Douglas J. TobiasProfessor, Chemistry |
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Research Interests |
Theoretical and Computational Chemistry, Biophysical Chemistry, Atmospheric Chemistry | |
| URL | www.chem.uci.edu/people/faculty/dtobias/ | |
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Academic Distinctions |
National Institutes of Health Predoctoral Trainee, 1987-1990 National Institutes of Health National Research Service Award,1991-1993 Elected Fellow of the American Association for the Advancement of Science, 2006 |
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| Appointments |
Postdoctoral Researcher, Department of Chemistry, University of Pennsylvania, 1991-1995 Guest Researcher, NIST Center for Neutron Research, National Institute of Standards and Technology, 1995-1997 Appointed to the UC Irvine Faculty, 1997 Assistant Professor, UC Irvine, 1997-2003 Assosiate Professor, UC Irvine, 2003-2005 Professor, UC Irvine, 2005-present Visiting Professor, Universite Joseph Fourier, Institut de Biologie Structurale, Grenoble, France, 2007 |
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Research Abstract |
Our research involves using atomic-scale computer simulation techniques based on classical and quantum mechanics to study the structure and dynamics of biological molecules and biomimetic materials, and aqueous interfaces with air that are important in atmospheric chemical processes. A substantial portion of our work is devoted to the development, implementation, and optimization of novel simulation methodology and analysis tools. Current areas of research in our lab include: Interactions of Peptides and Proteins with Lipids and Protein Folding in Membranes. Membrane proteins comprise roughly 25% of the genome and the majority of pharmaceutical targets, but relatively few structures of membrane proteins are known. In order to be able to predict their functions, we need to know how membrane proteins interact with membranes. In collaboration with Professor Stephen White in the UCI College of Medicine, we are modeling peptides and proteins in lipid bilayers, and developing methods for using simulations to refine low-resolution structures of membrane proteins determined by x-ray and neutron diffraction. We are also developing coarse grained models for studying generic aspects of the thermodynamics and kinetics of protein folding in membranes. Molecular Mechanism of Ion Channel Gating. Electrical signal propagation in excitable tissues such as nerves and muscles relies on the synchronized opening and closing of membrane-associated protein pores that are highly selective to specific ions and are sensitive to changes in transmembrane electrical potential. We are using molecular dynamics simulations to elucidate the molecular mechanism of voltage sensing and ion conduction by voltage-sensitive potassium and proton channels. Structure and Function of Pulmonary Surfactant Proteins. Pulmonary surfactant (PS) is a mixture of lipids and proteins that resides at the alveolar air/water interface and keeps the surface tension low during breathing, thereby providing stability to the expanding and contracting alveoli. We are simulating native and mutant PS proteins in lipid monolayers to predict their structures and to elucidate the role of particular residues in their function. The resulting insight will be applied to the development of synthetic replacement surfactant components to treat respiratory diseases associated with the lack of PS proteins, e.g. respiratory distress syndrome in premature infants. Dynamics of Native and Denatured Proteins and their Hydration Water. We are using molecular dynamics simulations to study several fundamental aspects of protein dynamics related to protein function and folding: the transition from an inactive, glassy state at low temperature to the active, liquid-like state at higher temperatures; the role of solvent in affacting the glass transition; the storage and dissipation of electronic and vibrational energy in photoexcited proteins; the dynamics of proteins and water molecules in denatured states. Structure and Reactivity at the Interfaces of Sea Salt and Organic Aerosols. The role of aqueous aerosols (small water droplets suspended in air) in atmospheric chemical processes are currently a subject of great interest to atmospheric chemists. The interfaces of aerosol particles are the sites of unique chemistry that does not take place in gas phase or bulk solution environments. We are using molecular dynamics simulations to provide an atomic scale view of the structure and dynamics at the interfaces of concentrated ionic solutions (e.g. sea salt aerosols) and water droplets coated with organic molecules (e.g. organic aerosols), and their interactions with reactive trace gases present in the atmosphere (e.g. OH radical and ozone). In addition to providing fundamental insight in to the physicochemical properties of these interfaces, our simulations are leading to the proposal of new mechanisms for reactions that could be important in the chemistry of the atmosphere. This work is being performed in collaboration with Professors Barbara Finlayson-Pitts, John Hemminger, and Sergey Nizkorodov in the Chemistry Department at UCI, Martina Roeselova in the Academy of Sciences of the Czech Republic in Prague, Chris Mundy at the Pacific Northwest National Lab, and Will Kuo at the Lawrence Livermore National Lab. Fundamental Aspects of Ion-Water Hydrogen Bonds. Ion-water hydrogen bonds play an important role in determining the reactivity and thermodynamic and transport properties of aqueous solutions. Recent advances in spectroscopic techniques have led to a renaissance of interest in the quantitative details of the structure, energetics, and dynamics of hydrogen bonds between water and ions. We are using ab initio molecular dynamics simulations, in which the forces between the atoms are computed from the electronic structure using density functional theory, to study the solvation of ions in clusters of water molecules and bulk solutions. Our calculations are providing new information regarding the role of electronic polarization and quantum nuclear motion in ion-water hydrogen bonds. |
