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Volumn 1, Issue 1, 2013, Pages 50-53

Stochastic physics, complex systems and biology

Author keywords

Evolutionary Time Scale; Nonequilibrium Phase Transition; Nonequilibrium Steady State; Stochastic Dynamic; Stochastic Gene Expression

Indexed keywords


EID: 84878542116     PISSN: 20954689     EISSN: 20954697     Source Type: Journal    
DOI: 10.1007/s40484-013-0002-6     Document Type: Article
Times cited : (24)

References (46)
  • 1
    • 0000389761 scopus 로고
    • The dynamic origin of increasing entropy
    • Mackey, M. C. (1989) The dynamic origin of increasing entropy. Rev. Mod. Phys., 61, 981–1015.
    • (1989) Rev. Mod. Phys. , vol.61 , pp. 981-1015
    • Mackey, M.C.1
  • 2
    • 84857354366 scopus 로고    scopus 로고
    • Markov processes follow from the principle of maximum caliber
    • PID: 22360170
    • Ge, H., Pressé, S., Ghosh, K. and Dill, K. A. (2012) Markov processes follow from the principle of maximum caliber. J. Chem. Phys., 136, 064108.
    • (2012) J. Chem. Phys. , vol.136 , pp. 064108
    • Ge, H.1    Pressé, S.2    Ghosh, K.3    Dill, K.A.4
  • 3
    • 0027940353 scopus 로고
    • Physics, computation, and why biology looks so different?
    • Hopfield, J. J. (1994) Physics, computation, and why biology looks so different? J. Theor. Biol., 171, 53–60.
    • (1994) J. Theor. Biol. , vol.171 , pp. 53-60
    • Hopfield, J.J.1
  • 4
    • 0037136522 scopus 로고    scopus 로고
    • Physics meets biology: bridging the culture gap
    • PID: 12239534, COI: 1:CAS:528:DC%2BD38XntFShuro%3D
    • Knight, J. (2002) Physics meets biology: bridging the culture gap. Nature, 419, 244–246.
    • (2002) Nature , vol.419 , pp. 244-246
    • Knight, J.1
  • 8
  • 10
    • 68849093960 scopus 로고    scopus 로고
    • Stochastic bifurcation, slow fluctuations, and bistability as an origin of biochemical complexity
    • PID: 19506761, COI: 1:CAS:528:DC%2BD1MXntVKhtLc%3D
    • Qian, H., Shi, P.-Z. and Xing, J. (2009) Stochastic bifurcation, slow fluctuations, and bistability as an origin of biochemical complexity. Phys. Chem. Chem. Phys., 11, 4861–4870.
    • (2009) Phys. Chem. Chem. Phys. , vol.11 , pp. 4861-4870
    • Qian, H.1    Shi, P.-Z.2    Xing, J.3
  • 11
    • 79957877141 scopus 로고    scopus 로고
    • Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reactions systems — an analytical theory
    • Qian, H. (2011) Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reactions systems — an analytical theory. Nonlinearity, 24, R19–R49.
    • (2011) Nonlinearity , vol.24 , pp. R19-R49
    • Qian, H.1
  • 13
    • 36149021145 scopus 로고
    • Fluctuations and irreversible processes
    • COI: 1:CAS:528:DyaG3sXntVKktg%3D%3D
    • Onsager, L. and Machlup, S. (1953) Fluctuations and irreversible processes. Phys. Rev., 91, 1505–1512.
    • (1953) Phys. Rev. , vol.91 , pp. 1505-1512
    • Onsager, L.1    Machlup, S.2
  • 14
    • 49349121146 scopus 로고
    • Gaussian stochastic processes in physics
    • Fox, R. F. (1978) Gaussian stochastic processes in physics. Phys. Rep., 48, 179–283.
    • (1978) Phys. Rep. , vol.48 , pp. 179-283
    • Fox, R.F.1
  • 15
    • 78649786267 scopus 로고    scopus 로고
    • Non-equilibrium phase transition in mesoscopic biochemical systems: from stochastic to nonlinear dynamics and beyond
    • PID: 20466813
    • Ge, H. and Qian, H. (2011) Non-equilibrium phase transition in mesoscopic biochemical systems: from stochastic to nonlinear dynamics and beyond. J. R. Soc. Interface, 8, 107–116.
