Anomalous lifetime statistics of ligand-receptor binding in a tethered polymer system

In this paper, motivated by observations of non-exponential decay times in the stochastic binding and release of ligand-receptor systems, exemplified by the work of Rogers et al on optically trapped DNA-coated colloids (Rogers et al 2013 Soft Matter 9 6412), we explore the general problem of polymer-mediated surface adhesion using a simplified model of the phenomenon in which a single polymer molecule, fixed at one end, binds through a ligand at its opposite end to a flat surface a fixed distance L away and uniformly covered with receptor sites. Working within the Wilemski-Fixman approximation to diffusion-controlled reactions, we show that for a flexible Gaussian chain, the predicted distribution of times f(t) for which the ligand and receptor are bound is given, for times much shorter than the longest relaxation time of the polymer, by a power law of the form t(-1/4). We also show when the effects of chain stiffness are incorporated into this model (approximately), the structure of f(t) is altered to t(-1/2). These results broadly mirror the experimental trends in the work cited above.

Correlation equations for average deposition rate coefficients of nanoparticles in a cylindrical pore

Nanoparticle deposition behavior observed at the Darcy scale represents an average of the processes occurring at the pore scale. Hence, the effect of various pore-scale parameters on nanoparticle deposition can be understood by studying nanoparticle transport at pore scale and upscaling the results to the Darcy scale. In this work, correlation equations for the deposition rate coefficients of nanoparticles in a cylindrical pore are developed as a function of nine pore-scale parameters: the pore radius, nanoparticle radius, mean flow velocity, solution ionic strength, viscosity, temperature, solution dielectric constant, and nanoparticle and collector surface potentials. Based on dominant processes, the pore space is divided into three different regions, namely, bulk, diffusion, and potential regions. Advection-diffusion equations for nanoparticle transport are prescribed for the bulk and diffusion regions, while the interaction between the diffusion and potential regions is included as a boundary condition. This interaction is modeled as a first-order reversible kinetic adsorption. The expressions for the mass transfer rate coefficients between the diffusion and the potential regions are derived in terms of the interaction energy profile. Among other effects, we account for nanoparticle-collector interaction forces on nanoparticle deposition. The resulting equations are solved numerically for a range of values of pore-scale parameters. The nanoparticle concentration profile obtained for the cylindrical pore is averaged over a moving averaging volume within the pore in order to get the 1-D concentration field. The latter is fitted to the 1-D advection-dispersion equation with an equilibrium or kinetic adsorption model to determine the values of the average deposition rate coefficients. In this study, pore-scale simulations are performed for three values of Peclet number, Pe = 0.05, 5, and 50. We find that under unfavorable conditions, the nanoparticle deposition at pore scale is best described by an equilibrium model at low Peclet numbers (Pe = 0.05) and by a kinetic model at high Peclet numbers (Pe = 50). But, at an intermediate Pe (e.g., near Pe = 5), both equilibrium and kinetic models fit the 1-D concentration field. Correlation equations for the pore-averaged nanoparticle deposition rate coefficients under unfavorable conditions are derived by performing a multiple-linear regression analysis between the estimated deposition rate coefficients for a single pore and various pore-scale parameters. The correlation equations, which follow a power law relation with nine pore-scale parameters, are found to be consistent with the column-scale and pore-scale experimental results, and qualitatively agree with the colloid filtration theory. These equations can be incorporated into pore network models to study the effect of pore-scale parameters on nanoparticle deposition at larger length scales such as Darcy scale.

Structure and Dynamics of Octamethylcyclotetrasiloxane Confined between Mica Surfaces

