• Proceedings of the KSR Conference
• /
• 2008.11b
• /
• pp.1403-1406
• /
• 2008

Periodic lattice structures such as the large space lattice structures and carbon nanotubes may take the extension-transverse shear-bending coupled vibrations, which can be well represented by the extended Timoshenko beam theory. In this paper, the spectrally formulated finite element model (simply, spectral element model) has been developed for extended Timoshenko beams and applied to some typical periodic lattice structures such as the armchair carbon nanotube, the periodic plane truss, and the periodic space lattice beam.

• Transactions of the Korean Society of Mechanical Engineers B
• /
• v.39 no.5
• /
• pp.415-423
• /
• 2015

In this study, we present a grid refinement model in the lattice Boltzmann method (LBM) for two-dimensional incompressible fluid flow. That is, the model combines the desirable features of the lattice Boltzmann method and stream function-vorticity formulations. In order to obtain an accurate result, very fine grid (or lattice) is required near the solid boundary. Therefore, the grid refinement model is used in the lattice Boltzmann method for stream function-vorticity formulation. This approach is more efficient in that it can obtain the same accurate solution as that in single-block approach even if few lattices are used for computation. In order to validate the grid refinement approach for the stream function-vorticity formulation, the numerical simulations of lid-driven cavity flows were performed and good results were obtained.

• Bulletin of the Korean Chemical Society
• /
• v.17 no.9
• /
• pp.808-813
• /
• 1996

To explore protein folding mechanism, we simulated a folding pathway in a simplified 3×3×3 cubic lattice. In the lattice folding Monte Carlo simulations, each of the 28 possible native packing pairs that exist in the native conformation was used as a conformational restraint. The native packing restraints in the lattice model could be considered as a disulfide linkage restraint in a real protein. The results suggest that proteins denatured with a small disulfide loop can, but not always, fold faster than proteins without any disulfide linkage and than proteins with a larger disulfide loop. The results also suggest that there is a rough correlation between loop size of the native packing restraint and folding time. That is, the order of native residue-residue packing interaction in protein folding is likely dependent on the residue-residue distance in primary sequence. The strength of monomer-monomer pairwise interaction is not important in the determination of the packing order in lattice folding. From the folding simulations of five strong folding lattice sequences, it was also found that the context encoded in the primary sequence, which we do not yet clearly understand, plays more crucial role in the determination of detailed folding kinetics. Our restrained lattice model approach would provide a useful strategy to the future protein folding experiments by suggesting a protein engineering for the fast or slow folding research.

• Molecules and Cells
• /
• v.45 no.7
• /
• pp.444-453
• /
• 2022

Multivalent macromolecular interactions underlie dynamic regulation of diverse biological processes in ever-changing cellular states. These interactions often involve binding of multiple proteins to a linear lattice including intrinsically disordered proteins and the chromosomal DNA with many repeating recognition motifs. Quantitative understanding of such multivalent interactions on a linear lattice is crucial for exploring their unique regulatory potentials in the cellular processes. In this review, the distinctive molecular features of the linear lattice system are first discussed with a particular focus on the overlapping nature of potential protein binding sites within a lattice. Then, we introduce two general quantitative frameworks, combinatorial and conditional probability models, dealing with the overlap problem and relating the binding parameters to the experimentally measurable properties of the linear lattice-protein interactions. To this end, we present two specific examples where the quantitative models have been applied and further extended to provide biological insights into specific cellular processes. In the first case, the conditional probability model was extended to highlight the significant impact of nonspecific binding of transcription factors to the chromosomal DNA on gene-specific transcriptional activities. The second case presents the recently developed combinatorial models to unravel the complex organization of target protein binding sites within an intrinsically disordered region (IDR) of a nucleoporin. In particular, these models have suggested a unique function of IDRs as a molecular switch coupling distinct cellular processes. The quantitative models reviewed here are envisioned to further advance for dissection and functional studies of more complex systems including phase-separated biomolecular condensates.

