Douglas James Tobias - Publications

Affiliations: 
Chemistry University of California, Irvine, Irvine, CA 
Area:
Theoretical and Computational Chemistry
Website:
http://www.faculty.uci.edu/profile.cfm?faculty_id=4581

137 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Wong EK, Prytkova V, Freites JA, Butts CT, Tobias DJ. Molecular mechanism of aggregation of the cataract-related γD-crystallin W42R variant from multiscale atomistic simulations. Biochemistry. PMID 31393108 DOI: 10.1021/acs.biochem.9b00208  0.48
2019 Tronin AY, Maciunas LJ, Grasty KC, Loll PJ, Ambaye HA, Parizzi AA, Lauter V, Geragotelis AD, Freites JA, Tobias DJ, Blasie JK. Voltage-Dependent Profile Structures of a Kv-Channel via Time-Resolved Neutron Interferometry. Biophysical Journal. PMID 31378315 DOI: 10.1016/j.bpj.2019.07.011  0.56
2019 Hall JE, Freites JA, Tobias DJ. Experimental and Simulation Studies of Aquaporin 0 Water Permeability and Regulation. Chemical Reviews. PMID 31026155 DOI: 10.1021/acs.chemrev.9b00106  0.48
2019 Freites JA, Németh-Cahalan KL, Hall JE, Tobias DJ. Cooperativity and allostery in aquaporin 0 regulation by Ca. Biochimica Et Biophysica Acta. Biomembranes. PMID 30802427 DOI: 10.1016/j.bbamem.2019.02.007  0.48
2019 Majumdar BB, Prytkova V, Wong EK, Freites JA, Tobias DJ, Heyden M. The role of conformational flexibility in Monte Carlo simulations of many-protein systems. Journal of Chemical Theory and Computation. PMID 30633517 DOI: 10.1021/acs.jctc.8b00894  0.48
2018 Capponi S, White SH, Tobias DJ, Heyden M. Structural Relaxation Processes and Collective Dynamics of Water in Biomolecular Environments. The Journal of Physical Chemistry. B. PMID 30566356 DOI: 10.1021/acs.jpcb.8b12052  0.56
2018 Allen HC, Tobias DJ. Preface: Special Topic on Ions in Water. The Journal of Chemical Physics. 148: 222501. PMID 29907038 DOI: 10.1063/1.5039655  0.48
2018 Kyrychenko A, Lim NM, Vasquez-Montes V, Rodnin MV, Freites JA, Nguyen LP, Tobias DJ, Mobley DL, Ladokhin AS. Refining Protein Penetration into the Lipid Bilayer Using Fluorescence Quenching and Molecular Dynamics Simulations: The Case of Diphtheria Toxin Translocation Domain. The Journal of Membrane Biology. PMID 29550876 DOI: 10.1007/s00232-018-0030-2  0.48
2017 Perrine KA, Parry KM, Stern AC, Van Spyk MHC, Makowski MJ, Freites JA, Winter B, Tobias DJ, Hemminger JC. Specific cation effects at aqueous solution-vapor interfaces: Surfactant-like behavior of Li(+) revealed by experiments and simulations. Proceedings of the National Academy of Sciences of the United States of America. PMID 29078311 DOI: 10.1073/pnas.1707540114  0.48
2017 Olivieri G, Parry KM, D'Auria R, Tobias DJ, Brown MA. Specific Anion Effects on Na+ adsorption at the aqueous solution-air interface: MD Simulations, SESSA Calculations and Photoelectron Spectroscopy Experiments. The Journal of Physical Chemistry. B. PMID 29072463 DOI: 10.1021/acs.jpcb.7b06981  0.32
2017 Karabadzhak AG, Petti LM, Barrera FN, Edwards APB, Moya-Rodríguez A, Polikanov YS, Freites JA, Tobias DJ, Engelman DM, DiMaio D. Two transmembrane dimers of the bovine papillomavirus E5 oncoprotein clamp the PDGF β receptor in an active dimeric conformation. Proceedings of the National Academy of Sciences of the United States of America. PMID 28808001 DOI: 10.1073/pnas.1705622114  0.48
2017 Götte L, Parry KM, Hua W, Verreault D, Allen HC, Tobias DJ. Solvent-Shared Ion Pairs at the Air-Solution Interface of Magnesium Chloride and Sulfate Solutions Revealed by Sum Frequency Spectroscopy and Molecular Dynamics Simulation. The Journal of Physical Chemistry. A. PMID 28758749 DOI: 10.1021/acs.jpca.7b05600  0.48
2017 Ulmschneider MB, Ulmschneider JP, Freites JA, von Heijne G, Tobias DJ, White SH. Transmembrane helices containing a charged arginine are thermodynamically stable. European Biophysics Journal : Ebj. PMID 28409218 DOI: 10.1007/s00249-017-1206-x  0.56
2017 Starek G, Freites JA, Bernèche S, Tobias DJ. Gating energetics of a voltage-dependent K(+) channel pore domain. Journal of Computational Chemistry. PMID 28211063 DOI: 10.1002/jcc.24742  0.48
2017 Olivieri G, Parry KM, Powell CJ, Tobias DJ, Brown MA. Simulated photoelectron intensities at the aqueous solution-air interface for flat and cylindrical (microjet) geometries. Physical Chemistry Chemical Physics : Pccp. PMID 28203664 DOI: 10.1039/c6cp07539h  0.32
