SWR due to the high energy barrier that prevents significant agglomeration of Ti NPs in quiescent liquid Na.

• Advances in nano research
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• 제1권3호
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• pp.133-151
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• 2013

The availability of advanced nanotechnological methodologies (experimental and theoretical) has widened the investigation of biological/organic matter in interaction with substrates. Minerals are good candidates as substrates because they may present a wide variety of physico-chemical properties and surface nanostructures that can be used to actively condense and manipulate the biomolecules. Scanning Probe Microscopy (SPM) is one of the best suited techniques used to investigate at a single molecule level the surface interactions. In addition, the recent availability of high performance computing has increased the possibility to study quantum mechanically the interaction phenomena extending the number of atoms involved in the simulation. In the present paper, firstly we will briefly introduce new SPM technological developments and applications to investigate mineral surfaces and mineral-biomolecule interaction, then we will present results on the specific RNA-mineral interaction and recent basics and applicative achievements in the field of the interactions between other fundamental biological molecules and mineral surfaces from both an experimental and theoretical point of view.

• 한국자기공명학회논문지
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• 제19권1호
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• pp.1-10
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• 2015

Refinements with atomistic molecular dynamics (MD) simulation have contributed to improving the qualities of NMR structures. In most cases, the calculations with atomistic MD simulation for NMR structures employ generalized-Born implicit solvent model (GBIS) to take into accounts solvation effects. Developments in algorithms and computational capacities have ameliorated GBIS to approximate solvation effects that explicit solvents bring about. However, the quantitative comparison of NMR structures in the latest GBIS and explicit solvents is lacking. In this study, we report the direct comparison of NMR structures that atomistic MD simulation coupled with GBIS and water molecules refined. Two model proteins, GB1 and ubiquitin, were recalculated with experimental distance and torsion angle restraints, under a series of simulated annealing time steps. Whereas the root mean square deviations of the resulting structures were apparently similar, AMBER energies, the most favored regions in Ramachandran plot, and MolProbity clash scores witnessed that GBIS-refined structures had the better geometries. The outperformance by GBIS was distinct in the structure calculations with sparse experimental restraints. We show that the superiority stemmed, at least in parts, from the inclusion of all the pairs of non-bonded interactions. The shorter computational times with GBIS than those for explicit solvents makes GBIS a powerful method for improving structural qualities particularly under the conditions that experimental restraints are insufficient. We also propose a method to separate the native-like folds from non-violating diverged structures.

• 한국산학기술학회논문지
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• 제7권2호
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• pp.168-174
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• 2006

본 연구는 분자동력학 시뮬레이션을 이용하여 탄소 나노튜브를 이용한 전계효과 이온-전송 소자를 분석하였다. 외부 전기장에 의해 단전자 전계효과 트랜지스터 및 나노크기의 데이터 저장 장치로 활용될 수 있는 원리를 규명하였다. 외부 전기장이 증가할수록 칼륨 원자는 채널을 빠르게 통과하였다. 낮은 외부 전계에서는 나노채널의 열적 파동이 칼륨 원자의 터널링에 영향을 주게 됨을 해석하였다. 이로서 외부 전계의 강도에 따라 칼륨원자의 채널을 터널링하는 효과를 제어할 수 있는 메커니즘을 도출하였다.

• Mycobiology
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• 제48권5호
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• pp.392-398
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• 2020

This study was conducted to understand the dynamics of microbial communities of soil microorganisms, and their distribution and abundance in the indigenous microorganisms (IMOs) manipulated from humus collected from the forest near the crop field. The soil microorganisms originated from humus and artificially cultured microbial-based soil amendments were characterized by molecular and biochemical analyses. The bacterial population (2 × 10⁶~13 × 10⁶ CFU/g sample) was approximately 100-fold abundant than the fungal population (2 × 10⁴~8 × 10⁴ CFU/g sample). The 16S rDNA and ITS sequence analyses showed that the bacterial and fungal communities in humus and IMOs were mainly composed of Bacillus and Pseudomonas, and Trichoderma and Aspergillus species, respectively. Some of the bacterial isolates from the humus and IMOs showed strong inhibitory activity against soil-borne pathogenic fungi Fusarium oxysporum and Sclerotinia sclerotiorum. These bacteria also showed the siderophore production activity as well as phosphate solubilizing activity, which are requisite traits for biological control of plant pathogenic fungi. These results suggest that humus and IMOs could be a useful resource for sustainable agriculture.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2009년도 제38회 동계학술대회 초록집
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• pp.359-359
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• 2010

Self-organized nanostructures of dots, holes or ripples produced by energetic ion bombardment have been reported in a wide variety of substrates. Ion bombardment on an alloy or compound also draws much attention because it can induce a surface composition modulation with a topographical surface structure evolution. V. B. Shenoy et al. further suggested that, in the case of alloy surfaces, the differences in the sputtering yields and surface diffusivities of the alloy components will lead to a lateral surface composition modulation [1]. In the present work, the classical molecular dynamics simulation of Ar bombardment on metallic alloys at room temperature revealed that this bombardment induces a surface composition modulation in layer-by-layer mode. In both the $Co_{0.5}Cu_{0.5}$ alloy and the CoAl B2 phase, the element of higher-sputtering yield is accumulated on the top surface layer, whereas it is depleted in lower layers. A kinetic model considering both the rearrangement and the sputtering of the substrate atoms agrees with the puzzling simulation results, which revealed that the rearrangement of the substrate atoms plays a significant role in the observed composition modulation.

