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ruvido's library [249 articles]

Recent papers added to ruvido's library ordered by importance.
  • Zonal methods for the parallel execution of range-limited N-body simulations
    Journal of Computational Physics, Vol. 221, No. 1. (20 January 2007), pp. 303-329.
    by Kevin J Bowers, Ron O Dror, David E Shaw
    posted to algorithm shaw by ruvido on 2008-02-12 15:12:53 as *****
  • A reappraisal of what we have learnt during three decades of computer simulations on water
    Journal of Molecular Liquids, Vol. 101, No. 1-3. (November 2002), pp. 219-260.
    by Bertrand Guillot
    posted to water by ruvido on 2008-02-09 22:06:06 as ***** along with 3 people loison softsimu onufriev
  • The Structure of the First Coordination Shell in Liquid Water
    Science, Vol. 304, No. 5673. (14 May 2004), pp. 995-999.
    by Ph Wernet, D Nordlund, U Bergmann, M Cavalleri, M Odelius, H Ogasawara, LA Naslund, TK Hirsch, L Ojamae, P Glatzel, LGM Pettersson, A Nilsson
    posted to water by ruvido on 2008-02-09 21:39:19 as ***** along with 3 people and 1 group gane5h samjlord rabio moernerlab
  • Coarse-grained model of entropic allostery.
    Phys Rev Lett, Vol. 93, No. 9. (27 August 2004)
    by RJ Hawkins, TC McLeish
    posted to allostery entropy by ruvido on 2007-12-29 19:58:30 as ***** along with 2 people lna higueruelo
  • A Computational Investigation of Allostery in the Catabolite Activator Protein
    J. Am. Chem. Soc., Vol. 129, No. 50. (19 December 2007), pp. 15668-15676.
    by L Li, VN Uversky, AK Dunker, SO Meroueh
    posted to allostery cap by ruvido on 2007-12-29 14:30:54 as ***** along with 1 person and 1 group sobolevnrm baker-group
  • Sequence-dependent DNA deformability studied using molecular dynamics simulations
    Nucl. Acids Res. (30 August 2007), gkm627.
    by Satoshi Fujii, Hidetoshi Kono, Shigeori Takenaka, Nobuhiro Go, Akinori Sarai
    posted to molecular_dynamics dna cap_dna by ruvido on 2008-09-15 11:02:35 as ** along with 2 people aalibes dna
  • Charge neutralization and DNA bending by the Escherichia coli catabolite activator protein
    Nucl. Acids Res., Vol. 30, No. 9. (1 May 2002), pp. 1879-1885.
    by Philip R Hardwidge, Jeff M Zimmerman, Maher
    posted to protein dna cap_dna cap by ruvido on 2008-09-15 11:00:24 as **
  • Induced Fit and the Entropy of Structural Adaptation in the Complexation of CAP and lambda-Repressor with Cognate DNA Sequences
    Biophys. J., Vol. 88, No. 5. (1 May 2005), pp. 3147-3157.
    by Surjit B Dixit, David Q Andrews, DL Beveridge
    posted to dna cap_dna allostery by ruvido on 2008-09-15 10:57:26 as **
  • DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations
    Biophys. J., Vol. 85, No. 5. (1 November 2003), pp. 2872-2883.
    by Filip Lankas, Jiri Sponer, Jorg Langowski, Thomas E Cheatham
    posted to molecular_dynamics dna cap_dna by ruvido on 2008-09-15 10:56:56 as ** along with 1 person onufriev
  • Catabolite activator protein: DNA binding and transcription activation
    Current Opinion in Structural Biology, Vol. 14, No. 1. (February 2004), pp. 10-20.
    by Catherine L Lawson, David Swigon, Katsuhiko S Murakami, Seth A Darst, Helen M Berman, Richard H Ebright
    posted to review protein cap_dna cap allostery by ruvido on 2008-09-15 10:56:08 as **
  • Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking
    Journal of Molecular Biology, Vol. 314, No. 1. (16 November 2001), pp. 75-82.
