jwagoner's library 86 articles Export

	On the Application of Ellipsoidal Harmonics to Potential Problems in Molecular Electrostatics and Magnetostatics [My Copy] Proceedings of the Royal Society of London. Series A, Mathematical and Physical Sciences (1934-1990), Vol. 349, No. 1656. (13 April 1976), pp. 125-139. by J. W. Perram, P. J. Stiles posted to ellipsoid pb by jwagoner on 2007-11-28 08:59:29 as
	Ab initio SCF calculations on electrostatically solvated molecules using a deformable three axes ellipsoidal cavity [My Copy] The Journal of Chemical Physics, Vol. 78, No. 2. (1983), pp. 834-838. by Daniel Rinaldi, Manuel, Jean L. Rivail posted to ellipsoid pb by jwagoner on 2007-11-28 08:36:18 as
	New Developments in the Continuum Representation of solvent Effects [My Copy] by Gomez-Jeria Morales-Lagos posted to electrostatics implicit by jwagoner on 2007-09-06 21:07:49 as
	Fast geometry optimizationin self-cosistent reaction field computations on solvated molecules [My Copy] Journal of Computational Chemistry, Vol. 13, No. 6. (1992), pp. 675-680. by Daniel Rinaldi, Jean-Louis Rivail, Noureddine Rguini posted to electrostatics implicit by jwagoner on 2007-09-06 20:59:59 as
	Article DOI Lookup [My Copy] JACS (1974) by Bauer posted to diffusion hard_sphere by jwagoner on 2007-08-29 22:13:27 as
	Rotational friction coefficients for spheroids with the slipping boundary condition [My Copy] The Journal of Chemical Physics, Vol. 60, No. 11. (1974), pp. 4354-4357. by Chih M. Hu, Robert Zwanzig posted to diffusion hard_sphere by jwagoner on 2007-08-29 22:09:39 as
	Nitroxide/Substrate Weak Hydrogen Bonding: Attitude and Dynamics of Collisions in Solution [My Copy] J. Am. Chem. Soc., Vol. 129, No. 22. (6 June 2007), pp. 7018-7027. by J. L. Russ, J. Gu, K. H. Tsai, T. Glass, J. C. Duchamp, H. C. Dorn posted to sasd by jwagoner on 2007-08-01 22:05:27 as
	Molecular dynamics simulation in the grand canonical ensemble [My Copy] Journal of Computational Chemistry, Vol. 28, No. 10. (2007), pp. 1763-1773. by Hossein Eslami, Florian Müller-Plathe posted to gcmd by jwagoner on 2007-07-27 01:16:05 as
	Guiding Bacteria with Small Molecules and RNA [My Copy] posted to int by jwagoner on 2007-07-27 01:12:32 as
	Constant temperature simulations using the Langevin equation with velocity Verlet integration [My Copy] Chemical Physics, Vol. 236, No. 1-3. (15 September 1998), pp. 243-252. by Germana M. Paterlini, David M. Ferguson posted to stochastic by jwagoner on 2007-06-27 21:02:05 as along with 1 person rpetrenko
	Proton Solvation and Transport in Aqueous and Biomolecular Systems: Insights from Computer Simulations [My Copy] J. Phys. Chem. B, Vol. 111, No. 17. (3 May 2007), pp. 4300-4314. by J. M. J. Swanson, C. M. Maupin, H. Chen, et al.M. K. Petersen, J. Xu, Y. Wu, G. A. Voth posted to int by jwagoner on 2007-06-22 00:19:28 as
	Algorithm for model validation: Theory and applications [My Copy] PNAS, Vol. 104, No. 16. (17 April 2007), pp. 6562-6567. by D. Sornette, A. B. Davis, K. Ide, K. R. Vixie, V. Pisarenko, J. R. Kamm posted to int statistics by jwagoner on 2007-06-21 23:53:59 as
	Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting [My Copy] PNAS, Vol. 104, No. 14. (3 April 2007), pp. 5830-5835. by Thomas M. Hansen, Reihani, Lene B. Oddershede, Michael A. Sorensen posted to int by jwagoner on 2007-06-21 23:51:34 as along with 2 people lshaw physics
	The Binomial Cell Model of Hydrophobic Solvation [My Copy] J. Phys. Chem. B, Vol. 108, No. 40. (7 October 2004), pp. 15830-15840. by V. V. Alexandrovsky, M. V. Basilevsky, I. V. Leontyev, M. A. Mazo, V. B. Sulimov posted to hydrophobic-interactions by jwagoner on 2007-06-18 23:52:59 as
	THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method [My Copy] Journal of Computational Chemistry, Vol. 13, No. 8. (1992), pp. 1011-1021. by Shankar Kumar, John M. Rosenberg, Djamal Bouzida, Robert H. Swendsen, Peter A. Kollman posted to pmf by jwagoner on 2007-06-18 23:30:43 as along with 11 people and 1 group jrperillaj edws Diego_Prada stephenbond dfgreen A_Coletta_Thesis sunnytov dgront sikorski bransfop allmensch Structural Biology Group TorVergata
