• EDISON SW 활용 경진대회 논문집
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• 제5회(2016년)
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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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• 제5권1호
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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.

• 접착 및 계면
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• 제4권4호
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• pp.1-6
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• 2003

대기압 플라즈마를 이용하여 폴리프로필렌 필름의 표면을 처리한 후 각각 극성 용매(water)와 비극성 용매(diiodomethane)를 사용한 접촉각 측정기로 필름 표면의 접촉각을 측정하였다. 측정된 접촉각을 이용해 표면 자유에너지 변화를 계산한 후 대기압 플라즈마 처리 전후의 폴리프로필렌 필름의 접촉각과 표면 자유에너지 상태를 비교, 분석하였다. 또한 대기압 플라즈마의 처리 조건을 바꿔가며 폴리프로필렌 필름 표면을 처리함으로써 접촉각과 표면 자유에너지가 각각의 처리 조건에 따라 어떠한 영향을 받는지 연구하였다. 대기압 플라즈마 처리 조건에 따라 접촉각 및 표면 자유에너지는 최적값을 보여주거나 일정한 값에 도달하는 경향을 보여 주었다.

• Elastomers and Composites
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• 제39권4호
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• pp.281-285
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• 2004

이 연구는 열분석법을 이용하여 간단하게 자유 라디칼 중합의 활성화 에너지를 결정하는 방법을 부틸 아크릴레이트을 모델로 하여 구했다. 활성화 에너지는 Kissinger, Osawa 및 half-width법인 다수의 주사 속도법 (multiple scanning-rate method)을 이용하여 $1^{\circ}C/min,\;2^{\circ}C/min,\;5^{\circ}C/min$, 그리고 $10^{\circ}C/min$로 측정하였으며 단수 주사 속도법인 Barret 법을 이용하여 구하였다. 열분석법에 의해 구해진 중합반응의 활성화 에너지는 개시반응, 성장반응 및 종결반응의 각각의 활성화 에너지에서 계산된 전체 중합반응에서의 활성화 에너지와 가깝게 접근하였다.

• EDISON SW 활용 경진대회 논문집
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• 제3회(2014년)
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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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• 제29권2호
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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.

• 대한기계학회논문집
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• 제16권12호
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• pp.2368-2375
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• 1992

본 연구에서는 축대칭 유동장치를 구성하여 열선 풍속계를 이용, 중심축에 따 른 난류쇠퇴양식을 살펴보고 동시에 난류에너지천이에 대한 세밀한 분석을 통하여 각 각 상류유동전개부, 수축부 및 자유분사류로 연속되는 3개의 유동 구조속에서 어떻게 천이해 갈 것인가를 측정하여 축대칭 유동의 난류구조 변천에 대한 기초 실험자료로 제시하고저 한다.

• Bulletin of the Korean Chemical Society
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• 제24권6호
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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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• 제20권7호
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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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• 제29권7호
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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.