2017 Wood ML, Freites JA, Tombola F, Tobias DJ. Atomistic Modeling of Ion Conduction Through the Voltage-Sensing Domain of the Shaker K(+) Ion Channel. The Journal of Physical Chemistry. B. PMID 28074656 DOI: 10.1021/acs.jpcb.6b12639  0.48
2016 Fields JB, Németh-Cahalan KL, Freites JA, Vorontsova I, Hall JE, Tobias DJ. Calmodulin Gates Aquaporin 0 Permeability through a Positively Charged Cytoplasmic Loop. The Journal of Biological Chemistry. PMID 27660387 DOI: 10.1074/jbc.M116.743724  0.48
2016 Olivieri G, Parry KM, Powell CJ, Tobias DJ, Brown MA. Quantitative interpretation of molecular dynamics simulations for X-ray photoelectron spectroscopy of aqueous solutions. The Journal of Chemical Physics. 144: 154704. PMID 27389231 DOI: 10.1063/1.4947027  0.32
2016 Prytkova V, Heyden M, Khago D, Freites JA, Butts CT, Martin RW, Tobias DJ. Multi-Conformation Monte Carlo: A Method for Introducing Flexibility in Efficient Simulations of Many-Protein Systems. The Journal of Physical Chemistry. B. PMID 27063730 DOI: 10.1021/acs.jpcb.6b00827  0.48
2015 Capponi S, Freites JA, Tobias DJ, White SH. Interleaflet mixing and coupling in liquid-disordered phospholipid bilayers. Biochimica Et Biophysica Acta. PMID 26657692 DOI: 10.1016/j.bbamem.2015.11.024  0.92
2015 Fields JB, Hollingsworth SA, Chreifi G, Heyden M, Arce AP, Magana-Garcia HI, Poulos TL, Tobias DJ. "Bind and Crawl" Association Mechanism of Leishmania major Peroxidase and Cytochrome c Revealed by Brownian and Molecular Dynamics Simulations. Biochemistry. PMID 26598276 DOI: 10.1021/acs.biochem.5b00569  1
2015 Khago D, Wong EK, Kingsley CN, Alfredo Freites J, Tobias DJ, Martin RW. Increased hydrophobic surface exposure in the cataract-related G18V variant of human γS-crystallin. Biochimica Et Biophysica Acta. PMID 26459004 DOI: 10.1016/j.bbagen.2015.09.022  1
2015 Fichou Y, Heyden M, Zaccai G, Weik M, Tobias DJ. Molecular Dynamics Simulations of a Powder Model of the Intrinsically Disordered Protein Tau. The Journal of Physical Chemistry. B. 119: 12580-9. PMID 26351734 DOI: 10.1021/acs.jpcb.5b05849  1
2015 Capponi S, Heyden M, Bondar AN, Tobias DJ, White SH. Anomalous behavior of water inside the SecY translocon. Proceedings of the National Academy of Sciences of the United States of America. 112: 9016-21. PMID 26139523 DOI: 10.1073/pnas.1424483112  1
2015 Freites JA, Tobias DJ. Voltage Sensing in Membranes: From Macroscopic Currents to Molecular Motions. The Journal of Membrane Biology. 248: 419-30. PMID 25972106 DOI: 10.1007/s00232-015-9805-x  1
2015 Fichou Y, Schirò G, Gallat FX, Laguri C, Moulin M, Combet J, Zamponi M, Härtlein M, Picart C, Mossou E, Lortat-Jacob H, Colletier JP, Tobias DJ, Weik M. Hydration water mobility is enhanced around tau amyloid fibers. Proceedings of the National Academy of Sciences of the United States of America. 112: 6365-70. PMID 25918405 DOI: 10.1073/pnas.1422824112  1
2015 Schirò G, Fichou Y, Gallat FX, Wood K, Gabel F, Moulin M, Härtlein M, Heyden M, Colletier JP, Orecchini A, Paciaroni A, Wuttke J, Tobias DJ, Weik M. Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins. Nature Communications. 6: 6490. PMID 25774711 DOI: 10.1038/ncomms7490  1
2015 Amcheslavsky A, Wood ML, Yeromin AV, Parker I, Freites JA, Tobias DJ, Cahalan MD. Molecular biophysics of Orai store-operated Ca2+ channels. Biophysical Journal. 108: 237-46. PMID 25606672 DOI: 10.1016/j.bpj.2014.11.3473  1
2015 Jungwirth P, Tobias DJ. A comment on "pH and the surface tension of water" (J. K. Beattie, A. M. Djerdjev, A. Gray-Weale, N. Kallay, J. Lützenkirchen, T. Preočanin, A. Selmani, J. Colloid Interface Sci. 422 (2014) 54.). Journal of Colloid and Interface Science. 448: 593. PMID 25442714 DOI: 10.1016/j.jcis.2014.09.054  1
2015 Vincent JC, Matt SM, Rankin BM, D'Auria R, Freites JA, Ben-Amotz D, Tobias DJ. Specific ion interactions with aromatic rings in aqueous solutions: Comparison of molecular dynamics simulations with a thermodynamic solute partitioning model and Raman spectroscopy Chemical Physics Letters. 638: 1-8. DOI: 10.1016/j.cplett.2015.06.061  1
2014 Conti Nibali V, D'Angelo G, Paciaroni A, Tobias DJ, Tarek M. On the Coupling between the Collective Dynamics of Proteins and Their Hydration Water. The Journal of Physical Chemistry Letters. 5: 1181-6. PMID 26274468 DOI: 10.1021/jz500023e  1
