Publications (43)146.13 Total impact
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ABSTRACT: Liquid helium does not obey the Gibbs fluctuationcompressibility relation, which was noted more than six decades ago. However, still missing is a clear explanation of the reason for the deviation or the correct fluctuationcompressibility relation for the quantum liquid. Here we present the fluctuationcompressibility relation valid for any grand canonical system. Our result shows that the deviation from the Gibbs formula arises from a nonextensive part of thermodynamic potentials. The particleexchange symmetry of manybody wave function of a strongly degenerate quantum gas is related to the thermodynamic extensivity of the system; a Bose gas does not always obey the Gibbs formula, while a Fermi gas does. Our fluctuationcompressibility relation works for classical systems as well as quantum systems. This work demonstrates that the application range of the GibbsBoltzmann statistical thermodynamics can be extended to encompass nonextensive open systems without introducing any postulate other than the principle of equal a priori probability.Physical review. E, Statistical, nonlinear, and soft matter physics. 06/2014; 89(61):062131.  [Show abstract] [Hide abstract]
ABSTRACT: Celltocell variation in gene expression, or noise, is a general phenomenon observed within cell populations. Transcription is known to be the key stage of gene expression where noise is generated, however, how variation in RNA polymerase (RNAP) concentration contributes to gene expression noise is unclear. Here, we quantitatively investigate how variations in absolute amounts of RNAP molecules affect noise in the expression of two fluorescent protein reporters driven by identical promoters. We find that intrinsic noise is independent of variation in RNAP concentrations, whereas extrinsic noise, which is variation in gene expression due to varying cellular environments, scales linearly with variation in RNAP abundance. Specifically, the propagation of RNAP abundance variation to expressed protein noise is inversely proportional to the concentration of RNAP, which suggests that the change in noise that results from RNAP fluctuations is determined by the fraction of promoters that is not occupied by RNAP.Nature Communications 01/2014; 5:4761. · 10.02 Impact Factor 
Article: Reaction Event Counting Statistics of Biopolymer Reaction Systems with Dynamic Heterogeneity
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ABSTRACT: We investigate the reaction event counting statistics (RECS) of an elementary biopolymer reaction in which the rate coefficient is dependent on states of the biopolymer and the surrounding environment and discover a universal kinetic phase transition in the RECS of the reaction system with dynamic heterogeneity. From an exact analysis for a general model of elementary biopolymer reactions, we find that the variance in the number of reaction events is dependent on the square of the mean number of the reaction events when the size of measurement time is small on the relaxation time scale of rate coefficient fluctuations, which does not conform to renewal statistics. On the other hand, when the size of the measurement time interval is much greater than the relaxation time of rate coefficient fluctuations, the variance becomes linearly proportional to the mean reaction number in accordance with renewal statistics. Gillespie’s stochastic simulation method is generalized for the reaction system with a rate coefficient fluctuation. The simulation results confirm the correctness of the analytic results for the time dependent mean and variance of the reaction event number distribution. On the basis of the obtained results, we propose a method of quantitative analysis for the reaction event counting statistics of reaction systems with rate coefficient fluctuations, which enables one to extract information about the magnitude and the relaxation times of the fluctuating reaction rate coefficient, without a bias that can be introduced by assuming a particular kinetic model of conformational dynamics and the conformation dependent reactivity. An exact relationship is established between a higher moment of the reaction event number distribution and the multitime correlation of the reaction rate for the reaction system with a nonequilibrium initial state distribution as well as for the system with the equilibrium initial state distribution.Journal of Chemical Theory and Computation 03/2012; 8(4):1415–1425. · 5.39 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: Fluctuating turnover times of a single enzyme become observable with the advent of modern cuttingedge, single enzyme experimental techniques. Although the conventional chemical kinetics and its modern generalizations could provide a good quantitative description for the mean of the enzymatic turnover times, to our knowledge there has not yet been a successful quantitative interpretation for the variance or the randomness of the enzymatic turnover times. In this review, we briefly review several theories in this field, and compare predictions of these theories to the randomness parameter data reported for βgalactosidase enzyme. We find