On Bifurcations of Equilibria of Intrinsically Curved, Electrically Charged, Rod-like Structures that Model DNA Molecules in Solution

DNA molecules in the familiar Watson–Crick double helical B form can be treated as though they have rod-like structures obtained by stacking dominoes 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. These “dominoes” are called base pairs. A recently developed theory of sequence-dependent DNA elasticity (Coleman, Olson, & Swigon, J. Chem. Phys. 118:7127–7140, 2003) takes into account the observation that the step from one base pair to the next can be one of several distinct types, each having its own mechanical properties that depend on the nucleotide composition of the step. In the present paper, which is based on that theory, emphasis is placed on the fact that, 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, which implies that each base pair is subject to not only the elastic forces and moments exerted on it by its neighboring base pairs but also to long range electrostatic forces 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 c of salt in the medium. When these electrostatic forces are taken into account, the equations of mechanical equilibrium for a DNA molecule with N + 1 base pairs are a system of μN non-linear equations, where μ, the number of kinematical variables describing the relative displacement and orientation of adjacent pairs is in general 6; it reduces to 3 when base-pair steps are assumed to be inextensible and non-shearable. As a consequence of the long-range electrostatic interactions of base pairs, the μN × μN Jacobian matrix of the equations of equilibrium is full. An efficient numerically stable computational scheme is here presented for solving those equations and determining the mechanical stability of the calculated equilibrium configurations. That scheme is employed to compute and analyze bifurcation diagrams in which c is the bifurcation parameter and to show that, for an intrinsically curved molecule, small changes in c can have a strong effect on stable equilibrium configurations. Cases are presented in which several stable configurations occur at a single value of c.      

DNA stretching modeled at the base pair level: Overtwisting and shear instability in elastic linkages

Stretching experiments on single DNA molecules indicate that, counterintuitive to expectations, DNA overwinds when stretched and, at large forces, undergoes a transition into an overstretched form indicated by a plateau on the force–displacement diagrams. It is believed that these effects are the result of non-linearities in the elastic response of DNA. We use a discrete, base pair level model to simulate the behavior of short DNA molecules, taking into account the sequence dependent physical properties of DNA alongside with the coupling between the kinematical step parameters, yet retaining the quadratic form of local elastic energy function. By constructing bifurcation diagrams of equilibrium configurations and studying the dependence on base pair combinations we show that the quadratic model is capable of explaining the overtwisting as a result of coupling between modes of deformation and overstretching as a result of shear instability.     

On Infinitesimal Shear

The setting for this note is the theory of infinitesimal strain in the context of classical linearized elasticity. As a body is subjected to a deformation the angle between a pair of material line elements through a typical point P is changed. The decrease in angle is called the shear of this pair of elements. Here, we determine all pairs of material line elements at P which are unsheared in a deformation. It is seen, in general, that corresponding to any given material line element in a given plane through P, there is one corresponding “companion” material line element such that the given element and its conjugate are unsheared in the deformation. There are two exceptions. If the plane through P is a plane of central circular section of the strain ellipsoid, then every material line element through P in this plane has an infinity of companion elements in this plane – all pairs of material line elements in the plane(s) of central circular section of the strain ellipsoid are unsheared. If the plane through P is not a plane of central circular section of the strain ellipsoid, then there are two exceptional material line elements through P such that neither of them has a companion material line element forming an unsheared pair with it. The directions of these exceptional elements in the plane are called “limiting directions”. It is seen that it is the pair of elements along the limiting directions in a plane which suffer the maximum shear in that plane. A geometrical construction is presented for the determination of the extensional strains along the pairs of elements which are unsheared. Also, it is shown that knowing one unsheared pair in a plane and their extensions is sufficient to determine the principal extensions and the principal axes in this plane. Expressions for all unsheared pairs in a given plane are given in terms of the normals to the planes of central circular sections of the strain ellipsoid. Finally, for a given material line element, a formula is derived for the determination of all other material line elements which form an unsheared pair with the given element.     