2014 Jardón-Valadez E, Bondar AN, Tobias DJ. Electrostatic interactions and hydrogen bond dynamics in chloride pumping by halorhodopsin. Biochimica Et Biophysica Acta. 1837: 1964-72. PMID 25256652 DOI: 10.1016/j.bbabio.2014.09.006  1
2014 Baer MD, Kuo IF, Tobias DJ, Mundy CJ. Toward a unified picture of the water self-ions at the air-water interface: a density functional theory perspective. The Journal of Physical Chemistry. B. 118: 8364-72. PMID 24762096 DOI: 10.1021/jp501854h  1
2014 Tronin AY, Nordgren CE, Strzalka JW, Kuzmenko I, Worcester DL, Lauter V, Freites JA, Tobias DJ, Blasie JK. Direct evidence of conformational changes associated with voltage gating in a voltage sensor protein by time-resolved X-ray/neutron interferometry. Langmuir : the Acs Journal of Surfaces and Colloids. 30: 4784-96. PMID 24697545 DOI: 10.1021/la500560w  1
2014 Kyrychenko A, Freites JA, He J, Tobias DJ, Wimley WC, Ladokhin AS. Structural plasticity in the topology of the membrane-interacting domain of HIV-1 gp41. Biophysical Journal. 106: 610-20. PMID 24507601 DOI: 10.1016/j.bpj.2013.12.032  1
2014 Nishino N, Hollingsworth SA, Stern AC, Roeselová M, Tobias DJ, Finlayson-Pitts BJ. Interactions of gaseous HNO3 and water with individual and mixed alkyl self-assembled monolayers at room temperature. Physical Chemistry Chemical Physics : Pccp. 16: 2358-67. PMID 24352159 DOI: 10.1039/c3cp54118e  1
2014 Baer MD, Tobias DJ, Mundy CJ. Investigation of interfacial and bulk dissociation of HBr, HCl, and HNO3 using density functional theory-based molecular dynamics simulations Journal of Physical Chemistry C. 118: 29412-29420. DOI: 10.1021/jp5062896  1
2013 Heyden M, Tobias DJ. Spatial dependence of protein-water collective hydrogen-bond dynamics. Physical Review Letters. 111: 218101. PMID 24313531 DOI: 10.1103/PhysRevLett.111.218101  1
2013 Richards-Henderson NK, Callahan KM, Nissenson P, Nishino N, Tobias DJ, Finlayson-Pitts BJ. Production of gas phase NO2 and halogens from the photolysis of thin water films containing nitrate, chloride and bromide ions at room temperature. Physical Chemistry Chemical Physics : Pccp. 15: 17636-46. PMID 24042539 DOI: 10.1039/c3cp52956h  1
2013 Reichow SL, Clemens DM, Freites JA, Németh-Cahalan KL, Heyden M, Tobias DJ, Hall JE, Gonen T. Allosteric mechanism of water-channel gating by Ca2+-calmodulin. Nature Structural & Molecular Biology. 20: 1085-92. PMID 23893133 DOI: 10.1038/nsmb.2630  1
2013 Stern AC, Baer MD, Mundy CJ, Tobias DJ. Thermodynamics of iodide adsorption at the instantaneous air-water interface. The Journal of Chemical Physics. 138: 114709. PMID 23534655 DOI: 10.1063/1.4794688  1
2013 Kyrychenko A, Tobias DJ, Ladokhin AS. Validation of depth-dependent fluorescence quenching in membranes by molecular dynamics simulation of tryptophan octyl ester in POPC bilayer. The Journal of Physical Chemistry. B. 117: 4770-8. PMID 23528135 DOI: 10.1021/jp310638f  1
2013 Tobias DJ, Stern AC, Baer MD, Levin Y, Mundy CJ. Simulation and theory of ions at atmospherically relevant aqueous liquid-air interfaces. Annual Review of Physical Chemistry. 64: 339-59. PMID 23331311 DOI: 10.1146/annurev-physchem-040412-110049  1
2013 Moussa SG, Stern AC, Raff JD, Dilbeck CW, Tobias DJ, Finlayson-Pitts BJ. Experimental and theoretical studies of the interaction of gas phase nitric acid and water with a self-assembled monolayer. Physical Chemistry Chemical Physics : Pccp. 15: 448-58. PMID 23160633 DOI: 10.1039/c2cp42405c  1
2012 Baer MD, Stern AC, Levin Y, Tobias DJ, Mundy CJ. Electrochemical Surface Potential Due to Classical Point Charge Models Drives Anion Adsorption to the Air-Water Interface. The Journal of Physical Chemistry Letters. 3: 1565-70. PMID 26285639 DOI: 10.1021/jz300302t  1
2012 Heyden M, Freites JA, Ulmschneider MB, White SH, Tobias DJ. Assembly and Stability of α-Helical Membrane Proteins. Soft Matter. 8: 7742-7752. PMID 23166562 DOI: 10.1039/C2SM25402F  1
2012 Andersson M, Bondar AN, Freites JA, Tobias DJ, Kaback HR, White SH. Proton-coupled dynamics in lactose permease. Structure (London, England : 1993). 20: 1893-904. PMID 23000385 DOI: 10.1016/j.str.2012.08.021  1
