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Volumn 2008, Issue 3, 2008, Pages

RNA secondary structures: Complex statics and glassy dynamics

Author keywords

Disordered systems (theory); Energy landscapes (theory); Sampling algorithms and rapid mixing; Structures and conformations (theory)

Indexed keywords


EID: 43149091475     PISSN: 17425468     EISSN: 17425468     Source Type: Journal    
DOI: 10.1088/1742-5468/2008/03/P03005     Document Type: Article
Times cited : (4)

References (52)
  • 5
    • 0000113876 scopus 로고    scopus 로고
    • Overlaps between RNA secondary structures
    • Higgs P G 1996 Overlaps between RNA secondary structures Phys. Rev. Lett. 76 704
    • (1996) Phys. Rev. Lett. , vol.76 , Issue.4 , pp. 704
    • Higgs, P.G.1
  • 7
    • 0000189939 scopus 로고    scopus 로고
    • Glassy transition in a disordered model for the RNA secondary structure
    • Pagnani A, Parisi G and Ricci-Tersenghi F 2000 Glassy transition in a disordered model for the RNA secondary structure Phys. Rev. Lett. 84 2026
    • (2000) Phys. Rev. Lett. , vol.84 , Issue.9 , pp. 2026
    • Pagnani, A.1    Parisi, G.2    Ricci-Tersenghi, F.3
  • 8
    • 33748714041 scopus 로고    scopus 로고
    • Comment on glassy transition in a disordered model for the RNA secondary structure
    • Hartmann AK 2001 Comment on glassy transition in a disordered model for the RNA secondary structure Phys. Rev. Lett. 86 1382
    • (2001) Phys. Rev. Lett. , vol.86 , Issue.7 , pp. 1382
    • Hartmann, A.K.1
  • 9
    • 41349099117 scopus 로고    scopus 로고
    • Statistical mechanics of secondary structures formed by random RNA sequences
    • Bundschuh R and Hwa T 2002 Statistical mechanics of secondary structures formed by random RNA sequences Phys. Rev. E 65 031903
    • (2002) Phys. Rev. , vol.65 , Issue.3 , pp. 031903
    • Bundschuh, R.1    Hwa, T.2
  • 10
    • 0036334292 scopus 로고    scopus 로고
    • Nature of the glassy phase of RNA secondary structure
    • Mézard M, Krzakala F and Müller M 2002 Nature of the glassy phase of RNA secondary structure Europhys. Lett. 57 752
    • (2002) Europhys. Lett. , vol.57 , Issue.5 , pp. 752
    • Mézard, M.1    Krzakala, F.2    Müller, M.3
  • 11
    • 41349120303 scopus 로고    scopus 로고
    • Dependence of RNA secondary structure on the energy model
    • Burghardt B and Hartmann AK 2005 Dependence of RNA secondary structure on the energy model Phys. Rev. E 71 021913
    • (2005) Phys. Rev. , vol.71 , pp. 021913
    • Burghardt, B.1    Hartmann, A.K.2
  • 12
  • 13
    • 5344222818 scopus 로고
    • Magnetic correlations in two-dimensional spin-glasses
    • Morgenstern I and Binder K 1980 Magnetic correlations in two-dimensional spin-glasses Phys. Rev. B 22 288
    • (1980) Phys. Rev. , vol.22 , Issue.1 , pp. 288
    • Morgenstern, I.1    Binder, K.2
  • 14
    • 0008268975 scopus 로고
    • The 2D+/-J Ising spin glass: Exact partition functions in polynomial time
    • Saul L and Kardar M 1994 The 2D+/-J Ising spin glass: exact partition functions in polynomial time Nucl. Phys. B 432 641
    • (1994) Nucl. Phys. , vol.432 , Issue.3 , pp. 641
    • Saul, L.1    Kardar, M.2
  • 15
    • 0001548761 scopus 로고
    • Spin glass with non-random interactions
    • Villain J 1977 Spin glass with non-random interactions J. Phys. C Solid State Phys. 10 1717
    • (1977) J. Phys. C Solid State Phys. , vol.10 , Issue.10 , pp. 1717
    • Villain, J.1
  • 16
    • 0010212094 scopus 로고
    • On the glassy nature of random directed polymers in two dimensions
    • Mezard M 1990 On the glassy nature of random directed polymers in two dimensions J. Physique 51 1831
    • (1990) J. Physique , vol.51 , Issue.17 , pp. 1831
    • Mezard, M.1
  • 18
    • 0002061484 scopus 로고
    • New Monte Carlo algorithm: Entropic sampling
    • Lee J 1993 New Monte Carlo algorithm: entropic sampling Phys. Rev. Lett. 71 211
