Appendix User Bibliography




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Chemistry


CHE050039

  1. R.D. Bach, In The Chemistry of Functional Groups Peroxides; Z. Rappoport Ed.; Wiley: New York, 2006, Chp 1.

  2. Bach, R.D.; Dmitrenko, O.; Estevez, C.M. Chemical Behavior of the Biradicaloid (HOONO) Singlet States of Peroxynitrous Acid. The Oxidation of Hydrocarbons, Sulfides and Selenides. J. Am. Chem. Soc. 2005, 127, 3140-3155.).

  3. Bach, R. D.; Dmitrenko, O The “Somersault” Mechanism for the P-459 Hydroxylation of Hydrocarbons. The Intervention of Transient Inverted metastable Hydroperoxides. J. Am. Chem. Soc. 2006, 128(1), 1474.

CHE050002

  1. Qian, X.; Ding, S.-Y.; Nimlos, M. R.; Johnson, D. K.; Himmel, M. E. Macromolecules 2005.

  2. Qian, X.; Nimlos, M. R.; Davis, M.; Johnson, D. K.; Himmel, M. E. Carbohydrate Research 2005, 340, 2319-2327.

MCA93S011

  1. M. Sliwinska-Bartkowiak, F. R. Hung, E. E. Santiso, B. Coasne, F. R. Siperstein and K. E. Gubbins, “Effect of confinement on freezing of CCl4 in cylindrical pores”, Adsorption 11, 391 (2005).

  2. S. Bhattacharya, B. Coasne, F. R. Hung and K. E. Gubbins, “A realistic molecular model for SBA-15: mimetic simulations and gas adsorption”, Langmuir, submitted (2006).

  3. S. Bhattacharya, B. Coasne, F. R. Hung and K. E. Gubbins, “Modeling triblock surfactant templated mesoporous silicas (MCF and SBA-15): a mimetic simulation study”, Stud. Surf. Sci. Catal., in press (2006).

  4. S. Bhattacharya and K.E. Gubbins, “Ultra-Large Mesopores in the Triblock Surfactant-Oil-Water-Inorganic Oxide System: Lattice Monte Carlo Simulations”, J. Chem. Phys., in press (2005).

  5. H. Bock, K.E. Gubbins and K.G. Ayappa, “Solid/Solid Phase Transitions in Confined Thin Films: A Zero Temperature Approach”, Journal of Chemical Physics 122, 094709 (2005).

  6. N. Chennamsetty, H. Bock, and K.E. Gubbins, “Coarse-Grained Potentials from Widom’s Particle Insertion Method”, Mol. Phys. 103, 3185 (2005).

  7. N. Chennamsetty, H. Bock, L.F. Scanu, F.R. Siperstein and K.E. Gubbins, “Cosurfactant and Cosolvent Effects on Surfactant Self-Assembly in Supercritical Carbon Dioxide”, Journal of Chemical Physics 122, 094710 (2005).

  8. B. Coasne, J. Czwartos, K. E. Gubbins, F. R. Hung and M. Sliwinska-Bartkowiak, “Confinement effects on freezing of binary mixtures” Stud. Surf. Sci. Catal., in press (2006).

  9. B. Coasne, J. Czwartos, K. E. Gubbins, F. R. Hung and M. Sliwinska-Bartkowiak, “Freezing of mixtures confined a slit nanopores” Adsorption 11, 311 (2005).

  10. B. Coasne and K.E. Gubbins and R.J-M. Pellenq, “Temperature Effect on Adsorption/Desorption Isotherms for a Simple Fluid Confined within Various Nanopores”, Adsorption 11, 289-294 (2005).

  11. B. Coasne, F. R. Hung, R. J.–M. Pellenq, F. R. Siperstein, and K. E. Gubbins, “Adsorption of simple gases in MCM-41 materials: the role of surface roughness”, Langmuir, in press (2006).

