• Molecules and Cells
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• v.45 no.1
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• pp.33-40
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• 2022

The various DNA-protein interactions associated with the expression of genetic information involve double-stranded DNA (dsDNA) bending. Due to the importance of the formation of the dsDNA bending structure, dsDNA bending properties have long been investigated in the biophysics field. Conventionally, DNA bendability is characterized by innate averaging data from bulk experiments. The advent of single-molecule methods, such as atomic force microscopy, optical and magnetic tweezers, tethered particle motion, and single-molecule fluorescence resonance energy transfer measurement, has provided valuable tools to investigate not only the static structures but also the dynamic properties of bent dsDNA. Here, we reviewed the single-molecule methods that have been used for investigating dsDNA bendability and new findings related to dsDNA bending. Single-molecule approaches are promising tools for revealing the unknown properties of dsDNA related to its bending, particularly in cells.

• Proceedings of the Korean Vacuum Society Conference
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• 2015.08a
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• pp.63.2-63.2
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• 2015

Controlling and sensing spin states of magnetic molecules such as metallo-porphyrins at the single molecule level is essential for spintronic molecular device applications. Axial coordinations of diatomic molecules to metallo-porphyrins also play key roles in dynamic processes of biological functions such as blood pressure control and immune response. However, probing such reactions at the single molecule level to understand their physical mechanisms has been rarely performed. Here we present on our single molecule association and dissociation experiments between diatomic and metallo-porphyrin molecules on Au(111) describing its adsorption structures, spin states, and dissociation mechanisms. We observed bright ring shapes in NO adsorbed metallo-porphyrin compelxes and explained them by considering tilted binding and precession motion of NO. Before NO exposure, Co-porphryin showed a clear zero-bias peak in scanning tunneling spectroscopy, a signature of Kondo effect in STS, whereas after NO exposures it formed a molecular complex, NO-Co-porphyrin, that did not show any zero-bias feature implying that the Kondo effect was switched off by binding of NO. Under tunneling junctions of scanning tunneling microscope, both positive and negative energy pulses. From the observed power law relations between dissociation rate and tunneling current, we argue that the dissociations were inelastically induced with molecular orbital resonances. Our study shows that single molecule association and dissociation can be used to probe spin states and reaction mechanisms in a variety of axial coordination between small molecules and metallo-porphyrins.

• Proceedings of the Korean Society for Technology of Plasticity Conference
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• 1999.03b
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• pp.173-178
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• 1999

In this study MD simulations have been performed to observe the behavior of a grain boundary in an a-Fe plate under 2-dimensional loading. In MD simulation the acceleration of every molecule can be achieved from the potential energy and the force interacting between each molecule and the integration of the motion equation by using Verlet method gives the displacement of each molecule. Initially four a-Fe rectangular plates having different misorientation angles of grain boundary were modeled by using the Johnson potential and Morse potential We compared the potential energy of the grain boundary system with that of the perfect structure model. Also we could obtain the width of the grain boundary by investigating the local potential energy distribution. The tensile loading for each grain boundary models was applied and the behavior of grin boundary was studied. From this study it was clarified that in the case using Johnson potential the obvious fracture mechanism occurs along the grain boundary in the case of Morse potential the diffusion of the grain boundary appears instead of the grain boundary fracture.

• 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.

• Proceedings of the Optical Society of Korea Conference
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• 2001.02a
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• pp.272-273
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• 2001

We demonstrate the first separation of neutral molecules using optical forces. Unlike laser atomic cooling or optical tweezers, optical separation technique requires the manipulation of only one component of the molecular motion. Thus the mixtures can be separated, in principle, with less complex schemes. When an Intense nonresonant laser beam is focused onto a beam of molecules, the interaction between the laser electric field and the induced dipole moment of a molecule invokes a mechanical force on the molecule proportional to the field gradient and the molecular polarizability ($\alpha$) to mass (m) ratio $\alpha$/m. (omitted)

• Journal of The Korean Association For Science Education
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• v.18 no.2
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• pp.161-171
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• 1998

The effects of computer-assisted instruction (CAl) using molecular-level animation upon students' conceptions, attitudes toward science instruction, and learning motivation were investigated. Treatment and control groups (2 classes) were selected from a girls middle school in Seoul, and taught about the motion of molecule for 5 class hours. Before instruction, the short-version Group Assessment of Logical Thinking (GALT) and the Patterns of Adaptive Survey were administered, and the grade for the previous science course was obtained. The GALT score was used as a blocking variable, and the others as covariates. After the instructions, the researcher-made conceptions test, the test of attitudes toward science instruction, and the motivation questionnaire were administered. The perception questionnaire of CAl was also administered to the treatment group. Although more students in the CAl group had sound understanding about the motion of molecule, the scores of the conceptions test for the two groups were not significantly different at .05 level of significance. The students in the CAl group, however, were found to have more positive attitudes toward science instruction and learning motivation. In the perception questionnaire of CAl, most students in the treatment group exhibited positive attitudes toward the CAl. However, some students mentioned that they were disturbed by noisy environments, and that they could not understand some content presented. Educational implications are discussed.

• 한국정보디스플레이학회:학술대회논문집
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• 2005.07a
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• pp.199-202
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• 2005

We have studied the origin of coherent director rotation [CDR] as well as memory behavior in thiol-ene polymer stabilized ferroelectric liquid crystal [FLC]. The ene constituents are found to be always located at the inter-layer space and induce the coherent director rotation motion of liquid crystal molecule. On the other hand, the thiols are more intersticed between ferroelectric liquid crystal molecules at intra-layer as the thiol gets longer, and these intersticed thiols enhance the multistability and the resolution of memory state of FLCs.

• Journal of the Korean Chemical Society
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• v.32 no.2
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• pp.94-102
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• 1988

A quantitative description of the principle of least motion is suggested. The reaction path function of electronic variables, its norm and the reaction path average energy, which are unique for a given reaction path on a potential energy surface of a reacting system, are defined and their characteristics are discussed. It is postulated that the norm of the function and the average energy can be used as a criterion for identification of the preferred path of a unimolecular isomerization reaction. For a molecule with a certain symmetry, the preferred path, with which Woodward-Hoffmann rule agrees, is immediately identified without laborious computation.

• Membrane Journal
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• v.4 no.2
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• pp.96-105
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• 1994

Theoretical model for membrane transport of large polye!ectroiyte is presented. When the electric field is applied, the molecular conformation quickly orients in the field direction showing overshooting orientation. the predicted dependence of overshoot time and orientation upon field intensity and molecular size aids to understand the dynamic motion of molecules in membrane transport. The dynamics of the overshoot is associated with self-trapping conformations of molecule. The understanding of these effects supports evidences for the electrophoretic filtration of polydectrolyte in the polymeric membrane. This paper shows one example for molecular study in the theoretical review paper of membrane transport.

• Journal of the Korean Chemical Society
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• v.28 no.1
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• pp.34-40
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• 1984

The reorientational motion of $C_6F_6$ in neat liquid is investigated in the temperature range 293∼333K by analyzing ${\nu}_2$ and ${\nu}_16$ bands of its Raman spectrum. Diffusion constants for the tumbling ($D_{\bo}$) and spinning ($D_{\parallel}$) motions are determined. The reorientation of the molecule seems to be distinctly anisotropic. Based on the hydrodynamic model, the tumbling motion of the figure axis of $C_6F_6$ is largely diffusional. On the other hand, the spinning motion of the same axis looks mostly inertial.