Non-local effects on the non-linear modes of vibration of carbon nanotubes under electrostatic actuation

Carbon nanotubes (CNTs) based NEMS with electrostatic sensing/actuation may be employed as sensors, in situations where it is fundamental to understand their dynamic behaviour. Due to displacements that are large in comparison with the thickness and to the non-linearity of the electrostatic force, these CNT based NEMS operate in the non-linear regime. The knowledge of the modes of vibration of a CNT provides a picture of what one may expect from its dynamic behaviour not only in free, but also in forced vibrations. In this paper, the non-linear modes of vibration of CNTs actuated by electrostatic forces are investigated. For that purpose, a p-version finite element type formulation is implemented, leading to ordinary differential equations of motion in the time domain. The formulation takes into account non-local effects, which influence the inertia and the stiffness of CNTs, as well as the electrostatic actuation. The ordinary differential equations of motion are transformed into algebraic equations of motion via the harmonic balance method (HBM) and then solved by an arc-length continuation method. Several harmonics are considered in the HBM. The importance of non-local effects, combined with the geometrical non-linearity and with the action of the electrostatic force, is analysed. It is found that different combinations of these effects can result in alterations of the natural frequencies, variations in the degrees of softening or hardening, changes in the frequency content of the free vibrations, and alterations in the mode shapes of vibration. It is furthermore found that the small scale, here represented by the non-local theory, has an effect on interactions between the first and higher order modes which are induced by the geometrical and material non-linearities of the system.     

The oscillatory behavior, static and dynamic analyses of a micro/nano gyroscope considering geometric nonlinearities and intermolecular forces

The nonlinear dynamic and static deflection of a micro/nano gyroscope under DC voltages and base rotation are investigated. The gyroscope undertakes two cou- pled bending motions along the drive and sense directions and subjected to electrostatic actuations and intermolecular forces. The nonlinear governing equations of motion for the system with the effect of electrostatic force, intermolecular tractions and base rotation are derived using extended Hamilton principle. Under constant voltage, the gyroscope finds the preformed shape. First, the deflection of the rnicro/nano gyroscope under electrostatic forces is obtained by static and dynamic analyses. Furthermore, the static and dynamic in- stability of the system are investigated. Afterward the oscillatory behavior of the pre-deformed micro/nano gyroscope around equilibrium is studied. The effects of intermolecular and nonlinear parameters on the static and dynamic de- flection, natural frequencies and instability of the micro/nano gyroscope are studied. The presented model can be used to exactly determine static and the dynamic behavior of vibratory micro/nano gyroscopes.     

Utilising μ-PIV and pressure measurements to determine the viscosity of a DNA solution in a microchannel

There is currently considerable interest in the development of micro-scale polymerase chain reaction (PCR) systems. Smaller sample volumes are required than for macro-scale systems, and faster process times are feasible. Although much attention has focused on the output of micro-PCR (μ-PCR), little attention has been devoted to the detailed fluid mechanics of such devices. There are many technical challenges associated with systems of these length scales.

In this paper the effect of PCR on biofluid viscosity is examined. A theoretical expression for viscosity in PCR is derived. Transmission electron microscopy is used to determine the geometry of a 240 base pair segment of an Escherichia coli (E. coli) DNA molecule and the results are used to predict the effect of PCR on biofluid viscosity.

Micro-particle image velocimetry (μ-PIV) and pressure transducer measurements of water, amplified and unamplified E. coli DNA solutions flowing in a polycarbonate microchannel are recorded. In a novel application of these established measurement techniques, the results are combined with curve fitting of a theoretical prediction for channel flow to estimate the viscosity of the E. coli solutions. The viscosity results are compared to the theoretical prediction for PCR viscosity and to measurements in a commercial viscometer. Viscosity measurements indicated no increase in fluid viscosity after PCR for a low molecular weight molecule.     