    • (1993) Phys. Rev. Lett. , vol.71 , Issue.2 , pp. 211
    • Lee, J.1
  • 19
    • 4243613377 scopus 로고
    • Multicanonical ensemble: A new approach to simulate first-order phase transitions
    • Berg B A and Neuhaus T 1992 Multicanonical ensemble: a new approach to simulate first-order phase transitions Phys. Rev. Lett. 68 9
    • (1992) Phys. Rev. Lett. , vol.68 , Issue.1 , pp. 9
    • Berg, B.A.1    Neuhaus, T.2
  • 20
    • 6644221271 scopus 로고    scopus 로고
    • Efficient, multiple-range random walk algorithm to calculate the density of states
    • Wang F G and Landau D P 2001 Efficient, multiple-range random walk algorithm to calculate the density of states Phys. Rev. Lett. 86 2050
    • (2001) Phys. Rev. Lett. , vol.86 , Issue.10 , pp. 2050
    • Wang, F.G.1    Landau, D.P.2
  • 21
    • 39749147672 scopus 로고    scopus 로고
    • Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram
    • Wang F G and Landau D P 2001 Determining the density of states for classical statistical models: a random walk algorithm to produce a flat histogram Phys. Rev. E 64 056101
    • (2001) Phys. Rev. , vol.64 , Issue.5 , pp. 056101
    • Wang, F.G.1    Landau, D.P.2
  • 22
    • 41349094233 scopus 로고    scopus 로고
    • Optimizing the ensemble for equilibration in broad-histogram Monte Carlo simulations
    • Trebst S, Huse DA and Troyer M 2004 Optimizing the ensemble for equilibration in broad-histogram Monte Carlo simulations Phys. Rev. E 70 046701
    • (2004) Phys. Rev. , vol.70 , pp. 046701
    • Trebst, S.1    Huse, D.A.2    Troyer, M.3
  • 23
    • 84950437936 scopus 로고
    • Annealing Markov Chain Monte Carlo with applications to ancestral inference
    • Geyer CJ and Thompson EA 1995 Annealing Markov Chain Monte Carlo with applications to ancestral inference J. Am. Stat. Assoc. 90 909
    • (1995) J. Am. Stat. Assoc. , vol.90 , Issue.431 , pp. 909
    • Geyer, C.J.1    Thompson, E.A.2
  • 25
    • 22944453404 scopus 로고    scopus 로고
    • Optimal allocation of replicas in parallel tempering simulations
    • Rathore N, Chopra M and dePablo J J 2005 Optimal allocation of replicas in parallel tempering simulations J. Chem. Phys. 122 024111
    • (2005) J. Chem. Phys. , vol.122 , Issue.2 , pp. 024111
    • Rathore, N.1    Chopra, M.2    Depablo, J.J.3
  • 26
    • 17444374268 scopus 로고    scopus 로고
    • ParQ: High-precision calculation of the density of states
    • Heilmann F and Hoffmann K H 2005 ParQ: high-precision calculation of the density of states Europhys. Lett. 70 155
    • (2005) Europhys. Lett. , vol.70 , Issue.2 , pp. 155
    • Heilmann, F.1    Hoffmann, K.H.2
  • 27
    • 0034612331 scopus 로고    scopus 로고
    • Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme
    • Isambert H and Siggia ED 2000 Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme Proc. Nat. Acad. Sci. 97 6515
    • (2000) Proc. Nat. Acad. Sci. , vol.97 , Issue.12 , pp. 6515
    • Isambert, H.1    Siggia, E.D.2
  • 29
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • Zuker M 1989 On finding all suboptimal foldings of an RNA molecule Science 244 48
    • (1989) Science , vol.244 , Issue.4900 , pp. 48
    • Zuker, M.1
  • 30
    • 0014238951 scopus 로고
    • Statistics of branching and hairpin helices for the dAT copolymer
    • de Gennes P-G 1968 Statistics of branching and hairpin helices for the dAT copolymer Biopolymers 6 715
    • (1968) Biopolymers , vol.6 , Issue.5 , pp. 715
    • De Gennes, P.-G.1
  • 31
    • 0002296942 scopus 로고
    • A new algorithm for Monte Carlo simulation of Ising spin systems
    • Bortz A B, Kalos M H and Lebowitz J L 1975 A new algorithm for Monte Carlo simulation of Ising spin systems J. Comput. Phys. 17 10
    • (1975) J. Comput. Phys. , vol.17 , Issue.1 , pp. 10
    • Bortz, A.B.1    Kalos, M.H.2    Lebowitz, J.L.3
  • 32
