• Title/Summary/Keyword: Molecular freedom

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Molecular Dynamics Study on Atomistic Details of the Melting of Solid Argon

  • Han, Joo-Hwan
    • Journal of the Korean Ceramic Society
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    • v.44 no.8
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    • pp.412-418
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    • 2007
  • The atomic scale details of the melting of solid argon were monitored with the aid of molecular dynamics simulations. The potential energy distribution is substantially disturbed by an increase in the interatomic distance and the random of set distance from the lattice points, with increasing temperature. The potential energy barriers between the lattice points decrease in magnitude with the temperature. Eventually, at the melting point, these barriers can be overcome by atoms that are excited with the entropy gain acquired when the atoms obtain rotational freedom in their atomic motion, and the rotational freedom leads to the collapse of the crystal structure. Furthermore, it was found that the surface of crystals plays an important role in the melting process: the surface eliminates the barrier for the nucleation of the liquid phase and facilitates the melting process. Moreover, the atomic structure of the surface varies with increasing temperature, first via surface roughening and then, before the bulk melts, via surface melting.

Molecular Dynamics Simulation on thermodynamic and Structural Properties of Liquid Hydrocarbons : Normal Alkanes

  • Im, Won-Pil;Won, Young-Do
    • Bulletin of the Korean Chemical Society
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    • v.15 no.10
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    • pp.852-856
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    • 1994
  • A series of aliphatic hydrocarbons, methane to hexane in the liquid state, are modeled with the molecular mechanical potential parameters treating all hydrogen degrees of freedom explicitly. Thermodynamic properties (heat capacities and heats of vaporization) are calculated from relatively short (20ps) molecular dynamics trajectories. The liquid state structures are also examined through various radial distribution functions. Molecular dynamics simulations reproduce experimentally measured properties within a few percent errors, thus indicate that the present set of all-hydrogen parameters is suitable for simulating macromolecular systems in bulk.

Molecular Dynamics Simulation Study for Transport Properties of Diatomic Liquids

  • Lee, Song-Hi
    • Bulletin of the Korean Chemical Society
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    • v.28 no.10
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    • pp.1697-1704
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    • 2007
  • We present results for transport properties of diatomic fluids by isothermal-isobaric (NpT) equilibrium molecular dynamics (EMD) simulations using Green-Kubo and Einstein formulas. As the molecular elongation of diatomic molecules increases from the spherical monatomic molecule, the diffusion coefficient increases, indicating that longish shape molecules diffuse more than spherical molecules, and the rotational diffusion coefficients are almost the same in the statistical error since random rotation decreases. The calculated translational viscosity decreases with the molecular elongation of diatomic molecule within statistical error bar, while the rotational viscosity increases. The total thermal conductivity decreases as the molecular elongation increases. This result of thermal conductivity for diatomic molecules by EMD simulations is again inconsistent with the earlier results of those by non-equilibrium molecular dynamics (NEMD) simulations even though the missing terms related to rotational degree of freedom into the Green-Kubo and Einstein formulas with regard to the calculation of thermal conductivity for molecular fluids are included.

Transport Properties of Dumbbell Molecules by Equilibrium Molecular Dynamics Simulations

  • Lee, Song-Hi
    • Bulletin of the Korean Chemical Society
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    • v.25 no.5
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    • pp.737-741
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    • 2004
  • We presents new results for transport properties of dumbbell fluids by equilibrium molecular dynamics (EMD) simulations using Green-Kubo and Einstein formulas. It is evident that the interaction between dumbbell molecules is less attractive than that between spherical molecules which leads to higher diffusion and to lower friction. The calculated viscosity, however, is almost independent on the molecular elongation within statistical error bar, which is contradicted to the Stokes' law. The calculated thermal conductivity increases and then decreases as molecular elongation increases. These results of viscosity and thermal conductivity for dumbbell molecules by EMD simulations are inconsistent with the earlier results of those by non-equilibrium molecular dynamics (NEMD) simulations. The possible limitation of the Green-Kubo and Einstein formulas with regard to the calculations of viscosity and thermal conductivity for molecular fluids such as the missing rotational degree of freedom is pointed out.

End-to-end Structural Restriction of α-Synuclein and Its Influence on Amyloid Fibril Formation

  • Hong, Chul-Suk;Park, Jae Hyung;Choe, Young-Jun;Paik, Seung R.
    • Bulletin of the Korean Chemical Society
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    • v.35 no.12
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    • pp.3542-3546
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    • 2014
  • Relationship between molecular freedom of amyloidogenic protein and its self-assembly into amyloid fibrils has been evaluated with ${\alpha}$-synuclein, an intrinsically unfolded protein related to Parkinson's disease, by restricting its structural plasticity through an end-to-end disulfide bond formation between two newly introduced cysteine residues on the N- and C-termini. Although the resulting circular form of ${\alpha}$-synuclein exhibited an impaired fibrillation propensity, the restriction did not completely block the protein's interactive core since co-incubation with wild-type ${\alpha}$-synuclein dramatically facilitated the fibrillation by producing distinctive forms of amyloid fibrils. The suppressed fibrillation propensity was instantly restored as the structural restriction was unleashed with ${\beta}$-mercaptoethanol. Conformational flexibility of the accreting amyloidogenic protein to pre-existing seeds has been demonstrated to be critical for fibrillar extension process by exerting structural adjustment to a complementary structure for the assembly.

