• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.1-13
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• 2014

Potential Energy Surface(PES)를 양자 계산을 통해 알아내는 것은 화학 반응을 이해하는 데에 큰 도움이 된다. 이를테면 Transition State(TS)의 configuration을 알 수 있고, 따라서 reaction path와 활성화 에너지 값을 예측하여, 진행시키고자 하는 화학반응의 이해를 도울 수 있다. 하지만 PES를 그리기 위해서는 해당 분자의 다양한 configuration에 대한 singlet point energy 계산이 필요하기 때문에, 계산적인 측면에서 많은 비용을 요구한다. 따라서 product와 reactant의 구조와 같은 critical point의 정보를 이용하여 최소한의 configuration을 sampling하여 전체 PES를 재구성하는 기계학습 알고리즘을 개발하여 다차원 PES 상에서의 화학반응의 예측을 가능하게 하고자 한다. 본 연구에서는 Barbaralane의 두 안정화 된 구조의 critical point로 하여 이 주변을 random normal distribution하여, B3LYP/6-31G(d) level의 DFT 계산을 통해 relaxed scanning하여 구조와 에너지를 구하였으며, 이 정보를 Support Vector Regression(SVR) 알고리즘을 적용하여 PES를 재구현하였으며, 반응경로와 TS의 구조 그리고 활성화 에너지를 구하였다. 또한 본 기계학습 알고리즘을 바닥상태에서 일어나는 반응이 아닌, 들뜬 상태와 전자 구조가 변하는 화학반응, avoid crossing, conical intersection과 같은 Non-adiabatic frame에서 일어나는 현상에 적용 가능성을 논하고자 한다.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.472-474
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• 2014

Carbon nanotubes (CNTs) have been intensively investigated since they have been considered as building blocks of nanoscience and nanotechnology. Theoretical and computational studies on CNTs have revealed their physical and chemical properties and helped researchers build various experimental devices to study them in depth. However, there have been only few systematic studies on detailed changes in electronic structures of CNTs due to geometrical structure modifications. In this regard, it is necessary to perform systematic investigations of the modifications in electronic structures of CNTs, as their geometrical configurations are altered, using the first-principles density functional theory. In other words, it is essential to determine the true equilibrium structure of CNTs. We are going to construct different atomic configurations of each nanotube by maintaining the original symmetries, but changing all the other bonding types one by one. Furthermore, as for CNTs, for example, the way the graphene sheet is wrapped is represented by a pair of indices (n,m) and electronic structures of CNTs vary depending on different indices. Therefore, we plan to study and discuss all the significant couplings between electronic and geometric structures in CNTs.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.439-441
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• 2014

단층 $MoS_2$는 현재 트랜지스터나 LED등에 활용을 연구중인 물질이다. 단층 $MoS_2$의 밴드구조는 약 1.8eV의 직접 밴드갭을 보이는 반도체로 알려져있다. 이 물질을 소자에 활용할 때 고유의 1.8 eV 직접 밴드갭을 이용한다. 다양한 분야에 소자로 응용되기 위해서는 밴드갭을 조절이 필요하다. 그래서 $MoS_2$의 밴드갭을 조절하는 연구가 행해져 왔는데 그 중 하나가 수소흡착 방법이다. 수소를 단층 $MoS_2$에 흡착시키면 금속 밴드구조를 보인다고 알려져 있다. 본 연구에서는 DFT (Density Functional Theory) 계산을 통하여 밴드갭을 조절하는 다른 방법 중에 하나인 역학적인 힘에 의해 전기적인 특성의 변화에 대한 기초연구를 진행하였다. 단층 $MoS_2$에 in-plane 방향으로 isotropic strain을 주었을 때 밴드갭이 0.68 eV에서 1.89 eV까지 변하는 것을 확인했다. 우리는 단층 $MoS_2$는 약간의 strain에도 밴드갭크기가 다소 많이 변할 뿐만 아니라 직접 밴드갭이 간접 밴드갭으로 변하는 것을 보였다. 심지어 10%정도 strain을 주면 금속으로 변할 것으로 예상된다. 밴드갭이 변하는 성질을 이용하여 센서등 여러 어플리케이션에 단층 $MoS_2$를 활용할 수 있을 것으로 예상된다.