  12. B. Coasne, F. R. Hung, F. R. Siperstein and K. E. Gubbins, “Molecular simulation of gas adsorption in realistic models of silica nanopores”, Ann. Chim-Sci. Mat. 30, 375 (2005).

  13. J. Czwartos, B. Coasne, K. E. Gubbins, F. R. Hung and M. Sliwinska-Bartkowiak, “Freezing and melting of azeotropic mixtures confined in nanopores: experiment and molecular simulation” Mol. Phys. 103, 3103 (2005).

  14. F. R. Hung, B. Coasne, K. E. Gubbins, F. R. Siperstein, and M. Sliwinska-Bartkowiak, “A Monte Carlo study of capillary condensation of krypton within realistic models of templated mesoporous silica materials”, Stud. Surf. Sci. Catal., in press (2006).

  15. F. R. Hung, B. Coasne, E. E. Santiso, K. E. Gubbins, F. R. Siperstein and M. Sliwinska-Bartkowiak, “Molecular modeling of freezing of simple fluids confined within carbon nanotubes”, J. Chem. Phys. 122, 144706 (2005).

  16. F.R. Hung, K.E. Gubbins, R. Radhakrishnan, K. Szostak, F. Beguin, G. Dudziak and M. Sliwinska-Bartkowiak, “Freezing/Melting of Lennard-Jones Fluids in Carbon Nanotubes”, Applied Physics Letters 86, 103110 (2005).

  17. S.K. Jain, J.P. Pikunic, R.J-M. Pellenq and K.E. Gubbins, “Effects of Activation on the Structure and Adsorption Properties of a Nanoporous Carbon using Molecular Simulation”, Adsorption 11, 355-360 (2005).

  18. M.K. Kostov, E.E. Santiso,A.M.George, K.E. Gubbins and M. Buongiorno Nardelli, “Dissociation of water on defective carbon substrates”, Phys. Rev. Lett. 95, 136105 (2005).

  19. J. Pikunic, P. Llewellyn, R. Pellenq and K.E. Gubbins, “Argon and Nitrogen Adsorption in Disordered Nanoporous Carbons: Simulation and Experiment”, Langmuir 21, 4431-4440 (2005).

  20. E. Santiso, A.M. George, C.H. Turner, M.K. Kostov, K.E. Gubbins, M.B . Nardelli, and M. Sliwinska Bartkowiak, Appl. Surf. Sci. 252, 766 (2005).

  21. E. Santiso, K.E. Gubbins, A.M. George, M.B . Nardelli, and M. Sliwinska-Bartkowiak, “Effect of Confinement on Chemical Reactions”, Adsorption 11, 349 (2005).

  22. J.R. Silbermann, S.H.L. Klapp, M. Schoen, N. Chennamsetty, H. Bock, and K.E. Gubbins, “Mesoscale Modeling of Complex Binary Fluid Mixtures. Towards an Atomistic Foundation of Effective Potentials”, J. Chem. Phys., in press (2006).

  23. A.Striolo, A.A. Chialvo, P.T. Cummings and K.E. Gubbins, “Simulated Water Adsorption in Chemically Heterogeneous Carbon Nanotubes”, Journal of Chemical Physics, in press (2005).

  24. Striolo, A.A. Chialvo, K.E. Gubbins and P.T. Cummings, “Water in Carbon Nanotubes: Adsorption Isotherms and Thermodynamic Properties from Molecular Simulation”, J. Chem. Phys., in press (2006).

  25. Striolo, K.E. Gubbins, A.A. Chialvo and P.T. Cummings, “The Effect of Pore Connectivity on Water Adsorption Isotherms in Non-Activated Graphitic Nanopores”, Adsorption 11, 337-341 (2005).

  26. Striolo, P.K. Naicker, A.A. Chialvo, P.T. Cummings and K.E. Gubbins, “Simulated Water Adsorption Isotherms in Hydrophilic and Hydrophobic Cylindrical Nanopores”, Adsorption 11, 397-401 (2005).