• Advances in nano research
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• 제5권2호
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• pp.141-169
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• 2017

In this paper, a nanobeam connected to a rotating molecular hub is considered. The vibration behavior of rotating functionally graded nanobeam based on Eringen's nonlocal theory and Euler-Bernoulli beam model is investigated. Furthermore, axial preload and porosity effect is studied. It is supposed that the material attributes of the functionally graded porous nanobeam, varies continuously in the thickness direction according to the power law model considering the even distribution of porosities. Porosity at the nanoscopic length scale can affect on the rotating functionally graded nanobeams dynamics. The equations of motion and the associated boundary conditions are derived through the Hamilton's principle and generalized differential quadrature method (GDQM) is utilized to solve the equations. In this paper, the influences of some parameters such as functionally graded power (FG-index), porosity parameter, axial preload, nonlocal parameter and angular velocity on natural frequencies of rotating nanobeams with pure ceramic, pure metal and functionally graded materials are examined and some comparisons about the influence of various parameters on the natural frequencies corresponding to the simply-simply, simplyclamped, clamped-clamped boundary conditions are carried out.

• Bulletin of the Korean Chemical Society
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• 제14권4호
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• pp.491-496
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• 1993

A class A ${\beta}$-lactamase from Staphylococcus aureus PC1 complexed with 3R,5R-clavulanate is studied. The starting geometry for the computation is the crystal structure of the ${\beta}$-lactamase. Docking of the clavulanate to the enzyme is done exploiting the requirements of electrostatic and shape complementarity between the enzyme and clavulanate. This structure is then hydrated by water molecules and refined by energy minimization and short molecular dynamics simulation. In the energy refined structure of this complex, the carboxyl group of the clavulanate is hydrogen bonded to Lys-234, and the the carbonyl carbon atom of the clavulanate is adjacent to the $O_{\gamma}$ of Ser-70. It is found that a crystallographic water molecule initially located at the oxyanion hole, which is formed by the two -NH group of Ser-70 and Gln-237, is replaced by the carbonyl oxygen atom of the 3R,5R-clavulanate after docking and energy reginement. The crystallographic water molecules are proved to be important in ligand binding. Glu-166 residue is found to be repulsive to the binding of clavulanate, which is in agreement with experimental observation. Arg-244 residue is found to be important to the binding of clavulanate as well as to interaction with C2 side chain of the clavulanate. The electron density redistribution of the clavulanate on binding to the ${\beta}$-lactamase in studied by an ab initio quantum-mechanical calculation. A significant redistribution of electron density of the clavulanate is induced by the enzyme, toward the enzyme, toward the transition state of the enzymatic reaction.

• 한국추진공학회:학술대회논문집
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• 한국추진공학회 2008년 영문 학술대회
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• pp.150-156
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• 2008

A program based on a 2-D CFD code has been developed to simulate a gas turbine engine. 2-D Navier-Stokes implicit code with $k-\omega$ turbulent model is used in compressor and turbine. Lumped method chemical equilibrium code with 10 species of molecular is applied to combustor with assuming perfect mixture and 100% combustion efficiency at constant pressure state. Fluid properties are shared on interfaces between engine components. Compressor supplies outlet temperature and pressure to combustor. At the same time, combustor also carries temperature and pressure to turbine. The back pressure of compressor outlet is transferred by inlet pressure of turbine. Unsteady phenomena in rotor-stator are covered by mixing-plane method. The running condition of engine can be determined only by given the inlet condition of compressor, the outlet condition of turbine, equivalence ratio and rotating speed.

• Animal cells and systems
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• 제16권3호
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• pp.224-229
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• 2012

The Korean shiner (Coreoleuciscus splendidus, Gobioninae), a small freshwater fish native to Korea Peninsula, widely inhabits in most of the major drainages in South Korea. Here we describe the development of 14 novel and polymorphic microsatellites for this species and its effective utilization in estimation of genetic diversity using 72 individuals from three sampling sites in different drainages. Loci were isolated from a microsatellite enrichment procedure using probe-labeled magnetic beads. A total of 242 alleles were detected across all loci with an average of 17.3 alleles per locus ranging 4 32. The loci varied levels of polymorphism as evident from its expecte heterozygosity ranging from 0.111 to 0.957. The average pairwise $F_{ST}$ between two populations examined shows significant differentiation ($F_{ST}$ = 0.215, p<0.05). The 14 microsatellite loci developed here will also be useful to explain for the genetic structures among geographically isolated populations and gene flow dynamics within drainages in this species as well as the closely related species.