• Journal of the Semiconductor & Display Technology
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• v.3 no.3
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• pp.27-29
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• 2004

The responses of hypothetical silicon nanotubes under torsion have been investigated using an atomistic simulation based on the Tersoff potential. A torque, proportional to the deformation within Hooke's law, resulted in the ribbon-like flattened shapes and eventually led to a breaking of hypothetical silicon nanotubes. Each shape change of hypothetical silicon nanotubes corresponded to an abrupt energy change and a singularity in the strain energy curve as a function of the external tangential force, torque, or twisted angle. The dynamics of silicon nanotubes under torsion can be modelled in the continuum elasticity theory.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.32 no.2
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• pp.170-176
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• 2008

Anti roll bar model for real time multibody vehicle dynamics model has been proposed using kinematic constraint. Anti roll bar have been modeled by kinematic relationship, and mass properties are neglected. Relative angle of torsion bar spring is computed by constraint about drop-link using Newton-Raphson iteration, and then the torque of torsion bar spring can be computed with the angle and torsion spring stiffness. Finally anti roll bar force acting on both knuckle can be calculated. To validate the proposed method, half car simulations of McPherson strut suspension and full car simulations are also carried out comparing with the ADAMS vehicle model with anti roll bar. CPU times are also measured to see the real-time capabilities of the proposed method.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.4
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• pp.102-108
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• 2016

With the rapid increase of data on protein-protein interactions, the need for delineating the 3D structures of huge protein complexes has increased. The protocols for determining nuclear magnetic resonance (NMR) structure can be applied to modeling complex structures coupled with sparse experimental restraints. In this report, I suggest the use of multiple rigid bodies for improving the efficiency of NMR-assisted structure modeling of huge complexes using CYANA. By preparing a region of known structure as a new type of residue that has no torsion angle, one can facilitate the search of the conformational spaces. This method has a distinct advantage over the rigidification of a region with synthetic distance restraints, particularly for the calculation of huge molecules. I have demonstrated the idea with calculations of decaubiquitins that are linked via Lys6, Lys11, Lys27, Lys29, Lys33, Lys48, or Lys63, or head to tail. Here, the ubiquitin region consisting of residues 1-70 was treated as a rigid body with a new residue. The efficiency of the calculation was further demonstrated in Lys48-linked decaubiquitin with ambiguous distance restraints. The approach can be readily extended to either protein-protein complexes or large proteins consisting of several domains.

• Proceedings of the Korean Society Of Semiconductor Equipment Technology
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• 2004.05a
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• pp.63-66
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• 2004

The responses of hypothetical silicon nanotubes under torsion have been investigated using an atomistic simulation based on the Tersoff potential. A torque, proportional to the deformation within Hooke's law, resulted in the ribbon-like flattened shapes and eventually led to a breaking of hypothetical silicon nanotubes. Each shape change of hypothetical silicon nanotubes corresponded to an abrupt energy change and a singularity in the strain energy curve as a function of the external tangential force, torque, or twisted angle. The dynamics of silicon nanotubes under torsion can be modelled in the continuum elasticity theory.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.16 no.12S
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• pp.1165-1174
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• 2003

The responses of hypothetical silicon nanotubes under torsion have been investigated using an atomistic simulation based on the Tersoff potential. A torque, proportional to the deformation within Hooke's law, resulted in the ribbon-like flattened shapes and eventually led to a breaking of hypothetical silicon nanotubes. Each shape change of hypothetical silicon nanotubcs corresponded to an abrupt energy change and a singularity in the strain energy curve as a function of the external tangential force, torque, or twisted angle. The dynamics o silicon nanotubes under torsion can be modelled in the continuum elasticity theory.

