• Interaction and multiscale mechanics
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• v.6 no.2
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• pp.157-172
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• 2013

This paper presented an investigation of macromolecular suspension in a grooved channel by using the dissipative particle dynamics (DPD) with finitely extensible non-linear elastic (FENE) bead spring chains model. Before studying the movement and evolution of macromolecules, the DPD method was first validated by modeling the simple fluid flow in the grooved channel. For both simple fluid flow and macromolecular suspension, the flow fields were analyzed in detail. It is found that the structure of the grooved channel with sudden contraction and expansion strongly affects the velocity distribution. As the width of the channel reduces, the horizontal velocity increases simultaneously. Vortices can also be found at the top and bottom corners behind the contraction section. For macromolecular suspension, the macromolecular chains influence velocity and density distribution rather than the temperature and pressure. Macromolecules tend to drag simple fluid particles, reducing the velocity with density and velocity fluctuations. Particle trajectories and evolution of macromolecular conformation were investigated. The structure of the grooved channel with sudden contraction and expansion significantly influence the evolution of macromolecular conformation, while macromolecules display adaptivity to adjust their own conformation and angle to suit the structure so as to pass the channel smoothly.

• Journal of Photoscience
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• v.11 no.1
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• pp.35-40
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• 2004

[Ru(2,2'-bipyridine)$_2$(4,4'-dicarboxy-2,2'-bipyridine)]$^{2+}$(RuBDc) is a very photostable probe that possesses favorable photophysical properties including long lifetime, high quantum yield, large Stokes' shift, and highly polarized emission. To evaluate the usefulness of this luminophore (RuBDc) for studying macromolecular dynamics, its intensity and anisotropy decays when conjugated to RNA bacteriophage MS2 were examined using frequency-domain fluorometry with a high-intensity, blue light-emitting diode (LED) as the modulated light source. The intensity decays were best fit by a sum of two exponentials, and the mean intensity decay time was 442.2 ns. The anisotropy decay data showed a single rotational correlation time (2334.9 ns), which is typical for a spherical molecule. The use of RuBDc enabled us to measure the rotational correlation time up to several microseconds. These results indicate that RuBDc can be useful for studying rotational diffusion of biological macromolecules.s.

• International Journal of Control, Automation, and Systems
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• v.4 no.3
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• pp.382-393
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• 2006

Mechanical system dynamics plays an important role in the area of computational structural biology. Elastic network models (ENMs) for macromolecules (e.g., polymers, proteins, and nucleic acids such as DNA and RNA) have been developed to understand the relationship between their structure and biological function. For example. a protein, which is basically a folded polypeptide chain, can be simply modeled as a mass-spring system from the mechanical viewpoint. Since the conformational flexibility of a protein is dominantly subject to its chemical bond interactions (e.g., covalent bonds, salt bridges, and hydrogen bonds), these constraints can be modeled as linear spring connections between spatially proximal representatives in a variety of coarse-grained ENMs. Coarse-graining approaches enable one to simulate harmonic and anharmonic motions of large macromolecules in a PC, while all-atom based molecular dynamics (MD) simulation has been conventionally performed with an aid of supercomputer. A harmonic analysis of a macroscopic mechanical system, called normal mode analysis, has been adopted to analyze thermal fluctuations of a microscopic biological system around its equilibrium state. Furthermore, a structure-based system optimization, called elastic network interpolation, has been developed to predict nonlinear transition (or folding) pathways between two different functional states of a same macromolecule. The good agreement of simulation and experiment allows the employment of coarse-grained ENMs as a versatile tool for the study of macromolecular dynamics.

• 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.

• Proceedings of the Korean Society of Rheology Conference
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• 2001.09a
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• pp.164.1-164
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• 2001

• Korea-Australia Rheology Journal
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• v.14 no.3
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• pp.129-138
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• 2002