2012 MacMillan AC, McIntire TM, Freites JA, Tobias DJ, Nizkorodov SA. Interaction of water vapor with the surfaces of imidazolium-based ionic liquid nanoparticles and thin films. The Journal of Physical Chemistry. B. 116: 11255-65. PMID 22900634 DOI: 10.1021/jp305029n  1
2012 Freites JA, Schow EV, White SH, Tobias DJ. Microscopic origin of gating current fluctuations in a potassium channel voltage sensor. Biophysical Journal. 102: L44-6. PMID 22713585 DOI: 10.1016/j.bpj.2012.04.021  1
2012 Gupta S, Dura JA, Freites JA, Tobias DJ, Blasie JK. Structural characterization of the voltage-sensor domain and voltage-gated K+-channel proteins vectorially oriented within a single bilayer membrane at the solid/vapor and solid/liquid interfaces via neutron interferometry. Langmuir : the Acs Journal of Surfaces and Colloids. 28: 10504-20. PMID 22686684 DOI: 10.1021/la301219z  1
2012 Schow EV, Freites JA, Nizkorodov A, White SH, Tobias DJ. Coupling between the voltage-sensing and pore domains in a voltage-gated potassium channel. Biochimica Et Biophysica Acta. 1818: 1726-36. PMID 22425907 DOI: 10.1016/j.bbamem.2012.02.029  1
2012 Funkner S, Niehues G, Schmidt DA, Heyden M, Schwaab G, Callahan KM, Tobias DJ, Havenith M. Watching the low-frequency motions in aqueous salt solutions: the terahertz vibrational signatures of hydrated ions. Journal of the American Chemical Society. 134: 1030-5. PMID 22124334 DOI: 10.1021/ja207929u  1
2012 Spudich EN, Ozorowski G, Schow EV, Tobias DJ, Spudich JL, Luecke H. A transporter converted into a sensor, a phototaxis signaling mutant of bacteriorhodopsin at 3.0 Å. Journal of Molecular Biology. 415: 455-63. PMID 22123198 DOI: 10.1016/j.jmb.2011.11.025  1
2012 Wood ML, Schow EV, Freites JA, White SH, Tombola F, Tobias DJ. Water wires in atomistic models of the Hv1 proton channel. Biochimica Et Biophysica Acta. 1818: 286-93. PMID 21843503 DOI: 10.1016/j.bbamem.2011.07.045  1
2012 Fleming PJ, Freites JA, Moon CP, Tobias DJ, Fleming KG. 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. Biochimica Et Biophysica Acta. 1818: 126-34. PMID 21816133 DOI: 10.1016/j.bbamem.2011.07.016  1
2011 Baer MD, Mundy CJ, McGrath MJ, Kuo IF, Siepmann JI, Tobias DJ. Re-examining the properties of the aqueous vapor-liquid interface using dispersion corrected density functional theory. The Journal of Chemical Physics. 135: 124712. PMID 21974557 DOI: 10.1063/1.3633239  1
2011 Andersson M, Freites JA, Tobias DJ, White SH. Structural dynamics of the S4 voltage-sensor helix in lipid bilayers lacking phosphate groups. The Journal of Physical Chemistry. B. 115: 8732-8. PMID 21692541 DOI: 10.1021/jp2001964  1
2011 Lewis T, Winter B, Stern AC, Baer MD, Mundy CJ, Tobias DJ, Hemminger JC. Dissociation of strong acid revisited: X-ray photoelectron spectroscopy and molecular dynamics simulations of HNO3 in water. The Journal of Physical Chemistry. B. 115: 9445-51. PMID 21688845 DOI: 10.1021/jp205510q  1
2011 Mihailescu M, Vaswani RG, Jardón-Valadez E, Castro-Román F, Freites JA, Worcester DL, Chamberlin AR, Tobias DJ, White SH. Acyl-chain methyl distributions of liquid-ordered and -disordered membranes. Biophysical Journal. 100: 1455-62. PMID 21402027 DOI: 10.1016/j.bpj.2011.01.035  1
2011 Richards NK, Wingen LM, Callahan KM, Nishino N, Kleinman MT, Tobias DJ, Finlayson-Pitts BJ. Nitrate ion photolysis in thin water films in the presence of bromide ions. The Journal of Physical Chemistry. A. 115: 5810-21. PMID 21291193 DOI: 10.1021/jp109560j  1
2011 Brubaker WD, Freites JA, Golchert KJ, Shapiro RA, Morikis V, Tobias DJ, Martin RW. Separating instability from aggregation propensity in γS-crystallin variants. Biophysical Journal. 100: 498-506. PMID 21244846 DOI: 10.1016/j.bpj.2010.12.3691  1
2011 Bondar AN, Woolf TB, Tobias DJ. Festschrift in the honor of Stephen H. White's 70th Birthday. The Journal of Membrane Biology. 239: 1-3. PMID 21191785 DOI: 10.1007/s00232-010-9337-3  1
2011 Schow EV, Freites JA, Cheng P, Bernsel A, von Heijne G, White SH, Tobias DJ. Arginine in membranes: the connection between molecular dynamics simulations and translocon-mediated insertion experiments. The Journal of Membrane Biology. 239: 35-48. PMID 21127848 DOI: 10.1007/s00232-010-9330-x  1
2010 Callahan KM, Casillas-Ituarte NN, Xu M, Roeselová M, Allen HC, Tobias DJ. Effect of magnesium cation on the interfacial properties of aqueous salt solutions. The Journal of Physical Chemistry. A. 114: 8359-68. PMID 20701343 DOI: 10.1021/jp103485t  1
