Publications
2012:
M. Heyden, J. A. Freites, M. B. Ulmschnieder, S. H. White, and D. J. Tobias, Proteins in biological membranes and how they get there, Soft Matter, accepted. [Invited Tutorial Review]
J. A. Freites, E. V. Schow, S. H. White, and D. J. Tobias, Microscopic origin of gating current fluctuations in a potassium channel voltage sensor, Biophys. J., accepted.
E. V. Schow, J. A. Freites, A. Nizkorodov, S. H. White, and D. J. Tobias, Coupling between the voltage-sensing and pore domains in a voltage-gated potassium channel, Biochim. Biophys. Acta - Biomembranes, accepted.
M. H. Cheng, K. M. Callahan, A. M. Margarella, D. J. Tobias, and J. C. Hemminger, Ambient pressure x-ray photoelectron spectroscopy and molecular dynamics simulation studies of liqid/vapor interfaces of aqueous NaCl, RbCl, and RbBr solutions, J. Phys. Chem. C 116, 4545-4555 (2012).
S. Funkner, G. Niehues, D. A. Schmidt, M. Heyden, K. M. Callahan, G. Schwaab, D. J. Tobias, and M. Havenith, Watching low frequency motions in aqueous salt solutions – the terahertz vibrational signatures of hydrated ions, J. Am. Chem. Soc. 134, 1030-1035 (2012).
P. J. Fleming, J. A. Freites, C. P. Moon, D. J. Tobias, and K. G. Fleming, Outer membrane phospholipase A in phospholipid bilayers: A model system for concerted computational and experimental investigations of amino acid side chain partitioning into lipid bilayers, Biochim. Biophys. Acta - Biomembranes 1818, 126-134 (2012).
M. L. Wood, E. V. Schow, J. A. Freites, S. H. White, F. Tombola, and D. J. Tobias, Water wires in atomistic models of the Hv1 proton channel, Biochim. Biophys. Acta - Biomembranes 1818, 286-293 (2012).
E. N. Spudich, G. Ozorowski, E. V. Schow, D. J. Tobias, J. L. Spudich, and H. Luecke, A transporter converted into a sensor, a phototaxis signaling mutant at 3.0 Å, J. Mol. Biol. 415, 455-463 (2012).
2011:
M. Heyden and D. J. Tobias, Hot and crowded: new insights into the dynamics of thermophilic enzymes from multiscale modeling, Biophys. J. 101, 2553-2554 (2011). [New & Notable commentary]
T. Lewis, B. Winter, A. C. Stern, M. D. Baer, C. J. Mundy, D. J. Tobias, and J. C. Hemminger, Does nitric acid dissociate at the aqueous solution interface?, J. Phys. Chem. C 115, 21183-21190 (2011). [Cover Article]
M. D. Baer, C. J. Mundy, M. J. McGrath, I.-F. W. Kuo, J. I. Siepmann, and D. J. Tobias, Re-examining the properties of the aqueous liquid-vapor interface using dispersion corrected density functional theory, J. Chem. Phys. 135, 124712 (2011).
T. Lewis, B. Winter, A. C. Stern, M. D. Baer, C. J. Mundy, D. J. Tobias, and J. C. Hemminger, Dissociation of strong acid revisited: x-ray photoelectron spectroscopy and molecular dynamics simulations of HNO3 in water, J. Phys. Chem. B 115, 9445-9451 (2011).
M. Andersson, J. A. Freites, D. J. Tobias, and S. H. White, Structural dynamics of the S4 voltage sensor helix in bilayers lacking lipid phosphates, J. Phys. Chem. B 115, 8732-8738 (2011).
N. K. Richards, L. M. Wingen, K. M. Callahan, N. Noshino, M. T. Kleinman, D. J. Tobias, and B. J. Finlayson-Pitts, Nitrate ion photolysis in thin water films in the presence of bromide ions, J. Phys. Chem. A, 115, 5810-5821 (2011).
M. Mihailescu, R. G. Vaswani, E. Jardón-Valadez, F. Castro-Román, J. A. Freites, D. L. Worcester, A. R. Chamberlin, D. J. Tobias, and S. H. White, Acyl-chain methyl distributions of liquid-ordered and -disordered membranes, Biophys. J. 100, 1455-1462 (2011).
W. D. Brubaker, J. A. Freites, K. J. Golchert, R. A. Shapiro, V. Morikis, D. J. Tobias, and R. W. Martin, Separating instability from aggregation propensity in gS-crystallin variants, Biophys. J. 100, 498-506 (2011).