Using a molecular model for octamethylcydotetrasiloxane (OMCTS), molecular dynamics simulations are carried out to probe the phase state of OMCTS confined between two mica surfaces in equilibrium With a reservoir. Molecular dynamics simulations are carried out for elevations ranging from 5 to 35 K above the melting point for the OMCTS model used in this study. The Helmholtz free energy is, computed for a specific confinement using the :two-phase thermodynamic (2PT) method. Analysis of the in-plane pair correlation functions did not reveal signatures of freezing even under an extreme confinement of two layers. OMCTS is found to orient with a wide distribution of orientations with respect to the mica surface, with a distinct preference for the surface parallel configuration in the contact layers. The self-intermediate scattering function is found to decay with increasing relaxation times as the surface separation is decreased, and the two-step relaxation in the scattering function, a signature of glassy dynamics, distinctly evolves as the temperature is lowered. However, even at 5 K above the melting point, we did not observe a freezing transition and the self-intermediate scattering functions relax within 200 ps for the seven-layered confined system. The self diffusivity and relaxation times obtained from the Kohlrausch-Williams-Watts stretched exponential fits to the late alpha-relaxation exhibit power law scalings with the packing fraction as predicted by mode coupling theory. A distinct discontinuity in the Helmholtz free energy, potential energy, and a sharp change in the local bond order parameter, Q(4), was observed at 230 K for a five-layered system upon cooling, indicative of a first-order transition. A freezing point depression of about 30 K was observed for this five-layered confined system, and at the lower temperatures, contact layers were found to be disordered with long-range order present only in the inner layers. These dynamical signatures indicate that confined OMCTS undergoes a slowdown akin to a fluid approaching a glass transition upon increasing confinement, and freezing under confinement would require substantial subcooling below the bulk melting point of OMCTS.

Depletion of nonlinearity in magnetohydrodynamic turbulence: Insights from analysis and simulations

It is shown how suitably scaled, order-m moments, D-m(+/-), of the Elsasser vorticity fields in three-dimensional magnetohydrodynamics (MHD) can be used to identify three possible regimes for solutions of the MHD equations with magnetic Prandtl number P-M = 1. These vorticity fields are defined by omega(+/-) = curl z(+/-) = omega +/- j, where z(+/-) are Elsasser variables, and where omega and j are, respectively, the fluid vorticity and current density. This study follows recent developments in the study of three-dimensional Navier-Stokes fluid turbulence Gibbon et al., Nonlinearity 27, 2605 (2014)]. Our mathematical results are then compared with those from a variety of direct numerical simulations, which demonstrate that all solutions that have been investigated remain in only one of these regimes which has depleted nonlinearity. The exponents q(+/-) that characterize the inertial range power-law dependencies of the z(+/-) energy spectra, epsilon(+/-)(k), are then examined, and bounds are obtained. Comments are also made on (a) the generalization of our results to the case P-M not equal 1 and (b) the relation between D-m(+/-) and the order-m moments of gradients of magnetohydrodynamic fields, which are used to characterize intermittency in turbulent flows.

Load-Unload Response Ratio and Accelerating Moment/Energy Release Critical Region Scaling and Earthquake Prediction

The main idea of the Load-Unload Response Ratio (LURR) is that when a system is stable, its response to loading corresponds to its response to unloading, whereas when the system is approaching an unstable state, the response to loading and unloading becomes quite different. High LURR values and observations of Accelerating Moment/Energy Release (AMR/AER) prior to large earthquakes have led different research groups to suggest intermediate-term earthquake prediction is possible and imply that the LURR and AMR/AER observations may have a similar physical origin. To study this possibility, we conducted a retrospective examination of several Australian and Chinese earthquakes with magnitudes ranging from 5.0 to 7.9, including Australia's deadly Newcastle earthquake and the devastating Tangshan earthquake. Both LURR values and best-fit power-law time-to-failure functions were computed using data within a range of distances from the epicenter. Like the best-fit power-law fits in AMR/AER, the LURR value was optimal using data within a certain epicentral distance implying a critical region for LURR. Furthermore, LURR critical region size scales with mainshock magnitude and is similar to the AMR/AER critical region size. These results suggest a common physical origin for both the AMR/AER and LURR observations. Further research may provide clues that yield an understanding of this mechanism and help lead to a solid foundation for intermediate-term earthquake prediction.

Fractals and Scaling in Fracture Induced by Microcrack Coalescence

A numerical model is proposed to simulate fracture induced by the coalescence of numerous microcracks, in which the condition for coalescence between two randomly nucleated microcracks is determined in terms of a load-sharing principle. The results of the simulation show that, as the number density of nucleated microcracks increases, stochastic coalescence first occurs followed by a small fluctuation, and finally a newly nucleated microcrack triggers a cascade coalescence of microcracks resulting in catastrophic failure. The fracture profiles exhibit self-affine fractal characteristics with a universal roughness exponent, but the critical damage threshold is sensitive to details of the model. The spatiotemporal distribution of nucleated microcracks in the vicinity of critical failure follows a power-law behaviour, which implies that the microcrack system may evolve to a critical state.

