• Interaction and multiscale mechanics
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• v.2 no.4
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• pp.353-374
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• 2009

A new seamless multiscale simulation was developed for coupling the continuum model with its molecular dynamics. Kriging-based Finite Element Method (K-FEM) is employed to model the continuum base of the entire domain, while the molecular dynamics (MD) is confined in a localized domain of interest. In the coupling zone, where the MD domain overlaps the continuum model, the overall Hamiltonian is postulated by contributions from the continuum and the molecular overlays, based on a quartic spline scaling parameter. The displacement compatibility in this coupling zone is then enforced by the Lagrange multiplier technique. A multiple-time-step velocity Verlet algorithm is adopted for its time integration. The validation of the present method is reported through numerical tests of one dimensional atomic lattice. The results reveal that at the continuum/MD interface, the commonly reported spurious waves in the literature are effectively eliminated in this study. In addition, the smoothness of the transition from MD to the continuum can be significantly improved by either increasing the size of the coupling zone or expanding the nodal domain of influence associated with K-FEM.

• Journal of the Korean Vacuum Society
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• v.12 no.S1
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• pp.36-39
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• 2003

Field-domain dynamics and current self-oscillations are theoretically studied in quantum-well (QW) negative-effective-mass (NEM) $p^{+}pp^{+}$ diodes when the electric field is applied along the direction of the well. The origin of current self-oscillations is the formation and traveling of electric-field domains in the p-base. We have accurately considered the scattering contributions from carrier-impurity, carrier-acoustic phonon, and carrier-optic phonon. It's indicated that, both the applied bias and the doping concentration largely influence the current patterns and self-oscillating frequencies, which lie in the THz range for the NEM $p^{+}pp^{+}$ diode with a submicrometer p-base. The complicated field-domain dynamics is presented with the applied bias as the controlling parameter.

• Journal of Magnetics
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• v.11 no.2
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• pp.74-76
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• 2006

Dynamic behaviors of transverse domain walls (TDWs) in rectangular shaped thin-film magnetic nanowires with different widths under applied magnetic fields less than the Walker field were studied by micromagnetic simulations. It was found that the velocity of stable TDWs in the viscous region increases from 147 to 419 m/s and their mass decreases from $6.24{\times}10^{-23}\;to\;2.70{\times}10^{-23}kg$ with increasing strength of the applied magnetic field ranging from 5 to 20 Oe for the nanowire with a dimension of 10 nm in thickness and $5{\mu}m$ in length, and 50 nm in width. With increasing the width of nanowires from 50 to 125 nm at a specific field strength of 5 Oe, the TDW's velocity also increases from 147 to 246 m/s and its mass decreases from $6.24{\times}10^{-23}\;to\;5.91{\times}10^{-23}kg$.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1995.04a
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• pp.81-81
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• 1995

It is well known that Src Homology 2(SH2) domain in many intracellular signal transduction proteins is very important. The domain has about 100 amino acid residues and bind phosphotyrosine-containing peptide with high affinity and specificity. Lck SH2 domain is a Src-like, lymphocyte-specific tyrosine kinase. An 11-residue phosphopeptide derived from the hamster polvoma middle-T antigen, EPQp YEEIPIYL, binds with an 1 nM dissociation constant to Lck SH2 domain. And it is known that the phosphotyrosine and isoleucine residues of the peptide are tightly bound by two well-defined pockets on Lck SH2 domain's surface. To investigate the conformational changes during complexation of SH2 domain with phosphopeptide we have performed the molecular dynamics simulation for Lck SH2 domain with peptide and peptide-free form at look in aqueous solution. More than 3000 water molecules were incorporated to solvate Lck SH2 domain and peptide. Periodic boundary condition has been applied in molecular dynamics simulation. Data analysis with the results of that simulation shows that the phosphopeptide makes primary interaction with the Lck SH2 domain at six central residues, The comparison of the complexed and uncomplexed SH2 domain structures in solution has revealed only relatively small change. But the hydrophilic and hydrophobic pockets in the protein surface show the conformational changes in spite of the small structural difference between the complex and peptide-free forms.