Dual input–output pairs for modeling hysteresis inspired by mem-models

We call attention to a dual-pair concept for modeling hysteresis involving instantaneous switching: Specifically, there are two input–output pairs for each hysteresis model under one specific input, namely a differential pair and an integral pair. Currently in engineering mechanics, only one pair is being recognized and utilized, not the other. Whereas this dual-pair concept is inherent in the differential and algebraic forms of memristors and memcapacitors, the concept has not been carried over to memristive system theory, nor to memcapacitive system theory. We show that the “zero-crossing” feature in memristors, memcapacitors, and memristive/memcapacitive models (i.e., the “mem-models”) is also a feature of the differential pairs of well-known non-mem-models, examples of which are Ramberg–Osgood, Bouc–Wen, bilinear hysteresis, and classical Preisach. The dual-pair concept thus connects mem-models and non-mem-models, thereby facilitating the modeling of hysteresis, and raising a set of scientific questions for further studies that might not otherwise come to awareness.     

Force flux and the peridynamic stress tensor

The peridynamic model is a framework for continuum mechanics based on the idea that pairs of particles exert forces on each other across a finite distance. The equation of motion in the peridynamic model is an integro-differential equation. In this paper, a notion of a peridynamic stress tensor derived from nonlocal interactions is defined. At any point in the body, this stress tensor is obtained from the forces within peridynamic bonds that geometrically go through the point. The peridynamic equation of motion can be expressed in terms of this stress tensor, and the result is formally identical to the Cauchy equation of motion in the classical model, even though the classical model is a local theory. We also establish that this stress tensor field is unique in a certain function space compatible with finite element approximations.     

Stochastic parameterization of shallow cumulus convection estimated from high-resolution model data

In this paper, we report on the development of a methodology for stochastic parameterization of convective transport by shallow cumulus convection in weather and climate models. We construct a parameterization based on Large-Eddy Simulation (LES) data. These simulations resolve the turbulent fluxes of heat and moisture and are based on a typical case of non-precipitating shallow cumulus convection above sea in the trade-wind region. Using clustering, we determine a finite number of turbulent flux pairs for heat and moisture that are representative for the pairs of flux profiles observed in these simulations. In the stochastic parameterization scheme proposed here, the convection scheme jumps randomly between these pre-computed pairs of turbulent flux profiles. The transition probabilities are estimated from the LES data, and they are conditioned on the resolved-scale state in the model column. Hence, the stochastic parameterization is formulated as a data-inferred conditional Markov chain (CMC), where each state of the Markov chain corresponds to a pair of turbulent heat and moisture fluxes. The CMC parameterization is designed to emulate, in a statistical sense, the convective behaviour observed in the LES data. The CMC is tested in single-column model (SCM) experiments. The SCM is able to reproduce the ensemble spread of the temperature and humidity that was observed in the LES data. Furthermore, there is a good similarity between time series of the fractions of the discretized fluxes produced by SCM and observed in LES.     

Effect of polymer bridging on rheological properties of dispersions of charged silica particles in the presence of low-molecular-weight physically adsorbed poly(ethylene oxide)

 The effect of a low-molecular-weight physically adsorbed poly(ethylene oxide) on the rheological behavior of aqueous dispersions of silica particles (as a model system) has been investigated. Particular attention is given to the evolution of the rheological behavior with increasing polymer concentration in the system at different volume fractions of the particles. Experiments were performed in the absence of salt and just the pH of the dispersion was adjusted to 9.5, a condition at which the system is electrostatically stable and electrostatic repulsive forces are long range in nature. It was observed that the shear viscosity and the linear viscoelastic functions of the dispersion at 55 vol% increase initially through the addition of polymer, reach a maximum, and then decrease to a minimum with further addition of polymer to the system. At higher polymer concentrations, there may be an increase in the viscosity of the dispersion owing to an increase in the concentration of free polymer chains in the medium causing depletion flocculation in the system. The increase in the rheological behavior of the dispersion at low polymer coverage is attributed to polymer bridging flocculation caused by a low-molecular-weight poly(ethylene oxide) in the system. Comparison of the data given here with the results of earlier studies on the viscosity behavior of the system in the presence of salt (0.01 M) indicates that the range of the electrostatic repulsion has a significant role in the rheological behavior of the system. Received: 7 February 2001 Accepted: 18 October 2001     