	Predicting coupling limits from an experimentally determined energy landscape [My Copy] PNAS, Vol. 104, No. 12. (20 March 2007), pp. 4907-4912. by Timothy O. Street, Christina M. Bradley, Doug Barrick posted to folding by jwagoner on 2007-06-09 00:03:04 as along with 1 person doktornoe
	Accurate, conformation-dependent predictions of solvent effects on protein ionization constants [My Copy] PNAS, Vol. 104, No. 12. (20 March 2007), pp. 4898-4903. by P. Barth, T. Alber, P. B. Harbury posted to pka by jwagoner on 2007-06-08 23:59:18 as
	Studies in Molecular Dynamics. VIII. The Transport Coefficients for a Hard-Sphere Fluid [My Copy] The Journal of Chemical Physics, Vol. 53, No. 10. (1970), pp. 3813-3826. by B. J. Alder, D. M. Gass, T. E. Wainwright posted to asasd diffusion hard_sphere by jwagoner on 2007-05-16 09:21:56 as
	Decay of the Velocity Autocorrelation Function [My Copy] Physical Review A, Vol. 1, No. 1. (January 1970), 18. by B. J. Alder, T. E. Wainwright posted to asasd diffusion hard_sphere by jwagoner on 2007-05-16 09:21:19 as along with 3 people softsimu weeks rschmid
	The Dewetting Transition and The Hydrophobic Effect [My Copy] J. Am. Chem. Soc., Vol. 129, No. 15. (18 April 2007), pp. 4847-4852. by N. Choudhury, B. M. Pettitt posted to hydrophobic-interactions by jwagoner on 2007-05-10 06:29:35 as
	Maintaining solvent accessible surface area under rotamer substitution for protein design [My Copy] Journal of Computational Chemistry, Vol. 28, No. 8. (2007), pp. 1336-1341. by Andrew Leaver-Fay, Glenn L. Butterfoss, Jack Snoeyink, Brian Kuhlman posted to sasa by jwagoner on 2007-05-10 01:35:38 as along with 2 people mijam jwm
	Micromechanical control of cell-cell interactions. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 14. (3 April 2007), pp. 5722-5726. by Elliot E. Hui, Sangeeta N. Bhatia posted to int by jwagoner on 2007-05-09 00:34:19 as along with 2 people yhkim guhjy
	Measuring Coexisting Densities from a Two-Phase Molecular Dynamics Simulation by Voronoi Tessellations [My Copy] J. Phys. Chem. B, Vol. 111, No. 13. (5 April 2007), pp. 3469-3475. by J. T. Fern, D. J. Keffer, W. V. Steele posted to int by jwagoner on 2007-05-08 23:59:06 as
	Global minimum structure searches via particle swarm optimization [My Copy] Journal of Computational Chemistry, Vol. 28, No. 7. (2007), pp. 1177-1186. by Seth T. Call, Dmitry, Alexander I. Boldyrev posted to int by jwagoner on 2007-04-23 21:27:02 as
	Metastable Liquid Clusters in Super- and Undersaturated Protein Solutions [My Copy] J. Phys. Chem. B, Vol. 111, No. 12. (29 March 2007), pp. 3106-3114. by O. Gliko, W. Pan, P. Katsonis, et al.N. Neumaier, O. Galkin, S. Weinkauf, P. G. Vekilov posted to int by jwagoner on 2007-04-23 21:19:06 as
	Proton Transfer and Associated Molecular Rearrangements in the Photocycle of Photoactive Yellow Protein: Role of Water Molecular Migration on the Proton Transfer Reaction [My Copy] J. Phys. Chem. B, Vol. 111, No. 11. (22 March 2007), pp. 2948-2956. by M. Kamiya, S. Saito, I. Ohmine posted to int by jwagoner on 2007-04-19 07:37:37 as
	Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. 3. Calculation and Parameterization of the Potentials of Mean Force of Pairs of Identical Hydrophobic Side Chains [My Copy] J. Phys. Chem. B, Vol. 111, No. 11. (22 March 2007), pp. 2925-2931. by M. Makowski, E. Sobolewski, C. Czaplewski, et al.A. Liwo, S. Oldziej, J. H. No, H. A. Scheraga posted to implicit by jwagoner on 2007-04-19 07:37:26 as
	Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. 1. Approximate Expression for the Free Energy of Hydrophobic Association Based on a Gaussian-Overlap Model [My Copy] J. Phys. Chem. B, Vol. 111, No. 11. (22 March 2007), pp. 2910-2916. by M. Makowski, A. Liwo, H. A. Scheraga posted to implicit by jwagoner on 2007-04-19 07:36:57 as