    • (2011) J. R. Soc. Interface , vol.8 , pp. 107-116
    • Ge, H.1    Qian, H.2
  • 16
    • 84859224635 scopus 로고    scopus 로고
    • Mesoscopic biochemical basis of isogenetic inheritance and canalization: stochasticity, nonlinearity, and emergent landscape
    • PID: 22428359
    • Qian, H. and Ge, H. (2012) Mesoscopic biochemical basis of isogenetic inheritance and canalization: stochasticity, nonlinearity, and emergent landscape. Mol. Cell. Biomech., 9, 1–30.
    • (2012) Mol. Cell. Biomech. , vol.9 , pp. 1-30
    • Qian, H.1    Ge, H.2
  • 18
    • 0030729125 scopus 로고    scopus 로고
    • A quantitative analysis of single protein-ligand complex separation with the atomic force microscope
    • PID: 17029898, COI: 1:CAS:528:DyaK2sXmvFSqt78%3D
    • Shapiro, B. E. and Qian, H. (1997) A quantitative analysis of single protein-ligand complex separation with the atomic force microscope. Biophys. Chem., 67, 211–219.
    • (1997) Biophys. Chem. , vol.67 , pp. 211-219
    • Shapiro, B.E.1    Qian, H.2
  • 19
    • 84861381646 scopus 로고    scopus 로고
    • How should we think about the ribosome?
    • PID: 22577819, COI: 1:CAS:528:DC%2BC38Xpt1yitLk%3D
    • Moore, P. B. (2012) How should we think about the ribosome? Annu. Rev. Biophys., 41, 1–19.
    • (2012) Annu. Rev. Biophys. , vol.41 , pp. 1-19
    • Moore, P.B.1
  • 20
    • 33646405732 scopus 로고    scopus 로고
    • The biological frontier of physics
    • COI: 1:CAS:528:DC%2BD28XkvF2mtLk%3D
    • Phillips, R. and Quake, S. R. (2006) The biological frontier of physics. Phys. Today, 59, 38–43.
    • (2006) Phys. Today , vol.59 , pp. 38-43
    • Phillips, R.1    Quake, S.R.2
  • 21
    • 23844508956 scopus 로고    scopus 로고
    • The nonequilibrium thermodynamics of small systems
    • COI: 1:CAS:528:DC%2BD2MXmslCgtrk%3D
    • Bustamante, C., Liphardt, J. and Ritort, F. (2005) The nonequilibrium thermodynamics of small systems. Phys. Today, 58, 43–48.
    • (2005) Phys. Today , vol.58 , pp. 43-48
    • Bustamante, C.1    Liphardt, J.2    Ritort, F.3
  • 22
    • 84863873310 scopus 로고    scopus 로고
    • Hill’s small systems nanothermodynamics: a simple macromolecular partition problem with a statistical perspective
    • PID: 23449763
    • Qian, H. (2012) Hill’s small systems nanothermodynamics: a simple macromolecular partition problem with a statistical perspective. J. Biol. Phys., 38, 201–207.
    • (2012) J. Biol. Phys. , vol.38 , pp. 201-207
    • Qian, H.1
  • 23
    • 5044227742 scopus 로고    scopus 로고
    • The evolution of molecular biology into systems biology
    • PID: 15470464, COI: 1:CAS:528:DC%2BD2cXotFGqurc%3D
    • Westerhoff, H. V. and Palsson, B. Ø. (2004) The evolution of molecular biology into systems biology. Nat. Biotechnol., 22, 1249–1252.
    • (2004) Nat. Biotechnol. , vol.22 , pp. 1249-1252
    • Westerhoff, H.V.1    Palsson, B.Ø.2
  • 24
    • 84861384820 scopus 로고    scopus 로고
    • Cooperativity in cellular biochemical processes: noiseenhanced sensitivity, fluctuating enzyme, bistability with nonlinear feedback, and other mechanisms for sigmoidal responses
    • PID: 22404682, COI: 1:CAS:528:DC%2BC38Xpt1yiurk%3D
    • Qian, H. (2012) Cooperativity in cellular biochemical processes: noiseenhanced sensitivity, fluctuating enzyme, bistability with nonlinear feedback, and other mechanisms for sigmoidal responses. Annu. Rev. Biophys., 41, 179–204.
    • (2012) Annu. Rev. Biophys. , vol.41 , pp. 179-204
    • Qian, H.1
  • 25
    • 70049116237 scopus 로고    scopus 로고
    • Strong inference for systems biology
    • PID: 19714210