the recently proposed kinetics for renewal reaction processes could provide an excellent quantitative interpretation of the randomness parameter data. From the analysis of the randomness parameter data of the single enzyme reaction, one can extract quantitative information about the mean lifetime of enzymesubstrate complex; the success or the failure probability of the catalytic reaction per each formation of ES complex; and the nonPoisson character of the reaction dynamics of the ES complex (which is beyond reach of the longstanding paradigm of the conventional chemical kinetics).Biophysical Journal 08/2011; 101(3):51924. · 3.67 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: We introduce a new method of solution for the Fredholm integral equations of the second kind. The method would be useful when the direct iterative approach leads to a divergent perturbation series solution. By using the method, we obtain an accurate expression of the propagator for diffusive dynamics of a pair of particles interacting via an arbitrary central potential and hydrodynamic interaction. We test the accuracy of the propagator expression by calculating the diffusioncontrolled geminate and bimolecular reaction rates. It is shown that our propagator expression provides very accurate results for the whole time region.The Journal of Chemical Physics 03/2011; 134(12):121102. · 3.12 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: We present a theory for a unified characterization of a substrate–receptor system with an arbitrary binding affinity distribution. On the basis of a universal expression obtained for the bound fraction isotherm of a monovalent receptor system, we propose a novel experimental analysis method for characterization of the receptor system, introducing a new type of experimental plot. From our analysis method, one can extract key physical parameters that mostly determine the shape of bound fraction isotherm, which include the mean binding affinity, the mean binding free energy, and the parameters that measure the magnitude of fluctuation and the asymmetry of the binding free energy distribution for receptor–substrate system, without any bias that can be introduced by presuming a particular functional form for the binding free energy distribution or for the bound fraction isotherm.Graphical abstractHighlights► We report a theory for an objective characterization of a substratereceptor system with an arbitrary binding affinity distribution. ►We propose a quantitative analysis method applicable to a heterogeneous receptor system with use of a novel experimental plot, named Θ0 plot. ►Our analysis method enables one toestimatekey physical parameters that mostly determine the shape of the bound fraction isotherm.Chemical Physics 01/2011; 384:3643. · 1.96 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: We report a robust quadratic relation between the inverse substrate concentration and the second moment, <t(2)>, of the catalytic turnover time distribution for enzyme reactions. The results hold irrespective of the mechanism and dynamics of the enzyme reaction and suggest a novel single molecule experimental analysis that provides information about reaction processes of the enzymesubstrate complex and ergodicity of the enzyme reaction system, which is beyond the reach of the conventional analysis for the mean reaction time, . It turns out that <t(2)>  2 (2) is linear in inverse substrate concentration for an ergodic homogeneous enzyme system given that the enzyme substrate encounter is a simple rate process, and its value at the high substrate concentration limit provides direct information about if any nonPoisson reaction process of the enzymesubstrate complex. For a nonergodic heterogeneous reaction system, the corresponding quantity becomes a quadratic function of the inverse substrate concentration. This leads us to suggest an ergodicity measure for single enzyme reaction systems. We obtain a simple analytic expression of the randomness parameter for the single catalytic turnover time, which could provide a quantitative explanation about the previously reported randomness data of the betagalactosidase enzyme. In obtaining the results, we introduce novel chemical kinetics applicable to a nonPoisson reaction network with arbitrary connectivity, as a generalization of the conventional chemical kinetics.The Journal of Physical Chemistry B 08/2010; 114(30):98407. · 3.61 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: New typeII structures of CdSe/InP and InP/CdSe coreshell nanocrystals which have staggered bandgap alignment were fabricated. Using a simple model for the wave function for electrons and holes in InP/CdSe and CdSe/InP core/shell nanocrystals showed the wave function of the electron and hole spread into the shell, respectively. The probability density of the InP/CdSe and CdSe/InP core/shell QDs also showed a similar tendency. As a result, the structure exhibits increased delocalization of electrons and holes, leading to a redshift in absorption and emission. Quantum yield increased in the InP/CdSe, however decreased in the CdSe/InP. The reason may be due to the surface trap and high activation barrier for detrapping in the InP