• Molecules and Cells
• /
• 제27권6호
• /
• pp.673-680
• /
• 2009

Conversion of the normal soluble form of prion protein, PrP ($PrP^C$), to proteinase K-resistant form ($PrP^{Sc}$) is a common molecular etiology of prion diseases. Proteinase K-resistance is attributed to a drastic conformational change from ${\alpha}$-helix to ${\beta}$-sheet and subsequent fibril formation. Compelling evidence suggests that membranes play a role in the conformational conversion of PrP. However, biophysical mechanisms underlying the conformational changes of PrP and membrane binding are still elusive. Recently, we demonstrated that the putative transmembrane domain (TMD; residues 111-135) of Syrian hamster PrP penetrates into the membrane upon the reduction of the conserved disulfide bond of PrP. To understand the mechanism underlying the membrane insertion of the TMD, here we explored changes in conformation and membrane binding abilities of PrP using wild type and cysteine-free mutant. We show that the reduction of the disulfide bond of PrP removes motional restriction of the TMD, which might, in turn, expose the TMD into solvent. The released TMD then penetrates into the membrane. We suggest that the disulfide bond regulates the membrane binding mode of PrP by controlling the motional freedom of the TMD.

• 한국진공학회:학술대회논문집
• /
• 한국진공학회 2009년도 제38회 동계학술대회 초록집
• /
• pp.16-17
• /
• 2010

Molecular spintronics has attracted attentions, which combines molecular electronics with the spin degree of freedom in electron transport. Among various molecules as candidates of the molecular spintronics, single molecule magnet (SMM) is one of the most promising material. SMM molecules show a ferromagnetic behavior even as a single molecule and hold the spin information even after the magnetic field is turned off. Here in this report, we show the spin behavior of SMM molecules adsorbed on the Au surface by combining the observation of Kondo peak in the STS and ESR-STM measurement. Kondo resonance state is formed near the Fermi level when degenerated spin state interacts with conduction electrons. ESR-STM detects the Larmor frequency of the spin in the presence of a magnet field. The sample include $MPc_2$ and $M_2Pc_3$ molecules ($M\;=\;Tb^{3+}$, $Dy^{3+}$, and $Y^{3+}$ Pc=phthalocyanine) whose critical temperature as a ferromagnet reaches 40 K. A clear Kondo peak was observed which is originated from an unpaired electron in the ligand of the molecule, which is the first demonstration of the Kondo peak originated from electron observed in the STS measurement. We also observed corresponding peaks in ESR-STM spectra. [1] In addition we found that the Kondo peak intensity shows a clear variation with the conformational change of the molecule; namely the azimuthal rotational angle of the Pc planes. This indicates that the Kondo resonance is correlated with the molecule electronic state. We examined this phenomena by using STM manipulation technique, where pulse bias application can rotate the relative azimuthal angle of the Pc planes. The result indicates that an application of ~1V pulse to the bias voltage can rotate the Pc plane and the Kondo peaks shows a clear variation in intensity by the molecule's conformational change.

• Korean Membrane Journal
• /
• 제5권1호
• /
• pp.43-53
• /
• 2003

The selectivity of a gas in the carbon molecular sieve membrane (CMSM) can be expressed as the ratio of the product of the diffusivity and the solubility of two different gases. The diffusivity is also expressed as the product of the entropy and the total energy (kinetic and potential energy) in the nano-sized pore of the membrane. The present study calculates the entropic-energy and selectivity of penetrant gases such as H$_2$, O$_2$, N$_2$, and CO$_2$ from the gas-in-a box theory to physically analyze the diffusivity of penetrant gas in slit-shaped pore of CMSM focusing on the restriction of gas motion based on the size difference between penetrant gas pairs. The contribution of each energy term is converted to entropic term separately. By the conjugated calculation for each entropic-energy, the entropic effects on diffusivity-selectivity for gas pairs such as H$_2$/N$_2$, CO$_2$/N$_2$, and O$_2$/N$_2$ were analyzed within active pore of CMSM. In the activated diffusion domain, the calculated value of entropic-selectivity lies between 9.25 and 111.6 for H$_2$/N$_2$, between 3.36 and 6.0 for CO$_2$/N$_2$, and between 1.25 and 16.94 for O$_2$/N$_2$, respectively. The size decrement of active pore in CMSM had the direct effect on the reduction of translational entropic-energy and the contribution of vibrational entropic-energy for N$_2$, O$_2$, and H$_2$ was almost negligible. However, the vibrational entropic term of CO$_2$ might extravagantly affect on the entropic-selectivity.