2010 Bondar AN, del Val C, Freites JA, Tobias DJ, White SH. Dynamics of SecY translocons with translocation-defective mutations. Structure (London, England : 1993). 18: 847-57. PMID 20637421 DOI: 10.1016/j.str.2010.04.010  1
2010 Schow EV, Freites JA, Gogna K, White SH, Tobias DJ. Down-state model of the voltage-sensing domain of a potassium channel. Biophysical Journal. 98: 2857-66. PMID 20550898 DOI: 10.1016/j.bpj.2010.03.031  1
2010 Klauda JB, Venable RM, Freites JA, O'Connor JW, Tobias DJ, Mondragon-Ramirez C, Vorobyov I, MacKerell AD, Pastor RW. Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. The Journal of Physical Chemistry. B. 114: 7830-43. PMID 20496934 DOI: 10.1021/jp101759q  1
2010 Wood K, Tobias DJ, Kessler B, Gabel F, Oesterhelt D, Mulder FA, Zaccai G, Weik M. The low-temperature inflection observed in neutron scattering measurements of proteins is due to methyl rotation: direct evidence using isotope labeling and molecular dynamics simulations. Journal of the American Chemical Society. 132: 4990-1. PMID 20302295 DOI: 10.1021/ja910502g  1
2010 Callahan KM, Casillas-Ituarte NN, Roeselová M, Allen HC, Tobias DJ. Solvation of magnesium dication: molecular dynamics simulation and vibrational spectroscopic study of magnesium chloride in aqueous solutions. The Journal of Physical Chemistry. A. 114: 5141-8. PMID 20201546 DOI: 10.1021/jp909132a  1
2010 Casillas-Ituarte NN, Callahan KM, Tang CY, Chen X, Roeselová M, Tobias DJ, Allen HC. Surface organization of aqueous MgCl2 and application to atmospheric marine aerosol chemistry. Proceedings of the National Academy of Sciences of the United States of America. 107: 6616-21. PMID 20133722 DOI: 10.1073/pnas.0912322107  1
2010 Harmon CW, Grimm RL, McIntire TM, Peterson MD, Njegic B, Angel VM, Alshawa A, Underwood JS, Tobias DJ, Gerber RB, Gordon MS, Hemminger JC, Nizkorodov SA. Hygroscopic growth and deliquescence of NaCl nanoparticles mixed with surfactant SDS. The Journal of Physical Chemistry. B. 114: 2435-49. PMID 20108956 DOI: 10.1021/jp909661q  0.32
2010 Sul S, Feng Y, Le U, Tobias DJ, Ge NH. Interactions of tyrosine in Leu-enkephalin at a membrane-water interface: an ultrafast two-dimensional infrared study combined with density functional calculations and molecular dynamics simulations. The Journal of Physical Chemistry. B. 114: 1180-90. PMID 20017523 DOI: 10.1021/jp9105844  1
2009 Krepkiy D, Mihailescu M, Freites JA, Schow EV, Worcester DL, Gawrisch K, Tobias DJ, White SH, Swartz KJ. Structure and hydration of membranes embedded with voltage-sensing domains. Nature. 462: 473-9. PMID 19940918 DOI: 10.1038/nature08542  1
2009 Miller Y, Thomas JL, Kemp DD, Finlayson-Pitts BJ, Gordon MS, Tobias DJ, Gerber RB. Structure of large nitrate-water clusters at ambient temperatures: simulations with effective fragment potentials and force fields with implications for atmospheric chemistry. The Journal of Physical Chemistry. A. 113: 12805-14. PMID 19817362 DOI: 10.1021/jp9070339  0.32
2009 Valiev M, D'Auria R, Tobias DJ, Garrett BC. Interactions of Cl- and OH radical in aqueous solution. The Journal of Physical Chemistry. A. 113: 8823-5. PMID 19591498 DOI: 10.1021/jp903625k  1
2009 Jaud S, Fernández-Vidal M, Nilsson I, Meindl-Beinker NM, Hübner NC, Tobias DJ, von Heijne G, White SH. Insertion of short transmembrane helices by the Sec61 translocon. Proceedings of the National Academy of Sciences of the United States of America. 106: 11588-93. PMID 19581593 DOI: 10.1073/pnas.0900638106  1
2009 Sengupta N, Maekawa H, Zhuang W, Toniolo C, Mukamel S, Tobias DJ, Ge NH. Sensitivity of 2D IR spectra to peptide helicity: a concerted experimental and simulation study of an octapeptide. The Journal of Physical Chemistry. B. 113: 12037-49. PMID 19496555 DOI: 10.1021/jp901504r  1
2009 D'Auria R, Tobias DJ. Relation between surface tension and ion adsorption at the air-water interface: a molecular dynamics simulation study. The Journal of Physical Chemistry. A. 113: 7286-93. PMID 19438204 DOI: 10.1021/jp810488p  1
2009 Tobias DJ, Sengupta N, Tarek M. Hydration dynamics of purple membranes. Faraday Discussions. 141: 99-116; discussion 1. PMID 19227353 DOI: 10.1039/b809371g  1
