Multiscale modeling of biological and soft matter

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dc.contributor Aalto-yliopisto fi
dc.contributor Aalto University en Falck, Emma 2012-02-17T06:49:45Z 2012-02-17T06:49:45Z 2005-03-15
dc.identifier.isbn 952-10-1688-4
dc.identifier.issn 1455-0563
dc.description.abstract The large range of spatial and temporal scales inherent in biological and soft matter is a challenge to modeling. To understand the physics of a cell membrane, one needs to start from Ångström-sized atoms and their motions in the femtosecond range, and go all the way to whole cells, whose diameters can be tens of micrometers and lifetimes of the order of days. All these scales can neither be probed by a single experimental technique, nor modeled using one simulation approach. What is needed is a range of techniques. Describing matter by a hierarchy of computational models, systematically linking the models at lower resolution to those at higher resolution, is termed multiscale modeling. Depending on the phenomenon one wishes to study, one may choose atomic-level models and algorithms, opt for a simplified or coarse-grained description, or decide on a combination of these. The aim of this Thesis is to describe modeling at atomic scale and mesoscale, i.e., at scales in the range 1-1000 nm and 1-1000 ns. We also focus on the systematic linking; how to reduce the degrees of freedom in an atomic-scale model to arrive at a coarse-grained description. Further, use of hybrid models that combine atomic and coarse-grained descriptions is discussed. We approach multiscale modeling through examples from biological and soft matter physics. Atomic-scale modeling is illustrated through molecular dynamics simulations of phospholipid/cholesterol bilayers. The effect of cholesterol on the free volume, packing, and diffusive properties of bilayers is investigated. We then link the atomic-scale model to one allowing us to reach length scales significantly larger than those reached in current-day state-of-the-art atomic-level simulations: the new model offers an eight-order-of-magnitude speed-up, enabling us to study the lateral structure of bilayers at length scales up to hundreds of nanometers at a modest computational cost. The simulation results point at the existence of cholesterol-rich domains with sizes in the ten-nanometer-range. From membrane systems we move to the realm of complex fluids. We use polymer chains and colloids in solution as examples of systems where hybrid models should be used. The solutes are modeled in microscopic detail, while the solvent is coarse-grained. The solvent model is cost-effective, yet correctly describes the hydrodynamic interactions between the solute particles. Using these models we are able to resolve a long-standing debate about dynamic scaling of two-dimensional polymers in solution, and obtain interesting results for collective diffusion in colloidal suspensions. en
dc.format.extent 97, [53]
dc.format.mimetype application/pdf
dc.language.iso en en
dc.publisher Helsinki University of Technology en
dc.publisher Teknillinen korkeakoulu fi
dc.relation.ispartofseries Internal report / Helsinki Institute of Physics en
dc.relation.ispartofseries 2005-01 en
dc.relation.haspart E. Falck, O. Punkkinen, I. Vattulainen, and T. Ala-Nissila. 2003. Dynamics and scaling of two-dimensional polymers in a dilute solution. Physical Review E (Rapid Communications) 68, pages 050102 (R) : 1-4. [article1.pdf] © 2003 American Physical Society. By permission.
dc.relation.haspart E. Falck, J. M. Lahtinen, I. Vattulainen, and T. Ala-Nissila. 2004. Influence of hydrodynamics on many-particle diffusion in 2D colloidal suspensions. The European Physical Journal E 13, pages 267-275. [article2.pdf] © 2004 EDP Sciences. By permission.
dc.relation.haspart E. Falck, M. Patra, M. Karttunen, M. T. Hyvönen, and I. Vattulainen. 2004. Lessons of slicing membranes: interplay of packing, free area, and lateral diffusion in phospholipid/cholesterol bilayers. Biophysical Journal 87, number 2, pages 1076-1091. [article3.pdf] © 2004 Biophysical Society. By permission.
dc.relation.haspart T. Murtola, E. Falck, M. Patra, M. Karttunen, and I. Vattulainen. 2004. Coarse-grained model for phospholipid/cholesterol bilayer. Journal of Chemical Physics 121, number 18, pages 9156-9165. [article4.pdf] © 2004 American Institute of Physics. By permission.
dc.relation.haspart E. Falck, M. Patra, M. Karttunen, M. T. Hyvönen, and I. Vattulainen. 2004. Impact of cholesterol on voids in phospholipid membranes. Journal of Chemical Physics 121, number 24, pages 12676-12689. [article5.pdf] © 2004 American Institute of Physics. By permission.
dc.subject.other Physics en
dc.subject.other Biotechnology en
dc.title Multiscale modeling of biological and soft matter en
dc.type G5 Artikkeliväitöskirja fi
dc.description.version reviewed en
dc.contributor.department Department of Engineering Physics and Mathematics en
dc.contributor.department Teknillisen fysiikan ja matematiikan osasto fi
dc.subject.keyword computer simulations en
dc.subject.keyword multiscale modeling en
dc.subject.keyword coarse-graining en
dc.subject.keyword stochastic rotation dynamics en
dc.subject.keyword molecular dynamics en
dc.subject.keyword Monte Carlo en
dc.subject.keyword inverse Monte Carlo en
dc.subject.keyword membrane en
dc.subject.keyword lipid bilayer en
dc.subject.keyword cholesterol en
dc.subject.keyword polymer dynamics en
dc.subject.keyword colloidal dynamics en
dc.subject.keyword dynamic scaling en
dc.identifier.urn urn:nbn:fi:tkk-004922
dc.type.dcmitype text en
dc.type.ontasot Väitöskirja (artikkeli) fi
dc.type.ontasot Doctoral dissertation (article-based) en
dc.contributor.lab Laboratory of Physics en
dc.contributor.lab Fysiikan laboratorio fi

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