CHE060043

  1. Ivanov, B. Chen, S. Raugei, and M.L. Klein, `Relative pKas from first principles molecular dynamics: The case of histidine deprotonation', J. Phys. Chem. B 110, 6365{6371 (2006).

  2. M.E. McKenzie and B. Chen, `Unravelling the peculiar nucleation mechanisms for non-ideal binary mixtures with atomistic simulations', J. Phys. Chem. B 110, 3511{3516 (2006).

CHE050094

  1. X Huang, R Zhou, and B. J. Berne. J. Phys. Chem. B, 109:3546, 2005.

  2. Lan Hua, Xuhui Huang, Ruhong Zhou, Pu Liu and Bruce J. Berne, ”Protein Surface Hydrophobicity Analysis” In preparation. (2006)

  3. P. Liu, X. Huang, R. Zhou, and B. J. Berne. Nature, 437:159, 2005.

  4. Pu Liu, Xuhui Huang, Ruhong Zhou, and Bruce J. Berne, ”Hydrophobic Aided Replica Exchange: an Efficient Algorithm for Protein Folding in Explicit Solvent” J. Phys. Chem. B. In press. (2006)

  5. Liu, P, Huang, X, Zhou, R, & Berne, B. J. (2005) Nature 437, 159.

  6. Liu, P, Kim, B, Friesner, R. A, & B.J.Berne. (2005) Proc. Natl. Acad. Sci. 102.

MCA01S024

  1. “Hybrid QM/MM and DFT Investigations of the Catalytic Mechanism and Inhibition of the Dinuclear Zinc Metallo--lactamase CcrA from Bacteroides fragilis” H. Park; K. M. Merz, Jr. J. Am. Chem. Soc. 2005, 127, 4232-4221.

  2. "Large Scale Validation of a Quantum Mechanics Based Scoring Function: Predicting the Binding Affinity and the Binding Mode of a Diverse set of Protein-Ligand Complexes” K. Raha; K. M. Merz Jr. J. Med. Chem. 2005, 48, 4558-4575.

  3. “The Effects of Fluorine Substitution on the Edge-to-Face Interaction of the Benzene Dimer” K. E. Riley; K. M. Merz, Jr. J. Phys. Chem. B., 2005, 109, 17752-17756.

  4. “Accurate Atomic and Molecular Calculations without Gradient Corrections: Scaled SVWNV Density Functional” K. E. Riley; E. N. Brothers; K. B. Ayers and K. M. Merz, Jr. J. Chem Theory Comput. 2005, 1, 546-533.

  5. “Pairwise Decomposition of Residue Interaction Energies using Semiempirical Quantum Mechanical Methods in Studies of Protein-Ligand Interaction” K. Raha; A. J. van der Vaart; K. E. Riley; L. M. Westerhoff; H. Kim and K. M. Merz Jr. J. Am. Chem. Soc. 2005, 127, 6583-6594.

  6. “Molecular Dynamics Simulations of the TEM-1 lactamase Complexed with Cephalothin” D. Suárez; N. Díaz; K. M. Merz, Jr.; T. L. Sordo J. Med. Chem. 2005, 48, 780-791.

  7. “Validation of the Binding Site Structure of the Cellular Retinol-Binding Protein (CRBP) by Ligand NMR Chemical Shift Perturbations” B. Wang; K. M. Merz, Jr. J. Am. Chem. Soc. 2005, 127, 5310-5311.

  8. “Refinement of Protein Crystal Structures Using Energy Restraints Derived from Linear-scaling Quantum Mechanics” N. Yu; H. P. Yennawar; K. M. Merz, Jr. Acta. Cryst. D. Biol. Cryst. 2005, 51, 322-332.