	Mechanical Stabilization Effect of Water on a Membrane-like System [My Copy] J. Am. Chem. Soc., Vol. 129, No. 9. (7 March 2007), pp. 2636-2641. by M. Castronovo, F. Bano, S. Raugei, et al.D. Scaini, M. Dell'angela, R. Hudej, L. Casalis, G. Scoles posted to int by jwagoner on 2007-04-19 07:33:40 as
	Determination of the friction coefficient of a Brownian particle by molecular-dynamics simulation [My Copy] The Journal of Chemical Physics, Vol. 118, No. 17. (2003), pp. 7888-7891. by Ould F. Kaddour, D. Levesque posted to fluctuation-dissipation by jwagoner on 2007-04-03 19:40:57 as
	Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations [My Copy] The Journal of Chemical Physics, Vol. 100, No. 12. (1994), pp. 9050-9063. by Dmitrii Beglov, Benoît Roux posted to implicit by jwagoner on 2007-04-02 20:20:25 as along with 2 people dmitry_s_yershov dfgreen
	Sodium chloride ion pair interaction in water: computer simulation [My Copy] Chemical Physics Letters, Vol. 105, No. 6. (6 April 1984), pp. 577-580. by Max Berkowitz, Omar A. Karim, Andrew J. Mccammon, Peter J. Rossky posted to pmf by jwagoner on 2007-03-30 22:58:48 as
	Hydration Dynamics and Time Scales of Coupled Water-Protein Fluctuations [My Copy] J. Am. Chem. Soc., Vol. 129, No. 11. (21 March 2007), pp. 3376-3382. by T. Li, A. A. Hassanali, Y. T. Kao, D. Zhong, S. J. Singer posted to solvation by jwagoner on 2007-03-20 19:01:56 as along with 2 people kjell cz
	Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models [My Copy] Journal of Computational Chemistry, Vol. 13, No. 8. (1992), pp. 952-962. by Shuichi Miyamoto, Peter A. Kollman posted to md by jwagoner on 2007-03-19 03:05:23 as along with 8 people oteri Lombardo_7 choonpeng A_Coletta_Thesis tji softsimu ashaytan robertvacha
	An algorithm for the representation and computation of supermolecular surfaces and volumes [My Copy] Journal of Computational Chemistry, Vol. 10, No. 5. (1989), pp. 628-634. by Heinrich R. Karfunkel, Veronique Eyraud posted to algorithm sasa by jwagoner on 2007-03-16 17:45:27 as
	Particle-Based Implicit Solvent Model for Biosimulations: Application to Proteins and Nucleic Acids Hydration [My Copy] Journal of Chemical Theory and Computation, Vol. 2, No. 6. (1 November 2006), pp. 1646-1656. by Nathalie Basdevant, Tap Ha-Duong, Daniel Borgis posted to implicit by jwagoner on 2007-03-16 17:26:28 as along with 2 people and 1 group Elena_Zubova sobolevnrm baker-group
	A semi-implicit solvent model for the simulation of peptides and proteins [My Copy] Journal of Computational Chemistry, Vol. 25, No. 8. (2004), pp. 1015-1029. by Nathalie Basdevant, Daniel Borgis, Tap Ha-Duong posted to implicit by jwagoner on 2007-03-16 17:24:10 as along with 1 person and 1 group sobolevnrm baker-group
	Ant colony system: a cooperative learning approach to the traveling salesman problem [My Copy] Evolutionary Computation, IEEE Transactions on In Evolutionary Computation, IEEE Transactions on, Vol. 1, No. 1. (1997), pp. 53-66. by M. Dorigo, L. M. Gambardella posted to algorithm by jwagoner on 2007-03-06 20:05:19 as along with 6 people and 1 group cafetai andreud kevinstuttgard dmeister damaru otavio Scout/Leader Systems
	Dynamical fluctuating charge force fields: Application to liquid water. [My Copy] J Chem Phys by Berne posted to md by jwagoner on 2007-03-06 10:23:58 as
	Implementation of ?-? interactions in molecular dynamics simulation [My Copy] Journal of Computational Chemistry, Vol. 28, No. 6. (2007), pp. 1091-1099. by Hitomi Yuki, Yoshikazu Tanaka, Masayuki Hata, Hidenori Ishikawa, Saburo Neya, Tyuji Hoshino posted to md by jwagoner on 2007-03-03 04:24:06 as along with 1 person choonpeng
	Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: All-atom molecular dynamics in implicit solvent [My Copy] Journal of Computational Chemistry, Vol. 28, No. 6. (2007), pp. 1068-1082. by Anna Jagielska, Harold A. Scheraga posted to fluctuation-dissipation integrator by jwagoner on 2007-03-03 04:22:22 as along with 2 people onufriev choonpeng