A.-N. Bondar, T. Woolf, and D. J. Tobias, Festschrift in honor of Stephen H. White’s 70th Birthday, J. Membrane Biol. 239, 1-3 (2011).
E. V. Schow, J. A. Freites, P. Cheng, A. Bernsel, G. von Heijne, S. H. White, and D. J. Tobias, Arginine insertion in membranes: on the connection between molecular dynamics simulations and translocon-mediated insertion experiments, J. Membrane Biol. 239, 35-48 (2011).
2010:
E. Jardón-Valadez, A.-N. Bondar, and D. J. Tobias, Coupling of retinal, protein, and water dynamics in squid rhodopsin, Biophys. J. 99, 2200-2207 (2010).
K. M. Callahan, N. N. Casillas-Ituarte, M. Xu, M. Roeselová, H. C. Allen, and D. J. Tobias, The effect of magnesium cation on the interfacial properties of aqueous salt solutions, J. Phys. Chem. A 114, 8359-8368 (2010).
A.-N. Bondar, C. Munoz del Val, J. A. Freites, D. J. Tobias, and S. H. White, Dynamics of SecY translocons with translocation-defective mutations, Structure 18, 847-857 (2010). [Featured Article]
J. B. Klauda, R. M. Venable, J. A. Freites, J. W. O’Conner, D. J. Tobias, C. Mondragon-Ramirez, I. Vorobyov, A. D. MacKerell Jr., and R. W. Pastor, Update of the CHARMM all-atom additive force fields for lipids: validation on six lipid types, J. Phys. Chem. B 114, 7830-7843 (2010).
E. V. Schow, J. A. Freites, K. Gogna, S. H. White, and D. J. Tobias, Down-state model of the voltage-sensing domain of a potassium channel, Biophys. J. 98, 2857-2866 (2010).
K. M. Callahan, N. N. Casillas-Ituarte, M. Xu, M. Roeselová, H. C. Allen, and D. J. Tobias, Solvation of magnesium cation: molecular dynamics simulation and vibrational spectroscopic study of magnesium chloride in aqueous solutions, J. Phys. Chem. A 114, 5141-5148 (2010). [Cover Article]
N. N. Casillas-Ituarte, K. M. Callahan, C. Y. Tang, X. Chen, M. Roeselová, D. J. Tobias, and H. C. Allen, Surface organization of aqueous MgCl2 and application to atmospheric marine aerosol chemistry, Proc. Natl. Acad. Sci. USA 107, 6616-6621 (2010).
K. Wood, D. J. Tobias, B. Kessler, D. Oesterhelt, G. Zaccai, F. A. A. Mulder, and M. Weik, The low temperature inflection observed in neutron scattering measurements of proteins is due to methyl rotation: direct evidence using isotope labeling, J. Am. Chem. Soc. 132, 4990-4991 (2010).
C. W. Harmon, R. L. Grimm, T. M. McIntire, M. D. Petersen, B. Njegic, V. M. Angel, A. Alshawa, J. S. Underwood, D. J. Tobias, R. B. Gerber, M. S. Gordon, J. C. Hemminger, and S. A. Nizkorodov, Hygroscopic growth and deliquescence of NaCl particles mixed with surfactant SDS, J. Phys. Chem. B 114, 2435-2449 (2010).
R. L. Grimm, D. J. Tobias, and J. C. Hemminger, D2O water interaction with textured carboxylic acid terminated monolayer surfaces characterized by temperature programmed desorption and molecular dynamics, J. Phys. Chem. C 114, 1570-1579 (2010).
J. Heyda, J. Vincent, D. J. Tobias, J. Dzubiella, and P. Jungwirth, Ion specificity at the peptide bond: molecular dynamics simulations of N-methylacetamide in aqueous salt solutions, J. Phys. Chem. B 114, 1213-1220 (2010).
S. Sul, Y. Feng, U. Le, D. J. Tobias, and N.-H. Ge, Interactions of tyrosine in Leu-enkephalin at a membrane-water interface: an ultrafast 2D IR study combined with DFT and MD simulation, J. Phys. Chem. B 114, 1180-1190 (2010).
2009:
D. Krepkiy, M. Mihailescu, J. A. Freites, E. V. Schow, D. L. Worcester, K. Gawrisch, D. J. Tobias, S. H. White, and K. J. Swartz, Structure and hydration of membranes embedded with voltage-sensing domains, Nature 462, 473-479 (2009).
