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Nanomechanics of biomolecules: focus on DNA
Y. Eugene Pak,김대식,Mohana Marimuthu,김상효 대한기계학회 2009 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.23 No.7
Nano-mechanical measurements and manipulations at the single-cell and single-molecular levels using the atomic force microscope (AFM) and optical tweezers are presenting fascinating opportunities to the researchers in bioscience and biotechnology. Single molecule biophysics technologies, due to their capability to detect transient states of molecules and biomolecular complexes, are the methods of choice for studies in DNA structure and dynamics, DNA-DNA and DNA-protein interactions, and viral DNA packaging. The aim of this review is to describe the recent developments of scientific tools and the knowledge gained in single molecule DNA mechanics such as DNA elasticity, electrostatics, condensation and interactions of DNA with surrounding fluids during its hydrodynamic flow.
Energy release rates for various defects under different loading conditions
Y. Eugene Pak,다네시와미시라,유승현 대한기계학회 2012 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.26 No.11
It is well known that the energy release rate associated with translation, rotation and self-similar expansion of defects in solids are expressed by the path-independent integrals J, L, and M, respectively. It is shown that these integrals for a crack or a circular hole may be obtained by first considering an elliptical cavity and then performing a limiting process. This obviates dealing with singularities at the crack tip. The energy release rates for these defects under various mechanical, thermal and electromechanical loading conditions are calculated.
Dhaneshwar Mishra,Y. Eugene Pak(박유근),Seung-Hyun Yoo(유승현) (사)한국CDE학회 2011 한국 CAD/CAM 학회 학술발표회 논문집 Vol.2011 No.1
Materials used for various applications are inherently inhomogeneous though we consider it homogeneous and isotropic for simplicity of analysis. Composite materials which are very common now a days for various applications in both large and small structures are designed in such a way that it has different layers and these layers have different material properties gives rise to the material inhomogeneity at the interfaces of these layers. Material inhomogeneity can cause stress concentration. Energy can be released or absorbed depending upon the elastic modulus mismatch between interfacing layers. The stress concentration along with energy release rate (GC) when reaches at its critical value can contribute to material failure. We have presented analytical solution for M-integral, the measure of energy release rate for self similar expansion in fiber, coating and matrix and studied the effect of material inhomogeneity by choosing different shear modulus ratio of fiber - matrix and coating ? matrix. The effect of coating thickness on energy release rate is also studied. It has been found that combination of stiffer fiber and softer coating in comparison to matrix absorbs energy while when fiber becomes softer and coating becomes stiffer with respect to matrix, it releases energy. Thickness of coating also have significant effect on energy release or absorb rate as in case of thicker coating, the energy release/absorb rate is smaller in both coating and matrix region while it increases significantly when we choose thinner coating. This study will be very helpful for understanding the energy release/absorb due to material inhomogeneity and coating thickness and thus help to understand the critical region of failures in such structures which can contribute for design improvements for composite structures with inclusions.
3-D Simulation of Nanopore Structure for DNA Sequencing
Park, Jun-Mo,Pak, Y. Eugene,Chun, Honggu,Lee, Jong-Ho American Scientific Publishers 2012 Journal of Nanoscience and Nanotechnology Vol.12 No.7
<P>In this paper, we propose a method for simulating nanopore structure by using conventional 3-D simulation tool to mimic the I-V behavior of the nanopore structure. In the simulation, we use lightly doped silicon for ionic solution where some parameters like electron affinity and dielectric constant are fitted to consider the ionic solution. By using this method, we can simulate the I-V behavior of nanopore structure depending on the location and the size of the sphere shaped silicon oxide which is considered to be an indicator of a DNA base. In addition, we simulate an Ionic Field Effect Transistor (IFET) which has basically the nanopore structure, and show that the simulated curves follow sufficiently the I-V behavior of the measurement data. Therefore, we think it is reasonable to apply parameter modeling mentioned above to simulate nanopore structure. The key idea is to modify electron affinity of silicon which is used to mimic the KCl solution to avoid band bending and depletion inside the nanopore. We could efficiently utilize conventional 3-D simulation tool to simulate the I-V behavior of nanopore structures.</P>
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서유정(Youjung Seo),박유근(Y. Eugene Pak) 대한기계학회 2017 대한기계학회 춘추학술대회 Vol.2017 No.11
The configurational forces on arbitrary-oriented line singularities that are subjected to far-field loads in an infinite isotropic solid are evaluated by the path-independent J<SUB>k</SUB> , M , and L-integrals. The translational forces, J<SUB>k</SUB>, acting on these singularities are obtained in closed-form expressions which are shown to be equivalent to the generalized Peach-Koehler force¹. The self-similar expansion forces, M, for the nuclei of strain are obtained when the normal stresses exists. Likewise, the rotational forces, L, for the concentrated couple moment exists only when the normal stresses are present.