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You searched for subject:(solvation response). Showing records 1 – 3 of 3 total matches.

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University of Notre Dame

1. Zachary Terranova. Exploring the Structure and Dynamics of Ionic Liquids Using Molecular Dynamics</h1>.

Degree: Chemistry and Biochemistry, 2014, University of Notre Dame

Experimental studies of solvation dynamics in imidazolium-based ionic liquids (ILs) have revealed complex kinetics over a broad range of time scales from femtoseconds to tens of nanoseconds. Microsecond-length molecular dynamics (MD) simulations of coumarin 153 (C153) in a series of imidazolium-based ILs were performed to reveal the molecular-level mechanism for solvation dynamics over the full range of time scales accessed in the experiments. An analysis of the structure of the IL in the vicinity of the probe molecule revealed preferential solvation by the cations. Despite this observation, decomposition of the solvation response into components from the anions and cations and also from translational and rotational motions show that translations of the anions are the dominant contributor to solvation dynamics. The kinetics for the translation of the anions into and out of the first solvation shell of the dye were found to mimic the kinetic profile of the solvation dynamics response. This mechanism for solvation dynamics contrasts dramatically with conventional polar liquids in which solvent rotations are generally responsible for the response. The structure and dynamics of water as measured experimentally in ILs have revealed local ion rearrangements that occur an order of magnitude faster than complete randomization of the liquid structure. Simulations of an isolated water molecule embedded in 1-butyl-3-methyl imidazolium hexafluorophosphate, [bmim][PF6], were performed to shed insight into the nature of these coupled water-ion dynamics. The theoretical calculations of the spectral diffusion dynamics and the infrared absorption spectra of the OD stretch of isolated HOD in [bmim][PF6] agree well with experiment. The infrared (IR) absorption lineshape of the OD stretch is narrow and blue-shifted in the IL compared to the OD stretch of HOD in H2O. Decomposition of the OD frequency time correlation function revealed the translation of the anions dominate the spectral diffusion dynamics. Advisors/Committee Members: S. Alex Kandel, Committee Member, Steven A. Corcelli, Committee Chair, Jeffrey Peng, Committee Member, J. Daniel Gezelter, Committee Member.

Subjects/Keywords: spectroscopy; linear response; ionic liquids; solvation response; solvation dynamics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Terranova, Z. (2014). Exploring the Structure and Dynamics of Ionic Liquids Using Molecular Dynamics</h1>. (Thesis). University of Notre Dame. Retrieved from https://curate.nd.edu/show/jh343r09c3f

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16th Edition):

Terranova, Zachary. “Exploring the Structure and Dynamics of Ionic Liquids Using Molecular Dynamics</h1>.” 2014. Thesis, University of Notre Dame. Accessed July 14, 2020. https://curate.nd.edu/show/jh343r09c3f.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7th Edition):

Terranova, Zachary. “Exploring the Structure and Dynamics of Ionic Liquids Using Molecular Dynamics</h1>.” 2014. Web. 14 Jul 2020.

Vancouver:

Terranova Z. Exploring the Structure and Dynamics of Ionic Liquids Using Molecular Dynamics</h1>. [Internet] [Thesis]. University of Notre Dame; 2014. [cited 2020 Jul 14]. Available from: https://curate.nd.edu/show/jh343r09c3f.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Terranova Z. Exploring the Structure and Dynamics of Ionic Liquids Using Molecular Dynamics</h1>. [Thesis]. University of Notre Dame; 2014. Available from: https://curate.nd.edu/show/jh343r09c3f

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

2. Li, Tanping. The Coupled Water-Protein Dynamics within Hydration Layer surrounding Protein and Semiclassical Approximation for Optical Response Funtion.

