Validity of the bead-spring model for describing the linear viscoelastic properties of single-strand DNA under strongly denaturing conditions

Using a normal mode analysis, we predict the infinite dilution linear viscoelastic properties of single-strand (ss) DNA molecules and compare the results to the linear viscoelastic data of Shusterman et al. (Phys Rev Let 92(4):048303, 2004) obtained by monitoring the diffusion of a fluorescently labeled terminus of the molecule. To compute the overall best global fit, we constrain the hydrodynamic interaction parameter, h*, equilibrium root mean square spring extension, b, and the number of Kuhn steps per spring, N _K,S, to be equal for the strands compared. The fits using the bead-spring model for all but 23,100 base ss-DNA strands match the experimental data at long times with significant deviations at intermediate and short times. However, parameters fitted separately to all individual strand lengths predict results well. The best fits to data for 2,400 and 6,700 base pairs yield N _K,S ∼12 and h* = 0.12. These values are similar to those found for conventional polymers such as polystyrene which have been successfully modeled with N _K,S ∼7 and h* = 0.15, indicating ss-DNA and polystyrene exhibit analogous hydrodynamic behavior.     

Theory of the influence of changes in salt concentration on the configuration of intrinsically curved, impenetrable, rod-like structures modeling DNA minicircles

DNA molecules in the familiar double helical B form are treated here as though they have rod-like structures obtained by stacking the nearly planar base pairs comprising them one on top of another with each rotated by approximately one-tenth of a full turn with respect to its immediate predecessor in the stack. As each base in a base pair is attached to the sugar-phosphate backbone chain of one of the two DNA strands that have come together to form the Watson-Crick structure, and each phosphate group in a backbone chain bears one electronic charge, two such charges are associated with each base pair. Thus, each base pair is subject to not only the elastic forces and moments exerted on it by its neighboring base pairs but also to electrostatic forces, of sequentially remote origin, that, because they are only partially screened out by positively charged counter ions, can render the molecule's equilibrium configurations sensitive to changes in the concentration of salt in the medium. As there are cases in which, even though the intramolecular electrostatic forces of repulsion are strong, the distance of closest approach has value equal to that of the impenetrable diameter of the molecule, the theory presented here takes into account self-contact. Examples are given of cases in which the theory predicts that the radius of gyration of the minimum energy configuration of a small (549 base pair) circularized DNA molecule (called a “DNA minicircle”) has a remarkably strong dependence on the salt concentration.     

Improvement of cold-wire response for measurement of temperature dissipation

This work aimed at improving fine-scale measurements using cold-wire anemometry. The dissipation ɛ _θ of the temperature variance was measured on the axis of a heated turbulent round jet. The measurements were performed with a constant current anemometer (CCA) operating fine Pt–10%Rh wires at very low overheat. The CCA developed for this purpose allowed the use of the current injection method in order to estimate the time constant of the wire. In the first part of the paper, it is shown that the time constants obtained for two wire diameters −d=1.2 and d=0.58 μm – compare well with those measured at the same time using two other methods (laser excitation and pulsed wire). Moreover, for these two wires, the estimated time constants were in good agreement with those obtained from a semi-empirical relation. In the second part of the paper, a compensation procedure – post-processing filtering – was developed in order to improved the frequency response of the cold-wire probes. The measurements carried out on the axis of the jet (Re _D =16 500, Re _λ  ≃ 167) showed that the frequency response of the 1.2 μm wire was significantly improved. In fact, the spectral characteristics of the compensated signal obtained with the 1.2 μm wire compared fairly well with those from the 0.58 μm wire. Moreover, the results indicated that the compensation procedure must be applied when the cut-off frequency of the cold-wire f _c is lower than two times the Kolmogorov frequency f _K. In the case where f _c ≃ 0.6f _K, the compensation procedure can reduce the error in the estimate of ɛ _θ by more than 20%. When f _c ≃ 2f _K, the effect of the compensation is reduced to about 5%. Received: 3 November 2000/Accepted: 23 March 2001     

Theory of Supercoiled Elastic Rings with Self-Contact and Its Application to DNA Plasmids