shell.Journal of Colloid and Interface Science 03/2010; 346(2):34751. · 3.17 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: We report that an external field can drive inherently extensive systems into nonextensive ones. For the correct grand canonical description of nonextensive systems, it is necessary to take into account the excess grand potential, X, in addition to the conventional grand potential proportional to the thermodynamic pressure, which has long been overlooked in the literature in this field. We present the statistical mechanical expression for X of a system as a functional of the external field imposed on the system, from which we establish the criterion for the external field that drives an inherently extensive macroscopic system into a nonextensive one.The Journal of Physical Chemistry B 06/2009; 113(23):79825. · 3.61 Impact Factor 
Article: Bandgap engineered reverse typeI CdTe/InP/ZnS coreshell nanocrystals for the nearinfrared.
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ABSTRACT: New quantum dots were fabricated with a core/shell/shell structure consisting of CdTe core/InP shell/ZnS shell of which the InP shell causes a redshift to the NIR region and the ZnS shell imparts photostability; toxicity tests on mammalian cells and NIR imaging of a mouse highlight their potential applications in biomedical imaging.Chemical Communications 04/2009; · 6.38 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: We present a theoretical model for description of real polyreceptor molecular wire sensors (MWS), whose conductance signal may dramatically reduce upon analyte binding to one of the receptors coupled to the molecular wire but may not vanish as completely as assumed in the ideal MWS model. For the present nonideal MWS model, we establish the exact relationship between analyte concentration and the sensory signal intensity. It turns out that, whereas the SternVolmer curve of the ideal MWS always has a positive curvature, the SternVolmer curve of the imperfect MWS can have a negative curvature, consistent with experimental data. We find that the MWS still performs better than the corresponding ideal monoreceptor sensor, unless the nonideality of the imperfect MWS is egregiously large. We establish the conditions for the imperfect polyreceptor MWS to have a sensitivity and detection limit superior to the traditional monoreceptor sensor.Analytical Chemistry 01/2009; 81(2):57883. · 5.70 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: On the basis of the recently developed optimized RouseZimm theory of chain polymers with excluded volume interactions, we calculate the longtime firstorder rate constant k(1) for endtoend cyclization of linear chain polymers. We first find that the optimized RouseZimm theory provides the longest chain relaxation times tau(1) of excluded volume chains that are in excellent agreement with the available Brownian dynamics simulation results. In the freedraining limit, the cyclization rate is diffusioncontrolled and k(1) is inversely proportional to tau(1), and the k(1) values calculated using the WilemskiFixman rate theory are in good agreement with Brownian dynamics simulation results. However, when hydrodynamic interactions are included, noticeable deviations are found. The main sources of errors are fluctuating hydrodynamic interaction and correlation hole effects as well as the nonMarkovian reaction dynamic effect. The physical natures of these factors are discussed, and estimates for the magnitudes of required corrections are given. When the corrections are included, the present theory allows the prediction of accurate k(1) values for the cyclization of finitelength chains in good solvents as well as the correct scaling exponent in the longchain limit.The Journal of Physical Chemistry B 06/2008; 112(19):62508. · 3.61 Impact Factor 
Article: Statistical mechanics of molecular adsorption: effects of adsorbate interaction on isotherms.
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ABSTRACT: We investigate a simple, exactly solvable model for interacting adsorbates. From the model study, we find that (1theta)(1) as a function of density of molecules in bulk media can have a positive curvature only in the presence of attractive interaction between adsorbed molecules. We propose a novel experimental observable, chi. Positive chi is the sufficient condition for the presence of attractive interactions between adsorbate molecules.Langmuir 04/2008; 24(6):256972. · 4.38 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: Jarzynski's equation (JE) has been known to relate free energy change of a system to statistical distribution of work done on the system for an arbitrary process. In the present work, we first establish the validity condition of JE for boundary switching processes. The validity condition of JE is examined for an example of spontaneous irreversible processes, for which, obviously, JE does not hold. We find that the free energy difference between two configurational states with different phasespace volume cannot be correctly estimated by JE for any adiabatic boundary switching process.Physical Review E 04/2008; 77(4 Pt 1):042101. · 2.31 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: We investigate the first passage times for the contact between the ends of a Rouse chain, whose initial separation is greater than a predefined contact distance, sigma, and equilibriumdistributed. An approximate analytic expression for the mean first passage time is obtained and compared with the results of previous theories and Brownian dynamics simulations. We find that the results of the present theory are in better agreement with Brownian dynamics simulation results than those of previously reported theories.The Journal of Physical Chemistry B 10/2007; 111(35):1046873. · 3.61 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: We present an exact theoretical test of Jarzynski's equality (JE) for reversible volumeswitching processes of an ideal gas system. The exact analysis shows that the prediction of JE for the free energy difference is the same as the work done on the gas system during the reversible process that is dependent on the shape of path of the reversible volumeswitching process.Physical Review E 08/2007; 76(1 Pt 1):012101. · 2.31 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: We investigate how the pulloff force in atomic force microscopy (AFM), which arises from a nanoscale water bridge between the AFM tip and the surface, is influenced by atomic scale (smaller than 0.6 nm) roughness in the surface. Adopting a lattice gas model for water, we have simulated the adhesion of a siliconnitride tip (with a 20nm diameter) to mica under ambient humidity. The pulloff force responds sensitively to both surface and tip roughness, and its humidity dependence changes significantly with slight variation in the tip and surface morphology. The change in the pulloff force due to roughness smaller than 0.6 nm can be larger than the change from doubling the tip radius. The roughness effect is large at low humidities and diminishes as humidity increases. Even at 80 percent humidity, the pulloff force varies considerably with changes in tipsurface geometry. On average, the pulloff force decreases with increasing tip roughness. However it decreases with surface roughness for small roughness (<0.2 nm), and then it increases for larger roughness. The pulloff force is also found to decrease with increasing average tipsurface distance at the point of initial contact, which shows the importance of spatial confinement of the water droplet.Journal of Physical Chemistry C  J PHYS CHEM C. 03/2007; 111(12).  [Show abstract] [Hide abstract]
ABSTRACT: We present a theory for describing the reaction process occurring in disordered media with energetically disordered trapping sites and spatial constraints. The theory is based on a generalized fractional reaction–diffusion equation, which describes the time evolution of the mean distribution of a particle performing a continuous time random walk on a fractal network. The motion of a particle is subdiffusive because of the spatial constraints and/or the random detrapping times described by a waiting time distribution given by ψ(t)~t−(1+α) with 0<α<1. Assuming that the reaction occurs at a separation of contact, the reaction and transport processes are decoupled and the kinetic information for the reaction is expressed in terms of the reactionfree Green's function obtained with the reflecting boundary condition at the separation of contact. The survival probability of a reactant pair is shown to decay asymptotically as τ−αds/2−1, where ds is the fracton dimension of the fractal network under consideration. We also check the validity of the analytical results by comparison with Monte Carlo simulation results.Journal of Physics Condensed Matter 01/2007; 19(6):065116. · 2.22 Impact Factor  [Show abstract] [Hide abstract]
ABSTRACT: The molecular wire approach has recently been proposed as a method to enhance the sensitivity of traditional chemosensors. In this paper, we present the exact quantitative relationship between analyte concentration and the signal for the ideal molecular wire sensor (MWS). The signal profile of a MWS differs from that of traditional chemosensors in that its SternVolmer curve has a positive curvature that increases with the number kappa of receptor units in each molecular wire composing the MWS. We find that the sensitivity of the MWS to the change of analyte concentration increases with kappa if kappa is less than a critical value kappa*; otherwise, it becomes a decreasing function of kappa. We also briefly comment on aspects of nonideal sensors.Analytical Chemistry 11/2005; 77(19):616973. · 5.70 Impact Factor 
Article: Erratum: ``Four wave mixing spectroscopy for a multilevel system'' [J. Chem. Phys. 115, 9266 (2001)]
Chemical Physics 04/2005; 122(16):9901. · 1.96 Impact Factor
Publication Stats
342  Citations  
146.13  Total Impact Points  
Top Journals
Institutions

2005–2014

ChungAng University
 Department of Chemistry
Sŏul, Seoul, South Korea


1992–2008

Seoul National University
 • Department of Chemistry
 • Division of Chemistry and Molecular Engineering
Seoul, Seoul, South Korea


2001–2005

Massachusetts Institute of Technology
 • Department of Chemistry
 • Department of Materials Science and Engineering
Cambridge, MA, United States


2000–2001

Korea University
Sŏul, Seoul, South Korea