2009 Moussa SG, McIntire TM, Szori M, Roeselová M, Tobias DJ, Grimm RL, Hemminger JC, Finlayson-Pitts BJ. Experimental and theoretical characterization of adsorbed water on self-assembled monolayers: understanding the interaction of water with atmospherically relevant surfaces. The Journal of Physical Chemistry. A. 113: 2060-9. PMID 19173586 DOI: 10.1021/jp808710n  1
2008 Baer M, Mathias G, Kuo IF, Tobias DJ, Mundy CJ, Marx D. Spectral signatures of the pentagonal water cluster in bacteriorhodopsin. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 9: 2703-7. PMID 19025752 DOI: 10.1002/cphc.200800473  0.36
2008 Wingen LM, Moskun AC, Johnson SN, Thomas JL, Roeselová M, Tobias DJ, Kleinman MT, Finlayson-Pitts BJ. Enhanced surface photochemistry in chloride-nitrate ion mixtures. Physical Chemistry Chemical Physics : Pccp. 10: 5668-77. PMID 18956101 DOI: 10.1039/b806613b  1
2008 Sengupta N, Jaud S, Tobias DJ. Hydration dynamics in a partially denatured ensemble of the globular protein human alpha-lactalbumin investigated with molecular dynamics simulations. Biophysical Journal. 95: 5257-67. PMID 18775960 DOI: 10.1529/biophysj.108.136531  1
2008 Brown MA, D'Auria R, Kuo IF, Krisch MJ, Starr DE, Bluhm H, Tobias DJ, Hemminger JC. Ion spatial distributions at the liquid-vapor interface of aqueous potassium fluoride solutions. Physical Chemistry Chemical Physics : Pccp. 10: 4778-84. PMID 18688520 DOI: 10.1039/b807041e  1
2008 Yu Y, Ezell MJ, Zelenyuk A, Imre D, Alexander L, Ortega J, Thomas JL, Gogna K, Tobias DJ, D'Anna B, Harmon CW, Johnson SN, Finlayson-Pitts BJ. Nitrate ion photochemistry at interfaces: a new mechanism for oxidation of alpha-pinene. Physical Chemistry Chemical Physics : Pccp. 10: 3063-71. PMID 18688369 DOI: 10.1039/b719495a  1
2008 D'Auria R, Kuo IF, Tobias DJ. Ab initio molecular dynamics study of the solvated OHCl- complex: implications for the atmospheric oxidation of chloride anion to molecular chlorine. The Journal of Physical Chemistry. A. 112: 4644-50. PMID 18444631 DOI: 10.1021/jp077669d  1
2008 Tarek M, Tobias DJ. The role of protein-solvent hydrogen bond dynamics in the structural relaxation of a protein in glycerol versus water. European Biophysics Journal : Ebj. 37: 701-9. PMID 18427802 DOI: 10.1007/s00249-008-0324-x  0.6
2008 Tobias DJ, Hemminger JC. Chemistry. Getting specific about specific ion effects. Science (New York, N.Y.). 319: 1197-8. PMID 18309069 DOI: 10.1126/science.1152799  1
2007 Wood K, Plazanet M, Gabel F, Kessler B, Oesterhelt D, Tobias DJ, Zaccai G, Weik M. Coupling of protein and hydration-water dynamics in biological membranes. Proceedings of the National Academy of Sciences of the United States of America. 104: 18049-54. PMID 17986611 DOI: 10.1073/pnas.0706566104  1
2007 Thomas JL, Tobias DJ, Mackerell AD. Direct comparisons of experimental and calculated neutron structure factors of pure solvents as a method for force field validation. The Journal of Physical Chemistry. B. 111: 12941-4. PMID 17958354 DOI: 10.1021/jp076501p  1
2007 Thomas JL, Roeselová M, Dang LX, Tobias DJ. Molecular dynamics simulations of the solution-air interface of aqueous sodium nitrate. The Journal of Physical Chemistry. A. 111: 3091-8. PMID 17402716 DOI: 10.1021/jp0683972  1
2007 Jaud S, Tobias DJ, Falke JJ, White SH. Self-induced docking site of a deeply embedded peripheral membrane protein. Biophysical Journal. 92: 517-24. PMID 17071664 DOI: 10.1529/biophysj.106.090704  1
2006 Castro-Román F, Benz RW, White SH, Tobias DJ. Investigation of finite system-size effects in molecular dynamics simulations of lipid bilayers. The Journal of Physical Chemistry. B. 110: 24157-64. PMID 17125387 DOI: 10.1021/jp064746g  1
2006 Curtis JE, Dirama TE, Carri GA, Tobias DJ. Inertial suppression of protein dynamics in a binary glycerol-trehalose glass. The Journal of Physical Chemistry. B. 110: 22953-6. PMID 17107124 DOI: 10.1021/jp0615499  1
2006 Freites JA, Tobias DJ, White SH. A voltage-sensor water pore. Biophysical Journal. 91: L90-2. PMID 17012321 DOI: 10.1529/biophysj.106.096065  0.56
2006 Benz RW, Nanda H, Castro-Román F, White SH, Tobias DJ. Diffraction-based density restraints for membrane and membrane-peptide molecular dynamics simulations. Biophysical Journal. 91: 3617-29. PMID 16950837 DOI: 10.1529/biophysj.106.084483  1