Methods are presented for obtaining exact analytical representations of supercoiled equilibrium configurations of impenetrable elastic rods of circular cross-section that have been pretwisted and closed to form rings, and a discussion is given of applications in the theory of the elastic rod model for DNA. When, as here, self-contact is taken into account, and the rod is assumed to be inextensible, intrinsically straight, transversely isotropic, and homogeneous, the important parameters in the theory are the excess link Δℒ (a measure of the amount the rod was twisted before its ends were joined), the ratio ω of the coefficients of torsional and flexural rigidity, and the ratio d of cross-sectional diameter to the length of the axial curve C. Solutions of the equations of equilibrium are given for cases in which self-contact occurs at isolated points and along intervals. Bifurcation diagrams are presented as graphs of Δℒ versus the writhe of C and are employed for analysis of the stability of equilibrium configurations. It is shown that, in addition to primary, secondary, and tertiary branches that arise by successive bifurcations from the trivial branch made up of configurations for which the axial curve is a circle, there are families of equilibrium configurations that are isolas in the sense that they are not connected to bifurcation branches by paths of equilibrium configurations compatible with the assumed impenetrability of the rod. Each of the isolas found to date is connected to a bifurcation branch by a path which, although made up of solutions of the governing equations, contains regions on which the condition of impenetrability does not hold. This revised version was published online in July 2006 with corrections to the Cover Date.     

Edge fracture in cone-plate and parallel plate flows

Edge fracture is an instability of cone-plate and parallel plate flows of viscoelastic liquids and suspensions, characterised by the formation of a `crack' or indentation at a critical shear rate on the free surface of the liquid. A study is undertaken of the theoretical, experimental and computational aspects of edge fracture. The Tanner-Keentok theory of edge fracture in second-order liquids is re-examined and is approximately extended to cover the Criminale-Ericksen-Filbey (CEF) model. The second-order theory shows that the stress distribution on the semi-circular crack is not constant, requiring an average to be taken of the stress; this affects the proportionality constant, K in the edge fracture equation −N _2c = KΓ/a, where N _2c is the critical second normal stress difference, Γ is the surface tension coefficient and a is the fracture diameter. When the minimum stress is used, K = 2/3 as found by Tanner and Keentok (1983). Consideration is given to the sources of experimental error, including secondary flow and slip (wall effect). The effect of inertia on edge fracture is derived. A video camera was used to record the inception and development of edge fracture in four viscoelastic liquids and two suspensions. The recorded image was then measured to obtain the fracture diameter. The edge fracture phenomenon was examined to find its dependence on the physical dimensions of the flow (i.e. parallel plate gap or cone angle), on the surface tension coefficient, on the critical shear rate and on the critical second normal stress difference. The critical second normal stress difference was found to depend on the surface tension coefficient and the fracture diameter, as shown by the theory of Tanner and Keentok (1983); however, the experimental data were best fitted by the equation −N _2c = 1.095Γ/a. It was found that edge fracture in viscoelastic liquids depends on the Reynolds number, which is in good agreement with the inertial theory of edge fracture. Edge fracture in lubricating grease and toothpaste is broadly consistent with the CEF model of edge fracture. A finite volume method program was used to simulate the flow of a viscoelastic liquid, obeying the modified Phan-Thien-Tanner model, to obtain the velocity and stress distribution in parallel plate flow in three dimensions. Stress concentrations of the second normal stress difference (N ₂) were found in the plane of the crack; the velocity distribution shows a secondary flow tending to aid crack formation if N ₂ is negative, and a secondary flow tending to suppress crack formation if N ₂ is positive. Received: 4 January 1999 Accepted: 19 May 1999     

Rheological and mechanical properties of silica colloids: from Newtonian liquid to brittle behaviour

Rheological and mechanical properties of aqueous mono-disperse silica suspensions (Ludox? HS40) are investigated as a function of particle volume fraction (ϕ _p ranging from 0.22 to 0.51) and water content, using shear rate tests, oscillatory methods, indentation and an ultrasonic technique. As the samples are progressively dried, four regimes are identified; they are related to the increasing particle content and the existence and behaviour of the electrical double layer (EDL) around each particle. For 0.22 ≤ ϕ _p ≤ 0.30), the suspensions are stable due to the strong electrostatic repulsion between particles and show Newtonian behaviour (I). As water is removed, the solution pH decreases and the ionic strength increases. The EDL thickness therefore slowly decreases, and screening of the electrostatic repulsion increases. For 0.31 ≤ ϕ _p ≤ 0.35, the suspensions become turbid and exhibit viscoelastic (VE) shear thinning behaviour (II), as they progressively flocculate. For 0.35 ≤ ϕ _p ≤ 0.47, the suspensions turn transparent again and paste-like, with VE shear thinning behaviour and high elastic modulus (III). At higher particle concentration, the suspensions undergo a glass transition and behave as an elastic brittle solid (IV, ϕ _p = 0.51).     