    by Shengfeng Chen, Angelo Gunasekera, Xiaoping Zhang, Thomas A Kunkel, Richard H Ebright, Helen M Berman
    posted to protein cap_dna cap allostery by ruvido on 2008-09-15 10:54:44 as **
  • Structure of the CAP-DNA Complex at 2.5 Å Resolution: A Complete Picture of the Protein-DNA Interface
    Journal of Molecular Biology, Vol. 260, No. 3. (19 July 1996), pp. 395-408.
    by Gary Parkinson, Christopher Wilson, Angelo Gunasekera, Yon W Ebright, Richard E Ebright, Helen M Berman
    posted to protein cap_dna cap allostery by ruvido on 2008-09-15 10:54:00 as **
  • Allostery and cooperativity revisited
    Protein Sci, Vol. 17, No. 8. (1 August 2008), pp. 1295-1307.
    by Qiang Cui, Martin Karplus
    posted to protein dynamics allostery by ruvido on 2008-09-12 11:20:02 as ** along with 2 people agrossfield tny
  • Probing single-molecule dynamics photon by photon
    The Journal of Chemical Physics, Vol. 117, No. 24. (2002), pp. 10965-10979.
    by Haw Yang, Sunney X Xie
    posted to subdiffusion protein models experimental by ruvido on 2008-09-09 15:22:22 as ** along with 1 person fornstar
  • Stochastic modeling in nanoscale biophysics: Subdiffusion within proteins
    (24 Jul 2008)
    by SC Kou
    posted to subdiffusion protein models dynamics by ruvido on 2008-09-09 09:41:54 as ** along with 1 person dah
  • The Rubik’s cube problem revisited: a statistical thermodynamic approach
    The European Physical Journal B - Condensed Matter and Complex Systems
    by C Lee, M Huang
    posted to rubik energy_landscape complex by ruvido on 2008-09-08 08:41:50 as **
  • Dynamic Distance Disorder in Proteins Is Caused by Trapping
    J. Phys. Chem. B, Vol. 110, No. 19. (18 May 2006), pp. 9363-9367.
    by G Luo, I Andricioaei, XS Xie, M Karplus
    posted to subdiffusion protein dynamics by ruvido on 2008-09-04 15:01:00 as ** along with 1 person allmensch
  • Fractional Brownian dynamics in proteins
    The Journal of Chemical Physics, Vol. 121, No. 20. (2004), pp. 10278-10283.
    by GR Kneller, K Hinsen
    posted to subdiffusion protein dynamics by ruvido on 2008-09-04 14:35:32 as **
  • Generalized Langevin Equation with Fractional Gaussian Noise: Subdiffusion within a Single Protein Molecule
    Physical Review Letters, Vol. 93, No. 18. (29 October 2004), 180603.
    by SC Kou, Sunney X Xie
    posted to subdiffusion protein dynamics by ruvido on 2008-09-04 14:33:58 as **
  • Networks for the allosteric control of protein kinases
    Current Opinion in Structural Biology, Vol. 16, No. 6. (December 2006), pp. 686-692.
    by Zhengshuang Shi, Katheryn A Resing, Natalie G Ahn
    posted to kinases allostery by ruvido on 2008-09-02 09:07:48 as ** along with 2 people lna choonpeng
  • Allosteric cooperativity in protein kinase A
    Proceedings of the National Academy of Sciences, Vol. 105, No. 2. (15 January 2008), pp. 506-511.
    by Larry R Masterson, Alessandro Mascioni, Nathaniel J Traaseth, Susan S Taylor, Gianluigi Veglia
    posted to kinases allostery by ruvido on 2008-09-02 09:06:58 as ** along with 2 people and 1 group cactus sobolevnrm baker-group
  • Protein states and proteinquakes.
    Proc Natl Acad Sci U S A, Vol. 82, No. 15. (August 1985), pp. 5000-5004.
    by A Ansari, J Berendzen, SF Bowne, H Frauenfelder, IE Iben, TB Sauke, E Shyamsunder, RD Young
    posted to dynamics energy_landscape experimental hierarchy models by ruvido on 2008-08-25 13:50:51 as ** along with 2 people aqeel kjell
  • Rate theories and puzzles of hemeprotein kinetics
    Science, Vol. 229, No. 4711. (26 July 1985), pp. 337-345.
