Lund University Publications
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Lund University Lund University Publications2000-01-01T00:00+00:001dailyMonte Carlo simulations of polyelectrolytes inside viral capsids
https://lup.lub.lu.se/search/publication/6b5a70bc-192c-4458-9860-622f13c8481c
Angelescu, DanielBruinsma, RLinse, Per2006Structural features of polyelectrolytes as single-stranded RNA or double-stranded DNA confined inside viral capsids and the thermodynamics of the encapsidation of the polyelectrolyte into the viral capsid have been examined for various polyelectrolyte lengths by using a coarse-grained model solved by Monte Carlo simulations. The capsid was modeled as a spherical shell with embedded charges and the genome as a linear jointed chain of oppositely charged beads, and their sizes corresponded to those of a scaled-down T=3 virus. Counterions were explicitly included, but no salt was added. The encapisdated chain was found to be predominantly located at the inner capsid surface, in a disordered manner for flexible chains and in a spool-like structure for stiff chains. The distribution of the small ions was strongly dependent on the polyelectrolyte-capsid charge ratio. The encapsidation enthalpy was negative and its magnitude decreased with increasing polyelectrolyte length, whereas the encapsidation entropy displayed a maximum when the capsid and polyelectrolyte had equal absolute charge. The encapsidation process remained thermodynamically favorable for genome charges ca. 3.5 times the capsid charge. The chain stiffness had only a relatively weak effect on the thermodynamics of the encapsidation.http://lup.lub.lu.se/record/908682http://dx.doi.org/10.1103/PhysRevE.73.041921wos:000237146400078scopus:33645991802engPhysical Review E (Statistical, Nonlinear, and Soft Matter Physics); 73(4) (2006)ISSN: 1539-3755Fysikalisk kemiMonte Carlo simulations of polyelectrolytes inside viral capsidscontributiontojournal/articleinfo:eu-repo/semantics/articletextUltrasound-induced acoustophoretic motion of microparticles in three dimensions
https://lup.lub.lu.se/search/publication/41366257-6656-4c64-b887-a1ebbaf771f2
Muller, P. B.Rossi, M.Marin, A. G.Barnkob, R.Augustsson, PerLaurell, ThomasKaehler, C. J.Bruus, H.2013We derive analytical expressions for the three-dimensional (3D) acoustophoretic motion of spherical microparticles in rectangular microchannels. The motion is generated by the acoustic radiation force and the acoustic streaming-induced drag force. In contrast to the classical theory of Rayleigh streaming in shallow, infinite, parallel-plate channels, our theory does include the effect of the microchannel sidewalls. The resulting predictions agree well with numerics and experimental measurements of the acoustophoretic motion of polystyrene spheres with nominal diameters of 0.537 and 5.33 mu m. The 3D particle motion was recorded using astigmatism particle tracking velocimetry under controlled thermal and acoustic conditions in a long, straight, rectangular microchannel actuated in one of its transverse standing ultrasound-wave resonance modes with one or two half-wavelengths. The acoustic energy density is calibrated in situ based on measurements of the radiation dominated motion of large 5-mu m-diameter particles, allowing for quantitative comparison between theoretical predictions and measurements of the streaming-induced motion of small 0.5-mu m-diameter particles.http://lup.lub.lu.se/record/4030646http://dx.doi.org/10.1103/PhysRevE.88.023006wos:000322918700010scopus:84883874034engPhysical Review E (Statistical, Nonlinear, and Soft Matter Physics); 88(2), no 023006 (2013)ISSN: 1539-3755MedicinteknikUltrasound-induced acoustophoretic motion of microparticles in three dimensionscontributiontojournal/articleinfo:eu-repo/semantics/articletextFoundation of fractional Langevin equation: Harmonization of a many-body problem
https://lup.lub.lu.se/search/publication/f0f5f653-08be-4c65-a51e-ff64168d7f2f
Lizana, LudvigAmbjörnsson, TobiasTaloni, AlessandroBarkai, EliLomholt, Michael A.2010In this study we derive a single-particle equation of motion, from first principles, starting out with a microscopic description of a tracer particle in a one-dimensional many-particle system with a general two-body interaction potential. Using a harmonization technique, we show that the resulting dynamical equation belongs to the class of fractional Langevin equations, a stochastic framework which has been proposed in a large body of works as a means of describing anomalous dynamics. Our work sheds light on the fundamental assumptions of these phenomenological models and a relation derived by Kollmann.http://lup.lub.lu.se/record/1616662http://dx.doi.org/10.1103/PhysRevE.81.051118wos:000278148400028scopus:77952338160engPhysical Review E (Statistical, Nonlinear, and Soft Matter Physics); 81(5) (2010)ISSN: 1539-3755BiofysikFoundation of fractional Langevin equation: Harmonization of a many-body problemcontributiontojournal/articleinfo:eu-repo/semantics/articletext