MCA06N048

  1. H. Frost, T. Duren, and R. Q. Snurr, J. Phys. Chem. B. 110, 9565 (2006).

  2. L. A. Clark, S. Chempath, and R. Q. Snurr, Langmuir 21, 2267 (2005).

Analytical and Surface Chemistry


CHE040001

  1. J. Phares, D. W. Grumbine, Jr., and F. J. Wunderlich, Phase Diagrams of Monomer Adsorption on Equilateral Triangular Lattices I: Repulsive First-neighbor Interactions, submitted to Physics Letters A, 30 September 2005.

CHE060010

  1. H. Huang, F. B. Prinz to be submitted.

  2. M. Nakamura, H. Huang, F. B. Prinz to be submitted.

CHE040030

  1. Hyman, M. P.; Medlin, J. W., "A Theoretical Study of the Adsorption and Dissociation of Oxygen on Pt(111) in the Presence of Homogeneous Electric Fields" J. Phys. Chem. B 2005, 109, 6304.

Organic and Macromolecular Chemistry


CHE030089

  1. Bojin, M. D.; Tantillo, D. J., submitted to Org. Biomol. Chem: “Nonclassical Carbocations as C–H Hydrogen Bond Donors”

  2. Gerkin, J. B.; Wang, S. C.; Preciado, A. B.; Park, Y. S.; Nishiguchi, G.; Tantillo, D. J.; Little, R. D. J. Org. Chem. 2005, 70, 4598-4608: “Remote Substituent Effects upon the Rearrangements of Housane Cation Radicals”

  3. Gutta, P.; Tantillo, D. J. Angew. Chem. Int. Ed. 2005, 44, 2719-2723: “Proton Sandwiches: Nonclassical Carbocations with 4-Coordinate Protons,” highlighted in the "Science Concentrates" section of the May 2, 2005 issue of C&EN.

  4. Ho, G. A. (undergraduate); Nouri, D. H.; Tantillo, D. J. J. Org. Chem. 2005, 70, 5139-5143: “The Cationic Cascade Route to Longifolene”

  5. Nouri, D. H.; Tantillo, D. J., submitted to J. Am. Chem. Soc.: “Hiscotropic Rearrangements: Hybrids of Electrocyclic and Sigmatropic Reactions”

  6. Nouri, D. H.; Tantillo, D. J. Curr. Org. Chem., in press: “They Came from the Deep: Syntheses, Applications and Biology of Ladderanes”

  7. Ponec, R.; Bultinck, P.; Gutta, P.; Tantillo, D. J., submitted to J. Org. Chem.: “Multicenter Bonding in Carbocations with Tetracoordinate Protons”

  8. Siebert, M. R. (undergraduate); Tantillo, D. J., submitted to J. Org. Chem: “Tetracoordinate Carbon as a Nucleophile? Interconversion of Carbenium Ions with Carbonium Ions Possessing Nearly Square Pyramidal Pentacoordinate Carbons”

  9. Wang, S. C.; Tantillo, D. J. Eur. J. Org. Chem., in press: “The Mechanism of Semibullvalene Bromination”

Physical Chemistry


CHE060008

  1. Dixit SB, Beveridge DL, Case DA, Cheatham TE, Guidice E, Lankas F, Lavery R, Maddocks JH, Osman R, Sklenar H, Thayer K, Varnai P. Biophys J. 2005 Sep 16; [Epub ahead of print]

CHE060045

  1. G. Brancato and M. E. Tuckerman. A polarizable multistate empirical valence bond model for proton transport in aqueous solution. J. Chem. Phys., 122:224507, 2005.

  2. R. Iftimie and M. E. Tuckerman. The molecular origin of the continuous infrared absorption in aqueous solutions of acids: A computational approach. Angew. Chem., 45:1144, 2006.

  3. H.-S. Lee and M. E. Tuckerman. Ab initio molecular dynamics with discrete variable representation basis set: Techniques and application to liquid water. J. Phys. Chem. A, xxxx:(in press), 2006.

