• Journal of Biomedical Engineering Research
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• v.24 no.5
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• pp.447-451
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• 2003

A new method for analyzing the bone-remodeling process using quasi-molecular dynamics was proposed in this study. The effect of pressure due to bone marrow, which could not be considered in previous methods, was also considered in this method. Bone-remodeling response of the 2D vertebral body of lumbar spine to a uniaxial compressive displacement of 1.8564mm. corresponding to approximately 2kN of compressive load, was studied. Converged shape change of the cortical shell and rearrangement of cancellous bone structure matched well with a normal shape of the vertebral body. The calculated responses in the spinal elements also shows closed results compared with experimental results.

• Bulletin of the Korean Chemical Society
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• v.29 no.2
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• pp.363-371
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• 2008

As a computational method for the discovery of the effective agonists for PPARd, we address the usefulness of molecular dynamics free energy (MDFE) simulation with explicit solvent in terms of the accuracy and the computing cost. For this purpose, we establish an efficient computational protocol of thermodynamic integration (TI) that is superior to free energy perturbation (FEP) method in parallel computing environment. Using this protocol, the relative binding affinities of GW501516 and its derivatives for PPARd are calculated. The accuracy of our protocol was evaluated in two steps. First, we devise a thermodynamic cycle to calculate the absolute and relative hydration free energies of test molecules. This allows a self-consistent check for the accuracy of the calculation protocol. Second, the calculated relative binding affinities of the selected ligands are compared with experimental IC50 values. The average deviation of the calculated binding free energies from the experimental results amounts at the most to 1 kcal/mol. The computational efficiency of current protocol is also assessed by comparing its execution times with those of the sequential version of the TI protocol. The results show that the calculation can be accelerated by 4 times when compared to the sequential run. Based on the calculations with the parallel computational protocol, a new potential agonist of GW501516 derivative is proposed.

• Bulletin of the Korean Chemical Society
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• v.33 no.11
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• pp.3805-3809
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• 2012

Results for molecular dynamics simulation method of small liquid drops of argon (N = 1200-14400 molecules) at 94.4 K through a Lennard-Jones intermolecular potential are presented in this paper as a preliminary study of drop systems. We have calculated the density profiles ${\rho}(r)$, and from which the liquid and gas densities ${\rho}_l$ and ${\rho}_g$, the position of the Gibbs' dividing surface $R_o$, the thickness of the interface d, and the radius of equimolar surface $R_e$ can be obtained. Next we have calculated the normal and transverse pressure tensor ${\rho}_N(r)$ and ${\rho}_T(r)$ using Irving-Kirkwood method, and from which the liquid and gas pressures ${\rho}_l$ and ${\rho}_g$, the surface tension ${\gamma}_s$, the surface of tension $R_s$, and Tolman's length ${\delta}$ can be obtained. The variation of these properties with N is applied for the validity of Laplace's equation for the pressure change and Tolman's equation for the effect of curvature on surface tension through two routes, thermodynamic and mechanical.

• Coupled systems mechanics
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• v.6 no.1
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• pp.41-54
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• 2017

Shape-memory alloys (SMA) have interesting behaviors and important mechanical properties due to the solid-solid phase transformation. These phenomena are dominated by the evolution of microstructures. In recent years, the microstructures in SMAs have been studied extensively and modeled using molecular dynamics (MD) simulations. However, it remains difficult to identify the crystal variants in the simulation results, which consist of large numbers of atoms. In the present work, a method is developed to identify the austenite phase and the monoclinic martensite crystal variants in MD results. The transformation matrix of each lattice is calculated to determine the corresponding crystal variant. Evolution of the volume fraction of the crystal variants and the microstructure in Ni-Ti SMAs under thermal and mechanical boundary conditions are examined. The method is validated by comparing MD-simulated interface normals with theoretical solutions. In addition, the results show that, in certain cases, the interatomic potential used in the current study leads to inconsistent monoclinic lattices compared with crystallographic theory. Thus, a specific modification is applied and the applicability of the potential is discussed.

• Current Applied Physics
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• v.18 no.11
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• pp.1327-1337
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• 2018

This paper investigates the vibration behavior of pristine and defected triangular graphene sheets; which has recently attracted the attention of researchers and compare these two types in natural frequencies and sensitivity. Here, the molecular dynamics method has been employed to establish a virtual laboratory for this purpose. After measuring the different parameters obtained by the molecular dynamics approach, these data have been analyzed by using the frequency domain decomposition (FDD) method, and the dominant frequencies and mode shapes of the system have been extracted. By analyzing the vibration behaviors of pristine triangular graphene sheets in four cases (right angle of 45-90-45 configuration, right angle of 60-90-30 configuration, equilateral triangle and isosceles triangle), it has been demonstrated that the natural frequencies of these sheets are higher than the natural frequency of a square sheet, with the same number of atoms, by a minimum of 7.6% and maximum of 26.6%. Therefore, for increasing the resonance range of sensors based on 2D materials, nonrectangular structures, and especially the triangular structure, can be considered as viable candidates. Although the pristine and defective equilateral triangular sheets have the highest values of resonance, the sensitivity of defective (45,90,45) triangular sheet is more than other configurations and then, defective (45,90,45) sheet is the worst choice for sensor applications.