Streamwise evolution of a high-Schmidt-number passive scalar in a turbulent plane wake

The concentration fluctuation c of diluted fluorescein dye, a high-Schmidt-number passive scalar (Sc=ν/D ≈ 2000, ν and D are the fluid momentum and dye diffusivities, respectively), is measured in the wake of a circular cylinder using a single-point laser-induced fluorescence (SPLIF) technique. The streamwise decay rate of the mean and rms values of c is slow in comparison to that of θ, the temperature fluctuation for which the molecular Prandtl number Pr=ν/κ is about 0.7 (κ is the thermal diffusivity). The comparison between mean and rms distributions of c and θ highlights the combined role the Reynolds and Schmidt numbers play in terms of dispersing the scalar. The streamwise evolution of the probability density functions (pdfs) of c and θ suggest that while p(θ) is approximately Gaussian in the intermediate wake (x/d ≈ 80), p(c) is strongly non-Gaussian, and depends on both x/d and Re. The skewness of c is larger than that of θ along the wake centreline. Arguably, the asymmetry of p(c) reflects the relatively strong organisation of the large-scale motion in the far-wake. Received: 27 July 2000/Accepted: 22 December 2000     

Scaling law in saddle-node bifurcations for one-dimensional maps: a complex variable approach

The study of transient dynamical phenomena near bifurcation thresholds has attracted the interest of many researchers due to the relevance of bifurcations in different physical or biological systems. In the context of saddle-node bifurcations, where two or more fixed points collide annihilating each other, it is known that the dynamics can suffer the so-called delayed transition. This phenomenon emerges when the system spends a lot of time before reaching the remaining stable equilibrium, found after the bifurcation, because of the presence of a saddle-remnant in phase space. Some works have analytically tackled this phenomenon, especially in time-continuous dynamical systems, showing that the time delay, τ, scales according to an inverse square-root power law, τ∼(μ−μ _c )^−1/2, as the bifurcation parameter μ, is driven further away from its critical value, μ _c . In this work, we first characterize analytically this scaling law using complex variable techniques for a family of one-dimensional maps, called the normal form for the saddle-node bifurcation. We then apply our general analytic results to a single-species ecological model with harvesting given by a unimodal map, characterizing the delayed transition and the scaling law arising due to the constant of harvesting. For both analyzed systems, we show that the numerical results are in perfect agreement with the analytical solutions we are providing. The procedure presented in this work can be used to characterize the scaling laws of one-dimensional discrete dynamical systems with saddle-node bifurcations.     

The effect of mixing particles of different size on the electrorheological response under steady shear flow

 The effect of mixing particles of different sizes on the electrorheological response of suspensions under steady shear flow was investigated. Two sizes, 15 μm and 50 μm, of monodisperse spherical sulfonated poly(styrene-co-divinylbenzene) particles were used. Several electrorheological fluids were made containing different proportions of small and large particles dispersed in silicone oil, but with constant overall particulate concentration. It was found that the mixed size system produced the highest electrorheological response under the shear rates used (10 s⁻¹ to 500 s⁻¹), which is the opposite trend to previous studies of bimodal systems with larger size ratios. Received: 21 December 2000 Accepted: 29 March 2001     

Radial filtration during constant-force squeeze flow of soft solids

Various soft solid suspensions were squeezed at constant force between polished and roughened circular glass plates and the time-dependence of the interplate separation was measured. The filterability of suspensions was quantified by their desorptivity S obtained from measurements of capillary suction time. The squeeze flow (SF) of suspensions for which S < 2 μm s^−1/2 was largely consistent with rheological theory, which neglected radial filtration: the relative motion between the liquid and solid phases of the suspension in the radial pressure gradient. Suspensions having S > 2 μm s^−1/2 showed SF behavior that was consistent with the presence of radial filtration.     

