• Bulletin of the Korean Chemical Society
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• 제33권3호
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• pp.980-986
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• 2012

In this paper we develop a minimalist model of single molecule spectroscopy in a dynamic environment. Our model is based upon a lattice system consisting of a probe molecule embedded in an Ising-model like environment. We assume that the probe molecule interacts with the Ising spins via a dipole-dipole potential, and calculate free energy curves and lineshapes of the system. To investigate fluctuation behavior of the system we exploit the metadynamics sampling method. In particular, using the method, we calculate the free energy curve of magnetization of the lattice and that of the transition energy of the probe molecule. Furthermore, we compare efficiencies of three different sampling methods used; unbiased, umbrella, and metadynamics sampling methods. Finally, we explore the lineshape behavior of the probe molecule as the system undergoes a phase transition from a sub-critical and to a super-critical temperature. We show that the transition energy of a probe molecule is broadly distributed due to the heterogeneous, local environments.

• BMB Reports
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• 제52권10호
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• pp.589-594
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• 2019

Single-molecule techniques have been used successfully to visualize real-time enzymatic activities, revealing transient complex properties and heterogeneity of various biological events. Especially, conventional force spectroscopy including optical tweezers and magnetic tweezers has been widely used to monitor change in DNA length by enzymes with high spatiotemporal resolutions of ~nanometers and ~milliseconds. However, DNA metabolism results from coordination of a number of components during the processes, requiring efficient monitoring of a complex of proteins catalyzing DNA substrates. In this min-review, we will introduce a simple and multiplexed single-molecule assay to detect DNA substrates catalyzed by enzymes with high-throughput data collection. We conclude with a perspective of possible directions that enhance capability of the assay to reveal complex biological events with higher resolution.

• International Journal of Oral Biology
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• 제43권2호
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• pp.53-59
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• 2018

In order to understand biological phenomena accurately, single molecule techniques using a physical research approach to molecular interactions have been developed, and are now widely being used to study complex biological processes. In this review, we discuss some of the single molecule methods which are composed of two major parts: single molecule spectroscopy and manipulation. In particular, we explain how these techniques work and introduce the current research which uses them. Finally, we present the oral biology research using the single molecule methods.

• 응용통계연구
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• 제26권4호
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• pp.569-579
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• 2013

단일 분자에서 발생한 발광의 세기 변화를 분석하는 문제는 단분자 분광학에서 반드시 필요하다. 본 연구에서는 카드뮴셀레나이드/황화아연의 중심-껍질 구조를 갖는 양자점에 대한 단분자 분광학 데이터에 대해 Poisson count data로서 베이지안 접근으로 모수에 대한 공액 감마분포와 변화점 개수에 대한 절단포아송 분포로 사전분포를 주고 다중변화점을 추정하였다.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2015년도 제49회 하계 정기학술대회 초록집
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• pp.63.2-63.2
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• 2015

Controlling and sensing spin states of magnetic molecules such as metallo-porphyrins at the single molecule level is essential for spintronic molecular device applications. Axial coordinations of diatomic molecules to metallo-porphyrins also play key roles in dynamic processes of biological functions such as blood pressure control and immune response. However, probing such reactions at the single molecule level to understand their physical mechanisms has been rarely performed. Here we present on our single molecule association and dissociation experiments between diatomic and metallo-porphyrin molecules on Au(111) describing its adsorption structures, spin states, and dissociation mechanisms. We observed bright ring shapes in NO adsorbed metallo-porphyrin compelxes and explained them by considering tilted binding and precession motion of NO. Before NO exposure, Co-porphryin showed a clear zero-bias peak in scanning tunneling spectroscopy, a signature of Kondo effect in STS, whereas after NO exposures it formed a molecular complex, NO-Co-porphyrin, that did not show any zero-bias feature implying that the Kondo effect was switched off by binding of NO. Under tunneling junctions of scanning tunneling microscope, both positive and negative energy pulses. From the observed power law relations between dissociation rate and tunneling current, we argue that the dissociations were inelastically induced with molecular orbital resonances. Our study shows that single molecule association and dissociation can be used to probe spin states and reaction mechanisms in a variety of axial coordination between small molecules and metallo-porphyrins.

• 대한화학회지
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• 제59권2호
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• pp.132-135
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• 2015

Bonding force and stiffness in amine-linked single-molecule junctions for Ag electrodes were measured using a home-built conducting atomic force microscope under ambient conditions at room temperature. For comparison, Au electrodes were used to measure the rupture force and stiffness of the molecular junctions. The traces of the force along with the conductance showed a characteristic saw-tooth pattern owing to the breaking of the metal atomic contacts or the metal-molecule- metal junctions. We found the rupture force and stiffness for Ag are smaller than those for Au electrodes. Furthermore, we observed that the force required to break the amine-Ag bond in the conjugated molecule, 1,4-benzenediamine, is smaller than in 1,4-butanediamine which is fully saturated. These results consist with the previous theoretical calculations for the binding energies of the nitrogen bonded to Ag or Au atoms.

• Bulletin of the Korean Chemical Society
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• 제30권5호
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• pp.1143-1146
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• 2009

[$Mn_{12}O_{12}(azo-L)_{16}(H_2O)_4$] (1), a new Mn12 single molecule magnet containing a photochromic azobenzene ligand, has been successfully synthesized by substitution of acetate ligand of Mn12 with 6-[4-{4-hexyloxyphenyl( azo)}-phenoxy]hexanoic-1-acid. The reversible photoisomerization of the azobenzene group was confirmed by UV-visible absorption spectroscopy. The temperature and field dependence of dc susceptibility and the temperature and the frequency dependence of ac susceptibility were measured for the cis and the trans isomer of 1. The magnetization value of the cis isomer in dc measurement is higher than that of the trans isomer. The cis isomer of 1 has a slower relaxation because cis-trans photoisomerization of the azobenzene group in peripheral ligands induces changes in its structure and dipole moment.

• 한국광학회:학술대회논문집
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• 한국광학회 2009년도 동계학술발표회 논문집
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• pp.431-432
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• 2009

• 한국광학회:학술대회논문집
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• 한국광학회 2004년도 제15회 정기총회 및 동계학술발표회
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• pp.180-181
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• 2004

• 대한화학회지
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• 제55권5호
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• pp.746-750
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• 2011

Fluorescence correlation spectroscopy (FCS) is an emerging fluorescence technique used to study the dynamics of proteins on a millisecond to microsecond time scale at the single-molecule level. Solution pH-modulated protein conformational changes can be manifested by binding rate, fluorescence lifetime, and binding specificity of a probe molecule. The fluorescence lifetime of Nile red (NR) bound to apomyoglobin (apoMb) was measured to be $6{\pm}0.3$ ns, much longer than that in water solution ($2.9{\pm}0.2$ ns). As the unfolding population of apoMb increased by lowering pH of solution, the fraction for the longer lifetime of NR decreased with an increasing fraction for the shorter lifetime of NR in water. Unlike 1-anilino-8-naphthalene sulfonic acid, which has many lifetimes due to nonspecific binding to the unfolded apoMb, NR bound to apoMb possesses only a single lifetime. These results suggest that NR binds specifically to native apoMb and thus can be utilized to probe the folding/unfolding dynamics of apoMb using FCS.