Y. Miller, J. L. Thomas, D. D. Kemp, B. J. Finlayson-Pitts, M. S. Gordon, D. J. Tobias, and R. B. Gerber, Structure of large nitrate-water clusters at ambient temperatures: simulations with effective fragment potentials and force fields with implications for atmospheric chemistry, J. Phys. Chem. A 113, 12805-12814 (2009).
C. J. Mundy, I.-F. W. Kuo, H.-S. Lee, M. E. Tuckerman, and D. J. Tobias, Hydroxide anion at the air-water interface, Chem. Phys. Lett. 481, 2-8 (2009). [Frontiers Article]
M. Valiev, R. D’Auria, D. J. Tobias, and B. C. Garrett, Interactions of Cl– and OH in aqueous solution, J. Phys. Chem. A 113, 8823-8825 (2009).
N. Sengupta, H. Maekawa, W. Zhuang, C. Toniolo, S. Mukamel, D. J. Tobias, and N.-H. Ge, Sensitivity of 2D IR spectra to peptide helicity: a concerted experimental and simulation study of an octapeptide, J. Phys. Chem. B 113, 12037-12049 (2009). [Cover Article]
D. J. Tobias, N. Sengupta, and M. Tarek, Molecular Dynamics Simulation Studies of Coupled Protein and Water Dynamics, in Proteins: Energy, Heat, and Signal Flow, eds. D. M. Leitner and J. E. Straub, Taylor and Francis/CRC Press, 361-386 (2009).
S. Jaud, M. Fernández-Vidal, I. Nilsson, N. M. Meindl-Beinker, N. Hübner, D. J. Tobias, G. von Heijne, and S. H. White, Insertion of transmembrane helices by the Sec61 translocon, Proc. Natl. Acad. Sci. USA 106, 11588-11593 (2009).
R. D’Auria and D. J. Tobias, On the relation between surface tension and ion adsorption at the air-water interface: a molecular dynamics simulation study, J. Phys. Chem. A 113, 7286-7293 (2009).
E. Jardón-Valadez, A. N. Bondar, and D. J. Tobias, Dynamics of internal water molecules in squid rhodopsin, Biophys. J. 96, 2572-2576 (2009).
D. J. Tobias, N. Sengupta, and M. Tarek, Hydration dynamics of purple membranes, Faraday Discuss. 141, 99-116 (2009).
M. Szöri, D. J. Tobias, and M. Roeselová, Microscopic wetting of mixed self-assembled monolayers: a molecular dynamics study, J. Phys. Chem. B 113, 4161-4169 (2009).
S. G. Moussa, T. M. McIntire, M. Szori, M. Roeselová, D. J. Tobias, R. L. Grimm, J. C. Hemminger, and B. J. Finlayson-Pitts, Experimental and theoretical characterization of water uptake on self-assembled monolayers: understanding the interaction of water with atmospherically relevant surfaces, J. Phys. Chem. A 113, 2060-2069 (2009).
2008:
M. Baer, G. Mathias, I-F. W. Kuo, D. J. Tobias, C. J. Mundy, and D. Marx, Spectral signatures of the pentagonal water cluster in bacteriorhodopsin, ChemPhysChem 9, 2703-2707 (2008).
L. M. Wingen, A. C. Moskun, S. N. Johnson, J. L. Thomas, M. Roeselová, D. J. Tobias, M. T. Kleinman, and B. J. Finlayson-Pitts, Enhanced photochemistry in chloride-nitrate ion mixtures, Phys. Chem. Chem. Phys. 10, 5668-5678 (2008). [Designated “Hot Article” by PCCP; Cover Article]
M. A. Brown, R. D’Auria, I.-F. W. Kuo, M. J. Krisch, D. E. Starr, K. Bluhm, D. J. Tobias, and J. C. Hemminger, Ion spatial distributions at the liquid-vapor interface of aqueous potassium fluoride solutions, Phys. Chem. Chem. Phys. 10, 4778-4784 (2008).
N. Sengupta, S. Jaud and D. J. Tobias, Hydration dynamics in a partially denatured ensemble of the globular protein human alpha-lactalbumin investigated with molecular dynamics simulations, Biophys. J. 95, 5257-5267 (2008).
D. J. Tobias and J. C. Hemminger, Getting specific about specific ion effects, Science 319, 1197-1198 (2008).
Y. Yu, M. J. Ezell, A. Zelenyuk, D. Imre, L. Alexander, J. Ortega, J. L. Thomas, K. Gogna, D. J. Tobias, B. D’Anna, C. Harmon, S. N. Johnson, and B. J. Finlayson-Pitts, A new pathway for oxidation of α-pinene through aqueous nitrate ion photochemistry, Phys. Chem. Chem. Phys. 10, 3063-3071 (2008).
