• Bulletin of the Korean Chemical Society
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• v.33 no.3
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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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• v.52 no.10
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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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• v.43 no.2
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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.

• The Korean Journal of Applied Statistics
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• v.26 no.4
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• pp.569-579
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• 2013

In the field of single-molecule spectroscopy, it is essential to analyze luminescence Intensity changes that result from a single molecule. With the CdSe/ZnS core-shell structured quantum dot photon emission data Bayesian multiple change-point estimation is done with the gamma prior for Poisson parameters and truncated Poisson distribution for the number of change-points.

• Proceedings of the Korean Vacuum Society Conference
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• 2015.08a
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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.

• Journal of the Korean Chemical Society
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• v.59 no.2
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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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• v.30 no.5
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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.

• Proceedings of the Optical Society of Korea Conference
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• 2009.02a
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• pp.431-432
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• 2009

• Proceedings of the Optical Society of Korea Conference
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• 2004.02a
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• pp.180-181
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• 2004

• Journal of the Korean Chemical Society
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• v.55 no.5
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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.