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Simulation of Relaxation Processes in Fluorescence, EPR and NMR Spectroscopy
Umeå University, Faculty of Science and Technology, Chemistry.
2004 (English)Doctoral thesis, comprehensive summary (Other academic)Alternative title
Simulering av Relaxationsprocesser inom Fluoresens, EPR och NMR Spektroskopi (Swedish)
Abstract [en]

Relaxation models are developed using numerical solutions of the Stochastic Liouville Equation of motion. Simplified descriptions such as the stochastic master equation is described in the context of fluorescence depolarisation experiments. Redfield theory is used in order to describe NMR relaxation in bicontinuous phases. The stochastic fluctuations in the relaxation models are accounted for using Brownian Dynamics simulation technique. A novel approach to quantitatively analyse fluorescence depolarisation experiments and to determine intramolecular distances is presented. A new Brownian Dynamics simulation technique is developed in order to characterize translational diffusion along the water lipid interface of bicontinuous cubic phases.

Place, publisher, year, edition, pages
Umeå: Kemi , 2004. , 34 p.
Keyword [en]
Physical chemistry, EPR, NMR, Energy migration, bicontinuous cubic phase, Stochastic Liouville Equation, Brownian Dynamics
Keyword [sv]
Fysikalisk kemi
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
URN: urn:nbn:se:umu:diva-244ISBN: 91-7305-666-9 (print)OAI: oai:DiVA.org:umu-244DiVA: diva2:142796
Public defence
2004-05-14, KB3A9, KBC, Biofysikalisk kemi, Umeå Universitet, Umeå, 10:00 (English)
Opponent
Supervisors
Available from: 2004-04-22 Created: 2004-04-22 Last updated: 2009-10-26Bibliographically approved
List of papers
1. A direct simulation of EPR slow-motion spectra of spin labelled phospholipids in liquid crystalline bilayers based on a molecular dynamics simulation of the lipid dynamics
Open this publication in new window or tab >>A direct simulation of EPR slow-motion spectra of spin labelled phospholipids in liquid crystalline bilayers based on a molecular dynamics simulation of the lipid dynamics
2001 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 3, no 23, 5311-5319 p.Article in journal (Refereed) Published
Abstract [en]

EPR line shapes can be calculated from the stochastic Liouville equation assuming a stochastic model for the reorientation of the spin probe. Here we use instead and for the first time a detailed molecular dynamics (MD) simulation to generate the stochastic input to the Langevin form of the Liouville equation. A 0.1 μs MD simulation at T = 50°C of a small lipid bilayer formed by 64 dipalmitoylphosphatidylcholine (DPPC) molecules at the water content of 23 water molecules per lipid was used. In addition, a 10 ns simulation of a 16 times larger system consisting of 32 DPPC molecules with a nitroxide spin moiety attached at the sixth position of the sn2 chain and 992 ordinary DPPC molecules, was used to investigate the extent of the perturbation caused by the spin probe. Order parameters, reorientational dynamics and the EPR FID curve were calculated for spin probe molecules and ordinary DPPC molecules. The timescale of the electron spin relaxation for a spin-moiety attached at the sixth carbon position of a DPPC lipid molecule is 11.9 × 107 rad s−1 and for an unperturbed DPPC molecule it is 3.5 × 107 rad s−1.

Place, publisher, year, edition, pages
RSC Publishing, 2001
National Category
Biophysics Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-3892 (URN)10.1039/B105618M (DOI)
Available from: 2004-04-22 Created: 2004-04-22 Last updated: 2012-06-01Bibliographically approved
2. The effect of memory in the Stochastic Liouville equation of motion. Electronic energy migration transfer between reorientating donor-donor, donor-acceptor chromophores
Open this publication in new window or tab >>The effect of memory in the Stochastic Liouville equation of motion. Electronic energy migration transfer between reorientating donor-donor, donor-acceptor chromophores
2004 In: Spectrochimica Acta Part A, ISSN 1386-1425, Vol. 61, no 1-2, 299-304 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:umu:diva-3893 (URN)
Available from: 2004-04-22 Created: 2004-04-22Bibliographically approved
3. Extended Förster theory of donor-donor energy migration in bifluorophoric macromomolecules: Part I. A new approach to quantitative analysis of time resolved fluorescence anisotropy
Open this publication in new window or tab >>Extended Förster theory of donor-donor energy migration in bifluorophoric macromomolecules: Part I. A new approach to quantitative analysis of time resolved fluorescence anisotropy
2000 In: Molecular Physics, Vol. 98, 1529-1537 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:umu:diva-3894 (URN)
Available from: 2004-04-22 Created: 2004-04-22Bibliographically approved
4. Extended Förster theory for determining intraprotein distances: 1. The K2-dynamics and fluorophore reorientation
Open this publication in new window or tab >>Extended Förster theory for determining intraprotein distances: 1. The K2-dynamics and fluorophore reorientation
2004 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, Vol. 108, no 44, 17243-17250 p.Article in journal (Refereed) Published
Abstract [en]