• 한국소음진동공학회:학술대회논문집
• /
• 한국소음진동공학회 2008년도 춘계학술대회논문집
• /
• pp.476-479
• /
• 2008

Understanding the dynamics of proteins is essential to gain insight into biological functions of proteins. The protein dynamics is delineated by conformational fluctuation (i.e. thermal vibration), and thus, thermal vibration of proteins has to be understood. In this paper, a simple mechanical model was considered for understanding protein's dynamics. Specifically, a mechanical vibration model was developed for understanding the large protein dynamics related to biological functions. The mechanical model for large proteins was constructed based on simple elastic model (i.e. Tirion's elastic model) and model reduction methods (dynamic model condensation). The large protein structure was described by minimal degrees of freedom on the basis of model reduction method that allows one to transform the refined structure into the coarse-grained structure. In this model, it is shown that a simple reduced model is able to reproduce the thermal fluctuation behavior of proteins qualitatively comparable to original molecular model. Moreover, the protein's dynamic behavior such as collective dynamics is well depicted by a simple reduced mechanical model. This sheds light on that the model reduction may provide the information about large protein dynamics, and consequently, the biological functions of large proteins.

• 한국전산구조공학회:학술대회논문집
• /
• 한국전산구조공학회 2006년도 정기 학술대회 논문집
• /
• pp.395-402
• /
• 2006

In analyzing the nano-scale phenomena or behaviors of nano devices or materials, it is often desirable to deal with more atoms than can be treated only with a full atomistic simulation. However, even now, it is advisable to apply the atomistic simulation to the narrow region where the deformation field changes rapidly but to apply the conventional continuum model to the region far from that region. This equivalent continuum model can be formulated by applying the Cauchy-Born rule to the exact atomistic potential as in the quasicontinuum method. To couple the atomistic model with the equivalent continuum model, continuum displacements are conformed to the molecular displacements at the discrete positions of the atoms within the bridging domain. To satisfy the coupling constraints, we apply the Lagrange multiplier method. The continuum model in the bridging model should be applied on the region where the deformation field changes gradually. Then we can make the nodal spacing in the continuum model be much larger than the atomic spacing. In the first step, we generate the atomic-resolution mesh with the nodal spacing equal to the atomic spacing, and then we eliminate the nodal degrees of freedom adaptively using the node deactivation techniques. We eliminate more DOFs as the regions are more far from the atomistic region. Computing time and computational resources can be greatly reduced by the present node deactivation technique in multi scale analysis.

• 한국정밀공학회:학술대회논문집
• /
• 한국정밀공학회 2006년도 춘계학술대회 논문집
• /
• pp.367-368
• /
• 2006

Today, the Artificial Intervertebral Disc (AID) is being developed by increasing the oblique of the endplate gradually. In other words, Ultra-high Molecular Weight Polyethylene (UHMWPE) which is apply to the sliding core of the AID, does not change the shape but alters the oblique of endplate. However, the unreasonable increase of degree of freedom (DOF) can result in the aggravation of the bone fusion and the initial stability and it can also lead to the increase of the concentrated force in core. For these reasons, it is necessary to develop the advanced techniques, which choose the most adequate DOF. In this study, the new optimized modeling of the sliding core and the endplate, the fatigue characteristics, the crack propagation and the formation mechanism of wearing debris was studied and the minimizing technique will be derived from this research.

• Bulletin of the Korean Chemical Society
• /
• 제30권2호
• /
• pp.429-434
• /
• 2009

The OH($X^2{\Pi},\;{\nu}$"=0, 1) internal state distributions from the reaction of electronically ground state oxygen atoms with HSi$Cl_3$ were measured using laser-induced fluorescence. The ground-state O$(^3P_J)$ atoms with kinetic energies above the reaction barrier were produced by photolysis of N$O_2$ at 355 nm. The OH product revealed strong vibrational population inversion, P(${\nu}$"=1)/P(${\nu}$"=0) = 4.0 ${\pm}$ 0.6, and rotational distributions in both vibrational states exhibit substantial rotational excitations to the limit of total available energy. However, no preferential populations in either of the two $\Lambda$ doublet states were observed from the micropopulations, which supports a mechanism involving a direct abstraction of hydrogen by the atomic oxygen. It was also found that the collision energy between O and HSi$Cl_3$ is effectively coupled into the excitation of the internal degrees of freedom of the OH product ($$ = 0.62, and $<\;f_{rot}>$ = 0.20). The dynamics appear consistent with expectations for the kinematically constrained reaction which supports the reaction type, heavy + light-heavy $\rightarrow$ heavy-light + heavy (H + LH′ $\rightarrow$ HL + H′). The dynamics of oxygen atom collision with HSi$Cl_3$ are discussed in comparison to those with Si$H_4$.

