• Macromolecular Research
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• v.17 no.10
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• pp.807-812
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• 2009

In this work, we focus on the tumbling dynamics of rod-like and semi-flexible polymers in mixed flows, which vary from simple shear to pure rotation. By employing a bead-rod model, the tumbling pathways and periods are examined with a focus on the angular distribution of their orientation. Under the mixed flows, the tumbling dynamics agreed well with earlier studies and confirmed the predicted scaling laws. We found that the angular distribution deviates from that of shear flow as the flow type approaches pure rotation. Finally, we investigated the angular distribution of $\lambda$-DNA in a shear flow and found that the present numerical simulations were in quantitative agreement with the previous experimental data.

• Bulletin of the Korean Chemical Society
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• v.29 no.11
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• pp.2103-2108
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• 2008

• Proceedings of the PSK Conference
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• 2002.10a
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• pp.312.2-312.2
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• 2002

The metal-ligand complex, ［Ru(phen)$_2$(dppz)]^{2＋}$ (phen = 1.10-phenanthroline, dppz = dipyrido［3.2-a:2', 3'-c］phenazine) (RuPD), was used as a spectroscopic probe for studying nucleic acid dynamics. The RuPD complex displays a long lifetime and a molecular light switch property upon DNA binding due to shielding of its dppz ligand from water. (omitted)

• Korean Chemical Engineering Research
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• v.62 no.1
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• pp.118-124
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• 2024

A neural network is utilized for preprocessing of de-noizing in electrocardiogram signals, retinal images, seismic waves, etc. However, the de-noizing process could provoke increase of computational time and distortion of the original signals. In this study, we investigated a neural network architecture to analyze measurement data without additional de-noizing process. From the dynamical behaviors of DNA in aqueous solution, our neural network model aimed to predict the mole fraction of each DNA in the solution. By adding white noise to the dynamics data of DNA artificially, we investigated the effect of the noise to neural network's predictions. As a result, our model was able to predict the DNA mole fraction with an error of O(0.01) when signal-to-noise ratio was O(1). This work can be applied as a efficient artificial intelligence methodology for analyzing DNA related to genetic disease or cancer cells which would be sensitive to background measuring noise.

• 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.

• 한국전산유체공학회:학술대회논문집
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• 2010.05a
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• pp.575-580
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• 2010

In this work, the electrophoretic motion of dsDNA molecule represented by a polymer through an artificial nano-pore in a membrane is simulated using the numerical method combining the lattice Boltzmann and Langevin molecular dynamic method. The polymer motion is represented by Langevin molecular dynamics technique while the fluid flow is taken into account by fluctuating lattice-Boltzmann method. The hydrodynamic interactions between the polymer and solvent in a confined space with a membrane having a hole are considered explicitly through the frictional and the random forces. The electric field intensity over the space is obtained from a finite difference method. Initially, the polymer is placed at one side of the space, and an electric field is applied to drive the polymer to the other side of the space through the nano-pore. In future, we plan to study the effect of the polymer size and the electric field on the electrophoretic velocity.

• Archives of Pharmacal Research
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• v.24 no.5
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• pp.455-465
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• 2001

The highly potent cytotoxic DNA-DNA cross-linker consists of two cyclopropa[c]pyrrolo[3,4-3]indol-4(5H)-ones insoles [(+)-CPI-I] joined by a bisamido pyrrole (abbreviated to "Pyrrole"). The Pyrrole is a synthetic analog of Bizelesin, which is currently in phase II clinical trials due to its excellent in vivo antitumor activity. The Pyrrole has 10 times more potent cytotoxicity than Bizelesin and mostly form DNA-DNA interstrand cross-links through the N3 of adenines spaced 7 bp apart. The Pyrrole requires a centrally positioned GC base pair for high cross-linking reactivity (i.e., $5^1$-T$AT_2$A*-$3^1$), while Bizelesin prefers purely AT-rich sequences (i.e., $5^1$-T$AT_4$A*-$3^1$, where /(equation omitted) represents the cross-strand adenine alkylation and A* represents an adenine alkylation) (Park et al., 1996). In this study, the high-field $^1$H-NMR and rMD studies are conducted on the 1 1-mer DNA duplex adduct of the Pyrrole where the 5′(equation omitted)TAGTTA*-3′sequence is cross-linked by the drug. A severe structural perturbation is observed in the intervening sequences of cross-linking site, while a normal B-DNA structure is maintained in the region next to the drug-modified adenines. Based upon these observations, we propose that the interplay between the bisamido pyrrole unit of the drug and central C/C base pair (hydrogen-bonding interactions) is involved in the process of cross-linking reaction, and sequence specificity is the outcome of those interactions. This study suggests a mechanism for the sequence specific cross-linking reaction of the Pyrrole, and provides a further insight to develop new DNA sequence selective and distortive cross-linking agents.

• Proceedings of the Korea Crystallographic Association Conference
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• 2000.05a
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• pp.26-26
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• 2000

• Interaction and multiscale mechanics
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• v.6 no.4
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• pp.395-409
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• 2013

Molecular dynamics (MD) systems are highly nonlinear and nonlocal, and the conventional model order reduction methods are ineffective for MD systems. The RBF-POD method (Lee and Chen, 2013) employed a radial basis function (RBF) approximated potential energies and inter-atomic forces of MD systems under the framework of the proper orthogonal decomposition (POD) method for the reduced-order modeling of MD systems. In this work, we focus on the numerical procedures of the RBF-POD method and demonstrate how to apply this approach to the modeling of ds-DNA molecules under stretching and bending conditions.

• Journal of Microbiology and Biotechnology
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• v.25 no.3
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• pp.307-316
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• 2015

Beginning from the recognition of FtsZ as a bacterial tubulin homolog in the early 1990s, many bacterial cytoskeletal elements have been identified, including homologs to the major eukaryotic cytoskeletal elements (tubulin, actin, and intermediate filament) and the elements unique in prokaryotes (ParA/MinD family and bactofilins). The discovery and functional characterization of the bacterial cytoskeleton have revolutionized our understanding of bacterial cells, revealing their elaborate and dynamic subcellular organization. As in eukaryotic systems, the bacterial cytoskeleton participates in cell division, cell morphogenesis, DNA segregation, and other important cellular processes. However, in accordance with the vast difference between bacterial and eukaryotic cells, many bacterial cytoskeletal proteins play distinct roles from their eukaryotic counterparts; for example, control of cell wall synthesis for cell division and morphogenesis. This review is aimed at providing an overview of the bacterial cytoskeleton, and discussing the roles and assembly dynamics of bacterial cytoskeletal proteins in more detail in relation to their most widely conserved functions, DNA segregation and coordination of cell wall synthesis.