• Transactions of the Korean Society of Mechanical Engineers A
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• v.23 no.7 s.166
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• pp.1223-1230
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• 1999

This paper addresses a novel optimization technique based on molecular dynamics simulation which has been utilized for physical model simulation at various disciplines. In this study, objective functions are considered to be potential functions, which depict molecular interactions. Comparisons of typical optimization method such as the steepest descent and the present method for several test functions are made. The present method shows applicability and stability in finding a global optimum.

• 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.

• 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.

• Bulletin of the Korean Chemical Society
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• v.23 no.3
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• pp.441-446
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• 2002

We have presented the results of thermodynamic, structural and dynamic properties of liquid benzene, toluene, and p-xylene in canonical (NVT) ensemble at 293.15 K by molecular dynamics (MD) simulations. The molecular model adopted for these molecules is a combination of the rigid body treatment for the benzene ring and an atomistically detailed model for the methyl hydrogen atoms. The calculated pressures are too low in the NVT ensemble MD simulations. The various thermodynamic properties reflect that the intermolecular interactions become stronger as the number of methyl group attached into the benzene ring increases. The pronounced nearest neighbor peak in the center of mass g(r) of liquid benzene at 293.15 K, provides the interpretation that nearest neighbors tend to be perpendicular. Two self-diffusion coefficients of liquid benzene at 293.15 K calculated from MSD and VAC function are in excellent agreement with the experimental measures. The self-diffusion coefficients of liquid toluene also agree well with the experimental ones for toluene in benzene and for toluene in cyclohexane.

• International Journal of Precision Engineering and Manufacturing
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• v.5 no.4
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• pp.28-35
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• 2004

Stimulated by novel phenomena observed in molecular aggregates, recent developments in engineering fields of microscopic scales are creating tremendous opportunities for future nanotechnology-based applications. Investigation in the field involves sub-nanosecond or sub-micrometer interactions between extremely small systems, but researches, to date in these physical extremes have been quite limited. Here, we shed light on some of nanoscale phenomena using molecular dynamics simulation: visualization of various phenomena of nanoscales and exploration of size-dependent mechanical properties.

• Carbon letters
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• v.11 no.4
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• pp.316-324
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• 2010

The effects of geometrical parameters on mechanical properties of graphite-vinylester nanocomposites and their constituents (matrix, reinforcement and interface) are studied using molecular dynamics (MD) simulations. Young's modulii of 1.3 TPa and 1.16 TPa are obtained for graphene layer and for graphite layers respectively. Interfacial shear strength resulting from the molecular dynamic (MD) simulations for graphene-vinylester is found to be 256 MPa compared to 126 MPa for graphitevinylester. MD simulations prove that exfoliation improves mechanical properties of graphite nanoplatelet vinylester nanocomposites. Also, the effects of bromination on the mechanical properties of vinylester and interfacial strength of the graphene.brominated vinylester nanocomposites are investigated. MD simulation revealed that, although there is minimal effect of bromination on mechanical properties of pure vinylester, bromination tends to enhance interfacial shear strength between graphite-brominated vinylester/graphene-brominated vinylester in a considerable magnitude.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.49 no.6
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• pp.815-822
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• 2016

The cationic biopolymer chitosan has several applications in medicine. Chitosan is the deacetylated derivative of chitin, the second most abundant naturally occurring polymer. Recent studies have investigated the relationship between chitosan and antibacterial activity. However, the molecular interactions and mechanisms have not been detailed. This study used molecular dynamics simulations to study interactions between chitosan and anionic bacterial membranes (POPE-POPG) and electrically neutral non-bacterial membranes (POPC). We calculated the free energy using umbrella sampling to compare the interactions between membranes and chitosan in different protonation states. Fully protonated chitosan interacted most strongly with the bacterial membranes, but weakly with non-bacterial membranes. These results suggest that electrostatic interactions are the main mechanism of the antibacterial activity of chitosan, and they provide insights into the design of novel antibacterial and antimicrobial agents.

• Interaction and multiscale mechanics
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• v.6 no.2
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• pp.127-136
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• 2013

In this study, atomistic simulations are performed to study the effect of Al solute on the behaviour of edge dislocation in Mg alloys. After the dissociation of an Mg basal edge dislocation into two Shockley partials using molecular mechanics, the interaction between the dislocation and Al solute at different temperatures is studied using molecular dynamics. It appears from the simulations that the critical shear stress increases with the Al solute concentration. Comparing with the solute effect at T = 0 K, however, the critical shear stress at a finite temperature is lower since the kinetic energy of the atoms can help the dislocation conquer the energy barriers created by the Al atoms. The velocity of the edge dislocation decreases as the Al concentration increases when the external shear stress is relatively small regardless of temperature. The Al concentration effect on the dislocation velocity is not significant at very high shear stress level when the solute concentration is below 4.0 at%. Drag coefficient B increases with the Al concentration when the stress to temperature ratio is below 0.3 MPa/K, although the effect is more significant at low temperatures.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.31 no.2 s.257
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• pp.237-244
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• 2007

In order to obtain mechanical properties of CNT/Polymer nano-composites, molecular dynamics simulation is performed. Overall system was modeled as a flexible unit cell in which carbon nanotubes are embedded into a polyethylene matrix for N $\sigma$ T ensemble simulation. COMPASS force field was chosen to describe inter and intra molecular potential and bulk effect was achieved via periodic boundary conditions. In CNT-polymer interface, only Lennard-Jones non-bond potential was considered. Using Parrinello-Rahman fluctuation method, mechanical properties of orthotropic nano-composites under various temperatures were successfully obtained. Also, we investigated thermal behavior of the short CNT reinforced nanocomposites system with predicting glass transition temperature.

• Bulletin of the Korean Chemical Society
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• v.31 no.9
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• pp.2581-2587
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• 2010

Nitration of tyrosine and tryptophan residues is common in cells under nitrative stress. However, physiological consequences of protein nitration are not well characterized on a molecular level due to limited availability of the 3D structures of nitrated proteins. Molecular dynamics (MD) simulation can be an alternative tool to probe the structural perturbations induced by nitration. In this study we developed molecular mechanics parameters for 3-nitrotyrosine (NIY) and 6-nitrotryptophan (NIW) that are compatible with the AMBER-99 force field. Partial atomic charges were derived by using a multi-conformational restrained electrostatic potential (RESP) methodology that included the geometry optimized structures of both $\alpha$- and $\beta$-conformers of a capped tripeptide ACE-NIY-NME or ACE-NIW-NME. Force constants for bonds and angles were adopted from the generalized AMBER force field. Torsional force constants for the proper dihedral C-C-N-O and improper dihedral C-O-N-O of the nitro group in NIY were determined by fitting the torsional energy profiles obtained from quantum mechanical (QM) geometry optimization with those from molecular mechanical (MM) energy minimization. Force field parameters obtained for NIY were transferable to NIW so that they reproduced the QM torsional energy profiles of ACE-NIW-NME accurately. Moreover, the QM optimized structures of the tripeptides containing NIY and NIW were almost identical to the corresponding structures obtained from MM energy minimization, attesting the validity of the current parameter set. Molecular dynamics simulations of thioredoxin nitrated at the single tyrosine and tryptophan yielded well-behaved trajectories suggesting that the parameters are suitable for molecular dynamics simulations of a nitrated protein.