K. Wood, A. Frölich, A. Paciaroni, M. Moulin, M. Härtlein, G. Zaccaï, D. J. Tobias, and M. Weik, Coincidence of hydration-water and soluble-protein dynamical transitions: direct measurements by neutron scattering and MD simulations, J. Am. Chem. Soc. 130, 4586-4587 (2008).
M. Tarek and D. J. Tobias, The role of protein-solvent hydrogen bond dynamics in the structural relaxation of a protein in glycerol versus in water, Eur. Biophys. J. 37, 701-709 (2008).
R. D’Auria, I.-F. W. Kuo, and D. J. Tobias, An ab initio molecular dynamics study of the solvated OHCl– complex: implications for the atmospheric oxidation of chloride ion to molecular chlorine, J. Phys. Chem. A 112, 4644-4650 (2008).
2007:
J. L. Thomas, D. J. Tobias, and A. D. MacKerell Jr., Direct comparisons of experimental and calculated neutron structure factors of pure solvents as a method for force field validation, J. Phys. Chem. B 111, 12941-12944 (2007).
K. Wood, M. Plazanet, F. Gabel, B. Kessler, D. Oesterhelt, D. J. Tobias, G. Zaccaï, and M. Weik, Coupling of protein and hydration-water dynamics in biological membranes, Proc. Natl. Acad. Sci. USA 104, 18049-18054 (2007).
M. J. Krisch, R. D’Auria, M. A. Brown, D. J. Tobias, J. C. Hemminger, M. Ammann, D. E. Starr, and H. Bluhm, The effect of an organic surfactant on the liquid-vapor interface of an electrolyte solution, J. Phys. Chem. C 111, 13497-13509 (2007).
J. L. Thomas, M. Roeselová, L. X. Dang, and D. J. Tobias, Molecular dynamics simulations of aqueous NaNO3 in interfacial environments, J. Phys. Chem. A 111, 3091-3098 (2007).
S. Jaud, D. J. Tobias, J. J. Falke, and S. H. White, Self-induced docking site of a deeply embedded peripheral membrane protein, Biophys. J. 92, 517-524 (2007) [Featured in Science Magazine’s Editor’s Choice].
2006:
J. A. Freites, D. J. Tobias, and S. H. White, A voltage sensor water pore, Biophys. J. 91, L90-L92 (2006).
F. Castro-Román, R. W. Benz, S. H. White, and D. J. Tobias, Investigation of finite system size effects in molecular dynamics simulations of lipid bilayers, J. Phys. Chem. B 110, 24157-24164 (2006).
R. W. Benz, H. Nanda, F. Castro-Roman, S. H. White, and D. J. Tobias, Diffraction based density restraints for membrane and membrane-peptide molecular dynamics simulations, Biophys. J. 91, 3617-3629 (2006).
J. E. Curtis, T. E. Dirama, G. A. Carri, and D. J. Tobias, Inertial suppression of protein dynamics in a binary glycerol-trehalose glass, J. Phys. Chem. B 110, 22953-22956 (2006).
P. Jungwirth, B. J. Finlayson-Pitts, D. J. Tobias, Introduction: structure and chemistry at aqueous interfaces, Chem. Rev. 106, 1137-1139 (2006).
P. Jungwirth and D. J. Tobias, Specific ion effects at the air/water interface, Chem. Rev. 106, 1259-1281 (2006).
L. X. Dang, T.-M. Chang, M. Roeselová, B. C. Garrett, and D. J. Tobias, On NO3––H2O interactions in aqueous solutions and at interfaces, J. Chem. Phys. 124, 066101 (2006).
M. Sprik, I. Siepmann, D. Tobias, M. Tuckerman, A tribute to Michael Klein, J. Phys. Chem. B 110, 3451-3453 (2006).
I.-F. W. Kuo, C. J. Mundy, B. L. Eggimann, M. J. McGrath, J. I. Siepmann, B. Chen, J. Vieceli, and D. J. Tobias, Structure and dynamics of the aqueous liquid-vapor interface: a comprehensive particle-based simulation study, J. Phys. Chem. B 110, 3738-3746 (2006).