2006 Kuo IF, Mundy CJ, Eggimann BL, McGrath MJ, Siepmann JI, Chen B, Vieceli J, Tobias DJ. Structure and dynamics of the aqueous liquid-vapor interface: a comprehensive particle-based simulation study. The Journal of Physical Chemistry. B. 110: 3738-46. PMID 16494432 DOI: 10.1021/jp056330t  1
2005 Vieceli J, Roeselova M, Potter N, Dang LX, Garrett BC, Tobias DJ. Molecular dynamics simulations of atmospheric oxidants at the air-water interface: solvation and accommodation of OH and O3. The Journal of Physical Chemistry. B. 109: 15876-92. PMID 16853017 DOI: 10.1021/jp051361+  0.36
2005 Gopalakrishnan S, Jungwirth P, Tobias DJ, Allen HC. Air-liquid interfaces of aqueous solutions containing ammonium and sulfate: spectroscopic and molecular dynamics studies. The Journal of Physical Chemistry. B. 109: 8861-72. PMID 16852054 DOI: 10.1021/jp0500236  1
2005 Brown EC, Mucha M, Jungwirth P, Tobias DJ. Structure and vibrational spectroscopy of salt water/air interfaces: predictions from classical molecular dynamics simulations. The Journal of Physical Chemistry. B. 109: 7934-40. PMID 16851926 DOI: 10.1021/jp0450336  1
2005 Mucha M, Frigato T, Levering LM, Allen HC, Tobias DJ, Dang LX, Jungwirth P. Unified molecular picture of the surfaces of aqueous acid, base, and salt solutions. The Journal of Physical Chemistry. B. 109: 7617-23. PMID 16851882 DOI: 10.1021/jp0445730  1
2005 Freites JA, Tobias DJ, von Heijne G, White SH. Interface connections of a transmembrane voltage sensor. Proceedings of the National Academy of Sciences of the United States of America. 102: 15059-64. PMID 16217012 DOI: 10.1073/pnas.0507618102  1
2005 Jaud S, Tobias DJ, Brant DA. Molecular dynamics simulations of aqueous pullulan oligomers. Biomacromolecules. 6: 1239-51. PMID 15877338 DOI: 10.1021/bm049463d  1
2005 Benz RW, Castro-Román F, Tobias DJ, White SH. Experimental validation of molecular dynamics simulations of lipid bilayers: a new approach. Biophysical Journal. 88: 805-17. PMID 15533925 DOI: 10.1529/biophysj.104.046821  1
2004 Roeselová M, Vieceli J, Dang LX, Garrett BC, Tobias DJ. Hydroxyl radical at the air-water interface. Journal of the American Chemical Society. 126: 16308-9. PMID 15600317 DOI: 10.1021/ja045552m  0.36
2004 Curtis JE, Tarek M, Tobias DJ. Methyl group dynamics as a probe of the protein dynamical transition. Journal of the American Chemical Society. 126: 15928-9. PMID 15584703 DOI: 10.1021/ja0480623  1
2003 Freites JA, Choi Y, Tobias DJ. Molecular dynamics simulations of a pulmonary surfactant protein B peptide in a lipid monolayer. Biophysical Journal. 84: 2169-80. PMID 12668426 DOI: 10.1016/S0006-3495(03)75023-1  0.48
2002 Tarek M, Tobias DJ. Single-particle and collective dynamics of protein hydration water: a molecular dynamics study. Physical Review Letters. 89: 275501. PMID 12513215  0.6
2002 Nordgren CE, Tobias DJ, Klein ML, Blasie JK. Molecular dynamics simulations of a hydrated protein vectorially oriented on polar and nonpolar soft surfaces. Biophysical Journal. 83: 2906-17. PMID 12496067 DOI: 10.1016/S0006-3495(02)75300-9  1
2002 Tarek M, Tobias DJ. Role of protein-water hydrogen bond dynamics in the protein dynamical transition. Physical Review Letters. 88: 138101. PMID 11955127  0.6
2001 Tarek M, Tobias DJ, Chen SH, Klein ML. Short wavelength collective dynamics in phospholipid bilayers: a molecular dynamics study. Physical Review Letters. 87: 238101. PMID 11736477  0.92
2000 Tarek M, Tobias DJ. The dynamics of protein hydration water: a quantitative comparison of molecular dynamics simulations and neutron-scattering experiments. Biophysical Journal. 79: 3244-57. PMID 11106628 DOI: 10.1016/S0006-3495(00)76557-X  0.6
2000 Knipping EM, Lakin MJ, Foster KL, Jungwirth P, Tobias DJ, Gerber RB, Dabdub D, Finlayson-Pitts BJ. Experiments and simulations of ion-enhanced interfacial chemistry on aqueous NaCl aerosols Science (New York, N.Y.). 288: 301-6. PMID 10764637 DOI: 10.1126/science.288.5464.301  1
1999 Tarek M, Tu K, Klein ML, Tobias DJ. Molecular dynamics simulations of supported phospholipid/alkanethiol bilayers on a gold(111) surface. Biophysical Journal. 77: 964-72. PMID 10423441 DOI: 10.1016/S0006-3495(99)76947-X  0.92
1999 Tarek M, Tobias DJ. Environmental dependence of the dynamics of protein hydration water [10] Journal of the American Chemical Society. 121: 9740-9741. DOI: 10.1021/ja990643i  0.92
