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  • Reaction Event Counting Statistics of Biopolymer Reaction Systems with Dynamic Heterogeneity
  • 강진규
    Views: 270, 2016.03.04 16:09:30
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    • Journal of Chemical Theory and Computation, 8 (4), 2012, pp 1415–1425
    • Yu Rim Lim †, Seong Jun Park †, Bo Jung Park †, Jianshu Cao *‡, Robert J. Silbey ‡, and Jaeyoung Sung *†§
      † Department of Chemistry, Chung-Ang University, Seoul 156-756, Korea
      ‡ Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
    • http://pubs.acs.org/doi/abs/10.1021/ct200785q

    201407300646201149223.JPG

    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.

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  • Views: 253
  • Nature Communications 9, Article number: 297 (2018)
  • Seong Jun Park1-3, Sanggeun Song1-3, Gil-Suk Yang1, Philip M. Kim4, Sangwoon Yoon2*, Ji-Hyun Kim1*, and Jaeyoung Sung1-3*
    1 Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea.
    2 Department of Chemistry, Chung-Ang University, Seoul 06974, Korea.
    3 National Institute of Innovative Functional Imaging, Chung-Ang University, Seoul 06974, Korea.
    4 Terrence Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics and Department of Computer Science, University of Toronto, Toronto M5S 3E1, Canada.
  • Gene expression is a complex stochastic process composed of numerous enzymatic reactions with rates coupled to hidden cell-state variables. Despite advances in single-cell technologies, the lack of a theory accurately describing the gene expression process has restricted a robust, quantitative unders...
Dec 18, 2017 20:33:39
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  • Views: 162
  • Science Advances Vol. 3, no. 9, e1700676 (2017)
  • Sung Hyun Kim, TakKyoon Ahn, Tao Ju Cui, Sweeny Chauhan, Jaeyoung Sung, Chirlmin Joo, and Doseok Kim*
    †Department of Physics and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, Republic of Korea.
    ‡Department of Bionanoscience, Kavli Institute of NanoScience, Delft University of Technology, 2628 CJ Delft, Netherlands.
    §Department of Chemistry, Chung-Ang University, Seoul, Republic of Korea.
  • At the core of homologous DNA repair, RecA catalyzes the strand exchange reaction. This process is initiated by a RecA loading protein, which nucleates clusters of RecA proteins on single-stranded DNA. Each cluster grows to cover the single-stranded DNA but may leave 1- to 2-nucleotide (nt) gaps betw...
Sep 11, 2017 08:34:54
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  • Views: 242
  • Physical Review Letters 119, 099801 (2017)
  • In-Chun Jeong, Sanggeun Song, Daehyun Kim, Seong Jun Park, Ji-Hyun Kim, and Jaeyoung Sung*
    †National Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea
    ‡Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
    §National Institute of Innovative Functional Imaging, Chung-Ang University, Seoul 06974, Korea
  • Comment on “Nonrenewal Statistics in the Catalytic Activity of Enzyme Molecules at Mesoscopic Concentrations” Figure 1 A system of N enzymes (a) under the synchronized initial condition and (b) in the steady state. Figure 2 Comparison between theory and simulation.
Sep 05, 2017 09:03:42
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  • Views: 241
  • The Journal of Physical Chemistry Letters, 8, 3152-3158 (2017)
  • Seong Jun Park†§⊥, Sanggeun Song†‡§⊥, In-Chun Jeong†‡§, Hye Ran Koh†‡, Ji-Hyun Kim*†, and Jaeyoung Sung*†‡§
    †National Creative Research Initiative Center for Chemical Dynamics in Living Cells, Chung-Ang University, Seoul 06974, Korea
    ‡Department of Chemistry, Chung-Ang University, Seoul 06974, Korea
    §National Institute of Innovative Functional Imaging, Chung-Ang University, Seoul 06974, Korea
  • Enzyme-to-enzyme variation in the catalytic rate is ubiquitous among single enzymes created from the same genetic information, which persists over the lifetimes of living cells. Despite advances in single-enzyme technologies, the lack of an enzyme reaction model accounting for the heterogeneous acti...
Jun 27, 2017 17:44:12
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  • Views: 376
  • Physical Review X 5, 031014 (2015)
  • Yu Rim Lim,1,* Ji-Hyun Kim,2,*,† Seong Jun Park,1 Gil-Suk Yang,1 Sanggeun Song,1 Suk-kyu Chang,1 Nam Ki Lee,3 and Jaeyoung Sung1,‡
    1Department of Chemistry and Institute of Innovative Functional Imaging, Chung-Ang University, Seoul 156-756, Korea.
    2Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139, U. S. A.
    3Department of Physics and School of Interdisciplinary Bioscience and Bioengineering, POSTECH, Pohang 790-784, Korea.
  • For quantitative understanding of probabilistic behaviors of living cells, it is essential to construct a correct mathematical description of intracellular networks interacting with complex cell environments, which has been a formidable task. Here, we present a novel model and stochastic kinetics fo...
Mar 04, 2016 16:18:44
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  • Views: 294
  • Nature Communications 5, Article number: 4761
  • Sora Yang, Seunghyeon Kim, Yu Rim Lim, Cheolhee Kim, Hyeong Jeon An, Ji-Hyun Kim, Jaeyoung Sung* & Nam Ki Lee*
  • Cell-to-cell 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 ...
