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Diego_Prada's library [90 articles]

Recent papers added to Diego_Prada's library.
  • On mean residence and first passage times in finite one-dimensional systems
    The Journal of Chemical Physics, Vol. 109, No. 13. (1998), pp. 5187-5193.
    by Arie B Haim, Joseph Klafter
    posted to stochastic_processes markov csn by Diego_Prada on 2008-05-10 11:47:32 as **
  • Conformational Study of the Alanine Dipeptide at the MP2 and DFT Levels
    J. Phys. Chem. A, Vol. 106, No. 13. (4 April 2002), pp. 3213-3218.
    by R Vargas, J Garza, BP Hay, DA Dixon
    posted to dialanine by Diego_Prada on 2008-05-07 15:38:46 as **
  • Some further applications of discrete path sampling to cluster isomerization
    Molecular Physics, pp. 891-908.
    by David J Wales
    posted to stochastic_processes free-energy by Diego_Prada on 2008-05-07 15:34:07 as **
  • Discrete path sampling
    Molecular Physics, pp. 3285-3305.
    by DJ Wales
    posted to stochastic_processes free-energy by Diego_Prada on 2008-05-07 15:32:10 as **
  • Annealed importance sampling of dileucine peptide
    (3 Apr 2007)
    by Edward Lyman, Daniel M Zuckerman
    posted to coarse-grained protein_dynamics struct_decorr by Diego_Prada on 2008-04-21 10:15:40 as **
  • Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model
    (24 Mar 2007)
    by Marty F Ytreberg, Svetlana, Daniel M Zuckerman
    posted to coarse-grained protein_dynamics struct_decorr by Diego_Prada on 2008-04-21 10:13:08 as **
  • Free energy landscapes of model peptides and proteins
    The Journal of Chemical Physics, Vol. 118, No. 8. (2003), pp. 3891-3897.
    by David A Evans, David J Wales
    posted to coarse-grained free-energy proteins by Diego_Prada on 2008-04-11 20:05:03 as **
  • Network and graph analyses of folding free energy surfaces
    Current Opinion in Structural Biology, Vol. 16, No. 1. (February 2006), pp. 71-78.
    by Amedeo Caflisch
    posted to free-energy protein_dynamics by Diego_Prada on 2008-04-11 19:59:28 as ** along with 4 people apaydin bilab mtw jlh64
  • Graph transformation method for calculating waiting times in Markov chains
    The Journal of Chemical Physics, Vol. 124, No. 23. (2006)
    by Semen A Trygubenko, David J Wales
    posted to free-energy markov by Diego_Prada on 2008-04-11 19:40:07 as **
  • Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states.
    J Chem Phys, Vol. 126, No. 15. (21 April 2007)
    by F Noé, I Horenko, C Schütte, JC Smith
    posted to markov protein_dynamics by Diego_Prada on 2008-03-30 16:22:35 as ** along with 1 person choonpeng
  • Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics
    The Journal of Chemical Physics, Vol. 126, No. 24. (2007)
    by Nina S Hinrichs, Vijay S Pande
    posted to markov protein_dynamics by Diego_Prada on 2008-03-30 16:17:53 as **
  • Statistically optimal analysis of samples from multiple equilibrium states
    (9 Jan 2008)
    by Michael R Shirts, John D Chodera
    posted to markov protein_dynamics stochastic_processes by Diego_Prada on 2008-03-30 16:14:48 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.
