Extension of nano-confined DNA: quantitative comparison between experiment and theory

The extension of DNA confined to nanochannels has been studied intensively and in detail. Yet quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose we performed new experiments, measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic buffer strength. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths the agreement is less good. We discuss possible reasons. Our approach allows, in principle, to measure the Kuhn length and effective width of a single DNA molecule and more generally of semiflexible polymers in solution.Comment: Revised version, 6 pages, 2 figures, 1 table, supplementary materia

A microfluidic device for the study of the orientational dynamics of microrods

We describe a microfluidic device for studying the orientational dynamics of microrods. The device enables us to experimentally investigate the tumbling of microrods immersed in the shear flow in a microfluidic channel with a depth of 400 mu and a width of 2.5 mm. The orientational dynamics was recorded using a 20 X microscopic objective and a CCD camera. The microrods were produced by shearing microdroplets of photocurable epoxy resin. We show different examples of empirically observed tumbling. On the one hand we find that short stretches of the experimentally determined time series are well described by fits to solutions of Jeffery's approximate equation of motion [Jeffery, Proc. R. Soc. London. 102 (1922), 161-179]. On the other hand we find that the empirically observed trajectories drift between different solutions of Jeffery's equation. We discuss possible causes of this orbit drift.Comment: 11 pages, 8 figure

Magnetic Dipole Absorption of Radiation in Small Conducting Particles

We give a theoretical treatment of magnetic dipole absorption of electromagnetic radiation in small conducting particles, at photon energies which are large compared to the single particle level spacing, and small compared to the plasma frequency. We discuss both diffusive and ballistic electron dynamics for particles of arbitrary shape. The conductivity becomes non-local when the frequency is smaller than the frequency \omega_c characterising the transit of electrons from one side of the particle to the other, but in the diffusive case \omega_c plays no role in determining the absorption coefficient. In the ballistic case, the absorption coefficient is proportional to \omega^2 for \omega << \omega_c, but is a decreasing function of \omega for \omega >> \omega_c.Comment: 25 pages of plain TeX, 2 postscipt figure

Caustics in turbulent aerosols

Networks of caustics can occur in the distribution of particles suspended in a randomly moving gas. These can facilitate coagulation of particles by bringing them into close proximity, even in cases where the trajectories do not coalesce. We show that the long-time morphology of these caustic patterns is determined by the Lyapunov exponents lambda_1, lambda_2 of the suspended particles, as well as the rate J at which particles encounter caustics. We develop a theory determining the quantities J, lambda_1, lambda_2 from the statistical properties of the gas flow, in the limit of short correlation times.Comment: 4 pages, 3 figure

Orientational correlations in confined DNA

We study how the orientational correlations of DNA confined to nanochannels depend on the channel diameter D by means of Monte Carlo simulations and a mean-field theory. This theory describes DNA conformations in the experimentally relevant regime where the Flory-de Gennes theory does not apply. We show how local correlations determine the dependence of the end-to-end distance of the DNA molecule upon D. Tapered nanochannels provide the necessary resolution in D to study experimentally how the extension of confined DNA molecules depends upon D. Our experimental and theoretical results are in qualitative agreement.Comment: Revised version including supplemental material, 7 pages, 8 figure

Understanding of the phase transformation from fullerite to amorphous carbon at the microscopic level

We have studied the shock-induced phase transition from fullerite to a dense amorphous carbon phase by tight-binding molecular dynamics. For increasing hydrostatic pressures P, the C60-cages are found to polymerise at P<10 GPa, to break at P~40 GPa and to slowly collapse further at P>60 GPa. By contrast, in the presence of additional shear stresses, the cages are destroyed at much lower pressures (P<30 GPa). We explain this fact in terms of a continuum model, the snap-through instability of a spherical shell. Surprisingly, the relaxed high-density structures display no intermediate-range order.Comment: 5 pages, 3 figure

Fingerprints of Random Flows?

We consider the patterns formed by small rod-like objects advected by a random flow in two dimensions. An exact solution indicates that their direction field is non-singular. However, we find from simulations that the direction field of the rods does appear to exhibit singularities. First, ` scar lines' emerge where the rods abruptly change direction by $\pi$. Later, these scar lines become so narrow that they ` heal over' and disappear, but their ends remain as point singularities, which are of the same type as those seen in fingerprints. We give a theoretical explanation for these observations.Comment: 21 pages, 11 figure

Collective versus single-particle effects in the optical spectra of finite electronic quantum systems

We study optical spectra of finite electronic quantum systems at frequencies smaller than the plasma frequency using a quasi-classical approach. This approach includes collective effects and enables us to analyze how the nature of the (single-particle) electron dynamics influences the optical spectra in finite electronic quantum systems. We derive an analytical expression for the low-frequency absorption coefficient of electro-magnetic radiation in a finite quantum system with ballistic electron dynamics and specular reflection at the boundaries: a two-dimensional electron gas confined to a strip of width a (the approach can be applied to systems of any shape and electron dynamics -- diffusive or ballistic, regular or irregular motion). By comparing with results of numerical computations using the random-phase approximation we show that our analytical approach provides a qualitative and quantitative understanding of the optical spectrum.Comment: 4 pages, 3 figure

Ergodic properties of a model for turbulent dispersion of inertial particles

We study a simple stochastic differential equation that models the dispersion of close heavy particles moving in a turbulent flow. In one and two dimensions, the model is closely related to the one-dimensional stationary Schroedinger equation in a random delta-correlated potential. The ergodic properties of the dispersion process are investigated by proving that its generator is hypoelliptic and using control theory

Semiclassical form factor for spectral and matrix element fluctuations of multi-dimensional chaotic systems

We present a semiclassical calculation of the generalized form factor which characterizes the fluctuations of matrix elements of the quantum operators in the eigenbasis of the Hamiltonian of a chaotic system. Our approach is based on some recently developed techniques for the spectral form factor of systems with hyperbolic and ergodic underlying classical dynamics and f=2 degrees of freedom, that allow us to go beyond the diagonal approximation. First we extend these techniques to systems with f>2. Then we use these results to calculate the generalized form factor. We show that the dependence on the rescaled time in units of the Heisenberg time is universal for both the spectral and the generalized form factor. Furthermore, we derive a relation between the generalized form factor and the classical time-correlation function of the Weyl symbols of the quantum operators.Comment: some typos corrected and few minor changes made; final version in PR