  4. P. Minary and M. E. Tuckerman. Reaction mechanism of 1,3-butadiene addition to the si(100)-2x1 surface. Journal of the American Chemical Society, 127:1110, 2005.

  5. J. A. Morrone, K. E. Haslinger, and M. E. Tuckerman. Ab initio molecular dynamics simulation of the structure and proton transport dynamics of methanol-water solutions. J. Phys. Chem. B, 110:3712, 2006.

  6. M. E. Tuckerman, A. Chandra, and D. Marx. Structure and dynamics of oh-(aq). Acc. Chem. Res., 39:151, 2006.

CHE060005

  1. S. Bubin, L. Adamowicz, and M. Cafiero, "Non-Born-Oppenheimer Calculations of Atoms and Molecules with Explicitly Correlated Gaussian Functions", Electronic Encyclopedia of Computational Chemistry (eECC), (2004, in press).

  2. M. Cafiero ''A new DFT Correlation Function for use with Exact Exchange '' Chem. Phys. Lett., Accepted, In Press.

  3. M. Cafiero and C. Gonzalez, ''Approximate self-consistent potentials for use in DFT XC functionals '' Phys. Rev. A.. 71, 42505 (2005).

  4. M. Cafiero and L Adamowicz, ''Nuclear Densities for DH2+,'' J. Chem. Phys. 122, 1 (2005)

  5. Godfrey-Kittle, A, and Cafiero, M " Evaluation of DFT methods for computing the binding nergies of homo-molecular and hetero-molecular dimers of monosubstituted benzene", In Review; Pranger, L. and Cafiero, M " Evaluation of DFT methods for computing the interaction nergies of hydrogen bonds to monosubstituted benzene", in preparation

  6. Godfrey_Kittle, M. Cafiero "Interaction energies for mono-substituted benzene ring dimers using DFT", In Review, PCCP.

CHE060007

  1. George C. McBane. Grand Valley State University, 2005. "PMP Molscat", a parallel version of Molscat version 14 available at http://faculty.gvsu.edu/mcbaneg/pmpmolscat

  2. Kirk A. Peterson and George C. McBane. A hierarchical family of three dimensional potential energy surfaces for He–CO. J. Chem. Phys., 123(8):084314, 2005.

MCA93S001

  1. N. Choudhury and B. M. Pettitt. Journal of the American Chemical Society, 2005, 127, 3556–3567.

  2. N. Choudhury and B. M. Pettitt. Journal of Physical Chemistry B, 2005, 109, 6422–6429.

  3. N. Choudhury and B. M. Pettitt. Molecular Simulation, 2005, 31, 457–463.

  4. J. Kurzak and B. M. Pettitt. J. Comp. Phys., 2005, 203(2), 731–743.

  5. J. Kurzak and B. M. Pettitt. Journal of Parallel and Distributed Computing, 2005, 65, 870–881.

  6. Graham L. Randall and B. Montgomery Pettitt and Gregory R. Buck and E. Lynn Zechiedrich. J. Phys. Cond. Matter, 2005. In press.

CHE930004

  1. Y. Kwon and K. B. Whaley, J. Low Temp. Phys. 140, 227 (2005).

  2. F. Paesani, Y. Kwon, and K. B. Whaley, Phys. Rev. Lett. 94, 153401 (2005).

  3. F. Paesani, R. Zillich, Y. Kwon, and K. B. Whaley, J. Chem. Phys. 122, 181106 (2005).

  4. H. D. Whitley, P. Huang, Y. Kwon, and K. Whaley, J. Chem. Phys. 123, 054307 (2005).

  5. R. E. Zillich, F. Paesani, Y. Kwon, and K. B. Whaley, J. Chem. Phys. 123, 114301 (2005).

CHE860003

  1. D. Wang and A. Kuppermann, Int. J. Quantum Chem. 106, 152 (2006)

MCA94P017

  1. Ayton, G. S.; Voth, G. A., Multiscale simulation of membrane bound proteins. J. Struct. Biol. 2006, (submitted).

  2. Blood, P. D.; Ayton, G. S.; Voth, G. A., Probing the molecular-scale lipid bilayer response to shear flow using nonequilibrium molecular dynamics. J. Phys. Chem. B 2005, 109, (39), 18673-18679.