M. Tarek and D. J. Tobias, Sub-nanosecond dynamics of proteins in solution: MD simulations and inelastic neutron scattering, in Neutrons in Biology, eds. T. Gutberlet, J. Fitter, and J. Katsaras, Springer-Verlag (2006).
2005:
J. A. Freites, D. J. Tobias, G. von Heijne, and S. H. White, Interface connections of a transmembrane voltage sensor, Proc. Natl. Acad. Sci. USA 102, 15059-15064 (2005).
J. Vieceli, M. Roeselova, N. Potter, L. X. Dang, B. C. Garrett, and D. J. Tobias, Molecular dynamics simulations of atmospheric oxidants at the air/water interface: solvation and accommodation of OH and O3, J. Phys. Chem. B 109, 15876-15892 (2005).
S. Gopalakrishnan, P. Jungwirth, D. J. Tobias, and H. C. Allen, Air-liquid interfaces of aqueous solutions containing ammonium and sulfate: spectroscopic and molecular dynamics studies, J. Phys. Chem. B 109, 8861-8872 (2005).
E. C. Brown, M. Mucha, P. Jungwirth, D. J. Tobias, Structure and vibrational spectroscopy of salt water/air interfaces: predictions from classical molecular dynamics simulations, J. Phys. Chem. B 109, 7934-7940 (2005).
M. Mucha, T. Frigato, L. Levering, H. C. Allen, D. J. Tobias, L. X. Dang, and P. Jungwirth, A unified molecular picture of the surfaces of aqueous acid, base, and salt solutions, J. Phys. Chem. B 109, 7617-7623 (2005).
S. Jaud, D. J. Tobias, and D. A. Brant, Molecular dynamics simulations of aqueous pullulan oligomers, Biomacromolecules 6, 1239-1251 (2005).
R. Benz, F. Castro-Roman, D. J. Tobias, and S. H. White, A new approach to experimental validation of molecular dynamics simulations of lipid bilayers, Biophys. J. 88, 805-817 (2005).
2004:
S. W. Hunt, M. Roeselova, W. Wang, L. M. Wingen, E. M. Knipping, D. J. Tobias, D. Dabdub, and B. J. Finlayson-Pitts, Formation of molecular bromine from the reaction of ozone with deliquesced NaBr aerosol: evidence for interface chemistry, J. Phys. Chem. A 108, 11559-11572 (2004).
Y. Dubowski, J. Vieceli, D. J. Tobias, A. Gomez, S. Nizkorodov, T. McIntire, and B. J. Finlayson-Pitts, Monitoring the oxidation of self-assembled monolayers in real time using ATR, J. Phys. Chem. A 108, 10473-10485 (2004).
M. Roeselova, J. S. Vieceli, L. X. Dang, B. C. Garrett, and D. J. Tobias, Hydroxyl radical at the air-water interface, J. Am. Chem. Soc. 126, 16308-16309 (2004).
J. Vieceli, M. Roeselova, and D. J. Tobias, Accommodation coefficients for water vapor at the air/water interface, Chem. Phys. Lett. 393, 249-255 (2004).
J. E. Curtis, M. Tarek, and D. J. Tobias, Methyl group dynamics as a probe of the protein dynamical transition, J. Am. Chem. Soc. 126, 15928-15929 (2004).
L. Vrbka, M. Mucha, B. Minofar, P. Jungwirth, E. C. Brown, and D. J. Tobias, Propensity of soft ions for the air/water interface, Curr. Opin. Coll. Int. Sci. 9, 67-73 (2004).
D. J. Tobias and J. A. Freites, Molecular Dynamics, in Encyclopedia of Nonlinear Dynamics, ed. A. Scott, Routledge, New York (2004).
J. Vieceli, O. L. Ma, and D. J. Tobias, Uptake and collision dynamics of gas phase ozone at unsaturated organic surfaces, J. Phys. Chem. A 108, 5806-5814 (2004).
2003:
M. Roeselova, P. Jungwirth, D. J. Tobias, and R. B. Gerber, Impact, trapping, and accommodation of hydroxyl radical and ozone at salt aerosol surfaces: a molecular dynamics study, J. Phys. Chem. B 107, 12690-12699 (2003).
P. Salvador, J. E. Curtis, D. J. Tobias, and P. Jungwirth, Polarizability of the nitrate anion and its solvation at the air/water interface, Phys. Chem. Chem. Phys. 5, 3572-3577 (2003).
M. Tarek, D. A. Neumann, and D. J. Tobias, Characterization of sub-nanosecond dynamics of the molten globule state of a-lactalbumin using quasielastic neutron scattering and molecular dynamics simulations, Chem. Phys. 292, 435-443 (2003).