• 대한화학회지
• /
• 제8권2호
• /
• pp.68-74
• /
• 1964

물은 용융점, 끓는점, 용융열 및 증발열등의 수소와 6족원소와의 화합물의 성질로부터 예측되는 값보다 훨씬 크고, ice-I녹을 때 부피의 감소가 일어나는 등 특이한 성질을 가지고 있다. 이와같은 성질들을 정량적으로 설명하려고 지금까지 많은 연구자들이 노력해왔다. 저자들은 물의 큰 표면자유에네르기와 용융시의 특수한 부피변화로 미루어 물의 구조모델을 다음과 같이 생각하였다. 즉, 얼음이 용융함에 따라 분자크기의 이동성 빈자리가 도입되면 물의 큰 표면에네르기 밀도로 말미암아 빈자리 주위의 물분자는 촘촘한 배열을 가지게 되면 빈자리에서 떨어져있는 분자는 ice-I의 구조를 가질것으로 생각된다. 빈자리 주위의 분자가 빈자리에 뛰어 들어갈 때는 이동자유도를 지니게 될 것이다. 저자들은 H. Eyring의 액체구조이론을 써서 물의 liquid partition function을 위에 말한 바와 같이 구조모델로부터 유도하고 물의 증기압, 용융 및 증발엔트로피 등 여러가지 열역학적 성질 및 몰부피를 계산하여 실측치와 좋은 일치를 얻었다.

• Bulletin of the Korean Chemical Society
• /
• 제14권6호
• /
• pp.713-717
• /
• 1993

The crystal structure of the potassium salt of penicillin V has been studied by the X-ray crystallographic methods. Crystal data are as follows; potassium 3,3-dimethyl-7-oxo-6-phenoxyacetoamido-4-thia-1- azabicyclo[3.2.0]-heptane-2${\alpha}$-carboxylate, $K^+{\cdot}C_{16}H_{18}N_2O_5S^-$, $M_r$= 388.5, triclinic, Pl, a= 9.371 (1), b= 12.497 (2), c= 15.313 (2) ${\AA},\;{\alpha}= 93.74\;(2),\;{\beta}=99.32\;(1),\;{\gamma}=90.17\;(1)^{\circ},\;V=1765.7\;(2)\;{\AA}^3$, Z=4, $D_m=1.461\;gcm^{-1},\;{\lambda}(Cu\;K{\alpha})=1.5418\;{\AA},\;{\mu}=40.1\;cm^{-1}$, F(000)=808, T=296 K. The structure was solved by the heavy atom and difference Fourier methods with intensity data measured on an automated four-circle diffractometer. The structure was refined by the full-matrix least-squares method to a final R= 0.081 for 3563 observed $[I_0{\geq}2{\sigam}(I_0)]$ reflections. The four independent molecules assume different overall conformations with systematically different orientations of the phenyl groups although the penam moieties have the same closed conformations. There are intramolecular hydrogen bonds between the exocyclic amide nitrogen and phenoxy oxygen atoms. The penam moiety is conformationally very restricted although the carboxyl and exocyclic amide groups apparently have certain rotational degrees of freedom but the phenyl group is flexible about the ether bond despite the presence of the intramolecular N-H${\cdots}$O hydrogen bond. There are complicated pseudo symmetric relationships in the crystal lattice. The penam moieties are related by pseudo 20.5 screw axes and the phenyl groups by pseudo centers of symmetry. The potassium ions, related by both pseudo symmetries, form an infinite zigzag planar chain parallel to the b axis. Each potassium ion is coordinated to seven oxygen atoms in a severely distorted pentagonal bipyramid configuration, forming the infinite hydrophilic channels which in turn form the molecular stacks. Between these stacks, there are only lipophilic interactions involving the phenyl groups.

• 한국식품과학회지
• /
• 제35권6호
• /
• pp.1053-1059
• /
• 2003

분석 중 소실되기 쉬운 야채음료의 비타민 C 함량을 HPLC를 이용하여 측정하였으며, 불확도인자로서 표준품의 무게, 순도, 분자량, 희석 등과 시료의 무게, 검정곡선, 회수율 및 정밀성 등이 작용하였다. 이러한 미심쩍음 정도와 더불어 계통오차와 우연오차 등 일련의 과정을 GUM(Guide to the expression of Uncertainty in Measurement)과 EURACHEM에 근거하여 수학적 처리 및 통계방법을 이용하여 측정불확도를 추정하였다. 추정방법은 각각의 인자들에 대하여 A-type또는 B-type으로 산출된 표준불확도 값을 합성하여 합성표준불확도를 산출하고, 확장불확도는 유효자유도로 산출된 포함인자를 곱하여 계산하였다. 야채와 과일이 혼합된 음료 중 비타민 C 함량은 27.53mg/100g이었으며, 포함인자(2.06)를 곱한 확장불확도는 0.63mg/100g로서 95% 신뢰도구간에서의 비타민C의 결과는 $27.53{\pm}0.63mg/100g$(95% 신뢰도 구간)과 같이 수치화하여 표현하였다. 비타민 C 분석의 경우 HPLC를 이용한 시료 분석의 회수율 및 정밀성(33%), 표준품 순도(23%), 표준용액 희석시(18%), 표준품 무게(10%), 시료 측정시(10%), 검정곡선(6%) 순으로 불확도를 추정할 수 있었다. 또한, 이를 통해서 시험원의 분석과정 중 불확도가 높게 산출된 실험과정에 대해서는 좀더 세심한 주의가 요구되며, 시료의 반복실험 시 재현성 있는 결과가 산출될 수 있도록 숙련도를 높일 필요가 있다.