  3. Blood, P. D.; Voth, G. A., Direct observation of BAR domain-induced membrane curvature via molecular dynamics simulation. Proc. Natl. Acad. Sci. U. S. A. 2006, (submitted).

  4. Chang, R.; Ayton, G. S.; Voth, G. A., Multiscale coupling of mesoscopic- and atomistic-level lipid bilayer simulations. J. Chem. Phys. 2005, 122, (24), 224716.

  5. Chen, H.; Ilan, B.; Wu, Y.; Burnham, C. J.; Zhu, F.; Tajkhorshid, K.; Schulten, K.; Voth, G. A., Electrostatics and charge delocalization in proton channels. I. The aquaporin channels and proton blockage. Biophys. J. 2006, (submitted).

  6. Chen, H.; Wu, Y.; Voth, G. A., Origins of proton transport behavior from selectivity domain mutations of the aquaporin-1 channel. Biophys. J. 2006, 90, L73-L75.

  7. Chu, J. W.; Voth, G. A., Allostery of actin filaments: Molecular dynamics simulations and coarse-grained analysis. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, (37), 13111-13116.

  8. Iyengar, S. S.; Day, T. J. F.; Voth, G. A., On the amphiphilic behavior of the hydrated proton: an ab initio molecular dynamics study. Int. J. Mass Spec. 2005, 241, (2-3), 197-204.

  9. Iyengar, S. S.; Petersen, M. K.; Day, T. J. F.; Burnham, C. J.; Teige, V. E.; Voth, G. A., The properties of ion-water clusters. I. The protonated 21-water cluster. J. Chem. Phys. 2005, 123, (8), 084309.

  10. Izvekov, S.; Voth, G. A., Ab initio molecular-dynamics simulation of aqueous proton solvation and transport revisited. J. Chem. Phys. 2005, 123, (4), 044505.

  11. Izvekov, S.; Voth, G. A., Multiscale coarse-graining of liquid state systems. J. Chem. Phys. 2005, 123, 134105-134117.

  12. Izvekov, S.; Voth, G. A., A multiscale coarse-graining method for biomolecular systems. J. Phys. Chem. B 2005, 109, 2469-2473.

  13. Izvekov, S.; Voth, G. A., Effective force field for liquid hydrogen fluoride from ab initio molecular dynamics simulation using the force-matching method. J. Phys. Chem. B 2005, 109, (14), 6573-6586.

  14. Jeon, J. G.; Voth, G. A., The dynamic stress responses to area change in planar lipid bilayer membranes. Biophys. J. 2005, 88, (2), 1104-1119.

  15. Paramore, S.; Ayton, G. S.; Mirijanian, D. T.; Voth, G. A., Extending a spectrin repeat unit I. Linear force-extension response. Biophys. J. 2006, 90, 92-100.

  16. Paramore, S.; Ayton, G. S.; Voth, G. A., Extending a spectrin repeat unit II. Rupture behavior. Biophys. J. 2006, 90, 101-111.

  17. Tepper, H. L.; Voth, G. A., Protons may leak through pure lipid bilayers via a concerted mechanism. Biophys. J. 2005, 88, (5), 3095-3108.

  18. Wang, F.; Voth, G. A., A linear-scaling self-consistent generalization of the multistate empirical valence bond method for multiple excess protons in aqueous systems. J. Chem. Phys. 2005, 122, 144105.

  19. Wu, Y.; Ilan, B.; Voth, G. A., Charge delocalization in proton channels. II. The synthetic LS2 channel and proton selectivity. Biophys. J. 2006, (submitted).