On Finite Shear

If a pair of material line elements, passing through a typical particle P in a body, subtend an angle Θ before deformation, and Θ+γ after deformation, the pair of material elements is said to be sheared by the amount γ. Here all pairs of material elements at P are considered for arbitrary deformations. Two main problems are addressed and solved. The first is the determination of all pairs of material line elements at P which are unsheared. The second is the determination of that pair of material line elements at P which suffers the maximum shear. All unsheared pairs of material elements in a given plane π(S) with normal S passing through P are considered. Provided π(S) is not a plane of central circular section of the C-ellipsoid at P (where C is the right Cauchy-Green strain tensor), it is seen that corresponding to any material element in π(S) there is, in general, one companion material element in π(S) such that the element and its companion are unsheared. There are, however, two elements in π(S) which have no companions. We call their corresponding directions \textit{limiting directions.} Equally inclined to the direction of least stretch in the plane π(S), the limiting directions play a central role. It is seen that, in a given plane π(S), the pair of material line elements which suffer the maximum shear lie along the limiting directions in π(S). If Θ _L is the acute angle subtended by the limitig directions in π(S) before deformation, then this angle is sheared into its supplement π−Θ _L so that the maximum shear γ^*;(S) is γ^*=π− 2 Θ _L . If S is given and C is known, then Θ _L may be determined immediately. Its calculation does not involve knowing the eigenvectors or eigenvalues of C. When all possible planes through P are considered, it is seen that the global maximum shear γ^* _G occurs for material elements lying along the limiting directions in the plane spanned by the eigenvectors of C corresponding to the greatest principal stretch λ₃ and the least λ₁. The limiting directions in this principal plane of C subtend the angle and . Generally the maximum shear does not occur for a pair of material elements which are originally orthogonal. For a given material element along the unit vector N, there is, in general, in each plane π(S passing through N at P, a companion vector M such that material elements along N and M are unsheared. A formula, originally due to Joly (1905), is presented for M in terms of N and S. Given an unsheared pair π(S), the limiting directions in π(S) are seen to be easily determined, either analytically or geometrically. Planar shear, the change in the angle between the normals of a pair of material planar elements at X, is also considered. The theory of planar shear runs parallel to the theory of shear of material line elements. Corresponding results are presented. Finally, another concept of shear used in the geology literature, and apparently due to Jaeger, is considered. The connection is shown between Cauchy shear, the change in the angle of a pair of material elements, and the Jaeger shear, the change in the angle between the normal N to a planar element and a material element along the normal N. Although Jaeger's shear is described in terms of one direction N, it is seen to implicitly include a second material line element orthogonal to N. Accepted: May 25, 1999     

The three-dimensional stationary instability in dynamic thermocapillary shallow cavities

In various configurations with thermal convection, three-dimensional stationary patterns occur that consist of pairs of counter-rotating longitudinal rolls. These rolls are investigated in this paper under a variety of experimental conditions. The liquids used are ethanol and the silicone oil hexamethyldisiloxane. The upper surface of the liquid volume is free and very flat because measures against menisci at the side and end walls have been taken. The temperature gradient is applied horizontally via thermally conducting but transparent sapphire end walls, leading to thermocapillary forces at the free surface in addition to the buoyant forces at normal earth's gravity. The geometry of the liquid volume is either rectangular or axisymmetrical (annular). The rectangular set-up is transparent and especially suited for optical observations of tracers in the bulk of the liquid. The annular set-up has the advantages of a large azimuthal (transversal) extent and the absence of side walls. In it a wavelength of λ≈1.3d was observed (where d is the depth of the liquid volume). Temperatures and velocities are measured and used to characterize the instability. Also the region of existence of the instability is studied in layers shallower than in earlier experiments in order to give a larger ratio between thermocapillary and buoyant forces. To find the onset of the instability when increasing the temperature gradient, the amplitude of the instability was derived from measurements and extrapolated. This yields a significantly lower threshold (Ma^c=2300 ± 1000 for d=5 mm) than previous experimental studies. One implementation of the annular gap experiment was performed under microgravity (experiment MAGIA), the other experiments under normal gravity. The results of the experiment under microgravity indicate the absence of the three-dimensional stationary pattern under the absence of gravity. Received: 14 August 2000/Accepted: 17 April 2001     