• Journal of the Computational Structural Engineering Institute of Korea
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• v.34 no.4
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• pp.191-197
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• 2021

To calculate the induced charge of atoms in molecular dynamics, linear equations for the induced charges need to be solved. As induced charges are determined at each time step, the process involves considerable computational costs. Hence, an efficient method for calculating the induced charge distribution is required when analyzing large systems. This paper introduces the Uzawa method for solving saddle point problems, which occur in linear systems, for the solution of the Lagrange equation with constraints. We apply the accelerated Uzawa algorithm, which reduces computational costs noticeably using the Schur complement and preconditioned conjugate gradient methods, in order to overcome the drawback of the Uzawa parameter, which affects the convergence speed, and increase the efficiency of the matrix operation. Numerical models of molecular dynamics in which two gold nanoparticles are placed under external electric fields reveal that the proposed method provides improved results in terms of both convergence and efficiency. The computational cost was reduced by approximately 1/10 compared to that for the Gaussian elimination method, and fast convergence of the conjugate gradient, as compared to the basic Uzawa method, was verified.

• Bulletin of the Korean Chemical Society
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• v.33 no.1
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• pp.167-170
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• 2012

A test-area molecular dynamics simulation method for the vapor-liquid interface of argon through a Lennard-Jones intermolecular potential is presented in this paper as a primary study of interfacial systems. We found that the calculated density profile along the z-direction normal to the interface is not changed with time after equilibration and that the values of surface tension computed from this test-area method are fully consistent with the experimental data. We compared the thermodynamic properties of vapor argon, liquid argon, and argon in the vapor-liquid interface. Comparisons are made with kinetic and potential energies, diffusion coefficient, and viscosity.

• Bulletin of the Korean Chemical Society
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• v.18 no.4
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• pp.415-424
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• 1997

Conformational flexibilities of the GlcNAc(β1,3)Gal(β)OMe are investigated through NMR spectroscopy and molecular modeling. Adiabatic energy map generated with a dielectric constant of 50 contains three local minima. All of the molecular dynamics simulations on three local minimum energy structures show fluctuations between two low energy structures, N2 at φ=80° and ψ=60° and N3 at φ=60° and ψ=-40°. We have presented adequate evidences to state that GlcNAc(β1,3)Gal(β)OMe exists in two conformationally discrete forms. Two state model of N2 and N3 conformers with a population ratio of 40:60 is used to calculate the effective cross relaxation rate and reproduces the experimental NOEs very well. Molecular dynamics simulation in conjunction with two state model proves successfully the dynamic equilibrium existed in GlcNAc(β1,3)Gal(β)OMe and can be considered as a powerful method to analyze the motional properties in the structure of carbohydrate. This observation also cautions against the indiscriminate use of a rigid model to analyze NMR data.

• Macromolecular Research
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• v.12 no.2
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• pp.178-188
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• 2004

We performed molecular dynamics (MD) simulations at 300 K on a series of poly(benzyl ether) (PBE) dendrimers having a different core functionalities. We used the rotational isomeric state Metropolis Monte Carlo (RMMC) method to construct the initial configuration in a periodic boundary cell (PBC) before the MD simulations were undertaken. To elucidate the effects that the structural features have on the chain dimension, the overall internal structure, and the morphology, we monitored the radii of gyration, R$\sub$g/ and the conformational changes during the simulations. The PBE dendrimers in a glassy state adopted less-extended structures when compared with the conformations obtained from the RMMC calculations. We found that R$\sub$g/ of the PBE dendrimer depends on the molecular weight, M, according to the relation, R$\sub$g/∼M$\^$0.22/. The radial distributions of the dendrimers were developed identically in the PBC, irrespective of the core functionality. A gradual decrease in radial density resulted from the fact that the terminal branch ends are distributed all over the molecule, except for the core region.

• 한국전산유체공학회:학술대회논문집
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• 2009.11a
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• pp.97-102
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• 2009

Translocation of biopolymers such as DNA and RNA through a nano-pore is an important process in biotechnology applications. The translocation process of a biopolymer through an artificial nano-pore in the presence of a fluid solvent is simulated. The polymer motion is simulated by Langevin molecular dynamics (MD) techniques while the solvent dynamics are taken into account by lattice-Boltzmann method (LBM). The hydrodynamic interactions are considered explicitly by coupling the polymer and solvent through the frictional and the random forces. From simulation results we found that the hydrodynamic interactions between polymer and solvent speed-up the translocation process. The translocation time ${\tao}_T$ scales with the chain length N as ${{\tau}_T}^{\propto}N^{\alpha}$. The value of scaling exponents($\alpha$) obtained from our simulations are $1.29{\pm}0.03$ and $1.41{\pm}0.03$, with and without hydrodynamic interactions, respectively. Our simulation results are in good agreement with the experimentally observed value of $\alpha$, which is equal to $1.27{\pm}0.03$, particularly when hydrodynamic interaction effects are taken into account.