1998 Tu K, Klein ML, Tobias DJ. Constant-pressure molecular dynamics investigation of cholesterol effects in a dipalmitoylphosphatidylcholine bilayer. Biophysical Journal. 75: 2147-56. PMID 9788908 DOI: 10.1016/S0006-3495(98)77657-X  0.92
1998 Lathrop RH, Casale M, Tobias DJ, Marsh JL, Thompson LM. Modeling protein homopolymeric repeats: possible polyglutamine structural motifs for Huntington's disease. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 6: 105-14. PMID 9783215  1
1997 Samuelson S, Tobias DJ, Martyna GJ. Modern computational methodology applied to the simulation of blocked trialanine peptide in vacuo, water clusters, and bulk water Journal of Physical Chemistry B. 101: 7592-7603.  0.92
1997 Tobias DJ, Tu K, Klein ML. Assessment of all-atom potentials for modeling membranes: Molecular dynamics simulations of solid and liquid alkanes and crystals of phospholipid fragments Journal De Chimie Physique Et De Physico-Chimie Biologique. 94: 1482-1502.  0.92
1996 Tobias DJ, Mar W, Blasie JK, Klein ML. Molecular dynamics simulations of a protein on hydrophobic and hydrophilic surfaces. Biophysical Journal. 71: 2933-41. PMID 8968566 DOI: 10.1016/S0006-3495(96)79497-3  0.92
1996 Tu K, Tobias DJ, Blasie JK, Klein ML. Molecular dynamics investigation of the structure of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer. Biophysical Journal. 70: 595-608. PMID 8789079 DOI: 10.1016/S0006-3495(96)79623-6  0.92
1996 Tarek M, Tobias DJ, Klein ML. Molecular dynamics investigation of the surface/bulk equilibrium in an ethanol-water solution Journal of the Chemical Society - Faraday Transactions. 92: 559-563.  0.92
1996 Tobias DJ, Klein ML. Molecular dynamics investigation of the lamellar liquid-crystal D-phase in the octylammonium chloride/ water system Molecular Simulation. 16: 219-228.  0.92
1996 Martyna GJ, Tuckerman ME, Tobias DJ, Klein ML. Explicit reversible integrators for extended systems dynamics Molecular Physics. 87: 1117-1157.  0.92
1995 Tu K, Tobias DJ, Klein ML. Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer. Biophysical Journal. 69: 2558-62. PMID 8599662 DOI: 10.1016/S0006-3495(95)80126-8  0.92
1995 Tobias DJ, Gesell J, Klein ML, Opella SJ. A simple protocol for identification of helical and mobile residues in membrane proteins. Journal of Molecular Biology. 253: 391-5. PMID 7473722 DOI: 10.1006/jmbi.1995.0561  0.92
1995 Tu K, Tobias DJ, Klein ML. Constant pressure and temperature molecular dynamics simulations of crystals of the lecithin fragments: Glycerylphosphorylcholine and dilauroylglycerol Journal of Physical Chemistry. 99: 10035-10042.  0.92
1994 Martyna GJ, Tobias DJ, Klein ML. Constant pressure molecular dynamics algorithms The Journal of Chemical Physics. 101: 4177-4189.  0.92
1993 Tobias DJ, Klein ML, Opella SJ. Molecular dynamics simulation of Pf1 coat protein. Biophysical Journal. 64: 670-5. PMID 8471719 DOI: 10.1016/S0006-3495(93)81426-7  0.92
1993 Karpen ME, Tobias DJ, Brooks CL. Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV. Biochemistry. 32: 412-20. PMID 8422350  0.92
1993 Tobias DJ, Martyna GJ, Klein ML. Molecular dynamics simulations of a protein in the canonical ensemble Journal of Physical Chemistry. 97: 12959-12966.  0.92
1992 Sneddon SF, Tobias DJ. The role of packing interactions in stabilizing folded proteins. Biochemistry. 31: 2842-6. PMID 1547226  0.92
1992 Tobias DJ, Sneddon SF, Brooks CL. Stability of a model beta-sheet in water. Journal of Molecular Biology. 227: 1244-52. PMID 1433296  0.92
1991 Tobias DJ, Brooks CL. Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides. Biochemistry. 30: 6059-70. PMID 2043644  0.92
1991 Tobias DJ, Mertz JE, Brooks CL. Nanosecond time scale folding dynamics of a pentapeptide in water. Biochemistry. 30: 6054-8. PMID 2043643  0.92
1990 Tobias DJ, Sneddon SF, Brooks CL. Reverse turns in blocked dipeptides are intrinsically unstable in water. Journal of Molecular Biology. 216: 783-96. PMID 2258940 DOI: 10.1016/0022-2836(90)90399-7  0.92
1989 Sneddon SF, Tobias DJ, Brooks CL. Thermodynamics of amide hydrogen bond formation in polar and apolar solvents. Journal of Molecular Biology. 209: 817-20. PMID 2585511  0.92
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