    • 0033185545 scopus 로고    scopus 로고
    • Transition matrix Monte Carlo method
    • Wang J S 1999 Transition matrix Monte Carlo method Comput. Phys. Commun. 121/122 22
    • (1999) Comput. Phys. Commun. , vol.121-122 , pp. 22
    • Wang, J.S.1
  • 33
    • 0034188570 scopus 로고    scopus 로고
    • Monte Carlo algorithms based on the number of potential moves
    • Wang JS and Lee LW 2000 Monte Carlo algorithms based on the number of potential moves Comput. Phys. Commun. 127 131
    • (2000) Comput. Phys. Commun. , vol.127 , Issue.1 , pp. 131
    • Wang, J.S.1    Lee, L.W.2
  • 34
    • 17944393733 scopus 로고    scopus 로고
    • Transition matrix Monte Carlo reweighting and dynamics
    • Wang J S, Tay T K and Swendsen R H 1999 Transition matrix Monte Carlo reweighting and dynamics Phys. Rev. Lett. 82 476
    • (1999) Phys. Rev. Lett. , vol.82 , Issue.3 , pp. 476
    • Wang, J.S.1    Tay, T.K.2    Swendsen, R.H.3
  • 37
    • 0001393762 scopus 로고    scopus 로고
    • Is the broad histogram random walk dynamics correct?
    • Wang JS 1999 Is the broad histogram random walk dynamics correct? Eur. Phys. J. B 8 287
    • (1999) Eur. Phys. J. , vol.8 , Issue.2 , pp. 287
    • Wang, J.S.1
  • 38
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • Kirkpatrick S, Gelatt C D Jr and Vecchi MP 1983 Optimization by simulated annealing Science 220 671
    • (1983) Science , vol.220 , Issue.4598 , pp. 671
    • Kirkpatrick, S.1    Gelatt, C.D.2    Vecchi, M.P.3
  • 40
    • 0041130319 scopus 로고
    • Low-temperature properties of the J Ising spin glass in two dimensions
    • Wang J S and Swendsen R H 1988 Low-temperature properties of the J Ising spin glass in two dimensions Phys. Rev. B 38 4840
    • (1988) Phys. Rev. , vol.38 , Issue.7 , pp. 4840
    • Wang, J.S.1    Swendsen, R.H.2
  • 41
    • 84901002994 scopus 로고    scopus 로고
    • Dynamics of the Wang-Landau algorithm and complexity of rare events for the three-dimensional bimodal Ising spin glass
    • Adler S, Trebst S, Hartmann A K and Troyer M 2004 Dynamics of the Wang-Landau algorithm and complexity of rare events for the three-dimensional bimodal Ising spin glass J. Stat. Mech. P07008
    • (2004) J. Stat. Mech. , vol.2004 , Issue.7 , pp. 07008
    • Adler, S.1    Trebst, S.2    Hartmann, A.K.3    Troyer, M.4
  • 43
    • 0001070119 scopus 로고
    • Algorithm AS 215: Maximum-likelihood estimation of the parameters of the generalized extreme-value distribution
    • Hosking J R M 1985 Algorithm AS 215: maximum-likelihood estimation of the parameters of the generalized extreme-value distribution Appl. Stat. 34 301
    • (1985) Appl. Stat. , vol.34 , Issue.3 , pp. 301
    • Hosking, J.R.M.1
  • 44
    • 0000552449 scopus 로고
    • Remark AS R76: A remark on algorithm AS 215: Maximum-likelihood estimation of the parameters of the generalized extreme-value distribution
    • Macleod A J 1989 Remark AS R76: a remark on algorithm AS 215: maximum-likelihood estimation of the parameters of the generalized extreme-value distribution Appl. Stat. 38 198
    • (1989) Appl. Stat. , vol.38 , Issue.1 , pp. 198
    • MacLeod, A.J.1
  • 50
    • 0002215069 scopus 로고
    • On a measure of divergence between two statistical populations defined by their probability distributions
    • Bhattacharyya A 1943 On a measure of divergence between two statistical populations defined by their probability distributions Bull. Cal. Math. Soc. 35 99
    • (1943) Bull. Cal. Math. Soc. , vol.35 , pp. 99
    • Bhattacharyya, A.1
  • 52
    • 0032364446 scopus 로고    scopus 로고
    • Accurate Monte Carlo estimation of very small p-values in Markov chains
    • Wilbur W H 1998 Accurate Monte Carlo estimation of very small p-values In Markov chains Comput. Stat. 13 153
    • (1998) Comput. Stat. , vol.13 , pp. 153
    • Wilbur, W.H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.