A detailed analysis of the previously developed (J. Chem. Phys. 1996, 105, 10896) extended Förster theory (EFT) is presented for analyzing electronic energy migration within pairs of donors (D). Synthetic data that mimics experimental time-correlated single photon counting data were generated and re-analyzed. To cover a wide dynamic range and various orientational restrictions, the rates of reorientation, as well as the orientational configurations of the interacting D-groups were varied. In general DD distances are recovered within an error limit of 5%, while the errors in orientational configurations are usually larger. The Maier−Saupe and cone potentials were used to generate an immense variety of orientational trajectories. The results obtained exhibit no significant dependence on the choice of potential function used for generating EFT data. Present work demonstrates how to overcome the classical “κ2-problem” and the frequently applied approximation of κ2 = 2/3 in the data analyses. This study also outlines the procedure for analyzing fluorescence depolarization data obtained for proteins, which are specifically labeled with D-groups. The EFT presented here brings the analyses of DDEM data to the same level of molecular detail as in ESR- and NMR-spectroscopy.

Keyword
Thimerosal, Ethylmercury, Mice, Autoimmunity
Identifiers
urn:nbn:se:umu:diva-2134 (URN)10.1021/jp040423d (DOI)
Available from: 2007-02-15 Created: 2007-02-15 Last updated: 2009-10-26Bibliographically approved
5. Ito diffusions on hypersurfaces with application to the Schwarz-P surface and nuclear magnetic resonance theory
Open this publication in new window or tab >>Ito diffusions on hypersurfaces with application to the Schwarz-P surface and nuclear magnetic resonance theory
2002 In: Journal of Chemical Physics, ISSN 0021-9606, Vol. 117, no 19, 8634-8643 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:umu:diva-3896 (URN)
Available from: 2004-04-22 Created: 2004-04-22Bibliographically approved
6. Nuclear magnetic relaxation study of the microstructure of a bicontinuous cubic phase
Open this publication in new window or tab >>Nuclear magnetic relaxation study of the microstructure of a bicontinuous cubic phase
2004 (English)In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, no 6, 4321-4329 p.Article in journal (Refereed) Published
Abstract [en]

A NMR relaxation and NMR translational diffusion study is performed on a bicontinuous cubic phase of the dodecyltrimethylammonium chloride/2H2O system with low water content. It is demonstrated how NMR relaxation measurements are combined with structural investigations of X-ray and NMR molecular diffusion measurements to create a consistent picture of the mesoscopic structure of the cubic phase. The 14N, spin-lattice (R1) and spin-spin relaxation rates (R2), were measured for the surfactant at two different field strengths and at four temperatures. The water and the surfactant translational diffusion coefficients were measured by NMR field gradient technique. The experimental spin relaxation rates, and translation diffusion coefficients were interpreted in a model based on a Brownian dynamics (BD) simulation of translational diffusion along curved interfaces (P. Håkansson, L. Persson and P.-O. Westlund, J. Chem. Phys., 2002,117(19), 8634-8643, ). The model surfaces used in our BD relaxation model are also frequently used in interpretations of X-ray crystallography and in free energy calculations on bicontinuous phases. One of our BD-models was able to quantify the influence of the water/lipid interface on the NMR relaxation and diffusion data. Together with X-ray data, a consistent picture of the microstructure for this system was obtained.

Place, publisher, year, edition, pages
Cambridge: Royal Society of Chemistry, 2004
Identifiers
urn:nbn:se:umu:diva-3897 (URN)10.1039/b408003c (DOI)
Available from: 2004-04-22 Created: 2004-04-22 Last updated: 2011-03-15Bibliographically approved

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