A cationic surfactant, cetyltrimethylammonium $\rho$-toluenesufonate (CTA$\rho$TS), forms long threadlike micelles in aqueous solution. The threadlike micelles make concentrated entanglement networks, so that the solution shows pronounced viscoelastic behavior as concentrated polymer systems do. However, a mechanism for a process responsible for the longest relaxation time of the threadlike micellar system is different from that of semi-dilute to concentrated polymer systems. The threadlike micellar system exhibits unique viscoelasticity described by a Maxwell model. The longest relaxation time of the threadlike micellar system is not a function of the concentration of CTA$\rho$TS, but changes with that of $\rho$-toluenesufonate ($\rho$$TS^{-}$) ions in the bulk aqueous phase supplied by adding sodium $\rho$-toluenesulfonate (NapTS). The rates of molecular motions in the threadlike micelles are not influenced by the concentration of $\rho$$TS^{-}$ anions, therefore, molecular motions in the threadlike micelles (micro-dynamics) are independent of the longest relaxation mechanism (macro-dynamics). A nonionic surfactant, oleyldimethylamineoxide (ODAO), forms long threadlike micelles in aqueous solution without any additives. The aqueous threadlike micellar system of ODAO also shows Maxwell type viscoelastic behavior. However, the relaxation mechanism for the longest relaxation process in the system should be different from that in the threadlike micellar systems of CTA$\rho$TS, since the system of ODAO does not contain additive anions. Because increase in the average degree of protonation of head groups of ODAO molecules in micelles due to adding hydrogen bromide causes the relaxation time remarkably longer, changes in micro-structure and micro-dynamics in the threadlike micelle are closely related to macro-dynamics in contrast with the threadlike micellar system of CTA$\rho$TS.

• Macromolecular Research
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• v.17 no.10
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• pp.807-812
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• 2009

In this work, we focus on the tumbling dynamics of rod-like and semi-flexible polymers in mixed flows, which vary from simple shear to pure rotation. By employing a bead-rod model, the tumbling pathways and periods are examined with a focus on the angular distribution of their orientation. Under the mixed flows, the tumbling dynamics agreed well with earlier studies and confirmed the predicted scaling laws. We found that the angular distribution deviates from that of shear flow as the flow type approaches pure rotation. Finally, we investigated the angular distribution of $\lambda$-DNA in a shear flow and found that the present numerical simulations were in quantitative agreement with the previous experimental data.

• Korea-Australia Rheology Journal
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• v.21 no.4
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• pp.235-244
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• 2009

Miscible polymer blends still have heterogeneity in their component chain concentration in the segmental length scale because of the chain connectivity (that results in the self-concentration of the segments of respective chains) as well as the dynamic fluctuation over various length scales. As a result, the blend components feel different dynamic environments to exhibit different temperature dependence in their segmental relaxation rates. This type of dynamic heterogeneity often results in a broad glass transition (sometimes seen as two separate transitions), a broad distribution of the local (segmental) relaxation modes, and the thermo-rheological complexity of this distribution. Furthermore, the dynamic heterogeneity also affects the global dynamics in the miscible blends if the component chains therein have a large dynamic asymmetry. Thus, the superficially simple miscible blends exhibit interesting dynamic behavior. This article gives a brief summary of the features of the segmental and global dynamics in those blends.

• Macromolecular Research
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• v.8 no.2
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• pp.53-58
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• 2000

Stabilities and structures of resorcinol formaldehyde resins (RF resins) and their dependence on solvent were studied by molecular mechanics and molecular dynamics. Dimers to decamers of the RF resins in the conditions of dielectric constant = 1.00, 21.01, 36.64, and 80.10 were calculated. The average distance between oxygen atoms in 1-hydroxyl groups of adjacent resorcinols of the resins became longer with increased dielectric constant of the environment. The number of intramolecular hydrogen bonds of the resins decreased by increasing the dielectric constant of the environment. The RF resin structure on the surface of fabric or steel cord was explained based on the present calculation.

• Macromolecular Research
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• v.10 no.6
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• pp.297-303
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• 2002

We have investigated the microstructural properties of a weakly charged polyelectrolyte modeled with both Hookean spring and Debye-Huckel potential, by employing a novel hybrid scheme of molecular dynamics (MD) and Monte Carlo (MC) simulations. Although the off-lattice pivot step facilitates the earlier computations stage, it gives rise to oscillations and hinders the stable equilibrium state. In order to overcome this problem, we adopt the MC off-lattice pivot step in early stage only, and then switch the computation to a pure MD step. The result shows that the computational speed-up compared to the previous method is entirely above 10 to 50, without loss of the accuracy. We examined the conformations of polyelectrolyte in solvents in terms of the end-to-end distance, radius of gyration, and structure factor with variations of the screening effects of solvent and the monomer charges. The emphasis can favorably be given on the elongation behavior of a polyelectrolyte chain, with observing the simultaneous snapshots.