Shear thickening and shear-induced agglomeration of chemical mechanical polishing slurries using electrolytes

Chemical mechanical polishing is a fundamental technology used in the semiconductor manufacturing industry to polish and planarize a wide range of materials for the fabrication of microelectronic devices. During the high-shear (～1,000,000 s^?1) polishing process, it is hypothesized that individual slurry particles are driven together to form large agglomerates (≥0.5 µm). These agglomerates are believed to trigger a shear-induced thickening effect and cause defects during polishing. We examined how the addition of various monovalent salts (CsCl, KCl, LiCl, and NaCl) and electrostatic stabilizing bases (KOH, NaOH, or CsOH) influenced the slurry’s thickening behavior. Overall, as the added salt concentration was increased from 0.02 to 0.15 M, the shear rate at which the slurry thickened (i.e., the critical shear rate) decreased. Slurries with added CsCl, NaCl, and LiCl thickened at comparable shear rates (～20,000–70,000 s^?1) and, in general, followed ion hydration theory (poorly hydrated ions caused the slurry to thicken at lower shear rates). However, slurries with added KCl portrayed thickening behavior at higher critical shear rates (～35,000–100,000 s^?1) than other chloride salts. Also, slurries stabilized with CsOH thickened at higher shear rates (～90,000–140,000 s^?1), regardless of the added salt cation or concentration, than the slurries with KOH or NaOH. The NaOH-stabilized slurries displayed thickening at the lowest shear rates (～20,000 s^?1). The thickening dependence on slurry base cation indicates the existence of additional close-range structure forces that are not predicted by the Derjaguin–Landau–Verwey–Overbeek colloidal stability theory.     

Stability and bifurcation for limit cycle oscillations of an airfoil with external store

In this paper, stability and local bifurcation behaviors for the nonlinear aeroelastic model of an airfoil with external store are investigated using both analytical and numerical methods. Three kinds of degenerated equilibrium points of bifurcation response equations are considered. They are characterized as (1) one pair of purely imaginary eigenvalues and two pairs of conjugate complex roots with negative real parts; (2) two pairs of purely imaginary eigenvalues in nonresonant case and one pair of conjugate complex roots with negative real parts; (3) three pairs of purely imaginary eigenvalues in nonresonant case. With the aid of Maple software and normal form theory, the stability regions of the initial equilibrium point and the explicit expressions of the critical bifurcation curves are obtained, which can lead to static bifurcation and Hopf bifurcation. Under certain conditions, 2-D tori motion may occur. The complex dynamical motions are considered in this paper. Finally, the numerical solutions achieved by the fourth-order Runge–Kutta method agree with the analytic results.     

The unraveling of a polymer chain in a strong extensional flow

By assuming that in a strong extensional flow a polymer molecule in dilute solution is quickly driven into a folded or kinked state in which drag and entropic elastic forces dominate over the Brownian force, we derive kink dynamics equations that describe the unraveling of the molecule in the extensional flow. Solving these equations numerically, we find that although the ends of the chain move, on average, affinely in the flow field until the chain is unfolded to about 1/3 of its fully extended length, large viscous stresses are produced because the solvent must flow around nonextending strands of polymer that lie between neighboring kinks. These predictions are compared with available experimental data and with other theoretical models.     

Exact traveling wave solutions in the coupled plane-base rotator model of DNA

The internal dynamics of the DNA base pairs is studied starting from the generalized coupled plane base-rotator model of DNA, obtained by Yomosa and later improved by Takeno and Homma. We conceive the double-stranded DNA as an anisotropically coupled spin chain simple model. The generalized Hamiltonian expressed in terms of quasi-spin operators is averaged over the generalized coherent states in the Perelomov sense, in order to obtain the classical non-linear evolution equations of this molecular system where the inhomogeneity has not been considered. This approach provides the equations of motion, which could be reduced to a nonlinear Schrödinger equation with a saturable nonlinearity. This non-linear equation, under certain restrictions in the parametric space, supports traveling periodic triangular, bell, bubble and kink like solutions.     