P. Jungwirth, J. E. Curtis, and D. J. Tobias, Polarizability and aqueous solvation of sulfate dianion, Chem. Phys. Lett. 367, 704-710 (2003).
D. J. Tobias, I. W. Kuo, A. Razmara, and M. Tarek, Protein Hydration Water, in Water in Confining Geometries, eds. J. P. Devlin and V. Buch, Springer-Verlag, pp. 213-225 (2003).
J. A. Freites, Y. Choi, and D. J. Tobias, Molecular dynamics simulation of a pulmonary surfactant protein B peptide in a lipid monolayer, Biophys. J. 84, 2169-2180 (2003).
2002:
M. Tarek and D. J. Tobias, Single particle and collective dynamics of protein hydration water: a molecular dynamics study, Phys. Rev. Lett. 89, art. no. 275501 (2002).
I. Kuo and D. J. Tobias, Thermal fluctuations of the unusually stable and symmetric superoxide tetrahydrate complex: an ab initio molecular dynamics study, J. Phys. Chem. A 105, 10969-10976 (2002).
C. E. Nordgren, D. J. Tobias, M. L. Klein, and J. K. Blasie, MD Simulations of a hydrated protein vectorially-oriented on polar and nonpolar soft surfaces, Biophys. J. 83, 2906-2917 (2002).
P. Jungwirth and D. J. Tobias, Ions at the air-water interface, J. Phys. Chem. B 106, 6361-6373 (2002).
M. Tarek and D. J. Tobias, The role of protein-water hydrogen bond dynamics in the protein dynamical transition, Phys. Rev. Lett. 88, art. no. 138101 (2002).
P. Jungwirth and D. J. Tobias, Chloride ion on aqueous clusters, at the air-water interface, and in liquid water: solvent effects on Cl– polarizability, J. Phys. Chem. A 106, 379-383 (2002).
2001:
P. Jungwirth and D. J. Tobias, The molecular structure of salt solutions: a new view of the interface with implications for heterogeneous atmospheric chemistry, J. Phys. Chem. B 105, 10468-10472 (2001).
M. Tarek, D. J. Tobias, S.-H. Chen, and M. L. Klein, Short wavelength collective dynamics in phospholipid bilayers: a molecular dynamics study, Phys. Rev. Lett. 87, art. no. 238101 (2001).
D. J. Tobias, Electrostatics calculations: recent methodological advances and applications to membranes, Current Opin. Struct. Biol. 11, 253-261 (2001).
M. Tarek and D. J. Tobias, Effects of solvent damping on side chain and backbone contributions to the protein boson peak, J. Chem. Phys., 115, 1607-1612 (2001).
I. Kuo and D. J. Tobias, Electronic polarization and hydration of the dimethylphosphate anion: an ab initio molecular dynamics study, J. Phys. Chem. B, 105, 5827-5832 (2001).
D. J. Tobias, P. Jungwirth, and M. Parrinello, Surface solvation of halogen anions in water clusters: an ab initio molecular dynamics study of the Cl–(H2O)6 complex, J. Chem. Phys. 114, 7036-7044 (2001).
D. J. Tobias, Membrane Simulations, in Computational biochemistry and biophysics, eds. O. M. Becker, A. D. MacKerell, Jr., B. Roux, and M. Watanabe. Marcel Dekker, New York, pp. 465-496 (2001).
2000:
M. Tarek, G. J. Martyna, and D. J. Tobias, Amplitudes and frequencies of protein dynamics: an analysis of discrepancies between neutron scattering and molecular dynamics simulations, J. Am. Chem. Soc. 122, 10450-10451 (2000).
C. F. Majkrzak, N. F. Berk, S. Krueger, J. A. Dura, M. Tarek, D. Tobias, V. Silin, C. W. Meuse, J. Woodward, and A. L. Plant, First-principles determination of hybrid bilayer membrane structure by phase sensitive neutron reflectometry, Biophys. J. 79, 3330-3340 (2000).
Y. Wadia, D. J. Tobias, R. Stafford, and B. J. Finlayson-Pitts, Real-time monitoring of the kinetics and gas phase products of the reaction of ozone with an unsaturated phospholipid at the air-water interface, Langmuir 16, 9321-9330 (2000).
M. Tarek and D. J. Tobias, The dynamics of protein hydration water: a quantitative comparison of molecular dynamics simulations and incoherent neutron scattering experiments, Biophys. J. 79, 3244-3257 (2000).
