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Volumn 105, Issue 34, 2008, Pages 12271-12276

Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations

Author keywords

Attractor; Cellular network; Entropy production; Landscape; Nongradient force; Stability

Indexed keywords

ARTICLE; BIOCHEMISTRY; CONCEPTUAL FRAMEWORK; CORRELATION ANALYSIS; ENTROPY; EVOLUTION; FORCE; LANDSCAPE; OSCILLATION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; STRUCTURE ANALYSIS;

EID: 50449104011     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0800579105     Document Type: Article
Times cited : (365)

References (37)
  • 2
    • 0037154231 scopus 로고    scopus 로고
    • Robustness of circadian rhythms with respect to molecular noise
    • Gonze D, Halloy J, Goldbeter A (2002) Robustness of circadian rhythms with respect to molecular noise. Proc Natl Acad Sci USA 99:673-678.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 673-678
    • Gonze, D.1    Halloy, J.2    Goldbeter, A.3
  • 3
    • 0036790975 scopus 로고    scopus 로고
    • Intrinsic and extrinsic contributions to stochasticity in gene expression
    • Swain PS, Elowitz MB, Siggia ED (2002) Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci USA 99:12795-12800.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 12795-12800
    • Swain, P.S.1    Elowitz, M.B.2    Siggia, E.D.3
  • 4
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81:2340-2361.
    • (1977) J Phys Chem , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 5
    • 0035193294 scopus 로고    scopus 로고
    • Stochasticity in transcriptional regulation: Origins, consequences, and mathematical representations
    • Kepler TB, Elston TC (2001) Stochasticity in transcriptional regulation: Origins, consequences, and mathematical representations. Biophys J 81:3116-3136.
    • (2001) Biophys J , vol.81 , pp. 3116-3136
    • Kepler, T.B.1    Elston, T.C.2
  • 6
    • 0036679175 scopus 로고    scopus 로고
    • Concentration fluctuations in a mesoscopic oscillating chemical reaction system
    • Qian H, Saffarian S, Elson EL (2002) Concentration fluctuations in a mesoscopic oscillating chemical reaction system. Proc Natl Acad Sci USA 99:10376-10381.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 10376-10381
    • Qian, H.1    Saffarian, S.2    Elson, E.L.3
  • 8
    • 0001658007 scopus 로고
    • eds Moss F, et al, Cambridge Univ Press, Cambridge, UK
    • Graham R (1989) in Noise in Nonlinear Dynamical Systems, eds Moss F, et al. (Cambridge Univ Press, Cambridge, UK), Vol 1, pp 225-278.
    • (1989) Noise in Nonlinear Dynamical Systems , vol.1 , pp. 225-278
    • Graham, R.1
  • 9
    • 0036829893 scopus 로고    scopus 로고
    • Number fluctuations and the threshold model of kinetic switches
    • Metzler R, Wolynes PG (2002) Number fluctuations and the threshold model of kinetic switches. Chem Phys 284:469-479.
    • (2002) Chem Phys , vol.284 , pp. 469-479
    • Metzler, R.1    Wolynes, P.G.2
  • 10
    • 0037418265 scopus 로고    scopus 로고
    • Stochastic gene expression as a many-body problem
    • Sasai M, Wolynes PG (2003) Stochastic gene expression as a many-body problem. Proc Natl Acad Sci USA 100:2374-2379.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 2374-2379
    • Sasai, M.1    Wolynes, P.G.2
  • 12
    • 0742288604 scopus 로고    scopus 로고
    • Potential in stochastic differential equations: Novel construction
    • Ao P (2004) Potential in stochastic differential equations: Novel construction. J Phys A Math Gen 37:L25-L30.
    • (2004) J Phys A Math Gen , vol.37
    • Ao, P.1
  • 13
    • 20344364613 scopus 로고    scopus 로고
    • Laws in Darwinian evolutionary theory
    • Ao P (2005) Laws in Darwinian evolutionary theory. Phys Life Rev 2:117-156.
    • (2005) Phys Life Rev , vol.2 , pp. 117-156
    • Ao, P.1
  • 14
    • 36749100036 scopus 로고    scopus 로고
    • Molecular level stochastic model for competence cycles in Bacillus subtilis
    • Schultz D, Jacob EB, Onuchic JN, Wolynes PG (2007) Molecular level stochastic model for competence cycles in Bacillus subtilis. Proc Natl Acad Sci USA 104:17582-17587.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 17582-17587
    • Schultz, D.1    Jacob, E.B.2    Onuchic, J.N.3    Wolynes, P.G.4
  • 15
    • 0000547916 scopus 로고    scopus 로고
    • Vector field formalism and analysis for a class of thermal ratchets
    • Qian H (1998) Vector field formalism and analysis for a class of thermal ratchets. Phys Rev Lett 81:3063-3066.
    • (1998) Phys Rev Lett , vol.81 , pp. 3063-3066
    • Qian, H.1
  • 16
    • 33748455499 scopus 로고    scopus 로고
    • Funneled landscape leads to robustness of cellular networks: MAPK signal transduction
    • Wang J, Huang B, Xia XF, Sun ZR (2006) Funneled landscape leads to robustness of cellular networks: MAPK signal transduction. Biophys J Lett 91:L54-L56.
    • (2006) Biophys J Lett , vol.91
    • Wang, J.1    Huang, B.2    Xia, X.F.3    Sun, Z.R.4
  • 17
    • 34047225832 scopus 로고    scopus 로고
    • Potential energy landscape and robustness of a gene regulatory network: Toggle switch
