• Proceeding of EDISON Challenge
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• 2016.03a
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• pp.37-54
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• 2016

The methods for estimating the change of free energy in dissipative particle dynamics (DPD) are discussed on the basis of fluctuation theorems. Fluctuation theorems are tactics to evaluate free energy changes from non-equilibrium work distributions and have several forms, as proposed by Jarzynski, Crooks, and Bennett. The validity of these methods however, has been shown merely with the molecular dynamics or Langevin dynamics. In this study, the appropriate forms of fluctuation theorems for dissipative particle dynamics, which has similar structure to that of Langevin dynamics, are suggested using Liouville's theorem, and they are proved equivalent to original fluctuation theorems. Work distribution functions, which are probability distribution functions of works exerted on the system within the systematic change, are the basics of fluctuation theorems and their shapes are turned out to be dependent on the phase space trajectory of the change of the system. The reliability of Jarzynski and Crooks methods is highly dependent on the number of simulations to measure works and the shapes of the work distribution functions. Bennett method, however, can evaluate free energy changes even when Jarzynski and Crooks methods fail to do so.

• Bulletin of the Korean Chemical Society
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• v.5 no.1
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• pp.27-32
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• 1984

To investigate the hydration effects on the conformational changes of N-pivaloly-L-prolyl-N-methyl-N'-isopropyl-L-alanin amide (PPMIA), the conformational free energy changes have been calculated by using an empirical potential function varying all the independent degrees of freedom of PPMIA backbones. It is found that cis conformers are folded by a strong intramolecular hydrogen bond involving both terminal CO and NH groups whereas trans conformers accommodate the open conformation. Conformers in the free state are proved to be less stable than in the hydrated state. The free energy changes of cis and trans PPMIA due to the hydration are -50.5 and -39.8 kcal/mole, their conformational energy changes are -52.3 and -41.0 kcal/mole, and their conformational entropy changes are -5.9 and -4.0 e.u., respectively. The free energy changes of cis PPMIA to trans PPMIA in the free and hydrated states are 5.3 and 16.0 kcal/mole, their conformational energy changes are 7.6 and 18.8 kcal/mole, and the entropy changes due to the conformational transitions correspond to 7.5 and 9.4 e.u., respectively. From these results, it is found that the bound water molecules play an important role in stabilizing the conformation of PPMIA.

• Journal of Adhesion and Interface
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• v.4 no.4
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• pp.1-6
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• 2003

After atmospheric pressure plasma treatment of polypropylene(PP) film surface, we measured the contact angle of the surface by using polar solvent (water) and non-polar solvent (diiodomethane). We also calculated the surface free energy of PP film by using the measured values of contact angles. And then we analyzed contact angle and surface free energy with changing the condition of atmospheric pressure plasma treatment. Upon each condition of atmospheric plasma treatment, contact angle and surface free energy showed an optimum value or leveled off.

• Elastomers and Composites
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• v.39 no.4
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• pp.281-285
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• 2004

In this paper, the simple way to evaluate the value of the activation energy for the overall rate of free radical polymerization by using DSC thermograms was studied using free radical polymerization or butylacrylate as a model. Activation ehergies were determined at heating rates of 1, 2, 5, and $10^{\circ}C/min$ by applying the multiple scanning-rate methods of Kissinger, Osawa, and half-width methods as well as the single rate method of Barrett. The value of the overall activation energy measured was closely matched with the values calculated from individual data. This work also demonstrated that the use of the isoconversional method was a simple and effective way to estimate the activation energy for the overall free radical polymerization.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.103-113
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• 2014

Hydrophobicity is the key concept to understand the role of water in protein folding, protein self-assembly, and protein-ligand interaction. Conventionally, hydrophobicity of amino acids in a protein has been argued based on hydrophobicity scales determined for individual free amino acids, assuming that those scales are unaltered when amino acids are embedded in a protein. Here, we investigate how the hydrophobicity of constituent amino acids depends on the protein context, in particular, on the total charge and secondary structures of a protein. To this end, we compute and analyze the hydration free energy - free energy change upon hydration quantifying the hydrophobicity - of three short proteins based on the integral-equation theory of liquids. We find that the hydration free energy of charged amino acids is significantly affected by the protein total charge and exhibits contrasting behavior depending on the protein net charge being positive or negative. We also observe that amino acids in the central ${\beta}$-strand sandwiched by ${\beta}$-sheets display more enhanced hydrophobicity than free amino acids, whereas those in the ${\alpha}$-helix do not clearly show such a tendency. Our results provide novel insights into the hydrophobicity of amino acids, and will be valuable for rationalizing and predicting the strength of water-mediated interaction involved in the biological activity of proteins.

• 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.

• Transactions of the Korean Society of Mechanical Engineers
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• v.16 no.12
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• pp.2368-2375
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• 1992

The transition of turbulent kinetic energy(TKE) balance along the centerline of the flow unit, which is composed of straight-duct, contraction and free-jet, has been investigated by the hot-wire anemometry. It is found that the mean turbulent kinetic energy is balanced by the dissipation in the internal flow region ; by the production and the dissipation, through contraction ; and by the dissipation, in initial region(X〈8D) of free-jet. But in the developing region (8D〈X〈20D) it is balanced by all of the three(ie, diffusion, production and dissipation). Finally, in the downstream of free-jet, the mean TKE is balanced again by dissipation like as the beginning. The decay-laws along the centerline are checked in the region of free jet as well as in the straightduct. After the developing region of free-jet also exist the decay-laws, the exponent of the axial turbulence being bigger than of the radial.

• Bulletin of the Korean Chemical Society
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• v.24 no.6
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• pp.805-808
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• 2003

Fundamental ideas of the free energy gradient method are briefly reviewed with three applications: the stable structures of glycine and ammonia-water molecule pair in aqueous solution and the transition state (TS) structure of a Menshutkin reaction $NH_3 + CH_3Cl → CH_3NH_3^+ + Cl^-$ in aqueous solution, which is the first example of full TS optimization of all internal degrees of freedom.

• Bulletin of the Korean Chemical Society
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• v.20 no.7
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• pp.815-818
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• 1999

The method of calculating the excess Helmholtz free energy from the averaged effective acceptance ratio for the Lennard-Jones fluid and the inverse twelve fluid has been slightly modified and applied to the two-center-Lennard-Jones liquid. The excess Helmholtz free energy is calculated directly from the average of the modified effective acceptance ratio through a single Metropolis Monte Carlo simulation. Therefore this method does not need any reference system. The results of the present method were satisfactory compared with those of the perturbation theories and the overlap ratio method.

• Journal of Advanced Marine Engineering and Technology
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• v.29 no.7
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• pp.729-735
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• 2005

This paper has dealt with the characteristics of mass and heat transfer of vertical flat plate with free convection. The theory of similarity transformations applied to the momentum and energy equations for free convection. To derive the similarity equation of mass transfer. the equation for conservation of species was added to the continuity. momentum and energy equations. The momentum, energy and species equations set numerically to obtain the velocity, temperature and mass fraction of species as dimensionless. For cases where momentum transport dominates, the thermal boundary layers are shorter than the momentum boundary layer. The relationships between momentum, energy and species were clarified from this study.