    J Chem Phys, Vol. 126, No. 15. (21 April 2007)
    by JD Chodera, N Singhal, VS Pande, KA Dill, WC Swope
    posted to markov protein_dynamics by Diego_Prada on 2008-03-30 16:13:45 as read along with 1 person allmensch
  • Thermally activated processes in polymer dynamics
    Physical Review E, Vol. 68, No. 6. (31 December 2003), 061111.
    by Lorenzo Bongini, Roberto Livi, Antonio Politi, Alessandro Torcini
    posted to hp_model by Diego_Prada on 2008-03-23 21:02:44 as read
  • Extended least action principle for steady flows under a prescribed flux
    (12 Jul 2005)
    by G Wolansky
    posted to leas_action by Diego_Prada on 2008-03-05 17:29:55 as **
  • Maximum entropy change and least action principle for nonequilibrium systems
    (8 Sep 2004)
    by Qiuping A Wang
    posted to information leas_action stochastic_processes by Diego_Prada on 2008-03-05 17:28:41 as *** along with 2 people scis0000001 Scis0000002
  • Stochastic embedding of dynamical systems
    (30 Sep 2005)
    by Jacky Cresson, Sébastien Darses
    posted to markov stochastic_processes by Diego_Prada on 2008-03-05 17:23:06 as **
  • Maximum path information and the principle of least action for chaotic system
    Chaos, Solitons & Fractals, Vol. 23, No. 4. (February 2005), pp. 1253-1258.
    by QA Wang
    posted to information by Diego_Prada on 2008-03-05 17:06:24 as read
  • Computing communities in large networks using random walks
    (14 Dec 2004)
    by Matthieu Latapy, Pascal Pons
    posted to communities networks by Diego_Prada on 2008-02-29 17:20:33 as **
  • Network Brownian Motion: A New Method to Measure Vertex-Vertex Proximity and to Identify Communities and Subcommunities
    Computational Science - ICCS 2004 (2004), pp. 1062-1069.
    by Haijun Zhou, Reinhard Lipowsky
    posted to communities networks by Diego_Prada on 2008-02-29 17:18:31 as **
  • Distance, dissimilarity index, and network community structure
    Physical Review E, Vol. 67, No. 6. (10 June 2003), 061901.
    by Haijun Zhou
    posted to communities networks by Diego_Prada on 2008-02-29 17:15:49 as **
  • Network landscape from a Brownian particle's perspective
    Physical Review E, Vol. 67, No. 4. (21 April 2003), 041908.
    by Haijun Zhou
    posted to communities networks by Diego_Prada on 2008-02-29 17:14:06 as **
  • Comparing community structure identification
    (18 Oct 2005)
    by Leon Danon, Jordi Duch, Albert Diaz-Guilera, Alex Arenas
    posted to communities networks by Diego_Prada on 2008-02-25 12:47:52 as read along with 2 people and 1 group nettraq fwkroon Philosophy_of_Information
  • Detecting Fuzzy Community Structures in Complex Networks with a Potts Model
    Physical Review Letters, Vol. 93, No. 21. (2004)
    by Jörg Reichardt, Stefan Bornholdt
    posted to communities networks by Diego_Prada on 2008-02-24 19:09:36 as read along with 3 people and 1 group fukken hannu marcio ThinkTank
  • From the Cover: Modularity and community structure in networks
    PNAS, Vol. 103, No. 23. (6 June 2006), pp. 8577-8582.
    by MEJ Newman
    posted to communities networks by Diego_Prada on 2008-02-21 13:14:38 as read along with 14 people and 3 groups aqeel ChaTo jfr yas balicea ddahlem cmm fukken kubyaddi adriandefroment gcalda hannu marcio phreeza T_lab FAB-lab ThinkTank
  • Finding and evaluating community structure in networks
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 69, No. 2. (2004)
    by MEJ Newman, M Girvan
    posted to communities networks by Diego_Prada on 2008-02-21 13:11:36 as read along with 4 people and 1 group lshaw gcalda RobMills hannu ThinkTank
  • Community structure in social and biological networks.