• Proceeding of EDISON Challenge
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• 2017.03a
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• pp.499-505
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• 2017

Photoisomerizing molecules which can transform their structure by the light irradiation have great deal for the application of photo-switching devices. And azobenzene is the representive type of the photoisomerizing molecules. It can transform their trans- structures into cis- structure as the light for certain wave lengths they receive. This property shows the potential of ON/OFF switching functionalization which can be used into the nano scale photo switch. Furthermore, many studies are interested in the organic linkers that connect the azobenzene and metal electrodes. We used S, $CH_2S$, $(CH_2)_4S$ as the linker to watch the influence of linkers for electronic properties. So We suggest a photoswitching device based on the vertical junction using the first-principles calculations with density functional theory and non-equilibrium Greens function (NEGF). By analyzing the electronic structure and tunneling current caused by the structural difference of the system between cis- and trans- azobenzene, the difference in switching mechanism, ON/OFF ratio and transmission will be watched as the linker changes. And finally We will suggest which linker would be the better for the optimal device architecture which can achieve high control of the ON/OFF photocurrent ratio. This result will show the potential of azobenzene-based photoswitch and provide the critical insight in constructing the optimal device architecture.

• Proceeding of EDISON Challenge
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• 2017.03a
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• pp.132-144
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• 2017

현재, 빛을 이용한 화학 연구가 활발히 진행되고 있고 이러한 연구는 양자역학을 기반으로 화학에서 상당히 중요한 부분을 차지하고 있다. 또한 컴퓨터의 발전에 따라 여러 계산 모델들이 개발되고 있다. 본 논문에서는 회전파 근사(Rotating Wave Approximation, RWA)를 통해 라비 진동을 이론적으로 확인하고, 가장 간단한 연속파 레이저와 두 에너지 준위에서 시작하여 레이저 펄스와 두 에너지 준위, 레이저 펄스와 이원자분자인 $Na_2$ 분자의 두 전자에너지 퍼텐셜 준위, 그리고 실제 시간 밀도 범함수 이론(Real-Time Time Dependent Density Functional Theory, RT-TDDFT)이란 제일원리계산을 통해 연속파 레이저와 $H_2$ 분자와 $C_2H_4$ 분자에서까지 관찰하였다. 이 연구를 통해 공명 전이의 경우 펄스의 면적이 ${\pi}$의 홀수 배일 때 완전한 입자수 전이가 일어나는 펄스 면적 정리를 확인할 수 있었고, 이원자분자인 $Na_2$의 경우엔 펄스의 지속시간도 입자수 전이에 영향을 미친다는 것을 확인하였다. 더 나아가 $H_2$ 분자와 $C_2H_4$ 분자에서는 RT-TDDFT 계산을 통해 라비 진동을 확인할 수 있었고, 두 종류의 기저함수간의 대조를 통해 기저함수 선택의 중요성을 알아보았고, 가장 중요하게는 레이저를 잘 조작하면 입자를 원하는 상태로 들뜨게 할 수 있다는 것이란 결론을 얻게 되었다.

• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.304-307
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• 2015

Carbon nanotubes (CNTs) have been widely accepted and used as the enhancer for polymer nano-composites due to their remarkable mechanical properties. Understandably, the CNT fiber-polymer matrix interface plays a major role in determining the properties of the CNT-polymer nano-composites. Here, using the LCAODFT Lab tool available on the EDISON Nano-Physics site, we performed first-principles density-functional theory calculations to determine the atomic configurations and binding energies of the CNTs in contact with polymers. For the polymer matrixes, we chose poly(acrylonitrile) (PAN), which is one of the most well-known polymer matrixes for the carbon nanofiber nanocomposites. Different chiralities and diameters of pristine CNTs were considered, and several PAN-CNT configurations were prepared based on the atomistic positions and directions of cyano group in PAN. The most favorable configuration of PAN was obtained when the PAN bound parallel to the surface of CNT. Our finding indicates the binding configurations are determined by the direction of the cyano group dominantly rather than the atomistic position of PAN, or the symmetry of CNTs. The result of increasing the length of CNT diameter suggests that PAN is inclinable to align evenly on the surface of relatively large size of CNT with the configuration parallel to the surface. These results obtained in this study will provide the starting point for the design of improved PAN-CNT composites for the next-generation ultra-strong and ultra-light carbon nanofibers.

• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.151-155
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• 2015

The molecular interactions between the nucleic acid bases and water molecules are important in organism. Despite Adenine-Thymine Hoogsteen base pair and Guanine-Cytosine Watson-Crick base pair have been demonstrated to be most stable in a gas phase, the effect of water on the stability of these base pairs remains elusive. Here we report the structural and thermodynamic characteristics on possible Adenine-Thymine and Guanine-Cytosine base pairs in a gas phase as well as in an aqueous phase by using quantum mechanical method and statistical mechanical calculations. First, we optimized the direct base-pair interaction energies of four Adenine-Thymine base pairs (Hoogsteen base pair, reverse Hoogsteen base pair, Watson-Crick base pair, and reverse Watson-Crick base pair) and three Guanine-Cytosine base pairs (GC1 base pair, GC2 base pair, and Watson Crick base pair) in a gas phase at the $B3LYP/6-31+G^{**}$ level. Then, the effect of solvent was quantified by the electronic reorganization energy and the solvation free energy by statistical mechanical calculations. Thereby, we discuss the effect of water on the stability of Adenine-Thymine and Guanine-Cytosine base pairs, and argue why Adenine-Thymine Watson-Crick base pair and Guanine-Cytosine Watson-Crick base pair are most stable in an aqueous environment.

• Proceeding of EDISON Challenge
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• 2016.03a
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• pp.62-66
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• 2016

Tumor suppressor protein p53 loses its function upon binding with the HDM2 protein, and inhibiting the p53-HDM2 interaction is critical to suppress tumor cell growth. Recently, the cyclized helix-loop-helix peptide (cHLH) mimicking the ${\alpha}-helix$ part of the p53 protein has been designed and found to exhibit high binding affinity with HDM2. Here, we report the structural and thermodynamic characteristics of the bound complex of the cHLH peptide with the HDM2 protein. We performed molecular dynamics simulations to investigate the structural features of the cHLH peptide as well as its complex with the HDM2. The binding free energy calculation based on the integral equation theory was also executed to quantify the binding affinity for the cHLH/HDM2 complex and to understand the factors contributing to the binding affinity. We found a variety of factors for the helix stability of the cHLH peptide as well as in the complexation with the HDM2, which may provide an insight into the development of anti-cancer drug designs.

• Proceeding of EDISON Challenge
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• 2016.03a
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• pp.163-166
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• 2016

Hydrophobicity is the key concept to understand the water plays in protein folding, protein aggregation, and protein-protein interaction. Traditionally, the hydrophobicity of protein is defined based on the scales of the hydrophobicity of residue, assuming that the hydrophobicity of free amino acids is maintained. Here, we explore how the hydrophobicity of constituting amino acids in protein rely on the protein context, in particular, on the total charge and secondary structures of a protein. To this end, we calculate and investigate the hydration free energy 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 total charge being positive or negative. We also observe that amino acids in the ${\beta}-sheets$ display more enhanced the hydrophobicity than amino acids in the loop, whereas those in the ${\alpha}-helix$ do not clearly show such a tendency. And the salt-bridge forming amino acids also exhibit increase of the hydrophobicity than that with no salt bridge. 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.

• Proceeding of EDISON Challenge
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• 2013.04a
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• pp.256-259
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• 2013

We investigate co-doping effects of conjugated P-N B-N with increasing of N concentration in the graphene sheets using a first principles based on the density functional theory. N doping sites of the graphene consider two possible sites (pyridinic and porphyrin-like). Energy calculation shows that additional doping of B atom in the porphyrin-like N doped graphene ($V+B-N_x$) is hard to form. At the low chemical potential of N, one N atom with additional doping in the graphene ($V+P-N_1$, $P/B-N_1$) has low formation energy on the other hand at high chemical potential of N, high concentration of N ($V+P-N_4$, $P/B-N_3$) in the graphene is governing conformation. From the results of electronic band structure calculation, it is found that $V+P-N_4$ and $P/B-N_3$ cases change the Fermi energy therefore type change is occurred. On the other hand, the cases of $V+P-N_1$ and N+B recover the electronic structure of pristine graphene.