  20. Wu, Y.; Voth, G. A., A computational study of the closed and open states of the influenza A M2 proton channel. Biophys. J 2005, 89, 2402-2411.

  21. Xu, J.; Voth, G. A., Computer simulation of explicit proton translocation in cytochrome c oxidase: the D-pathway. Proc. Natl. Acad. Sci. USA. 2005, 102, (19), 6795-800.

  22. Izvekov, S.; Voth, G. A., Multiscale coarse-graining of mixed phospholipid/cholesterol bilayers. J. Chem. Theor. Comp. 2006, 2, 637-648.

  23. Paramore, S.; Voth, G. A., Examining the influence of linkers and tertiary structure in the forced unfolding of multiple-repeat spectrin molecules. Biophys. J. 2006, Submitted.

  24. Shi, Q.; Izvekov, S.; Voth, G. A., Mixed atomistic and coarse-grained molecular dynamics simulation of a membrane bound ion channel. J. Phys. Chem. B 2006, (submitted).

  25. Shi, Q.; Voth, G. A., Multi-scale modeling of phase separation in mixed lipid bilayers. Biophys. J. 2005, 89, (4), 2385-2394.

  26. Wang, Y. T.; Izvekov, S.; Yan, T. Y.; Voth, G. A., Multiscale coarse-graining of ionic liquids. J. Phys. Chem. B 2006, 110, (8), 3564-3575.

  27. Wang, Y. T.; Voth, G. A., Unique spatial heterogeneity in ionic liquids. J. Am. Chem. Soc. 2005, 127, (35), 12192-12193.

  28. Wang, Y.; Voth, G. A., Spatial heterogeneity in ionic liquids. ACS Symp. Ser. Ionic Liquids 2006, (in press).

  29. Xu, J.; Voth, G. A., Free energy profiles for H+ conduction in the D-pathway of cytochrome c oxidase: a study of the wild type and N98D mutant enzymes. Biochim. Biophys. Acta. 2006, (in press).

  30. Yan, T.; Burnham, C. J.; Wang, Y.; Gao, X.; Voth, G. A., On the structure and dynamics of ionic liquids: Comparisons between a polarizable model and a non-polarizable model. 2006, (submitted).

  31. Zhou, J.; Izvekov, S.; Voth, G. A., Multiscale coarse-graining of peptides. I. Structure. J. Chem. Theor. Comp. 2006, (submitted).

MCA01S018

  1. O.S. ANDERSEN, R.E. KOEPPE 2nd and B. ROUX, ”Gramicidin channels”, IEEE Trans Nanobioscience 4, 10-20 (2005)

  2. V. M. Anisimov and G. Lamoureux and I.V. Vorobyov and N. Huang and B. Roux and A.D. MacKerell Jr. Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator. J Chem Theory Comp 1, 153–168 (2005).

  3. V.M. ANISIMOV, G. LAMOUREUX, I.V. VOROBYOV, N. HUANG, B. ROUX, and A. D. MACKERELL Jr., ”Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator” J. Chem. Theo. Comp. 1, 153-168 (2005).

  4. N.K. BANAVALI and B. ROUX, ”Free energy landscape of A-DNA to B-DNA conversion in aqueous solution”, j. Am. Chem. Soc. 127, 6866-6876 (2005).

  5. GILQUIN, S. BRAUD, M.A. ERIKSSON, B. ROUX, T.D. BAILEY, B.T. PRIEST, M.L. GARCIA, A. MENEZ A, and S. GASPARINI. ”A variable residue in the pore of Kv1 channels is critical for the high affinity of blockers from sea anemone and scorpions”, J. Biol. Chem. 280, 27093-27102 (2005).

  6. N.K. BANAVALI and B. ROUX, ”The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulation.” Structure 13, 1715-1723 (2005).

  7. N. K. Banavali, B. Roux, Free energy landscape of A-DNA to B-DNA conversion in aqueous solution, J. Am. Chem. Soc. 127 (2005) 6866–6876.