• Proceedings of the Korean Magnestics Society Conference
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• 2000.09a
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• pp.121-146
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• 2000

A novel system of magneto-optical microscope magnetometer (MOMM), capable of simultaneous local problems of magnetic properties as well as real-time magnetic domain evolution imaging of ferromagnetic thin films with 400-nm spatial resolution, New findings in domain reveral dynamics of Co-based multilayers: The reversal ratio of V/R is a governing physical parameter. The activation volumes of wall-motion and nucleation processes are generally unequal. Submicron-scale local coercivity variation determines domain reversal dynamics. A thermally activated relaxation process during domain reversal is existed on the submicron-scale in realistic films. Local variation of magnetic properties should be considered for a realistic simulation. The fantastic capabilities of the MOMM can open many possibilities to broaden and deepen our understanding of domain reversal phenomena in ferromagnetic thin films.

• BMB Reports
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• v.29 no.4
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• pp.380-385
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• 1996

Ovomucoid third domain is a serine proteinase inhibitor protein which consists of 56 amino acid residues. A fifty picosecond molecular dynamics (MD) simulation was carried out for ovomucoid third domain protein with 5 $\AA$ layer of water molecules. A comparison of main chain atoms in the MD averaged structure with the crystal structure showed that most of the backbone structures are maintained during the simulation. Investigation of the intramolecular hydrogen bondings indicated that most of the interactions between main chain atoms were conserved, whereas those between side chains were reorganized for the period of the simulation. Especially, the side chain interactions around the scissile bond of reactive site P1 (Met18) were found to be more extensive for the MD structures. During the simulation, hydrogen bonds were maintained between the side chains of Glu19 and Arg21 as well as those of Thr17 and Glu19. Extensive side chain interactions observed in the MD structures may shed light on the question of why protein proteinase inhibitors are strong inhibitors for proteinases rather than good substrates.

• Korea-Australia Rheology Journal
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• v.21 no.1
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• pp.1-12
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• 2009

This paper reports the suitability of a domain decomposition technique for the hybrid simulation of dilute polymer solution flows using Eulerian Brownian dynamics and Radial Basis Function Networks (RBFN) based methods. The Brownian Configuration Fields (BCF) and RBFN method incorporates the features of the BCF scheme (which render both closed form constitutive equations and a particle tracking process unnecessary) and a mesh-less method (which eliminates element-based discretisation of domains). However, when dealing with large scale problems, there appear several difficulties: the high computational time associated with the Stochastic Simulation Technique (SST), and the ill-condition of the system matrix associated with the RBFN. One way to overcome these disadvantages is to use parallel domain decomposition (DD) techniques. This approach makes the BCF-RBFN method more suitable for large scale problems.

• 한국기계연구소 소보
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• s.18
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• pp.87-97
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• 1988

The algorithm for relation of contact status, track shift, and contact force caused from wheel/rail contact geometry is presented. Grafting this algorithm into a algorithm of general program analyzing mechanical system, the program for time domain simulation of railway vehicle dynamics, called CASOTD, was developed. In addition, as applied example of CASOTD, the dynamic simulation of railway vehicle running on a rail joint and a irregularly alinemented rail is done in this paper.

• Journal of the Korean Physical Society
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• v.73 no.12
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• pp.1899-1903
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• 2018

The effects of introducing hybrid lipids to a lipid bilayer containing saturated and unsaturated lipids immersed in water were studied. The lipid and water molecules were modeled as coarse-grained particles. All particles were simulated by using the dissipative particle dynamics method. The results showed that the hybrid lipids accumulated at the interface between the saturated and the unsaturated lipid domains. The relation between the hybrid lipid concentration and the equilibrium domain size was obtained. Moreover, the sizes of the simulated lipid domains are consistent with that given by the lipid raft definition.

• Proceedings of the Korean Magnestics Society Conference
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• 2001.04a
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• pp.104-105
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• 2001