    Proc Natl Acad Sci U S A, Vol. 99, No. 12. (11 June 2002), pp. 7821-7826.
    by M Girvan, ME Newman
    posted to communities networks by Diego_Prada on 2008-02-21 13:08:23 as read along with 22 people and 5 groups pridkett korakot mrm rasca jtowle PiersYoung zqshen schaal shivaram yas lyongu herdivineshadow jirlong fwkroon adriandefroment gcalda noby andreacapocci Evangelia marcio pipkin stefanoallesina Philosophy_of_Information Blog_and_Wiki_Research GraphVis UCD_SmallWorldGraphVis T_lab
  • Energy landscapes and properties of biomolecules
    Physical Biology, Vol. 2, No. 4. (December 2005), S86.
    by David J Wales
    posted to free-energy hot by Diego_Prada on 2008-02-19 11:10:33 as **** along with 1 person mtw
  • Importance of Metastable States in the Free Energy Landscapes of Polypeptide Chains
    Physical Review Letters, Vol. 99, No. 17. (2007)
    by Stefan Auer, Mark A Miller, Sergei V Krivov, Christopher M Dobson, Martin Karplus, Michele Vendruscolo
    posted to free-energy hot by Diego_Prada on 2008-02-19 10:53:07 as *****
  • Free energy disconnectivity graphs: Application to peptide models
    The Journal of Chemical Physics, Vol. 117, No. 23. (2002), pp. 10894-10903.
    by Sergei V Krivov, Martin Karplus
    posted to free-energy by Diego_Prada on 2008-02-19 10:28:36 as *****
  • Potential Energy Surfaces and Conformational Transitions in Biomolecules: A Successive Confinement Approach Applied to a Solvated Tetrapeptide
    Physical Review Letters, Vol. 88, No. 3. (2 January 2002), 038101.
    by Sergei V Krivov, Sergei F Chekmarev, Martin Karplus
    posted to free-energy by Diego_Prada on 2008-02-19 10:26:36 as ****
  • One-Dimensional Free-Energy Profiles of Complex Systems: Progress Variables that Preserve the Barriers.
    J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, Vol. 110, No. 25. (29 June 2006), pp. 12689-12698.
    by SV Krivov, M Karplus
    posted to free-energy by Diego_Prada on 2008-02-19 10:24:24 as ****
  • Hidden complexity of free energy surfaces for peptide (protein) folding.
    Proc Natl Acad Sci U S A, Vol. 101, No. 41. (12 October 2004), pp. 14766-14770.
    by SV Krivov, M Karplus
    posted to free-energy proteins by Diego_Prada on 2008-02-19 10:22:29 as **** along with 4 people apaydin dimka bilab Fernando_FF
  • Exploration of the free-energy surface of a three-helix peptide with stochastic optimization methods
    International Journal of Quantum Chemistry, Vol. 99, No. 5. (2004), pp. 854-863.
    by T Herges, A Schug, W Wenzel
    posted to free-energy protein_dynamics by Diego_Prada on 2008-02-19 10:19:16 as **
  • From A to B in free energy space
    The Journal of Chemical Physics, Vol. 126, No. 5. (2007)
    by Davide Branduardi, Francesco L Gervasio, Michele Parrinello
    posted to free-energy hot by Diego_Prada on 2008-02-19 10:14:26 as ***** along with 2 people ruvido kdesmond
  • The Meaning of Component Analysis: Decomposition of the Free Energy in Terms of Specific Interactions
    Journal of Molecular Biology, Vol. 254, No. 5. (15 December 1995), pp. 801-807.
    by S Boresch, M Karplus
    posted to free-energy pca by Diego_Prada on 2008-02-19 10:11:40 as **** along with 1 person dmobley
  • Free-energy landscape of the villin headpiece in an all-atom force field.
    Structure (Camb), Vol. 13, No. 4. (April 2005), pp. 661-668.
    by T Herges, W Wenzel
    posted to free-energy protein_dynamics by Diego_Prada on 2008-02-19 10:10:21 as *** along with 2 people nigham fjc1
  • Escaping free-energy minima.
