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dc.contributor.advisorFrediani, Luca
dc.contributor.authorSteindal, Arnfinn Hykkerud
dc.date.accessioned2013-05-08T12:51:31Z
dc.date.available2013-05-08T12:51:31Z
dc.date.issued2013-01-22
dc.description.abstractThis thesis presents the development of theoretical models for the calculations of one- and two-photon absorption, and computational studies on solvated systems and biomolecules. The photon-absorbing chromophore is described by density functional theory, while the effects of the surroundings are taken into account by means of polarizable embedding models. The theory and implementation of a three-layered fully polarizable method is presented in this thesis. In this method, the short-range electrostatic potential due to the solvent is treated by a polarizable molecular mechanics force field, while the long-range effects are described by a dielectric continuum. This QM/MM/PCM implementation was tested on three organic molecules solvated in water and shown to converge faster with respect to system size compared to calculations using quantum mechanics/molecular mechanics (QM/MM) only. Further, the parallelization of the QM/MM module in the Dalton program is decribed, making it possible to do calculations on large molecular systems with the use of modern supercomputers. This implementation was used to calculate the one- and two-photon absorption properties in fluorescent proteins, demonstrating the importance of describing the protein surrounding the chromophore by a polarizable embedding.en
dc.description.doctoraltypeph.d.en
dc.description.popularabstractKvantemekanikk er nødvendig hvis man vil beregne om et molekyl vil absorberer lys. For store molekylære systemer vil slike beregninger ikke være mulig å gjennomføre, selv på de største datamaskiner som finnes. Grunnen til det er at disse metodene skalerer minst kvadratisk med størrelsen på systemet - hvis et molekyl er ti ganger større enn et annet vil det ta hundre ganger så lang tid å kjøre beregningen. Vi har utviklet en metode der kun de delene av de molekylære systemene som faktisk absorberer lyset blir beskrevet av kvantemekanikk. Resten av systemet blir beskrevet av en langt enklere modell, med polariserbare omgivelser. I tillegg har vi parallelisert programmet som kjører disse beregningene, slik at beregninger kan kjøre på kraftige superdatamaskiner ved bruk av mange prosessorer samtidig. Programmet har blant annet blitt bruk til å beregne en- og to-foton absorpsjon i grønt fluorescerende protein, og beregningene viser at vår metode gir en god beskrivelse av omgivelsene.en
dc.description.sponsorshipNOTUR for tungregningsfasiliteter, Norges forskningsråd gjennom senter for fremragende forskning (CTCC), og Tromsø Forskingsstiftelse gjennom SURFINT prosjektet.en
dc.descriptionThe papers of this thesis are not available in Munin: <br/>1. A. H. Steindal, K. Ruud, L. Frediani, K. Aidas and J. Kongsted: 'Excitation energies in solution: the fully polarizable QM/MM/PCM method', Journal of Physical Chemistry B (2011), vol.115(12):3027–3037. Available at <a href=http://dx.doi.org/10.1021/jp1101913>http://dx.doi.org/10.1021/jp1101913</a> <br/>2. A. H. Steindal, J. M. H. Olsen, L. Frediani, J. Kongsted and K. Ruud: 'Parallelization of the polarizable embedding scheme for higher-order response functions', Molecular Physics (2012), Vol. 110, no.19-20. Available at <a href=http://dx.doi.org/10.1080/00268976.2012.721016>http://dx.doi.org/10.1080/00268976.2012.721016</a> <br/>3. A. H. Steindal, J. M. H. Olsen, K. Ruud, L. Frediani and J. Kongsted: 'A combined quantum mechanics and molecular mechanics study of the one- and two-photon absorption in the green fluorescent protein', Physical Chemistry Chemical Physics (2012), vol.14:5440-5451. Available at <a href=http://dx.doi.org/10.1039/C2CP23537D>http://dx.doi.org/10.1039/C2CP23537D</a> <br/>4. M. T. P. Beerepoot, A. H. Steindal, J. M. H. Olsen, K. Ruud, L. Frediani, B. O. Brandsdal and J. Kongsted: 'A polarizable embedding DFT study of one-photon absorption in fluorescent proteins' (manuscript) <br/>5. N. H. List, J. M. H. Olsen, H. J. Aa. Jensen, A. H. Steindal and J. Kongsted: 'Molecular-level insight into the spectral tuning mechanism of the DsRed chromophore', Journal of Physical Chemistry Letters (2012), vol.3(23):3513–3521. Available at <a href=http://dx.doi.org/10.1021/jz3014858>http://dx.doi.org/10.1021/jz3014858</a>en
dc.identifier.isbn978-82-8236-086-9
dc.identifier.isbn978-82-8236-087-6
dc.identifier.urihttps://hdl.handle.net/10037/5148
dc.identifier.urnURN:NBN:no-uit_munin_4862
dc.language.isoengen
dc.publisherUniversitetet i Tromsøen
dc.publisherUniversity of Tromsøen
dc.rights.accessRightsopenAccess
dc.rights.holderCopyright 2013 The Author(s)
dc.subject.courseIDDOKTOR-004en
dc.subjectVDP::Matematikk og Naturvitenskap: 400::Kjemi: 440::Teoretisk kjemi, kvantekjemi: 444en
dc.subjectVDP::Mathematics and natural science: 400::Chemistry: 440::Theoretical chemistry, quantum chemistry: 444en
dc.titleUnderstanding and predicting one- and two-photon absorption properties of molecular complexesen
dc.typeDoctoral thesisen
dc.typeDoktorgradsavhandlingen


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