    • Beard, D. A. and Kushmerick, M. J. (2009) Strong inference for systems biology. PLoS Comput. Biol., 5, e1000459.
    • (2009) PLoS Comput. Biol. , vol.5
    • Beard, D.A.1    Kushmerick, M.J.2
  • 26
    • 62549132572 scopus 로고    scopus 로고
    • Darwinian evolution in the light of genomics
    • PID: 19213802, COI: 1:CAS:528:DC%2BD1MXivFSgtro%3D
    • Koonin, E. V. (2009) Darwinian evolution in the light of genomics. Nucleic Acids Res., 37, 1011–1034.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1011-1034
    • Koonin, E.V.1
  • 27
    • 0032489015 scopus 로고    scopus 로고
    • The cell as a collection of protein machines: preparing the next generation of molecular biologists
    • PID: 9476889, COI: 1:CAS:528:DyaK1cXhtFGisL8%3D
    • Alberts, B. (1998) The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell, 92, 291–294.
    • (1998) Cell , vol.92 , pp. 291-294
    • Alberts, B.1
  • 28
    • 0037119587 scopus 로고    scopus 로고
    • Stochastic gene expression in a single cell
    • PID: 12183631, COI: 1:CAS:528:DC%2BD38XmsVOht7c%3D
    • Elowitz, M. B., Levine, A. J., Siggia, E. D. and Swain, P. S. (2002) Stochastic gene expression in a single cell. Science, 297, 1183–1186.
    • (2002) Science , vol.297 , pp. 1183-1186
    • Elowitz, M.B.1    Levine, A.J.2    Siggia, E.D.3    Swain, P.S.4
  • 29
    • 33645027986 scopus 로고    scopus 로고
    • Stochastic protein expression in individual cells at the single molecule level
    • PID: 16541077, COI: 1:CAS:528:DC%2BD28XitlKgu7k%3D
    • Cai, L., Friedman, N. and Xie, X. S. (2006) Stochastic protein expression in individual cells at the single molecule level. Nature, 440, 358–362.
    • (2006) Nature , vol.440 , pp. 358-362
    • Cai, L.1    Friedman, N.2    Xie, X.S.3
  • 31
    • 77953351106 scopus 로고    scopus 로고
    • Physical origins of entropy production, free energy dissipation, and their mathematical representations
    • Ge, H. and Qian, H. (2010) Physical origins of entropy production, free energy dissipation, and their mathematical representations. Phys. Rev. E, 81, 051133.
    • (2010) Phys. Rev. E , vol.81 , pp. 051133
    • Ge, H.1    Qian, H.2
  • 32
    • 82455192486 scopus 로고    scopus 로고
    • Stochastic theory of nonequilibrium steady states and its applications (Part I)
    • Zhang, X.-J., Qian, H. and Qian, M. (2012) Stochastic theory of nonequilibrium steady states and its applications (Part I). Phys. Rep., 510, 1–86.
    • (2012) Phys. Rep. , vol.510 , pp. 1-86
    • Zhang, X.-J.1    Qian, H.2    Qian, M.3
  • 33
    • 83255165435 scopus 로고    scopus 로고
    • Stochastic theory of nonequilibrium steady states (Part II): Applications in chemical biophysics
    • COI: 1:CAS:528:DC%2BC3MXhs1yms7vP
    • Ge, H., Qian, M. and Qian, H. (2012) Stochastic theory of nonequilibrium steady states (Part II): Applications in chemical biophysics. Phys. Rep., 510, 87–118.
    • (2012) Phys. Rep. , vol.510 , pp. 87-118
    • Ge, H.1    Qian, M.2    Qian, H.3
  • 35
    • 37049235151 scopus 로고
    • The theory of open systems in physics and biology
    • Von Bertalanffy, L. (1950) The theory of open systems in physics and biology. Science, 111, 23–29.
    • (1950) Science , vol.111 , pp. 23-29
    • Von Bertalanffy, L.1
  • 36
    • 33748107406 scopus 로고    scopus 로고
    • Phosphorylation energy hypothesis: open chemical systems and their biological functions
    • PID: 17059360, COI: 1:CAS:528:DC%2BD2sXlslSitr8%3D
    • Qian, H. (2007) Phosphorylation energy hypothesis: open chemical systems and their biological functions. Annu. Rev. Phys. Chem., 58, 113–142.