    Proc Natl Acad Sci U S A, Vol. 99, No. 20. (1 October 2002), pp. 12562-12566.
    by A Laio, M Parrinello
    posted to free-energy by Diego_Prada on 2008-02-19 10:04:16 as **** along with 4 people AndreaColetta apaydin baaden and_ped10
  • Design of amino acid sequences to fold into C[sub alpha]-model proteins
    The Journal of Chemical Physics, Vol. 123, No. 5. (2005)
    by A Amatori, G Tiana, L Sutto, Ferkinghoff J Borg, A Trovato, RA Broglia
    posted to coarse-grained by Diego_Prada on 2008-02-18 18:48:21 as ****
  • Low Frequency Motion in Proteins
    Journal of Computational Physics, Vol. 151 (May 1999), pp. 169-189.
    by P Dauber-Osguthorpe, DJ Osguthorpe, PS Stern, J Moult
    posted to gnm by Diego_Prada on 2008-02-18 18:45:02 as read
  • Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability
    Physical Review Letters, Vol. 80, No. 12. (23 March 1998), 2733.
    by Ivet Bahar, Ali R Atilgan, Melik C Demirel, Burak Erman
    posted to gnm by Diego_Prada on 2008-02-18 18:41:25 as read along with 1 person choonpeng
  • Important fluctuation dynamics of large protein structures are preserved upon coarse-grained renormalization
    International Journal of Quantum Chemistry, Vol. 90, No. 2. (2002), pp. 822-837.
    by Pemra Doruker, Robert L Jernigan, Isabelle Navizet, Rigoberto Hernandez
    posted to coarse-grained gnm by Diego_Prada on 2008-02-18 18:39:25 as read
  • Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis
    Physical Review Letters, Vol. 77, No. 9. (1996), 1905.
    by Monique M Tirion
    posted to gnm by Diego_Prada on 2008-02-18 18:36:27 as read along with 1 person aqeel
  • Comparison of mode analyses at different resolutions applied to nucleic acid systems.
    Biophys J, Vol. 89, No. 5. (November 2005), pp. 2939-2949.
    by AW Van Wynsberghe, Q Cui
    posted to coarse-grained csn gnm pca by Diego_Prada on 2008-02-18 18:18:29 as **** along with 2 people aqeel eckart_bindewald
  • Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis
    Protein Sci, Vol. 3, No. 6. (1 June 1994), pp. 936-943.
    by S Hayward, A Kitao, N Go
    posted to gnm pca by Diego_Prada on 2008-02-18 18:15:23 as **** along with 1 person saravan
  • Global ribosome motions revealed with elastic network model
    Journal of Structural Biology, Vol. 147, No. 3. (September 2004), pp. 302-314.
    by Yongmei Wang, AJ Rader, Ivet Bahar, Robert L Jernigan
    posted to coarse-grained gnm by Diego_Prada on 2008-02-18 18:10:07 as read along with 3 people aqeel eckart_bindewald ffranca
  • Folding core predictions from network models of proteins
    Polymer, Vol. 45, No. 2. (January 2004), pp. 659-668.
    by AJ Rader, Ivet Bahar
    posted to coarse-grained gnm by Diego_Prada on 2008-02-18 18:07:31 as read along with 1 person choonpeng
  • Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data.
    Proteins, Vol. 57, No. 3. (15 November 2004), pp. 468-480.
    by NA Temiz, E Meirovitch, I Bahar
    posted to coarse-grained gnm by Diego_Prada on 2008-02-18 18:04:46 as read along with 2 people apaydin aqeel
  • Collective deformations in proteins determined by a mode analysis of molecular dynamics trajectories
    Polymer, Vol. 43, No. 2. (January 2002), pp. 431-439.
    by Pemra Doruker, Ivet Bahar, Canan Baysal, Burak Erman
    posted to gnm pca protein_dynamics by Diego_Prada on 2008-02-18 17:48:28 as read
  • Elastic Properties of Proteins: Insight on the Folding Process and Evolutionary Selection of Native Structures
    Journal of Molecular Biology, Vol. 321, No. 5. (30 August 2002), pp. 909-921.
    by Cristian Micheletti, Gianluca Lattanzi, Amos Maritan
    posted to coarse-grained gnm go by Diego_Prada on 2008-02-18 17:44:17 as read along with 2 people and 2 groups barry Einat structural_bioinformatics Bioinformatics
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