Conformations and dynamics of strongly charged biomolecules

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dc.contributor Aalto-yliopisto fi
dc.contributor Aalto University en
dc.contributor.author Punkkinen, Olli
dc.date.accessioned 2012-08-21T12:45:52Z
dc.date.available 2012-08-21T12:45:52Z
dc.date.issued 2009
dc.identifier.isbn 978-951-22-9917-1
dc.identifier.isbn 978-951-22-9915-7 (printed) #8195;
dc.identifier.issn 1795-4584
dc.identifier.uri https://aaltodoc.aalto.fi/handle/123456789/4619
dc.description.abstract This Thesis is based on analytical and numerical calculations concerning strongly charged biomolecules. The study concentrates on statistical properties of strongly charged biopolymers in the presence of neutralizing counterions and reservoir salt ions, involving applications on deoxyribonucleic acid (DNA), which is a key molecule in human cells. The Thesis starts from constructing a theory that explains the counter- and coion distributions around an arbitrary strongly charged surface, and moves to applications involving statistical conformations of highly stretched DNA, and dynamics of settling the DNA chain in the presence of a large amount of reservoir salt. Studies on ion-distributions around a charged surface concentrate on finding a theoretical description in the limit where electrostatic interactions between the ions and the charged surface are so strong that they dominate over the translational entropy of the counter- and coions. In particular we explain how the added electrolyte or salt modifies the ion distributions compared to the zero salt case, a topic which is highly relevant for bioapplications that take place under physiological salt concentration. Application on the DNA overstretching transition involves the evaluation of the response of the chain to a strong external stretching force. Here we explain how the force needed to extend the chain depends on the added electrolyte concentration. We concentrate on finding the conformation of the chain over the persistence length of DNA, and the equation of state for DNA as a function of the stretching force. Studies on dynamical properties of DNA concern the sedimentation velocity of a long DNA chain under physiological salt conditions that it is typically described using the self-avoiding walk (SAW) model. Here we show that in the limit of large polymer or Reynolds number, the chain goes through a crossover in its shape, transforming from slightly perturbed SAW chain into an elongated configuration along the direction of sedimentation. We present a model that couples the instant configuration in a non-linear way to the settling velocity of the chain. This way the scaling laws for both the radius of gyration of the chain characterizing its size, and for the diffusion coefficient of the chain characterizing its dynamics, are found to be in agreement with numerical simulations. en
dc.format.extent Verkkokirja (1078 KB, 100 s.)
dc.format.mimetype application/pdf
dc.language.iso en en
dc.publisher Teknillinen korkeakoulu en
dc.relation.ispartofseries TKK dissertations, 170 en
dc.relation.haspart [Publication 1]: O. Punkkinen, A. Naji, R. Podgornik, I. Vattulainen, and P.-L. Hansen. 2008. Ionic cloud distribution close to a charged surface in the presence of salt. Europhysics Letters, volume 82, number 4, 48001. en
dc.relation.haspart [Publication 2]: Olli Punkkinen, Ali Naji, Ilpo Vattulainen, and Rudi Podgornik. 2009. Distribution of ion clouds with respect to a charged surface in the presence of bulk salt. Helsinki Institute of Physics preprint HIP-2009-12/TH. en
dc.relation.haspart [Publication 3]: Olli Punkkinen, Per Lyngs Hansen, Ling Miao, and Ilpo Vattulainen. 2005. DNA overstretching transition: ionic strength effects. Biophysical Journal, volume 89, number 2, pages 967-978. © 2005 Biophysical Society. By permission. en
dc.relation.haspart [Publication 4]: V. Lehtola, O. Punkkinen, and T. Ala-Nissila. 2007. Polymer scaling and dynamics in steady-state sedimentation at infinite Péclet number. Physical Review E, volume 76, number 5, 051802. © 2007 American Physical Society. By permission. en
dc.subject.other Physics en
dc.title Conformations and dynamics of strongly charged biomolecules en
dc.type G5 Artikkeliväitöskirja fi
dc.contributor.department Teknillisen fysiikan laitos fi
dc.subject.keyword strong coupling en
dc.subject.keyword overcharging en
dc.subject.keyword overstretching en
dc.subject.keyword sedimentation en
dc.identifier.urn URN:ISBN:978-951-22-9917-1
dc.type.dcmitype text en
dc.type.ontasot Väitöskirja (artikkeli) fi
dc.type.ontasot Doctoral dissertation (article-based) en


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