Degree: PhD, Biophysics, 2011, The Ohio State University

We report experimental and theoretical studies on water and protein dynamics following photoexcitation of apomyoglobin. Using site-directed mutation and with femtosecond resolution, we experimentally observed relaxation dynamics with a biphasic distribution of time scales, 5 and 87 ps, around the site Trp7. Theoretical studies using both linear response and direct nonequilibrium molecular dynamics (MD) calculations reproduced the biphasic behavior. Further constrained MD simulations with either frozen protein or frozen water revealed the molecular mechanism of slow hydration processes and elucidated the role of protein fluctuations. Observation of slow water dynamics in MD simulations requires protein flexibility, regardless of whether the slow Stokes shift component results from the water or protein contribution. The initial dynamics in a few picoseconds represents fast local motions such as reorientations and translations of hydrating water molecules, followed by slow relaxation involving strongly coupled water-protein motions. We observed a transition from one isomeric protein configuration to another after 10 ns during our 30 ns ground-state simulation. For one isomer, the surface hydration energy dominates the slow component of the total relaxation energy. For the other isomer, the slow component is dominated by protein interactions with the chromophore. In both cases, coupled water-protein motion is shown to be necessary for observation of the slow dynamics. Such biologically important water-protein motions occur on tens of picoseconds. One significant discrepancy exists between theory and experiment, the large inertial relaxation predicted by simulations but clearly absent in experiment. Further improvements required in the theoretical model are discussed. Linear response theory has been reported to give good approximations with the nonequilibrium relaxation of Stokes shift in the studies of solvation dynamics. It breaks down for Trp-140 (W140) in Staphylococcus nuclease. Two isomers are found in the electronic ground state of Trp on the time scale of 35 nanosecond simulation. Isomerization of local structure around W151 is crucial to explain the mechanism how linear response theory deviates from the nonequilibrium process. Advisors/Committee Members: Zhong, Dongping (Committee Chair), Singer, Sherwin (Advisor).

Subjects/Keywords: Biophysics; solvation dynamics; linear response theory; optical response cunction

Response in Solvation Dynamics… …Zhong DP, “Ultrafast solvation dynamics at binding and active sites of photolyases”, Proc.Natl… …Zhong DP, “Mapping solvation dynamics at the function site of flavodoxin in three redox states… …C, Liu ZY, Wang LJ, Sancar A, Zhong DP, “Ultrafast solvation dynamics at binding and… …State Equilibrium Fluctuations . . . . . . . 3.3.2 Nonequilibrium Solvation Dynamics versus… 

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Li, T. (2011). The Coupled Water-Protein Dynamics within Hydration Layer surrounding Protein and Semiclassical Approximation for Optical Response Funtion. (Doctoral Dissertation). The Ohio State University. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=osu1312484867

Chicago Manual of Style (16th Edition):

Li, Tanping. “The Coupled Water-Protein Dynamics within Hydration Layer surrounding Protein and Semiclassical Approximation for Optical Response Funtion.” 2011. Doctoral Dissertation, The Ohio State University. Accessed July 14, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1312484867.

MLA Handbook (7th Edition):

Li, Tanping. “The Coupled Water-Protein Dynamics within Hydration Layer surrounding Protein and Semiclassical Approximation for Optical Response Funtion.” 2011. Web. 14 Jul 2020.

Vancouver:

Li T. The Coupled Water-Protein Dynamics within Hydration Layer surrounding Protein and Semiclassical Approximation for Optical Response Funtion. [Internet] [Doctoral dissertation]. The Ohio State University; 2011. [cited 2020 Jul 14]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1312484867.