	A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field [My Copy] The Journal of Chemical Physics, Vol. 108, No. 24. (1998), pp. 10220-10230. by David van der Spoel, Paul J. van Maaren, Herman J. C. Berendsen posted to gct by jwagoner on 2007-03-02 21:33:14 as along with 3 people r2s2 A_Coletta_Thesis softsimu
	Computational chemistry approach to protein kinase recognition using 3D stochastic van der Waals spectral moments [My Copy] Journal of Computational Chemistry, Vol. 28, No. 6. (2007), pp. 1042-1048. by Humberto González-Díaz, Liane Saíz-Urra, Reinaldo Molina, Yenny González-Díaz, Angeles Sánchez-González posted to int by jwagoner on 2007-03-01 17:54:35 as along with 1 person and 1 group whitead Jiang Research Group
	Molecular dynamics with coupling to an external bath [My Copy] The Journal of Chemical Physics, Vol. 81, No. 8. (1984), pp. 3684-3690. by H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Dinola, J. R. Haak posted to tcouple by jwagoner on 2007-02-28 18:47:16 as along with 12 people and 1 group georgwachter A_Coletta_Thesis rdf r2s2 dsmueller Lombardo_7 gsub lillekatt allmensch tji choonpeng jteyra Structural Biology Group TorVergata
	A generalized direct-particle-deletion scheme for the calculation of chemical potential and solubilities of small- and medium-sized molecules in amorphous polymers [My Copy] Journal of Computational Chemistry, Vol. 28, No. 5. (2007), pp. 877-889. by Martin R. Siegert, Matthias Heuchel, Dieter Hofmann posted to particle-deletion by jwagoner on 2007-02-21 19:50:39 as
	An ant algorithm for the conformational analysis of flexible molecules [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2007), NA. by Frits Daeyaert, Marc De Jonge, Luc Koymans, Maarten Vinkers posted to algorithm conformational-analysis by jwagoner on 2007-02-21 19:45:06 as along with 6 people and 1 group npt11tpn BragilMassoud gane5h samjlord rsantana superpyrin moernerlab
	From the Cover: Hydrophobic interaction and hydrogen-bond network for a methane pair in liquid water [My Copy] PNAS, Vol. 104, No. 8. (20 February 2007), pp. 2626-2630. by Je-Luen Li, Roberto Car, Chao Tang, Ned S. Wingreen posted to hydrophobic-interactions by jwagoner on 2007-02-21 19:43:50 as
	Electrostatics at the oilâwater interface, stability, and order in emulsions and colloids [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 8. (20 February 2007), pp. 2585-2590. by Mirjam E. Leunissen, Alfons van Blaaderen, Andrew D. Hollingsworth, Matthew T. Sullivan, Paul M. Chaikin posted to int by jwagoner on 2007-02-21 19:35:10 as along with 2 people kedmond ghunter
	A domain decomposition parallel processing algorithm for molecular dynamics simulations of systems of arbitrary connectivity [My Copy] pp. 170-186. by D. Brown posted to domain-decomposition by jwagoner on 2007-02-19 18:14:41 as along with 1 person and 1 group rblake uiuc-cs
	The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii [My Copy] The Journal of Physical Chemistry A, Vol. 101, No. 16. (1 April 1997), pp. 3005-3014. by Di Qiu, Peter S. Shenkin, Frank P. Hollinger, W. Clark Still posted to gb by jwagoner on 2007-02-16 22:54:27 as along with 4 people chemrahul82 GermanErlenkamp mijam dfgreen

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int	13
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dynamics	7
hybrid	7
gcmc	6
gcmd	6
hydrophobic-interactions	6
model	6
fluctuation-dissipation	5
hydrodynamic-interactions	5
diffusion	4
hard_sphere	4
algorithm	3
integrator	3
md	3
asasd	2
electrostatics	2
ellipsoid	2
hybrid-model	2
pb	2
pmf	2
sasa	2
stochastic-boundary-conditions	2
conformational-analysis	1
domain-decomposition	1
folding	1
friection	1
gb	1
gct	1
interfacial-water	1
particle-deletion	1
phase-equilibria	1
pka	1
sasd	1
solvation	1
statistics	1
surface-area	1
tcouple	1
tensor	1
traveling-salesman	1

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