• The Transactions of The Korean Institute of Electrical Engineers
• /
• v.59 no.6
• /
• pp.1126-1130
• /
• 2010

Speech production can be viewed as a filtering operation in which a sound source excites a vocal tract filter. The vocal tract is modeled as a chain of cylinders of varying cross-sectional area in linear prediction acoustic tube modeling. In this modeling the most common implementation assumes equal length of tube sections. Therefore, to model complex vocal tract shapes, a large number of tube sections are needed. This paper proposes a new vocal tract model with unfixed sectionlengths, which uses the reduced lattice filter for modeling the vocal tract. This model transforms the lattice filter to reduced structure and the Burg algorithm to modified version. When the conventional and the proposed models are implemented with the same order of linear prediction analysis, the proposed model can produce more accurate results than the conventional one. To implement a system within similar accuracy level, it may be possible to reduce the stages of the lattice filter structure. The proposed model produces the more similar vocal tract shape than the conventional one.

• 한국가시화정보학회:학술대회논문집
• /
• 2005.12a
• /
• pp.103-106
• /
• 2005

Lattice Boltzmann method is a new numerical method of investigating the fluid flow which have been solved by Navier-Stokes equation recently. It is known that making the single and parallel algorithms of the Lattice Boltzmann equation is easier than those of Navier-Stokes equations. Also, we can simulate the two phase flow using either the 'Interaction Potential model ' introduced by Shan and Chen. In this paper, we first compared the 3D cavity results of Lattice Boltzmann method with other numerical results for validation and showed the 3D phase transition and its simple application by using the ' Interaction Potential model'

• Journal of Mechanical Science and Technology
• /
• v.16 no.10
• /
• pp.1327-1335
• /
• 2002

The shock wave process represents an abrupt change in fluid properties, in which finite variations in pressure, temperature, and density occur over the shock thickness which is comparable to the mean free path of the gas molecules involved. This shock wave fluid phenomenon is simulated by using the finite difference lattice Boltzmann method (FDLBM). In this paper, a new model is proposed using the lattice BGK compressible fluid model in FDLBM for the purpose of speeding up the calculation as well as stabilizing the numerical scheme. The numerical results of the proposed model show good agreement with the theoretical predictions.

• Journal of Mechanical Science and Technology
• /
• v.17 no.12
• /
• pp.2034-2041
• /
• 2003

This study introduced a lattice Boltzmann computational scheme capable of modeling thermo hydrodynamic flows with simpler equilibrium particle distribution function compared with other models. The equilibrium particle distribution function is the local Maxwelian equilibrium function in this model, with all the constants uniquely determined. The characteristics of the proposed model is verified by calculation of the sound speeds, and the shock tube problem. In the lattice Boltzmann method, a thermal fluid or compressible fluid model simulates the reflection of a weak shock wave colliding with a sharp wedge having various angles $\theta$$\sub$w/. Theoretical results using LBM are satisfactory compared with the experimental result or the TVD.

• Structural Engineering and Mechanics
• /
• v.41 no.5
• /
• pp.645-662
• /
• 2012

Deteriorative effects of steel corrosion on the structural response of reinforced concrete are simulated for varying degrees of corrosion. The simulation approach is based on a three-dimensional irregular lattice model of the bulk concrete, in which fracture is modeled using a crack band approach that conserves fracture energy. Frame elements and bond link elements represent the reinforcing steel and its interface with the concrete, respectively. Polylinear stress-slip properties of the link elements are determined, for several degrees of corrosion, through comparisons with direct pullout tests reported in the literature. The link properties are then used for the lattice modeling of reinforced concrete beams with similar degrees of corrosion of the main reinforcing steel. The model is successful in simulating several important effects of steel corrosion, including increased deflections, changes in flexural cracking behavior, and reduced yield load of the beam specimens.

• Bulletin of the Korean Chemical Society
• /
• v.18 no.9
• /
• pp.965-972
• /
• 1997

An approximate molecular theory of classical fluids based on the nonrandom lattice statistical-mechanical theory is presented. To obtain configurational Helmholtz free energy and equation of state (EOS), the lattice-hole theory of the Guggenheim combinatorics is approximated by introducing the nonrandom two-fluid theory. The approximate nature in the derivation makes the model possible to unify the classical lattice-hole theory and to describe correctly the configurational properties of real fluids including macromolecules. The theory requires only two molecular parameters for a pure fluid. Results obtained to date have demonstrated that the model correlates quantitatively the first- and second-order thermodynamic properties of real fluids. The basic simplicity of the model can readily be generalized to multicomponent systems. The model is especially relevant to (multi) phase equilibria of systems containing molecularly complex species.