Measurements of concentration per size class in a dense polydispersed jet using planar laser-induced fluorescence and phase Doppler techniques

In dense two-phase flows, it is well known that phase Doppler anemometry is not well suited for the measurement of concentration and mass flux. Laser diagnostics based on fluorescence can provide the dispersed phase concentration but without discrimination between size classes. We present a new method of coupling the two techniques, in order to extract the local value of concentration and flux per size class. The method is applied to an axisymmetric turbulent jet, laden with polydispersed droplets 1–90 μm. Droplet concentration profiles are obtained in the development zone (x/d ₀ < 20) of the dense jet and are used to study droplet dispersion. The results are then introduced into the momentum transport equations to analyze the influence of droplets on the carrier phase. We show that the local decrease of the rate of variation of mean momentum with mass loading is due both to an increase in interfacial transfer rate and to a decrease in turbulent diffusion effects. Received: 20 November 2000 / Accepted: 3 April 2001     

Comparison of the vortex shedding behavior of a single plate and a plate array

This study compares the shedding behavior around and downstream of a single plate positioned in a flow field alone with the shedding behavior around and downstream of the same plate positioned in an array of identical plates. The shedding frequencies and corresponding Strouhal numbers based on chord [S _r (c)] and based on thickness [S _r (t)] are obtained using a hot-wire anemometer. In comparison with the plate positioned as a single plate, the same plate placed in a plate array shows increases in S _r (c) of up to 55.5% and produces a dominant peak in the power spectra that is wider by a factor of 3.5. In contrast to the single-plate results, which exhibit step changes in S _r (c) of about 0.6 at c/t ≈ 6, 8 and 11, the plate positioned in an array shows only one abrupt transition at c/t ≈ 4. Received: 26 January 1999/Accepted: 7 February 2000     

Irradiation-Induced Solute Clustering in a Low Nickel FeMnNi Ferritic Alloy

Understanding the radiation embrittlement of reactor pressure vessel (RPV) steels is required to be able to operate safely a nuclear power plant or to extend its lifetime. The mechanical properties degradation is partly due to the clustering of solute under irradiation. To gain knowledge about the clustering process, a Fe−1.1 Mn−0.7 Ni (at.%) alloy was irradiated in a test reactor at two fluxes of 0.15 and 9 ×10¹⁷ n _E > 1MeV .m^− 2.s^− 1 and at increasing doses from 0.18 to 1.3 ×10²⁴ n _E > 1MeV .m^− 2 at 300°C. Atom probe tomography (APT) experiments revealed that the irradiation promotes the formation in the α iron matrix of Mn/Mn and/or Ni/Ni pair correlations at low dose and Mn–Ni enriched clusters at high dose. These clusters dissolve partially after a thermal treatment at 400°C. Based on a comparison with thermodynamic calculations, we show that the solute clustering under irradiation can just result from an induced mechanism.     

Stiffening and Contraction Induced by Dexamethasone in Alveolar Epithelial Cells

Background  The structural integrity of the alveolar monolayer, which is compromised during lung inflammation, is determined by the balance between cell–cell and cell-matrix tethering forces and the centripetal forces owing to cell viscoelasticity and contraction. Dexamethasone is an anti-inflammatory glucocorticoid with protective effects in lung injury. Aim  To determine the effects of Dexamethasone on the stiffness and contractility of alveolar epithelial cells. Methods  Cell stiffness (G′) and average traction exerted by the cell (T) were measured by magnetic twisting cytometry and by traction microscopy, respectively. A549 cells were treated 24 h with Dexamethasone (1 μM) or vehicle (control). G′ and T were measured before and 5 min after challenge with the inflammatory mediator Thrombin (0.5 U/ml). Changes induced by Dexamethasone in actin cytoskeleton polymerization were assessed by the fluorescent ratio between F-actin and G-actin obtained by staining cells with phalloidin and DNase I. Results  Dexamethasone significantly increased G′ and T by 56% (n = 11; p < 0.01) and by 80% (n = 17; p < 0.05), respectively. Dexamethasone also increased F/G-actin ratio from 2.68 ± 0.07 to 2.96 ± 0.09 (n = 10; p < 0.05). The relative increase in stiffness and contraction induced by Thrombin in control cells was significantly (p < 0.05) reduced by Dexamethasone treatment: from 190 to 98% in G′ and from 318 to 105% in T. Conclusion  The cytoskeleton remodelling and the increase in cell stiffness and contraction induced by Dexamethasone could account for its protective effect in the alveolar epithelium when subjected to inflammatory challenge.     

