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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6

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Department: search.filters.department.Department of Mechanical EngineeringSubject: search.filters.subject.Mathematical physics

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Now showing 1 - 4 of 4
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    PublicationOpen Access
    Buckling of stiff polymers: influence of thermal fluctuations
    (American Physical Society (APS), 2007) Emanuel, Marc; Mohrbach, Herve; Schiessel, Helmut; Kulic, Igor M.; Department of Mechanical Engineering; Department of Mechanical Engineering; Sayar, Mehmet; Faculty Member; College of Engineering; 109820
    The buckling of biopolymers is a frequently studied phenomenon The influence of thermal fluctuations on the buckling transition is, however, often ignored and not completely understood. A quantitative theory of the buckling of a wormlike chain based on a semiclassical approximation of the partition function is presented. The contribution of thermal fluctuations to the force-extension relation that allows one to go beyond the classical Euler buckling is derived in the linear and nonlinear regimes as well. It is shown that the thermal fluctuations in the nonlinear buckling regime increase the end-to-end distance of the semiflexible rod if it is confined to two dimensions as opposed to the three-dimensional case. The transition to a buckled state softens at finite temperature. We derive the scaling behavior of the transition shift with increasing ratio of contour length versus persistence length.
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    PublicationOpen Access
    Twist-writhe partitioning in a coarse-grained DNA minicircle model
    (American Physical Society (APS), 2010) Department of Mechanical Engineering; Department of Physics; Department of Mechanical Engineering; Department of Physics; Sayar, Mehmet; Avşaroğlu, Barış; Kabakçıoğlu, Alkan; Faculty Member; Faculty Member; College of Engineering; College of Sciences; 109820; N/A; 49854
    Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular-dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long chains without sacrificing the characteristic structural properties of the DNA molecule, such as its helicity, backbone directionality, and the presence of major and minor grooves. The model parameters are extracted directly from full-atomistic simulations of DNA oligomers via Boltzmann inversion; therefore, our results can be interpreted as an extrapolation of those simulations to presently inaccessible chain lengths and simulation times. Using this model, we measure the twist/writhe partitioning in DNA minicircles, in particular its dependence on the chain length and excess linking number. We observe an asymmetric supercoiling transition consistent with experiments. Our results suggest that the fraction of the linking number absorbed as twist and writhe is nontrivially dependent on chain length and excess linking number. Beyond the supercoiling transition, chains of the order of one persistence length carry equal amounts of twist and writhe. For longer chains, an increasing fraction of the linking number is absorbed by the writhe.
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    PublicationOpen Access
    Junction formation during desiccation cracking
    (American Physical Society (APS), 2006) Toga, K. B.; Department of Mechanical Engineering; Department of Mechanical Engineering; Alaca, Burhanettin Erdem; Faculty Member; College of Engineering; 115108
    In order to provide a sound physical basis for the understanding of the formation of desiccation crack networks, an experimental study is presented addressing junction formation. Focusing on junctions, basic features of the network determining the final pattern, provides an elemental approach and imparts conceptual clarity to the rather complicated problem of the evolution of crack patterns. Using coffee-water mixtures a clear distinction between junction formation during nucleation and propagation is achieved. It is shown that for the same drying suspension, one can switch from the well-known symmetric triple junctions that are unique to the nucleation phase to propagation junctions that are purely dictated by the variations of the stress state. In the latter case, one can even manipulate the path of a propagating crack in a deterministic fashion by changing the stress state within the suspension. Clear microscopic evidence is provided for the formation of propagation junctions, and material inhomogeneity is observed to be reflected by a broad distribution of angles, in stark contrast to shrinkage cracks in homogeneous solid films.
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    PublicationOpen Access
    Equilibrium polyelectrolyte bundles with different multivalent counterion concentrations
    (American Physical Society (APS), 2010) Holm, Christian; Department of Mechanical Engineering; Department of Mechanical Engineering; Sayar, Mehmet; Faculty Member; College of Engineering; 109820
    We present the results of molecular-dynamics simulations on the salt concentration dependence of the formation of polyelectrolyte bundles in thermodynamic equilibrium. Extending our results on salt-free systems we investigate here deficiency or excess of trivalent counterions in solution. Our results reveal that the trivalent counterion concentration significantly alters the bundle size and size distribution. The onset of bundle formation takes place at earlier Bjerrum length values with increasing trivalent counterion concentration. For the cases of 80%, 95%, and 100% charge compensation via trivalent counterions, the net charge of the bundles decreases with increasing size. We suggest that competition among two different mechanisms, counterion condensation and merger of bundles, leads to a nonmonotonic change in line-charge density with increasing Bjerrum length. The investigated case of having an abundance of trivalent counterions by 200% prohibits such a behavior. In this case, we find that the difference in effective line-charge density of different size bundles diminishes. In fact, the system displays an isoelectric point, where all bundles become charge neutral.