P. Jungwirth and D. J. Tobias, Surface effects on aqueous ionic solvation: a molecular dynamics study of NaCl at the air/water interface from infinite dilution to saturation, J. Phys. Chem. B 104, 7702-7706 (2000).
E. Knipping, M. J. Lakin, K. L. Foster, P. Jungwirth, D. J. Tobias, R. B. Gerber, D. Dabdub, and B. J. Finlayson-Pitts, Experiments and simulations of ion-enhanced interfacial chemistry on aqueous NaCl aerosols, Science 288, 301-306 (2000).
1999:
M. Tarek and D. J. Tobias, Environmental dependence of the dynamics of protein hydration water, J. Am. Chem. Soc. 121, 9740-9741 (1999).
M. Tarek, K. Tu, M. L. Klein, and D. J. Tobias, Molecular dynamics simulations of supported phospholipid/alkanethiol bilayers on a gold(111) surface, Biophys. J. 77, 964-972 (1999).
D. J. Tobias, A workshop on MD simulations, in Hydration processes in biology: theoretical and experimental approaches, ed. M. C. Bellissent-Funel, IOS Press, Amsterdam, pp. 387-409 (1999).
D. J. Tobias, Water and membranes: molecular details from MD simulations, in Hydration processes in biology: theoretical and experimental approaches, ed. M. C. Bellissent-Funel, IOS Press, Amsterdam, pp. 293-310 (1999).
1998:
K. Tu, M. L. Klein, and D. J. Tobias, Constant pressure molecular dynamics investigation of cholesterol effects in a dipalmitoylphosphatidylcholine bilayer, Biophys. J. 75, 2147-2156 (1998).
R. H. Lathrop, M. Casale, D. J. Tobias, J. L. Marsh, and L. M. Thompson, Modeling protein homopolymeric repeats: possible polyglutamine structural motifs for Huntington's disease, in Proc. Intl. Conf. on Intelligent Systems for Molecular Biology, eds. J. Glasgow et al., AAAI Press, Menlo Park (1998).
1997:
D. J. Tobias, K. Tu, and M. L. Klein, Assessment of all-atom potentials for modeling membranes: molecular dynamics simulations of solid and liquid alkanes and crystals of phospholipid fragments, J. Chim. Phys. Phys.-Chim. Biol. 94, 1482-1502 (1997).
S. Samuelson, D. J. Tobias, and G. J. Martyna, Modern computational methodology applied to the simulation of blocked alanine tripeptide in vacuum, water, clusters, and bulk water, J. Phys. Chem. 101, 7592-7603 (1997).
D. J. Tobias, K. Tu, and M. L. Klein, Atomic-scale molecular dynamics simulations of lipid membranes, Curr. Opin. Coll. Int. Sci. 2, 15-26 (1997).
1996:
D. J. Tobias, W. Mar, J. K. Blasie, and M. L. Klein, Molecular dynamics simulations of a protein on hydrophobic and hydrophilic surfaces, Biophys. J. 71, 2933-2941 (1996).
D. J. Tobias and M. L. Klein, Molecular dynamics investigation of the lamellar liquid crystal D-phase in the octylammonium chloride/water system, Mol. Sim. 16, 219-228 (1996).
G. J. Martyna, M. E. Tuckerman, D. J. Tobias, and M. L. Klein, Explicit reversible integrators for extended systems dynamics, Mol. Phys. 87, 1117-1157 (1996).
D. J. Tobias and M. L. Klein, Molecular dynamics simulations of a calcium carbonate/calcium sulfonate reversed micelle in solution, J. Phys. Chem. 100, 6637-6648 (1996).
M. Tarek, D. J. Tobias, and M. L. Klein, Molecular dynamics investigation of the surface-bulk equilibrium in an ethanol/water solution, J. Chem. Soc., Faraday Trans. 92, 559-563 (1996).
D. J. Tobias, K. Tu, and M. L. Klein, Molecular dynamics simulations of lipid bilayers, in Monte Carlo and molecular dynamics of condensed matter systems, K. Binder and G. Ciccotti, Eds., SIF, Bologna (1996).
K. Tu, D. J. Tobias, J. K. Blasie, and M. L. Klein, Molecular dynamics investigation of the structure of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer, Biophys. J. 70, 595-608 (1996).
M. Tarek, D. J. Tobias, and M. L. Klein, Molecular dynamics investigation of an ethanol/water solution, Physica A 231, 117-122 (1996).