Determination of the Kinetic Energy Release Originating from the Reverse Critical Energy in Unimolecular ion Dissociation

  • Yeh, In-Chul;Lee, Tae-Geol;Kim, Myung-Soo
    • Bulletin of the Korean Chemical Society
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    • v.15 no.3
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    • pp.241-245
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    • 1994
  • A method has been developed to estimate the kinetic energy release originating from the reverse critical energy in unimolecular ion dissociation. Contribution from the excess energy was estimated by RRKM theory, the statistical adiabatic model and the modified phase space calculation. This was subtracted from the experimental kinetic energy release distribution (KERD) via deconvolution. The present method has been applied to the KERDs in $H_2$, loss from $C_6H_6^+$ and HF loss from ${CH_2CF_2}^+$. In the present formalism, not only the energy in the reaction coordinate but also the energy in some transitional vibrational degrees of freedom at the transition state is thought to contribute to the experimental kinetic energy release. Details of the methods for treating the transitional modes are found not to be critical to the final outcome. For a reaction with small excess energy and large reverse critical energy. KERD is shown to be mainly governed by the reverse critical energy.

Experimental and ab initio Computational Studies on Dimethyl-(4-{4-{3-methyl-3-phenyl-cyclobutyl)-thiazol-2-yl]-hydrazonomethyl}-phenyl)-amine

  • Yuksektepe, Cigdem;Saracoglu, Hanife;Caliskan, Nezihe;Yilmaz, Ibrahim;Cukurovali, Alaaddin
    • Bulletin of the Korean Chemical Society
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    • v.31 no.12
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    • pp.3553-3560
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    • 2010
  • A new hydrazone derivative compound has been synthesized and characterized by IR, $^1H$-NMR, $^{13}C$-NMR and UV-vis. spectroscopy techniques, elemental analysis and single-crystal X-ray diffraction (XRD). The new compound crystallizes in monoclinic space group C2/c. In addition to the crystal structure from X-ray experiment, the molecular geometry, vibrational frequencies and frontier molecular orbitals analysis of the title compound in the ground state have been calculated by using the HF/6-31G(d, p), B3LYP/6-311G(d, p) and B3LYP/6-31G(d, p) methods. The computed vibrational frequencies are used to determine the types of molecular motions associated with each of the observed experimental bands. To determine conformational flexibility, molecular energy profile of (1) was obtained by semi-empirical (AM1) calculation with respect to a selected degree of torsional freedom, which was varied from $-180^{\circ}$ to $+180^{\circ}$ in steps of $10^{\circ}$. Molecular electrostatic potential of the compound was also performed by the theoretical method.

극소공기막을 갖는 공기윤활 슬라이더 베어링의 윤활해석에 관한 연구

  • Hwang, Pyung;Yang, Seung-Han
    • Proceedings of the Korean Society of Tribologists and Lubrication Engineers Conference
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    • 1996.04b
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    • pp.94-98
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    • 1996
  • The static characteristics of air-lubricated slider bearing were performed using direct numerical method. The equations of motion of slider bearing are solved simultaneously with the Reynolds equation for three degrees of freedom. The molecular rarefaction effect is considered. The models implemented include the first-order slip, the second-order slip, and the Boltzmann equation model derived by Fukui and Kaneko(FK model)

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The Effect of the Collision Process Between Molecules on the Rates of Thermal Relaxation of the Translational-Rotational-Vibrational Energy Exchange (분자간 충돌과정에 따른 병진-회전-진동에너지의 이완율)

  • Heo, Joong-Sik
    • Transactions of the Korean Society of Mechanical Engineers B
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    • v.28 no.12
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    • pp.1494-1500
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    • 2004
  • A zero-dimensional direct simulation Monte Carlo(DSMC) model is developed for simulating diatomic gas including vibrational kinetics. The method is applied to the simulation of two systems: vibrational relaxation of a simple harmonic oscillator and translational-rotational-vibrational energy exchange process under heating and cooling. In the present DSMC method, the variable hard sphere molecular model and no time counter technique are used to simulate the molecular collision kinetics. For simulation of diatomic gas flows, the Borgnakke-Larsen phenomenological model is adopted to redistribute the translational and internal energies.

A Study on the Mechanical Properties of Knit Fabric Using 3D Printing -Focused on PLA, TPU Filament- (3D프린팅을 이용한 편성물의 역학적 특성 연구 -PLA, TPU 필라멘트를 중심으로-)

  • Han, Yoojung;Kim, Jongjun
    • Journal of Fashion Business
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    • v.22 no.4
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    • pp.93-105
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    • 2018
  • Using FDM 3D printing, yarn shape and composition were modeled and 3D printed with PLA and TPU filaments currently used for apparel. Based on this, mechanical characteristics were measured to determine 3D printing yarn according to type of filaments in the 3D printed output and deformation and recovery characteristics due to differences in structure type. As a result of examining tensile and shear characteristics of PLA and TPU 3D printing compiles, TPU overall was measured with significantly lower stress than PLA. This is due to high elasticity of TPU's character, revealing that it has better flexibility than PLA. In addition, during deformation due to external forces, the more freedom between the head and foot parts of the loop, and the lower the force associated with each other, the more flexible it is. TPU revealed that it was easier to tension and recovery from tensile deformation than PLA, indicating potential for clothing materials using 3D printing. If high-molecular materials, such as PLA flexibility, it is likely to provide some flexibility through development of styles, including degree of freedom in modeling. Based on this, we provide basic data for developing 3D printing textures that can be satisfied with textile for apparel.