    • (2007) Annu. Rev. Phys. Chem. , vol.58 , pp. 113-142
    • Qian, H.1
  • 37
    • 50449104011 scopus 로고    scopus 로고
    • Potential landscape and flux framework of nonequilibrium networks: robustness, dissipation, and coherence of biochemical oscillations
    • PID: 18719111, COI: 1:CAS:528:DC%2BD1cXhtVOhtrrK
    • Wang, J., Xu, L. and Wang, E. K. (2008) Potential landscape and flux framework of nonequilibrium networks: robustness, dissipation, and coherence of biochemical oscillations. Proc. Natl. Acad. Sci. USA, 105, 12271–12276.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 12271-12276
    • Wang, J.1    Xu, L.2    Wang, E.K.3
  • 38
    • 77957734642 scopus 로고    scopus 로고
    • Kinetic paths, time scale, and underlying landscapes: a path integral framework to study global natures of nonequilibrium systems and networks
    • PID: 20886967
    • Wang, J., Zhang, K. and Wang, E. K. (2010) Kinetic paths, time scale, and underlying landscapes: a path integral framework to study global natures of nonequilibrium systems and networks. J. Chem. Phys., 133, 125103.
    • (2010) J. Chem. Phys. , vol.133 , pp. 125103
    • Wang, J.1    Zhang, K.2    Wang, E.K.3
  • 39
    • 79957710315 scopus 로고    scopus 로고
    • Quantifying the Waddington landscape and biological paths for development and differentiation
    • PID: 21536909, COI: 1:CAS:528:DC%2BC3MXmsF2jsbg%3D
    • Wang, J., Zhang, K., Xu, L. and Wang, E. K. (2011) Quantifying the Waddington landscape and biological paths for development and differentiation. Proc. Natl. Acad. Sci. USA, 108, 8257–8262.
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 8257-8262
    • Wang, J.1    Zhang, K.2    Xu, L.3    Wang, E.K.4
  • 40
    • 84865327667 scopus 로고    scopus 로고
    • Analytical mechanics in stochastic dynamics: most probable path, large-deviation rate function and Hamilton-Jacobi equation
    • Ge, H. and Qian, H. (2012) Analytical mechanics in stochastic dynamics: most probable path, large-deviation rate function and Hamilton-Jacobi equation. Int. J. Mod. Phys. B, 26, 1230012.
    • (2012) Int. J. Mod. Phys. B , vol.26 , pp. 1230012
    • Ge, H.1    Qian, H.2
  • 41
    • 0034614637 scopus 로고    scopus 로고
    • The hallmarks of cancer
    • PID: 10647931, COI: 1:CAS:528:DC%2BD3cXks1CktA%3D%3D
    • Hanahan, D. and Weinberg, R. A. (2000) The hallmarks of cancer. Cell, 100, 57–70.
    • (2000) Cell , vol.100 , pp. 57-70
    • Hanahan, D.1    Weinberg, R.A.2
  • 42
    • 38749098685 scopus 로고    scopus 로고
    • Cancer as robust intrinsic state of endogenous molecular-cellular network shaped by evolution
    • PID: 17766049, COI: 1:CAS:528:DC%2BD1cXhslartLc%3D
    • Ao, P., Galas, D., Hood, L. and Zhu, X.-M. (2008) Cancer as robust intrinsic state of endogenous molecular-cellular network shaped by evolution. Med. Hypotheses, 70, 678–684.
    • (2008) Med. Hypotheses , vol.70 , pp. 678-684
    • Ao, P.1    Galas, D.2    Hood, L.3    Zhu, X.-M.4
  • 44
    • 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
  • 45
    • 51349120674 scopus 로고    scopus 로고
    • Emerging of stochastic dynamical equalities and steady state thermodynamics from Darwinian dynamics
    • PID: 21949462
    • Ao, P. (2008) Emerging of stochastic dynamical equalities and steady state thermodynamics from Darwinian dynamics. Commun. Theor. Phys., 49, 1073–1090.
    • (2008) Commun. Theor. Phys. , vol.49 , pp. 1073-1090
    • Ao, P.1


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