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| Publications | "Insertion of Transmembrane Helices by the Sec61 Translocon," S. Jaud, M. Fernandez-Vidal, I. Nilsson, N. M. Meindl-Beinker, N. Hubner, D. J. Tobias, G. von Heijne, and S. H. White, Proc. Natl. Acad. Sci. USA, in press (2009). | |
| "Experimental and Theoretical Characterization of Water Uptake on Self-Assembled Monolayers: Understanding the Interaction of Water with Atmospherically Relevant Surfaces," S. G. Moussa, T. M. McIntire, M. Szori, M. Roeselova, D. J. Tobias, R. L. Grimm, J. C. Hemminger, and B. J. Finlayson-Pitts, J. Phys. Chem. B 113, 2060-2069 (2009). | ||
| "Dynamics of Internal Water Molecules in Squid Rhodopsin," E. Jardon-Valadez, A. N. Bondar, and D. J. Tobias, Biophys. J. 96, 2572-2576 (2009). | ||
| "Hydration Dynamics of Purple Membranes," D. J. Tobias, N. Sengupta, and M. Tarek, Faraday Discuss. 141, 99-116 (2009). | ||
| "Hydration Dynamics in a Partially Denatured Ensemble of the Globular Protein Human Alpha-Lactalbumin Investigated with Molecular Dynamics Simulations," N. Sengupta, S. Jaud, and D. J. Tobias, Biophys. J. 95, 5257-5267 (2008). | ||
| "Getting Specific About Specific Ion Effects," D. J. Tobias and J. C. Hemminger, Science 319, 1197-1198 (2008). | ||
| "An Ab Initio Molecular Dynamics Study of the Solvated OHCl Complex: Implications for the Atmospheric Oxidation of Chloride Ion to Molecular Chlorine," R. D'Auria, I.-F. W. Kuo, and D. J. Tobias, J. Phys. Chem. A 105, 4644-4650 (2008). | ||
| "Enhanced Photochemistry in Chloride-Nitrate Ion Mixtures," L. M. Wingen, A. C. Moskun, S. N. Johnson, J. L. Thomas, M. Roeselova, D. J. Tobias, D. J. Tobias, M. T. Kleinman, and B. J. Finlayson-Pitts, Phys. Chem. Chem. Phys. 10, 5668-5678 (2008). | ||
| "Coupling of Protein and Hydration-Water Dynamics in Biological Membranes," K. Wood, M. Plazanet, F. Gabel. B. Kessler, D. Oesterhelt, D. J. Tobias. G. Zaccai, and M. Weik, Proc. Natl. Acad. Sci. USA 104, 18049-18054 (2007). | ||
| "The Effect of an Organic Surfactant on the Liquid-Vapor Interface of an Electrolyte Solution," M. J. Krisch, R. D'Auria, M. A. Brown, D. J. Tobias, J. C. Hemminger, M. Ammann, D. E. Starr, and H. Bluhm, J. Phys. Chem. C 111, 13497-13509 (2007). | ||
| "Self-Induced Docking Site of a Deeply Embedded Peripheral Membrane Protein," S. Jaud, D. J. Tobias, J. J. Falke, and S. H. White, Biophys. J. 92, 517-524 (2007). | ||
| "Specific Ion Effects at the Air/Water Interface," P. Jungwirth and D. J. Tobias, Chem. Rev. 106, 1259-1281 (2006). | ||
| "A Voltage Sensor Water Pore" J. A. Freites, D. J. Tobias, and S. H. White, Biophys. J. 91, L90-L92 (2006). | ||
| "Interface Connections of a Transmembrane Voltage Sensor," J. A. Freites, D. J. Tobias, G. von Heijne, and S. H. White, Proc. Natl. Acad. Sci. USA 102, 15059-15064 (2005). | ||
| "Uptake and Collision Dynamics of Gas Phase Ozone at Unsaturated Organic Surfaces," J. Vieceli, O. L. Ma, and D. J. Tobias, J. Phys. Chem. A 108, 5806-5814 (2004). | ||
| "Molecular Dynamics Simulations of a Pulmonary Surfactant Protein B Peptide in a Lipid Monolayer," J. A. Freites, Y. Choi and D. J. Tobias, Biophys. J. 84, 2169-2180 (2003). | ||
| "Ions at the Air/Water Interface," P. Jungwirth and D. J. Tobias, J. Phys. Chem. B 106, 6361-6373 (2002). | ||
| "Role of Protein-Water Hydrogen Bond Dynamics in the Protein Dynamical Transition," M. Tarek and D. J. Tobias, Phys. Rev. Lett. 88, 138101 (2002). | ||
| "The Molecular Structure of Salt Solutions: A New View of the Interface with Implications for Heterogeneous Atmospheric Chemistry," P. Jungwirth and D. J. Tobias, J. Phys. Chem. B 105, 10468-10472 (2001). | ||
| "Experiments and Molecular/Kinetics Simulations of Ion-Enhanced Interfacial Chemistry on Aqueous NaCl Aerosols," E. Knipping, M. J. Lakin, P. Jungwirth, D. J. Tobias, R. B. Gerber, D. Dabdub, and B. J. Finlayson-Pitts, Science 288, 301-306 (2000). | ||
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Professional Societies |
American Chemical Society American Physical Society American Association for the Advancement of Science Biophysical Society |
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| Research Centers | AirUCI Environmental Molecular Sciences Institute | |
| Institute for Surface and Interface Science (ISIS) | ||
| Center for Biomembrane Systems | ||
| Institute for Genomics and Bioinformatics (IGB) | ||
| Center for Complex Bio Systems (CCBS) | ||
| Institute for Complex Adaptive Matter (ICAM) | ||
| Link to this profile | http://www.faculty.uci.edu/profile.cfm?faculty_id=4581 | |
| Last updated | 07/03/2009 | |
