• International Journal of Highway Engineering
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• v.19 no.6
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• pp.23-30
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• 2017

PURPOSES : In this paper, the applicability of DEM to a coarse graining method was evaluated by simulating a series of minicone tests for cement paste. METHODS : First, the fundamental physical quantities that are used in a static liquid bridge model were presented with three basic quantities based on the similarity principle and coarse graining method. Then, the scale factors and surface tensions for six different sizes of particles were determined using the relationship between the physical quantities and the basic quantities. Finally, the determined surface tensions and radii were utilized to simulate the fluidal behavior of cement paste under a minicone test condition, and the final shape of the cement paste with reference DEM particle radii was compared with the final shape of the others. RESULTS : The simulations with adjusted surface tensions for five different radii of particles and surface tension showed acceptable agreement with the simulation with regard to the reference size of the particle, although disagreement increases as the sizes of the particle radii increase. It seems reasonable to increase the particle radii by at least 0.196 cm considering the computational time reduction of 162 min. CONCLUSIONS : The coarse graining method based on the similarity principle is applicable for simulating the behavior of fluidal materials when the behavior of the materials can be described by a static liquid bridge model. However, the maximum particle radius should be suggested by considering not only the scale factor but also the relationship of the particle size and number with the radius of the curve of the boundary geometry.

• Proceedings of the KSME Conference
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• 2004.11a
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• pp.400-403
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• 2004

We present a coarse-graining model to describe the mechanical behaviors of multi-walled carbon nanotubes. To find the atomic configuration in membrane-like nanostructure i.e. carbon nanotube, we employ interpolation functions and the associated element-variables that are defined in the subdivided region. Tersoff-Brenner potential is adopted for interaction of bonded atoms and also van der Waals force for non-bonded interaction. Moreover, we simulate the coarse-graining multi-walled carbon nanotubes with defects and its result is compared with that of perfect multi-walled carbon nanotubes.

• Journal of the KSME
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• v.56 no.5
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• pp.32-34
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• 2016

이 글에서는 액틴의 기계적 물성치를 측정한 연구 중 coarse-grained 기법을 이용한 전산해석 연구에 대해 소개하고자 한다.

• Proceedings of the Korea Water Resources Association Conference
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• 1998.05b
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• pp.3-3
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• 1998

In this pressentation it is argued that the heterogeneity of a hydrologic attribute which may seem to be nonstationary at one scale, may become stationary at a larger scale. The fundamental reason for transformation from nonstationarity to stationarity whith the increase in scale is the phenomenon of coarse-graining of the hydrologic processes with increasing scale. Due to the phenomenon of aliasing, a particular scale hydrologic process heterogeneity which is observed as a nonstationary process at that scale, may be observed as a stationary process at a higher(larger) scale whose size is bigger than the stationary extent of the lower scale heterogeneity. As one goes through a hierarchical sequence of larger and larger scales for observations, one would eliminate nonstationarities which emerge at some lower scales at the expense of losing information on the high frequency fluctuations of the lower scale heterogeneities which will no longer be observed at the larger sampling scales. We call this phenimenon as the "coarse-graining in hydrologic observations". In this presentation, it is also argued that by the coarse-graining of hydrologic processes due to the averaging and aliasing operations at increasing scales, the conservation laws corresponging to these scales may still be quite parsimonious, and need not be more complicated as the scales get larger. It is shown that shen a higher(larger) scale process is formed by averaging a lower(smaller) scale process in time or space, the high frequency components of the lower scale process will be eliminated by the averaging operation. Thereby, the resuliiting average hydrologic dynamics, free from the effects of the high frequency components of the lower scale process, can still be quite simple in form. This is demonstrated by means of some recent upscaling work on the solute teansport conservation equation for hetergeneous aquifers. By means of this solute transport example, it is also shown that for the ensemble average form of a hydrologic conservation equation to be equivalent to its volume-average form at any scale, the parameter functions of that conservation equation at the immediately lower scale must be ergodic.

• Interaction and multiscale mechanics
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• v.4 no.3
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• pp.219-237
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• 2011

Recent advances in scientific computing enable the full atomistic simulation of DNA molecules. However, there exists length and time scale limitations in molecular dynamics (MD) simulation for large DNA molecules. In this work, a two-level homogenization of DNA molecules is proposed. A wavelet projection method is first introduced to form a coarse-grained DNA molecule represented with superatoms. The coarsened MD model offers a simplified molecular structure for the continuum description of DNA molecules. The coarsened DNA molecular structure is then homogenized into a three-dimensional beam with embedded molecular properties. The methods to determine the elasticity constants in the continuum model are also presented. The proposed continuum model is adopted for the study of mechanical behavior of DNA loop.

• International Journal of Control, Automation, and Systems
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• v.4 no.3
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• pp.382-393
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• 2006

Mechanical system dynamics plays an important role in the area of computational structural biology. Elastic network models (ENMs) for macromolecules (e.g., polymers, proteins, and nucleic acids such as DNA and RNA) have been developed to understand the relationship between their structure and biological function. For example. a protein, which is basically a folded polypeptide chain, can be simply modeled as a mass-spring system from the mechanical viewpoint. Since the conformational flexibility of a protein is dominantly subject to its chemical bond interactions (e.g., covalent bonds, salt bridges, and hydrogen bonds), these constraints can be modeled as linear spring connections between spatially proximal representatives in a variety of coarse-grained ENMs. Coarse-graining approaches enable one to simulate harmonic and anharmonic motions of large macromolecules in a PC, while all-atom based molecular dynamics (MD) simulation has been conventionally performed with an aid of supercomputer. A harmonic analysis of a macroscopic mechanical system, called normal mode analysis, has been adopted to analyze thermal fluctuations of a microscopic biological system around its equilibrium state. Furthermore, a structure-based system optimization, called elastic network interpolation, has been developed to predict nonlinear transition (or folding) pathways between two different functional states of a same macromolecule. The good agreement of simulation and experiment allows the employment of coarse-grained ENMs as a versatile tool for the study of macromolecular dynamics.

• Korea-Australia Rheology Journal
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• v.19 no.2
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• pp.51-59
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• 2007

A polyelectrolyte chain confined in a slit nanochannel exhibits a structural transition from the one in free space. In this paper, the effect of the long-range electrostatic interactions between the xanthan polyelectrolyte and the slit wall on the confined xanthan conformation is investigated via the Brownian dynamics simulation. A neutral and two negatively charged surfaces of polydimethylsiloxane (PDMS) and glass are combined to make four kinds of slit channels with different charge characteristics: i) neutral-neutral, ii) glass-glass, iii) neutral-PDMS and iv) neutral-glass walls. Their walls are characterized by uniform surface charge densities determined from experimental data of zeta potential. Both the nonmonotonic chain size variation and the loss of long-range bond vector correlation, previously observed under confinement in the PDMS-PDMS slit, are also found in the neutral slit, demonstrating the nonelectrostatic origin of such crossover behaviors. As expected, the effect of wall charges is negligible at sufficiently high medium ionic strength of 100mM but it becomes significant in the opposite limit of 0.01mM. In the latter case, the high charge density of glass walls strengthens the effective confinement of a negatively charged polyelectrolyte and produces a xanthan structure comparable to that confined in a much narrower neutral slit. The obtained structural data suggest the possibility of controlling the structure of confined polyelectrolytes by the modification of surface charge characteristics of micro/nanofluidic devices in combination with the adjustment of the medium ionic strength.