Stability of an Initially, Stably Stratified Fluid Subjected to a Step Change in Temperature

The onset of convective instability in an initially quiescent, stably stratified fluid layer between two horizontal plates is analyzed with linear theory. The bottom boundary is heated suddenly from below, subjected to a step change in surface temperature. The critical time t _c to mark the onset of Rayleigh-Bénard convection is predicted by propagation theory. This theory uses the length scaled by , where α denotes thermal diffusivity. Under the normal mode analysis the dimensionless disturbance equations are obtained as a function of τ(=αt/d ²) and ζ(=Z/), where d is the fluid layer depth and Z is the vertical distance. The resulting equations are transformed to self-similar ones by using scaling and finally fixing τ as τ_c under the frame of coordinates τ and ζ. For a given γ, Pr and τ_c, the minimum value of Ra is obtained from the marginal stability curve. Here γ denotes the temperature ratio to represent the degree of stabilizing effect, Pr is the Prandtl number and Ra is the Rayleigh number. With γ=0, the minimum Ra value approaches the well-known value of 1708 as τ_c increases. However, it is inversely proportional to τ_c ^3/2 as τ_c decreases. With increasing γ, the system becomes more stable. It is interesting that in the present system, propagation theory produces the stability criteria to bound the available experimental data over the whole domain of time. Received 5 November 2001 and accepted 29 March 2002 Published online: 2 October 2002 RID="*" ID="*" This work has been supported by both SK Chemicals Co. Ltd. and LG Chemical Ltd., Seoul under the Brain Korea 21 Project of the Ministry of Education. Communicated by H.J.S. Fernando     

Free volume dependence of polymer viscosity

The Simha–Somcynsky (S–S) equation of state (eos) was used to compute the free volume parameter, h, from the pressure–volume–temperature (PVT) dependencies of eight molten polymers. The predicted by eos variation of h with T and P was confirmed by the positron annihilation lifetime spectroscopy; good agreement was found for h(P = constant) = h(T) as well as for h(T = constant) = h(P). Capillary shear viscosity (η) data of the same polymers (measured at three temperatures and six pressures up to 700 bars), were plotted as logη vs 1/h, the latter computed for T and P at which η was measured. In previous works, such a plot for solvents and silicone oils resulted in a “master curve” for the liquid, in a wide range of T and P. However, for molten polymers, no superposition of data onto a “master curve” could be found. The superposition could be obtained allowing the characteristic pressure reducing parameter, P*, to vary. The necessity for using a “rheological” characteristic pressure reducing parameter, P*_R = κP*, with κ = 1 to 2.1 indicates that the free volume parameter extracted from the thermodynamic equilibrium data may not fully describe the dynamic behavior. After eliminating possibility of other sources for the deviation, the most likely culprit seems to be the presence of structures in polymer melts at temperatures above the glass transition, T _g. For example, it was observed that for amorphous polymers at T ≅ 1.52T _g the factor κ = 1, and the deviation vanish.     

Axial annular flow of plastic fluids: dead zones and plug-free flow

In axial annular flow, the shear stress decreases from its value τ(κR) at the inner cylinder to 0 at r = λR and increases from then on to τ(R) at the outer cylinder. For plastic fluids with a yield stress τ _c, λ will be such that flow commences when τ(κR) = τ(R) = τ _c. For fluids with position-dependent yield stresses (electro- and magnetorheological fluids are examples), the situation is more complex. While it is possible that yielding and flow occur everywhere, it is also possible that flow occurs only in parts of the fluid-filled space, and a dead zone (region in which the fluid is at rest) close to one of the walls exists. In that case, the fluid will flow no matter how small the applied pressure difference is. If P is large enough, the dead zone ceases to exist and flow without any plug is possible. The fluid flows as if no yield stress exists.