Capstan friction model for DNA ejection from bacteriophages

Bacteriophages infect cells by attaching to the outer membrane and injecting their DNA into the cell.The phage DNA is then transcribed by the cell's transcription machinery.A number of physical mechanisms by which DNA can be translocated from the phage capsid into the cell have been identified. A fast ejection driven by the elastic and electrostatic potential energy of the compacted DNA within the viral capsid appears to be used by most phages, at least to initiate infection.In recent in vitro experiments, the speed of DNA translocation from a lambda phage capsid has been measured as a function of ejected length over the entire duration of the event.Here a mechanical model is proposed that is able to explain the observed dependence of exit velocity on ejected length, and that is also consistent with the accepted picture of the geometric arrangement of DNA within the viral capsid.Comment: 4 pages, 2 figure

Electromigration dispersion in Capillary Electrophoresis

In a previous paper (S. Ghosal and Z. Chen Bull. Math. Biol. 2010, vol. 72, pg. 2047) it was shown that the evolution of the solute concentration in capillary electrophoresis is described by a nonlinear wave equation that reduced to Burger's equation if the nonlinearity was weak. It was assumed that only strong electrolytes (fully dissociated) were present. In the present paper it is shown that the same governing equation also describes the situation where the electrolytic buffer consists of a single weak acid (or base). A simple approximate formula is derived for the dimensionless peak variance which is shown to agree well with published experimental data.Comment: 10 pages, 2 figure

Does buckling instability of the pseudopodium limit how well an amoeba can climb?

The maximum force that a crawling cell can exert on a substrate is a quantity of interest in cell biomechanics. One way of quantifying this force is to allow the cell to crawl against a measurable and adjustable restraining force until the cell is no longer able to move in a direction opposite to the applied force. Fukui et al.[1] reported on an experiment where amoeboid cells were imaged while they crawled against an artificial gravity field created by a centrifuge. An unexpected observation was that the net applied force on the amoeba did not seem to be the primary factor that limited its ability to climb. Instead, it appeared that the amoeba stalled when it was no longer able to support a pseudopodium against the applied gravity field. The high g-load bend the pseudopodium thereby preventing its attachment to the target point directly ahead of the cell. In this paper we further refine this idea by identifying the bending of the pseudopodium with the onset of elastic instability of a beam under its own weight. It is shown that the principal features of the experiment may be understood through this model and an estimate for the limiting g-load in reasonable accord with the experimental measurements is recovered.Comment: 7 pages, 2 figure

Anomalous diffusion in an electrolyte saturated paper matrix

Diffusion of colored dye on water saturated paper substrates has been traditionally exploited with great skill by renowned water color artists. The same physics finds more recent practical applications in paper based diagnostic devices deploying chemicals that react with a bodily fluid yielding colorimetric signals for disease detection. During spontaneous imbibition through the tortuous pathways of a porous electrolyte saturated paper matrix, a dye molecule undergoes diffusion in a complex network of pores. The advancing front forms a strongly correlated interface that propagates diffusively but with an enhanced effective diffusivity. We measure this effective diffusivity and show that it is several orders of magnitude greater than the free solution diffusivity and has a significant dependence on the solution pH and salt concentration in the background electrolyte. We attribute this to electrically mediated interfacial interactions between the ionic species in the liquid dye and spontaneous surface charges developed at porous interfaces, and introduce a simple theory to explain this phenomenon.Comment: 1

Selection of Dominant Characteristic Modes

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.The theory of characteristic modes is a popular physics based deterministic approach which has found several recent applications in the fields of radiator design, electromagnetic interference modelling and radiated emission analysis. The modal theory is based on the approximation of the total induced current in an electromagnetic structure in terms of a weighted sum of multiple characteristic current modes. The resultant outgoing field is also a weighted summation of the characteristic field patterns. Henceforth, a proper modal measure is an essential requirement to identify the modes which play a dominant role for a frequency of interest. The existing literature of significance measures restricts itself for ideal lossless structures only. This paper explores the pros and cons of the existing measures and correspondingly suggests suitable alternatives for both radiating and scattering applications. An example is presented in order to illustrate the proposed modal method for approximating the shielding response of a slotted geometry