    by H Frauenfelder, PG Wolynes
    posted to dynamics energy_landscape experimental hierarchy by ruvido on 2008-08-25 12:03:27 as **
  • Conformational Substates in Proteins
    Annual Review of Biophysics and Biophysical Chemistry, Vol. 17, No. 1. (1988), pp. 451-479.
    by H Frauenfelder, F Parak, RD Young
    posted to dynamics energy_landscape experimental hierarchy by ruvido on 2008-08-25 12:02:13 as **
  • Looking into the energy landscape of myoglobin
    Nat Struct Mol Biol, Vol. 2, No. 10. (October 1995), pp. 848-851.
    by Thorn D Leeson, DA Wiersma
    posted to dynamics energy_landscape hierarchy protein by ruvido on 2008-08-25 11:52:41 as **
  • Complexity in proteins
    Nat Struct Mol Biol, Vol. 2, No. 10. (October 1995), pp. 821-823.
    by Hans Frauenfelder
    posted to dynamics hierarchy protein by ruvido on 2008-08-25 11:50:00 as **
  • Multi-basin dynamics of a protein in a crystal environment
    Physica D: Nonlinear Phenomena, Vol. 107, No. 2-4. (1 September 1997), pp. 225-239.
    by Angel E García, Raphael Blumenfeld, Gerhard Hummer, James A Krumhansl
    posted to dynamics hierarchy protein subdiffusion by ruvido on 2008-08-25 11:12:58 as **
  • The energy landscape in non-biological and biological molecules
    Nat Struct Mol Biol, Vol. 5, No. 9. (1998), pp. 757-759.
    by Hans Frauenfelder, Daan T Leeson
    posted to energy_landscape hierarchy by ruvido on 2008-08-25 10:31:16 as ** along with 1 person aleperd
  • Allostery: an illustrated definition for the 'second secret of life'
    Trends in biochemical sciences (13 August 2008)
    by Aron W W Fenton
    posted to allostery review by ruvido on 2008-08-25 09:36:27 as ** along with 1 person and 2 groups barry structural_bioinformatics McCammon
  • Constrained spin-dynamics description of random walks on hierarchical scale-free networks
    Physical Review E, Vol. 69, No. 3. (23 March 2004), 036111.
    by Jae D Noh, Heiko Rieger
    posted to dynamics fractals networks subdiffusion by ruvido on 2008-08-21 18:54:22 as **
  • Dynamics on Ultrametric Spaces
    Physical Review Letters, Vol. 55, No. 15. (7 October 1985), 1634.
    by Andrew T Ogielski, DL Stein
    posted to dynamics fractals models subdiffusion by ruvido on 2008-08-21 18:43:58 as ** along with 1 person alexphys
  • Continuous-Time Random Walks on Fractals
    Physical Review Letters, Vol. 53, No. 14. (1 October 1984), 1301.
    by A Blumen, J Klafter, BS White, G Zumofen
    posted to dynamics fractals models subdiffusion by ruvido on 2008-08-21 18:41:13 as **
  • Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects
    The Journal of Chemical Physics, Vol. 123, No. 14. (2005)
    by Burak Alakent, Mehmet C Camurdan, Pemra Doruker
    posted to dynamics hierarchy protein subdiffusion by ruvido on 2008-08-21 18:16:13 as **
  • Hierarchical structure of the energy landscape of proteins revisited by time series analysis. I. Mimicking protein dynamics in different time scales
    The Journal of Chemical Physics, Vol. 123, No. 14. (2005)
    by Burak Alakent, Mehmet C Camurdan, Pemra Doruker
    posted to dynamics hierarchy protein subdiffusion by ruvido on 2008-08-21 18:15:42 as **
  • Biological Physics
    Reviews of Modern Physics, Vol. 71, No. 2. (1 March 1999), S419.
    by Hans Frauenfelder, Peter G Wolynes, Robert H Austin
    posted to biology physics review by ruvido on 2008-08-21 18:09:38 as **
  • Anomalous Diffusion and Relaxation Close to Thermal Equilibrium: A Fractional Fokker-Planck Equation Approach
    Physical Review Letters, Vol. 82, No. 18. (3 May 1999), 3563.
    by Ralf Metzler, Eli Barkai, Joseph Klafter
    posted to dynamics subdiffusion by ruvido on 2008-08-19 14:06:34 as **
  • Protein Conformational Dynamics Probed by Single-Molecule Electron Transfer
    Science, Vol. 302, No. 5643. (10 October 2003), pp. 262-266.