• Proceedings of the KSME Conference
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• 2004.11a
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• pp.410-415
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• 2004

Molecular dynamics simulations of nanoimprint lithography in which a stamp with patterns is pressed onto amorphous poly-(methylmethacrylate) (PMMA) surface are performed to study the deformation of polymer. Force fields including bond, angle, torsion, inversion, van der Waals and electrostatic potential are used to describe the intermolecular and intramolecular force of PMMA molecules and stamp. Periodic boundary condition is used in horizontal direction and $Nos\acute{e}$-Hoover thermostat is used to control the system temperature. As the simulation results, the adhesion forces between stamp and polymer are calculated and the mechanism of deformation are investigated. The effects of the adhesion force and friction force on the polymer deformation are also studied to analyze the pattern transfer in nanoimprint lithography. The mechanism of polymer deformation is investigated by means of inspecting the indentation process, molecular configurational properties, and molecular configurational energies.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.29 no.6 s.237
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• pp.852-859
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• 2005

Molecular dynamics simulations of nanoimprint lithography in which a stamp with patterns is pressed onto amorphous poly-(methylmethacrylate) (PMMA) surface are performed to study the deformation of polymer. Force fields including bond, angle, torsion, inversion, van der Waals and electrostatic potential are used to describe the intermolecular and intramolecular force of PMMA molecules and stamp. Periodic boundary condition is used in horizontal direction and Nose-Hoover thermostat is used to control the system temperature. As the simulation results, the adhesion forces between stamp and polymer are calculated and the mechanism of deformation are investigated. The effects of the adhesion and friction forces on the polymer deformation are also studied to analyze the pattern transfer in nanoimprint lithography. The mechanism of polymer deformation is investigated by means of inspecting the indentation process, molecular configurational properties, and molecular configurational energies.

• Proceedings of the KSME Conference
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• 2007.05a
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• pp.337-342
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• 2007

In this study, molecular dynamics simulation of nano imprint lithography in which patterned stamp is pressed onto amorphous polyethylene(PE) surface are performed to study the behaviour of polymer. Force fields including bond, angle, torsion, and Lennard Jones potential are used to describe the inter-molecular and intra-molecular force of PE molecules and stamp, substrate. Periodic boundary condition is used in horizontal direction and canonical NVT ensemble is used to control the system temperature. As the simulation results, the behaviour of polymer is investigated during the imprinting process. The mechanism of polymer deformation is studied by means of inspecting the surface shape, volume, density, atom distribution. Deformation of the polymer resist was found for various of the stamp geometry and the alignment state of the polymer molecules.

• BMB Reports
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• v.40 no.2
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• pp.261-269
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• 2007

The structure and dynamics of a 37-residue antimicrobial peptide gaegurin 4 (GGN4) isolated from the skin of the native Korean frog, Rana rugosa, was determined in SDS micelles by NMR spectroscopy. The solution structure of the peptide in SDS micelles was determined from 352 NOE-derived distance constraints and 22 backbone torsion angle constraints. Dynamic properties for the amide backbone were characterized by $^1H-^{15}N $heteronuclear NOE experiments. The structural study revealed two amphipathic helices spanning residues 2-10 and 16-32 and that the helices were connected by a flexible loop. An intraresidue disulfide bridge was formed between residues Cys31 and Cys37 near the C-terminus. The loop region (11-15) connecting the two helices are were slightly more flexible than these helices themselves. From the fact that since there is no contact NOEs between two helices, it is implied that the GGN4 peptide shows an independent motion of both helices which has an angle of about $ 60^{\circ}-120^{\circ}$ from each other.

• Tribology and Lubricants
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• v.21 no.4
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• pp.177-184
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• 2005

The molecular dynamics simulation of nanoimprint lithography (NIL) using $SiO_2$ stamp and amorphous poly-(methylmethacrylate) (PNMA) film is performed to study pattern transfer in NIL. Force fields including bond, angle, torsion, van der Waals and electrostatic potential are used to describe the intermolecular and intramolecular force of PMMA molecules and $SiO_2$ stamp. Nose-Hoover thermostat is used to control the system temperature and cell multipole method is adopted to treat long range interactions. The deformation of PMMA film is observed during pattern transfer in the NIL process. For the detail analysis of deformation characteristics, the distributions of density and stress in PMHA film are calculated. The adhesion and friction forces are obtained by dividing the PMMA film into subregions and calculating the interacting force between subregion and stamp. Their effects on the pattern transfer are also discussed as varying the indentation depth and speed.