On the limits of added-mass theory in separated flows and with varying initial conditions

It remains unclear to what extent inviscid added-mass theory accounts for the forces exerted on an accelerating body subjected to separated flow. In this study, reactant forces and velocity-field data are systematically acquired using experimental measurements and simulations of an accelerating circular flat plate. Cases accelerated from rest are compared to cases accelerated from a steady flow state. When the added-mass forces predicted by potential theory and the resistance forces associated with the instantaneous plate velocity are accounted for, the remaining (residual) forces comprise approximately 20% of the peak force, even at high accelerations. In addition, the computed residual forces during accelerations both from rest and steady-state cases yield good collapse with respect to one another, indicating that the total forces are not a strong function of the initial state of the wake. These results suggests that inviscid added-mass theory is inadequate to predict the full reactant force even in the ‘ideal’ condition of impulsive motion from rest.     

黏度、极性及配副因素在DLC薄膜固液复合设计中的影响

本文中系统研究了类金刚石(Diamond-like carbon,简称DLC)固体润滑薄膜与一系列不同黏度的烷烃、醇类液体润滑介质的复合润滑性能,并深入探讨了介质黏度、极性及摩擦配副在固液复合设计中的影响规律.我们发现所用DLC薄膜在所考察润滑介质中均表现出较好的稳定性及亲和性,而摩擦行为则呈现较大的差异:在非极性烷烃化合物润滑环境下,DLC/DLC和钢/钢摩擦副的摩擦系数随介质黏度的增加改变不大,钢/DLC摩擦副的摩擦系数则随着介质黏度的升高而逐渐降低;在极性的醇类介质中,钢/钢摩擦副的摩擦系数随着介质黏度的增大先下降后急剧上升,而钢/DLC和DLC/DLC摩擦副的摩擦系数随介质黏度的升高而降低.总之,介质黏度、极性和摩擦配副对体系润滑行为有很大影响,在进行固液复合润滑体系设计时,需综合考虑三者的相互作用关系.     

两性离子聚合物润滑的研究进展

两性离子聚合物是指高分子链上含有相同数量阴、阳离子的有机高分子材料,其因强亲水性和反聚电解质效应而在润滑方面得到广泛研究.一方面,两性离子聚合物可通过静电相互作用将润滑体系中的游离水吸附在材料表面,提高其润滑性能;另一方面,两性离子聚合物表面水合程度易受到润滑体系中盐离子类型和浓度影响,改变其润滑行为.本文中首先介绍摩擦过程中存在的润滑形式,然后总结并分析两性离子聚合物结构及典型两性离子聚合物(例如磺酸根阴离子型两性离子聚合物、磷酸根阴离子型两性离子聚合物和羧酸根阴离子型两性离子聚合物)的润滑行为和机理,最后阐述和展望两性离子聚合物在润滑方面的研究存在的问题和前景.     

Invariants for Rari- and Multi-Constant Theories with Generalization to Anisotropy in Biological Tissues

The rari-constant theory of linear elasticity is based on the assumption that elasticity in solids is caused by only pair potentials with coaxial forces acting between atoms. The strain energy of each pair potential depends on the square of the strain between the atoms in the pair. This strain can be determined by taking the inner product of the strain tensor with a structural tensor that is the tensor product of a unit vector with itself. It is shown that the 15 independent constants in the rari-constant theory can be generated by a complete set of 15 structural tensors. It is also shown that the 6 additional independent constants in the multi-constant theory can be generated by taking the inner product of 6 of these structural tensors with the square of the strain tensor. A generalization of these results for nonlinear elasticity is discussed with reference to recent work which compares the structural and generalized structural tensor approaches to modeling fibrous tissues.