• Proceedings of the KSME Conference
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• 2005.11a
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• pp.234.2-234.2
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• 2005

• Bulletin of the Korean Chemical Society
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• v.29 no.5
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• pp.1059-1062
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• 2008

• Journal of Mechanical Science and Technology
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• v.16 no.11
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• pp.1440-1447
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• 2002

Adhesion of a hemispherical tip to the flat surface in nano-structures is simulated using the molecular dynamics technique. The tip and plates are modeled with the Lennard-Jones molecules. The simulation focuses on the deformation of the tip. Detailed descriptions on the evolution of interaction force, the energy dissipation due to adhesion hysteresis, the forma- tion-growth-breakage of adhesive junction as well as the evolution of molecular distribution during the process are presented. The effects of the tip size, the maximum tip approach, the tip temperature, and the affinity between the tip and the mating plate are also discussed.

• 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 Magnetic Resonance Society
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• v.22 no.4
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• pp.139-143
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• 2018

Short antimicrobial peptide, A4W, have been studied by molecular dynamics (MD) simulation in an explicit dodecylphosphocholine (DPC) micelle. Peptide was aligned with DPC micelle and transferred new peptide-micelle coordinates within the same solvent box using specific micelle topology parameters. After initial energy minimization and equilibration, the conformation and orientation of the peptide were analyzed from trajectories obtained from the RMD (restrained molecular dynamics) or the subsequent free MD. Also, the information of solvation in the backbone and the side chain of the peptide, hydrogen bonding, and the properties of the dynamics were obtained. The results showed that the backbone residues of peptide are either solvated using water or in other case, they relate to hydrogen bonding. These properties could be a critical factor against the insertion mode of interaction. Most of the peptide-micelle interactions come from the hydrophobic interaction between the side chains of peptide and the structural interior of micelle system. The interaction of peptide-micelle, electrostatic potential and hydrogen bonding, between the terminal residues of peptide and the headgroups in micelle were observed. These interactions could be effect on the structure and flexibility of the peptide terminus.

• Journal of the Korean Society for Precision Engineering
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• v.12 no.4
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• pp.135-142
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• 1995

Recently, the analysis of microcutting with submicrometer depth of cut is tried to get a more high quality surface product, but to get a valuable result another method instead of conventional finite element method must be considered because finite element method is impossible for a very small focused region and mesh size. As the alternative method, Molecular Dynamics or Statics is suggested and accepted in the field of microcutting, indentation and crack propagation. In this paper using Molecular Dynamics simulation, the phenomena of microcutting with subnanometer chip thickness is studied and the cutting mechanism for tool edge configuration is evaluated. As the result of simulation the atomistic chip formation is achieved.

• Proceedings of the KSME Conference
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• 2001.11a
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• pp.252-257
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• 2001

With the help of newly arrived technology such as PC clustering, molecular dynamics (MD) seems to be promising for large-scale materials simulations. A cost-effective cluster is set up using commodity PCs connected over Ethernet with fast switching devices and free software Linux. Executing MD simulations in the parallel sessions makes it possible to carry out large-scale materials simulations at acceptable computation time and costs. In this study, the MD computer code for fracture simulation is modified to comply with MPI (Message Passing Interface) specification, and runs on the PC cluster in parallel mode flawlessly. It is noted that PC clusters can provide a rather inexpensive high-performance computing environment comparing to supercomputers, if properly arranged.

• Advances in concrete construction
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• v.4 no.4
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• pp.305-317
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• 2016

Porous materials such as concrete could be subjected to aggressive ions transport. Durability of cement paste is extremely depended on water and ions penetration into its interior sections. These ions transport could lead different damages depending on reactivity of ions, their concentrations and diffusion coefficients. In this paper, chloride diffusion process in cement hydrates is simulated at atomistic scale using molecular dynamics. Most important phase of cement hydrates is calcium silicate hydrate (C-S-H). Tobermorite, one of the most famous crystal analogues of C-S-H, is used as substrate in the simulation model. To conduct simulation, a nanopore is considered in the middle of simulation cell to place water molecules and aggressive ions. Different chloride salts are considered in models to find out which one is better for calculation of the transport properties. Diffusion coefficients of water molecules and chloride ions are calculated and validated with existing analytical and experimental works. There are relatively good agreements among simulation outputs and experimental results.

• Journal of the Korean Vacuum Society
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• v.4 no.S2
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• pp.139-147
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• 1995

The mechanism of the ionized cluster beam deposition has been studied using Molecular Dynamics Simulation. The Embedded Atom Method(EAM) potential were used in the simulation. The impact of a Au95-cluster on Au(100) substrate was studied for the impact energies 0.15-10eV/atom. The dependency of the impact energy of cluster beam was observed. For the cluster energy impact of 10eV per atom, the defects on surface were created and the cluster embedded into substrate as an amorphous state. For the energy of 0.5eV per atom, the defect free homoepitaxial growth was observed and atomic scale nucleation was formated, which are in good agreement with experiment. Thus molecular dynamics simulation is very useful to study the mechanism of the ionized cluster beam deposition.

• Tribology and Lubricants
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• v.32 no.1
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• pp.9-17
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• 2016

Contact between solid surfaces is one of the most important factors that influence dynamic behavior in micro/nanoscale. Although numerous theories and experimental results on contact behavior have been proposed, a thorough investigation for nanomaterials is still not available owing to technical difficulties. Therefore, molecular dynamics simulation was performed to investigate the contact behavior of nanomaterials, and the application of conventional contact theories to nanoscale was assessed in this work. Particularly, the contact characteristics of cylindrical nanowires were examined via simulation and contact theories. For theoretical analysis, various contact models were utilized and work of adhesion, Hamaker constant and elastic modulus those are required for calculation of the models were obtained from both indentation simulation and tensile simulation. The contact area of the cylindrical nanowire was assessed directly through molecular dynamics simulation and compared with the results obtained from the theories. Determination of the contact area of the nanowires was carried out via simulation by counting each atom, which is within the equilibrium length. The results of the simulation and theoretical calculations were compared, and it was estimated that the discrepancy in the results calculated between the simulation and the theories was less than 10 except in the case of the smallest nanowires. As the result, it was revealed that contact models can be effectively utilized to assess the contact area of nanomaterials.