    • Kim KY, Wang J (2007) Potential energy landscape and robustness of a gene regulatory network: Toggle switch. PLoS Comput Biol 3:e60.
    • (2007) PLoS Comput Biol , vol.3
    • Kim, K.Y.1    Wang, J.2
  • 18
    • 34250320968 scopus 로고    scopus 로고
    • Quantifying robustness and dissipation cost of yeast cell cycle network: The funneled energy landscape perspectives
    • Han B, Wang J (2007) Quantifying robustness and dissipation cost of yeast cell cycle network: The funneled energy landscape perspectives. Biophys J 92:3755-3763.
    • (2007) Biophys J , vol.92 , pp. 3755-3763
    • Han, B.1    Wang, J.2
  • 19
    • 43149090775 scopus 로고    scopus 로고
    • Intrinsic noise, dissipation cost, and robustness of cellular networks: The underlying energy landscape of MAPK signal transduction
    • Lapidus S, Han B, Wang J (2008) Intrinsic noise, dissipation cost, and robustness of cellular networks: The underlying energy landscape of MAPK signal transduction. Proc Natl Acad Sci USA 105:6039-6044.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 6039-6044
    • Lapidus, S.1    Han, B.2    Wang, J.3
  • 20
    • 0026320866 scopus 로고
    • The energy landscapes and motions of proteins
    • Frauenfelder H, Sligar SG, Wolynes PG (1991) The energy landscapes and motions of proteins. Science 254:1598-1603.
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 22
    • 0038266221 scopus 로고    scopus 로고
    • Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding
    • Wang J, Verkhivker GM (2003) Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding. Phys Rev Lett 90:188101.
    • (2003) Phys Rev Lett , vol.90 , pp. 188101
    • Wang, J.1    Verkhivker, G.M.2
  • 24
    • 0000907353 scopus 로고
    • The roles of mutation, inbreeding, crossbreeding and selection in evolution
    • Wright S (1932) The roles of mutation, inbreeding, crossbreeding and selection in evolution. in Proceedings of the Sixth International Congress on Genetics. 1:356-366.
    • (1932) Proceedings of the Sixth International Congress on Genetics , vol.1 , pp. 356-366
    • Wright, S.1
  • 27
    • 0015050422 scopus 로고
    • The existence and completeness of various potentials for the equations of Stokes flow
    • Kanwal RP (1971) The existence and completeness of various potentials for the equations of Stokes flow. Int J Eng Sci 9:375-386.
    • (1971) Int J Eng Sci , vol.9 , pp. 375-386
    • Kanwal, R.P.1
  • 29
    • 0030271945 scopus 로고    scopus 로고
    • At the heart of the budding yeast cell cycle
    • Nasmyth K (1996) At the heart of the budding yeast cell cycle. Trends Genet 12:405-412.
    • (1996) Trends Genet , vol.12 , pp. 405-412
    • Nasmyth, K.1
  • 31
    • 41349109494 scopus 로고    scopus 로고
    • Mesoscopic nonequilibrium thermodynamics of single macromolecules and dynamic entropy-energy compensation
    • Qian H (2001) Mesoscopic nonequilibrium thermodynamics of single macromolecules and dynamic entropy-energy compensation. Phys Rev E 65:016102.
    • (2001) Phys Rev E , vol.65 , pp. 016102
    • Qian, H.1
  • 32
    • 41549149539 scopus 로고    scopus 로고
    • Least dissipation cost as a design principle for robustness and function of cellular networks
    • Han B, Wang J (2008) Least dissipation cost as a design principle for robustness and function of cellular networks. Phys Rev E 77:031922.
    • (2008) Phys Rev E , vol.77 , pp. 031922
    • Han, B.1    Wang, J.2
  • 33
    • 34047130839 scopus 로고    scopus 로고
    • Roles of noise in single and coupled multiple genetic oscillators
    • Yoda M, Ushikubo T, Inoue W, Sasai M (2007) Roles of noise in single and coupled multiple genetic oscillators. J Chem Phys 126:115101.
    • (2007) J Chem Phys , vol.126 , pp. 115101
    • Yoda, M.1    Ushikubo, T.2    Inoue, W.3    Sasai, M.4
  • 34
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403:335-338.
    • (2000) Nature , vol.403 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2
  • 35
    • 0038241770 scopus 로고    scopus 로고
    • Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli
    • Atkinson MR, Savageau MA, Myers JT, Ninfa AJ (2003) Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113:597-607.
    • (2003) Cell , vol.113 , pp. 597-607
    • Atkinson, M.R.1    Savageau, M.A.2    Myers, J.T.3    Ninfa, A.J.4
  • 36
    • 37549018348 scopus 로고    scopus 로고
    • Ordered phosphorylation governs oscillation of a three-protein circadian clock
    • Rust MJ, Markson JS, Lane WS, Fisher DS, O'Shea EK (2007) Ordered phosphorylation governs oscillation of a three-protein circadian clock. Science 318:809-812.
    • (2007) Science , vol.318 , pp. 809-812
    • Rust, M.J.1    Markson, J.S.2    Lane, W.S.3    Fisher, D.S.4    O'Shea, E.K.5
  • 37
    • 0037041888 scopus 로고    scopus 로고
    • Synthetic gene network for entraining and amplifying cellular oscillations
    • Hasty J, Dolnik M, Rottschaer V, Collins JJ (2002) Synthetic gene network for entraining and amplifying cellular oscillations. Phys Rev Lett 88:148101.
    • (2002) Phys Rev Lett , vol.88 , pp. 148101
    • Hasty, J.1    Dolnik, M.2    Rottschaer, V.3    Collins, J.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.