Mar 04, 2016 16:16:16
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  • Views: 270
  • Journal of Chemical Theory and Computation, 8 (4), 2012, pp 1415–1425
  • Yu Rim Lim †, Seong Jun Park †, Bo Jung Park †, Jianshu Cao *‡, Robert J. Silbey ‡, and Jaeyoung Sung *†§
    † Department of Chemistry, Chung-Ang University, Seoul 156-756, Korea
    ‡ Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
  • 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 h...
Mar 04, 2016 16:09:30
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  • Views: 174
  • Bulletin of Korean Chemical Society, Vol. 33, No. 3, 2012, 963-970
  • Yu Rim Lim, Seong Jun Park, Sangyoub Lee,‡ and Jaeyoung Sung*
    Department of Chemistry, Chung-Ang University Seoul 156-756, Korea. *E-mail: jaeyoung@cau.ac.kr
    ‡Department of Chemistry, Seoul National University, Seoul 151-742, Korea
  • We review novel chemical kinetics proposed for quantitative description of fluctuations in reaction times and in the number of product molecules in a heterogeneous biological system, and discuss quantitative interpretation of randomness parameter data in enzymatic turnover times of β-galactosidase. ...
Mar 04, 2016 16:07:16
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  • Views: 222
  • Biophysical Journal, Volume 101, Issue 3, Pages 519–524
  • Seongeun Yang,† Jianshu Cao,‡ Robert J. Silbey,‡* and Jaeyoung Sung†*
    †Department of Chemistry, Chung-Ang University, Seoul, Korea; and ‡Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
  • Fluctuating turnover times of a single enzyme become observable with the advent of modern cutting-edge, 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 turnov...
Mar 04, 2016 16:05:40
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  • Views: 133
  • Chemical Physics, Volume 384, Issues 1–3, Pages 36–43
  • Bo Jung Park, Won Jung, Jaeyoung Sung*
    Department of Chemistry, Chung-Ang University, Seoul 156-756, Republic of Korea
  • 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 fo...
Mar 04, 2016 16:04:50
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Mar 04, 2016 16:02:49
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Mar 04, 2016 16:01:06
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  • Views: 154
  • Langmuir, 24 (6), 2008, pp 2569–2572
  • Je Hyun Bae ,† Yu Rim Lim ,† and Jaeyoung Sung *
    Department of Chemistry, Chung-Ang University, Seoul 156-756 Korea
  • We investigate a simple, exactly solvable model for interacting adsorbates. From the model study, we find that (1 - θ)^(-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 ...
Mar 04, 2016 15:55:09
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  • Views: 219
  • The Journal of Physical Chemistry B, 112 (19), 2008, pp 6250–6258
  • Ji-Hyun Kim ,‡ Woojin Lee ,‡ Jaeyoung Sung ,*§ and Sangyoub Lee *‡
    Department of Chemistry, Seoul National University, Seoul 151-747, South Korea, and Department of Chemistry, Chung-Ang University, Seoul 156-756, South Korea
  • On the basis of the recently developed optimized Rouse-Zimm theory of chain polymers with excluded volume interactions, we calculate the long-time first-order rate constant k1 for end-to-end cyclization of linear chain polymers. We first find that the optimized Rouse-Zimm theory provides the longest...
Mar 04, 2016 15:54:05
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  • Views: 229
  • Journal of Physics: Condensed Matter 19 (2007) 065116 (14pp)
  • Ji-Hyun Kim1, Dann Huh1, Jinuk Lee1, Sangyoub Lee*1,4, Jaeyoung Sung2, Kazuhiko Seki3 and M Tachiya3,4
    1 Department of Chemistry, Seoul National University, Seoul 151-747, Korea
    2 Department of Chemistry, Chung-Ang University, Seoul 156-756, Korea
    3 National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 5, Higashi 1-1-1, Tsukuba, Ibaraki 305-8565, Japan
  • 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 o...
Mar 04, 2016 15:51:42
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  • Views: 236
  • The Journal of Physical Chemistry B, 111 (35), 2007, pp 10468–10473
  • Changsun Eun ,†§ Ji-Hyun Kim ,‡ Jinuk Lee ,‡ Je Hyun Bae ,† Yu Rim Lim ,† Sangyoub Lee ,*‡ and Jaeyoung Sung *†
    Department of Chemistry, Chung-Ang University, Seoul 156-756, Korea, and Department of Chemistry, Seoul National University, Seoul 151-747, Korea
  • 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, ó, and equilibrium-distributed. An approximate analytic expression for the mean first passage time is obtained and compared with the resul...
Mar 04, 2016 15:49:38
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  • Views: 235
  • Chemical Physics Letters, Volume 415, Issues 1–3, Pages 10–14
  • Jaeyoung Sung(a,b) Robert J. Silbey(a)*
    a. Department of Chemistry, Massachusetts Institute of Technology, Building 6-123, 77 Massachusetts Avenue, Cambridge, MA 02139-4307, USA
    b. Department of Chemistry, Chung-Ang University, Seoul 156-756, Republic of Korea
  • We present an exact form for counting statistics of single-molecule (SM) reaction events for a molecule with arbitrary hidden dynamical processes coupled to the reaction, examples of which can be found in many single biopolymer experiments. The result suggests a novel SM experimental observable, H, ...
Mar 04, 2016 15:46:32
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