  8. N. K. Banavali, B. Roux, The N-terminal end of the catalytic domain of Src kinase Hck is a conformational switch implicated in long-range allosteric regulation, Structure 13 (2005) 1715–1723.

  9. S. BERNCHE and B. ROUX, ”A gate in the selectivity filter of potassium channels”, Structure (Camb) 13, 591-600 (2005).

  10. Baron Chanda, Osei Kwame Asamoah, Rikard Blunck, Benoˆıt Roux, and Francisco Bezanilla. Gating charge displacement in voltage-gated ion channels involves limited transmembrane movement. Nature, 436:852–856, 2005.

  11. CHANDA, O. K. ASAMOAH, R. BLUNCK, B. ROUX, F. BEZANILLA. ”Gating charge displacement in voltage-gated ion channels involves limited transmembrane movement”, Nature 436, 852-856 (2005).

  12. J. Cordero, L. Cuello, Y. Zhao, V. Jogini, D. M. Cortes, B. Roux and E. Perozo. “Molecular Determinants of Gating at the Potassium Channel Selectivity Filter” Nature Structural Biology (2006, in press).

  13. V. JOGININ and B. ROUX. ”Electrostatics of the intracellular vestibule of K+ channels.” J. Mol. Biol. 354, 272-288 (2005).

  14. KUTLUAY, B. ROUX, L. HEGINBOTHAM, ”Rapid intracellular TEA block of the KcsA potassium channel”, Biophys. J. 88, 1018-1029 (2005).

  15. P. LAGUE, B. ROUX and R.W. PASTOR. ”Molecular Dynamics Simulations of the Influenza Hemagglutinin Fusion Peptide in Micelles and Bilayers: Conformational Analysis of Peptide and Lipids”, J. Mol. Biol., (2005).

  16. G. Lamoureux, E. Harder, I. V. Vorobyov, B. Roux, A. D. MacKerell Jr. A polarizable model of water for molecular dynamics simulations of biomolecules Chem Phys Letters 2006, in press

  17. G. Lamoureux, B. Roux. Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field J Phys Chem B 2006, in press

  18. G. LAMOUREUX, E. HARDER. I. V. VOROBYOV, B. ROUX, A. D. MACkERELL JR. ”A polarizable model of water for molecular dynamics simulations of biomolecules” Chem. Phys. Letters. 418, 245 (2006).

  19. G. LAMOUREUX, B. ROUX. ”Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field” J. Phys. Chem. (2006, in press)

  20. S.Y. NOSKOV, G. LAMOUREUX, and B. ROUX. ”Molecular Dynamics Study of Hydration in Ethanol-Water Mixtures Using a Polarizable Force Field” J. Phys. Chem. B 109, 6705-6713 (2005).

  21. B. ROUX, ”Ion conduction and selectivity in K+ channels”, Ann. Rev. Biomol. Struc. Dyn. 34, 153-171 (2005).

  22. B. ROUX. ”The art of dissecting the function of a potassium channel”, Neuron 47, 777-778 (2005).

  23. H.-J. WOO and B. ROUX, ”Chemical Theory and Computation Special Feature: Calculation of absolute protein-ligand binding free energy from computer simulations”, Proc. Nat. Acad. Sci. USA 102, 6825-6830 (2005).

  24. H.-J. WOO and B. ROUX, ”Chemical Theory and Computation Special Feature: Calculation of absolute protein-ligand binding free energy from computer simulations”, Proc. Nat. Acad. Sci. USA 102, 6825-6830 (2005).

MCA04N010

  1. Thomas A. Manz, Andrew E. Fenwick, Khamphee Phomphrai, Ian P. Rothwell, Kendall T. Thomson, “The Nature of Aryloxide and Arylsulfide Ligand Bonding in Dimethyltitanium Complexes Containing Cyclopentadienyl Ligation,” Dalton Transactions (4): 668-674 (2005).
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