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401 related items for PubMed ID: 16483195

  • 1. Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality.
    Kosztin I, Barz B, Janosi L.
    J Chem Phys; 2006 Feb 14; 124(6):64106. PubMed ID: 16483195
    [Abstract] [Full Text] [Related]

  • 2. Calculating potentials of mean force from steered molecular dynamics simulations.
    Park S, Schulten K.
    J Chem Phys; 2004 Apr 01; 120(13):5946-61. PubMed ID: 15267476
    [Abstract] [Full Text] [Related]

  • 3. Estimation of free-energy differences from computed work distributions: an application of Jarzynski's equality.
    Echeverria I, Amzel LM.
    J Phys Chem B; 2012 Sep 13; 116(36):10986-95. PubMed ID: 22849340
    [Abstract] [Full Text] [Related]

  • 4. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.
    Hu H, Lu Z, Parks JM, Burger SK, Yang W.
    J Chem Phys; 2008 Jan 21; 128(3):034105. PubMed ID: 18205486
    [Abstract] [Full Text] [Related]

  • 5. Extending the fluctuation theorem to describe reaction coordinates.
    Paramore S, Ayton GS, Voth GA.
    J Chem Phys; 2007 Feb 07; 126(5):051102. PubMed ID: 17302463
    [Abstract] [Full Text] [Related]

  • 6. Direct determination of reaction paths and stationary points on potential of mean force surfaces.
    Li G, Cui Q.
    J Mol Graph Model; 2005 Oct 07; 24(2):82-93. PubMed ID: 16005650
    [Abstract] [Full Text] [Related]

  • 7. Dynamic information for cardiotoxin protein desorption from a methyl-terminated self-assembled monolayer using steered molecular dynamics simulation.
    Hung SW, Hsiao PY, Chieng CC.
    J Chem Phys; 2011 May 21; 134(19):194705. PubMed ID: 21599080
    [Abstract] [Full Text] [Related]

  • 8. Hummer and Szabo-like potential of mean force estimator for bidirectional nonequilibrium pulling experiments/simulations.
    Nicolini P, Procacci P, Chelli R.
    J Phys Chem B; 2010 Jul 29; 114(29):9546-54. PubMed ID: 20597536
    [Abstract] [Full Text] [Related]

  • 9. Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method.
    Khavrutskii IV, Dzubiella J, McCammon JA.
    J Chem Phys; 2008 Jan 28; 128(4):044106. PubMed ID: 18247929
    [Abstract] [Full Text] [Related]

  • 10. Equilibrium free energy estimates based on nonequilibrium work relations and extended dynamics.
    Atilgan E, Sun SX.
    J Chem Phys; 2004 Dec 01; 121(21):10392-400. PubMed ID: 15549919
    [Abstract] [Full Text] [Related]

  • 11. Calculating free-energy profiles in biomolecular systems from fast nonequilibrium processes.
    Forney MW, Janosi L, Kosztin I.
    Phys Rev E Stat Nonlin Soft Matter Phys; 2008 Nov 01; 78(5 Pt 1):051913. PubMed ID: 19113161
    [Abstract] [Full Text] [Related]

  • 12. A potential of mean force estimator based on nonequilibrium work exponential averages.
    Chelli R, Procacci P.
    Phys Chem Chem Phys; 2009 Feb 28; 11(8):1152-8. PubMed ID: 19209357
    [Abstract] [Full Text] [Related]

  • 13. Entropy-energy decomposition from nonequilibrium work trajectories.
    Nummela J, Yassin F, Andricioaei I.
    J Chem Phys; 2008 Jan 14; 128(2):024104. PubMed ID: 18205440
    [Abstract] [Full Text] [Related]

  • 14. Rosenbluth-sampled nonequilibrium work method for calculation of free energies in molecular simulation.
    Wu D, Kofke DA.
    J Chem Phys; 2005 May 22; 122(20):204104. PubMed ID: 15945710
    [Abstract] [Full Text] [Related]

  • 15. Single-file diffusion of confined water inside SWNTs: an NMR study.
    Das A, Jayanthi S, Deepak HS, Ramanathan KV, Kumar A, Dasgupta C, Sood AK.
    ACS Nano; 2010 Mar 23; 4(3):1687-95. PubMed ID: 20201566
    [Abstract] [Full Text] [Related]

  • 16. A differential fluctuation theorem.
    Maragakis P, Spichty M, Karplus M.
    J Phys Chem B; 2008 May 15; 112(19):6168-74. PubMed ID: 18331019
    [Abstract] [Full Text] [Related]

  • 17. Stiff Spring Approximation Revisited: Inertial Effects in Nonequilibrium Trajectories.
    Nategholeslam M, Gray CG, Tomberli B.
    J Phys Chem B; 2017 Jan 19; 121(2):391-403. PubMed ID: 27959538
    [Abstract] [Full Text] [Related]

  • 18. On the use of local diffusion models for path ensemble averaging in potential of mean force computations.
    Calderon CP.
    J Chem Phys; 2007 Feb 28; 126(8):084106. PubMed ID: 17343439
    [Abstract] [Full Text] [Related]

  • 19. Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality.
    West DK, Olmsted PD, Paci E.
    J Chem Phys; 2006 Nov 28; 125(20):204910. PubMed ID: 17144743
    [Abstract] [Full Text] [Related]

  • 20. Biased sampling of nonequilibrium trajectories: can fast switching simulations outperform conventional free energy calculation methods?
    Oberhofer H, Dellago C, Geissler PL.
    J Phys Chem B; 2005 Apr 14; 109(14):6902-15. PubMed ID: 16851777
    [Abstract] [Full Text] [Related]

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