Council of Science Editors:

Li T. The Coupled Water-Protein Dynamics within Hydration Layer surrounding Protein and Semiclassical Approximation for Optical Response Funtion. [Doctoral Dissertation]. The Ohio State University; 2011. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=osu1312484867

3. F. Tramonto. MICROSCOPIC STUDIES OF STATIC AND DYNAMIC PROPERTIES IN QUANTUM LIQUIDS AND GASES.

Degree: 2015, Università degli Studi di Milano

In this thesis I present studies of a number of quantum many-body Bose systems via Quantum Monte Carlo methods. We investigated the dynamic structure factor of a hard-sphere Bose system simulated at T=0 at different densities, from the dilute to the strongly interacting regimes. By increasing the density we observed the spectrum evolves from the weakly interacting Bogoliubov to a phonon-maxon-roton dispersion, but also the emergence of a broad multi-quasiparticle component. For a system with sphere radius and density corresponding to superfluid 4He at equilibrium, we found good agreement with the spectrum in the roton region. In another work, a liquid of distinguishable 4He atoms near freezing at T=1 K was studied to compute the equation of state and static density response function. The results of this study have been used to improve the description of the superfluid-to-solid transition within the Density Functional Theory. Measurements of crystallization kinetics in supercooled liquid p-H2 – o-D2 mixtures showed a slowdown with respect to the pure counterparts. In order to contribute to the interpretation of these results we simulated these metastable mixtures. We found differences in the quantum delocalization of the two isotopic molecules, which result in different effective sizes. We characterized also the differences in the local order around the molecules of each species. These results revealed that the observed slowdown is due to purely quantum effects. Finally, in a QMC study of ion Ar+ doped 4He nanodroplets at T=1 K, we computed density profiles, energies, and investigated local order around the Ar+ ion. We found stable solid structures around the ion composed of three solvation shells having the shape of platonic solids: an icosahedron, a dodecahedron, and, again, an icosahedron, with 12, 20, and 12 4He atoms, going from the inner to the outer shell respectively. These results confirmed the interpretation of experimental measurements of the abundances of [email protected] nanodroplets. Advisors/Committee Members: tutor: D. E. Galli, coordinatore: M. R. F. Bersanelli, GALLI, DAVIDE EMILIO, BERSANELLI, MARCO RINALDO FEDELE.

Subjects/Keywords: excited states; collective modes; rotons; phonons; maxons; dynamic structure factor; static structure factor; static density response function; bosons; hard spheres; 4He; helium; superfluidity; superfluid 4He; quantum liquid; quantum solid; quantum gas; Bose statistics; quantum Monte Carlo; path integral Monte Carlo; path integral ground state; 4He nanodroplets; argon; argon ion; cation; supercooled liquid; crystallization; para-hydrogen; ortho-deuterium; binary mixtures; solvation shells; icosahedron; dodecahedron; Settore FIS/03 - Fisica della Materia

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Tramonto, F. (2015). MICROSCOPIC STUDIES OF STATIC AND DYNAMIC PROPERTIES IN QUANTUM LIQUIDS AND GASES. (Thesis). Università degli Studi di Milano. Retrieved from http://hdl.handle.net/2434/260418

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16th Edition):

Tramonto, F.. “MICROSCOPIC STUDIES OF STATIC AND DYNAMIC PROPERTIES IN QUANTUM LIQUIDS AND GASES.” 2015. Thesis, Università degli Studi di Milano. Accessed July 14, 2020. http://hdl.handle.net/2434/260418.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7th Edition):

Tramonto, F.. “MICROSCOPIC STUDIES OF STATIC AND DYNAMIC PROPERTIES IN QUANTUM LIQUIDS AND GASES.” 2015. Web. 14 Jul 2020.

Vancouver:

Tramonto F. MICROSCOPIC STUDIES OF STATIC AND DYNAMIC PROPERTIES IN QUANTUM LIQUIDS AND GASES. [Internet] [Thesis]. Università degli Studi di Milano; 2015. [cited 2020 Jul 14]. Available from: http://hdl.handle.net/2434/260418.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Tramonto F. MICROSCOPIC STUDIES OF STATIC AND DYNAMIC PROPERTIES IN QUANTUM LIQUIDS AND GASES. [Thesis]. Università degli Studi di Milano; 2015. Available from: http://hdl.handle.net/2434/260418

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

.