1995:
D. J. Tobias, J. Gesell, M. L. Klein, and S. J. Opella, A simple protocol for identification of helical and mobile residues in membrane proteins, J. Mol. Biol. 253, 391-395 (1995).
M. Tarek, D. J. Tobias,and M. L. Klein, Molecular dynamics simulations of tetradecyltrimethylammonium bromide monolayers at the air/water interface, J. Phys. Chem. 99, 1393-1402 (1995).
K. Tu, D. J. Tobias, and M. L. Klein, Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholinebilayer, Biophys. J. 69, 2558-2562 (1995).
K. Tu, D. J. Tobias, and M. L. Klein, Constant pressure and temperature molecular dynamics simulation of crystals of the lecithin fragments: glycerylphosphorylcholine and dilauroylglycerol, J. Phys. Chem. 99, 10035-10042 (1995).
1994:
G. J. Martyna, D. J. Tobias, and M. L. Klein, Constant pressure molecular dynamics algorithms, J. Chem. Phys. 101, 4177-4189 (1994).
D. J. Tobias, G. J. Martyna, and M. L. Klein, Molecular dynamics simulations of a protein in the canonical ensemble, J. Phys. Chem. 97, 12959-12966 (1994).
1993:
D. J. Tobias, M. L. Klein, and S. J. Opella, Molecular dynamics simulation of Pf1 coat protein, Biophys. J. 64, 670-675 (1993).
M. Karpen, D. J. Tobias, and C. L. Brooks III, Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV, Biochemistry 32, 412-420 (1993).
1992:
S. F. Sneddon and D. J. Tobias, The role of packing interactions in stabilizing folded proteins, Biochemistry 31, 2842-2846 (1992).
D. J. Tobias, S. F. Sneddon, and C. L. Brooks III, Stability of a model beta-sheet in water, J. Mol. Biol. 227, 1244-1252 (1992).
D. J. Tobias and C. L. Brooks III, Conformational equilibria in the alanine dipeptide in the gas phase and aqueous solution: a comparison of theoretical results, J. Phys. Chem. 96, 3864-3870, (1992).
1991:
T. Lazaridus, D. J. Tobias, C. L. Brooks III, and M. Paulaitis, Reaction paths and free energy profiles for conformational transitions: an internal coordinate approach, J. Chem. Phys. 95, 7612-7625 (1991).
C. L. Brooks III, W. S. Young, and D. J. Tobias, Molecular dynamics on supercomputers, Int. J. Supercomp. Appl. 5, 98-112 (1991).
J. E. Mertz, D. J. Tobias, C. L. Brooks III, and U. C. Singh, Vector and parallel algorithms for molecular dynamics simulations of macromolecules on shared memory computers, J. Comp. Chem. 12, 1270-1277 (1991).
D. J. Tobias, S. F. Sneddon, and C. L. Brooks III, The stability of protein secondary structures in aqueous solution, in Advances in biomolecular simulations, 174-199, American Institute of Physics, New York (1991).
D. J. Tobias and C. L. Brooks III, Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides, Biochemistry 30, 6059-6070 (1991).
D. J. Tobias, J. E. Mertz, and C. L. Brooks III, Nanosecond folding dynamics of a pentapeptide in water, Biochemistry 30, 6054-6058 (1991).
1990:
D. J. Tobias, S. F. Sneddon, and C. L. Brooks III, Reverse turns in blocked dipeptides are intrinsically unstable in water, J. Mol. Biol. 216, 783-796 (1990).
D. J. Tobias and C. L. Brooks III, Thermodynamics of solvophobic effects: a molecular dynamics study of n-butane in carbon tetrachloride and water, J. Chem. Phys. 92, 2582-2592 (1990).
1989:
S. F. Sneddon, D. J. Tobias, and C. L. Brooks III, Thermodynamics of amide hydrogen bond formation in polar and apolar solvents, J. Mol. Biol. 209, 817-820 (1989).
D. J. Tobias, C. L. Brooks III, and S. H. Fleischman, Conformational flexibility in free energy simulations, Chem. Phys. Lett. 156, 256-260 (1989).
1988:
D. J. Tobias and C. L. Brooks III, Molecular dynamics with internal coordinate constraints, J. Chem. Phys. 89, 5115-5127 (1988).
1987:
D. J. Tobias and C. L. Brooks III, Calculation of free energy surfaces using the methods of thermodynamic perturbation theory, Chem. Phys. Lett. 142, 472-476 (1987).