    by Haw Yang, Guobin Luo, Pallop Karnchanaphanurach, Tai-Man Louie, Ivan Rech, Sergio Cova, Luying Xun, Sunney X Xie
    posted to dynamics experimental subdiffusion by ruvido on 2008-08-19 13:14:51 as ** along with 1 person and 1 group alexfuerstenberg moernerlab
  • Fractals without anomalous diffusion
    Physical Review E, Vol. 49, No. 3. (1 March 1994), R1785.
    by Raffaella Burioni, Davide Cassi
    posted to fractals random_walk subdiffusion by ruvido on 2008-06-10 19:47:19 as **
  • Diffusion in hierarchies
    Physical Review A, Vol. 38, No. 8. (15 October 1988), 4261.
    by Karl H Hoffmann, Paolo Sibani
    posted to random_walk subdiffusion by ruvido on 2008-06-10 19:46:42 as ** along with 1 person baronka
  • RNA dynamics: it is about time
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Hashim M Al-Hashimi, Nils G Walter
    posted to rna by ruvido on 2008-06-10 17:09:24 as ** along with 1 person barry
  • How We See Ourselves and How We See Others
    Science, Vol. 320, No. 5880. (30 May 2008), pp. 1177-1180.
    by Emily Pronin
    posted to other psichology by ruvido on 2008-05-30 14:08:59 as ** along with 1 person aung
  • Hierarchies and logarithmic oscillations in the temporal relaxation patterns of proteins and other complex systems.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 20. (28 September 1999), pp. 11085-11089.
    by R Metzler, J Klafter, J Jortner
    posted to fractals hierarchy random_walk subdiffusion by ruvido on 2008-05-29 11:02:17 as **
  • Random walks with feedback on fractal lattices
    Physical Review E, Vol. 66, No. 3. (2002), 031106.
    by Beatrix M Schulz, Michael Schulz, Steffen Trimper
    posted to fractals random_walk subdiffusion by ruvido on 2008-05-28 20:14:33 as **
  • Subdiffusion and localization in the one-dimensional trap model
    Physical Review E, Vol. 67, No. 2. (27 February 2003), 026128.
    by EM Bertin, JP Bouchaud
    posted to random_walk subdiffusion by ruvido on 2008-05-28 20:12:04 as **
  • Random walk and trapping processes on scale-free networks
    Physical Review E, Vol. 70, No. 4. (25 October 2004), 046116.
    by Lazaros K Gallos
    posted to random_walk by ruvido on 2008-05-28 20:10:43 as **
  • Probing microscopic origins of confined subdiffusion by first-passage observables
    Proceedings of the National Academy of Sciences, Vol. 105, No. 15. (15 April 2008), pp. 5675-5680.
    by S Condamin, V Tejedor, R Voituriez, O Benichou, J Klafter
    posted to fractals random_walk subdiffusion by ruvido on 2008-05-28 20:04:36 as ** along with 1 person ARobson
  • Kinetic and Structural Studies of the Allosteric Conformational Changes Induced by Binding of cAMP to the cAMP Receptor Protein from Escherichia coli
    Biochemistry, Vol. 45, No. 2. (17 January 2006), pp. 373-380.
    by E Fic, A Polit, Z Wasylewski
    posted to cap kinetics by ruvido on 2008-05-27 15:43:50 as **
  • Protein dynamics and 1/f noise.
    Biophys. J., Vol. 63, No. 2. (1 August 1992), pp. 594-598.
    by TG Dewey, JG Bann
    posted to dynamics fractals protein by ruvido on 2008-05-21 16:14:20 as ** along with 1 person wilbur
  • Fractals in Molecular Biophysics
    Oxford University Press (1997)
    by Thomas G Dewey
    posted to dynamics fractals protein by ruvido on 2008-05-21 15:54:47 as **
  • Probing dynamical disorder kinetics with chemical relaxation techniques
    Chemical Physics, Vol. 161, No. 3. (15 April 1992), pp. 339-350.
    by Gregory T Dewey
    posted to dynamics fractals protein by ruvido on 2008-05-21 15:51:28 as **
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