Similarity consideration of structural bifurcation buckling

Many structural bifurcation buckling problems exhibit a scaling or power law property. Dimensional analysis is used to analyze the general scaling property. The concept of a new dimensionless number, the response number-Rn, suggested by the present author for the dynamic plastic response and failure of beams, plates and so on, subjected to large dynamic loading, is generalized in this paper to study the elastic, plastic, dynamic elastic as well as dynamic plastic buckling problems of columns, plates as well as shells. Structural bifurcation buckling can be considered when Rn(n) reaches a critical value.

Calculations of longitudinal and transverse velocity structure functions using a vortex model of isotropic turbulence

The longitudinal structure function (LSF) and the transverse structure function (TSF) in isotropic turbulence are calculated using a vortex model. The vortex model is composed of the Rankine and Burgers vortices which have the exponential distributions in the vortex Reynolds number and vortex radii. This model exhibits a power law in the inertial range and satisfies the minimal condition of isotropy that the second-order exponent of the LSF in the inertial range is equal to that of the TSF. Also observed are differences between longitudinal and transverse structure functions caused by intermittency. These differences are related to their scaling differences which have been previously observed in experiments and numerical simulations.

Finite Element Solutions for Plane Strain Mode I Crack with Strain Grading Effect

In this paper, a new phenomenological theory with strain gradient effects is proposed to account for the size dependence of plastic deformation at micro- and submicro-length scales. The theory fits within the framework of general couple stress theory and three rotational degrees of freedom omega(i) are introduced in addition to the conventional three translational degrees of freedom mu(i). omega(i) is called micro-rotation and is the sum of material rotation plus the particles' relative rotation. While the new theory is used to analyze the crack tip field or the indentation problems, the stretch gradient is considered through a new hardening law. The key features of the theory are that the rotation gradient influences the material character through the interaction between the Cauchy stresses and the couple stresses; the term of stretch gradient is represented as an internal variable to increase the tangent modulus. In fact the present new strain gradient theory is the combination of the strain gradient theory proposed by Chen and Wang (Int. J. Plast., in press) and the hardening law given by Chen and Wang (Acta Mater. 48 (2000a) 3997). In this paper we focus on the finite element method to investigate material fracture for an elastic-power law hardening solid. With remotely imposed classical K fields, the full field solutions are obtained numerically. It is found that the size of the strain gradient dominance zone is characterized by the intrinsic material length l(1). Outside the strain gradient dominance zone, the computed stress field tends to be a classical plasticity field and then K field. The singularity of stresses ahead of the crack tip is higher than that of the classical field and tends to the square root singularity, which has important consequences for crack growth in materials by decohesion at the atomic scale. (C) 2002 Elsevier Science Ltd. All rights reserved.

Creep response of sandwich beams with a metallic foam core

The creep response of metallic foam sandwich beams in 3-point bend is investigated numerically for the case of a metallic foam core and two steel faces. The face sheets are treated as elastic, while the foam core is modeled by a viscoplastic extension of the Deshpande-Fleck yield surface. This power-law creeping constitutive law has been implemented within the commercial finite element code ABAQUS. It is found that the beams creep by a variety of competing mechanisms, depending upon the choice of material properties and the geometric parameters. A failure map is constructed and effect of rate dependence on the load-deflection curves is quantified, and compared against the available experimental data.

What is indentation hardness?

Using dimensional analysis and finite element calculations, we derive simple scaling relationships for loading and unloading curve, contact depth, and hardness. The relationship between hardness and the basic mechanical properties of solids, such as Young's modulus, initial yield strength, and work-hardening exponent, is then obtained. The conditions for 'piling-up' and 'sinking-in' of surface profiles during indentation are determined. A method for estimating contact depth from initial unloading slope is examined. The work done during indentation is also studied. A relationship between the ratio of hardness to elastic modulus and the ratio of irreversible work to total work is discovered. This relationship offers a new method for obtaining hardness and elastic modulus. Finally, a scaling theory for indentation in power-law creep solids using self-similar indenters is developed. A connection between creep and 'indentation size effect' is established.

Scaling, Dimensional Analysis, and Indentation Measurements

We provide an overview of the basic concepts of scaling and dimensional analysis, followed by a review of some of the recent work on applying these concepts to modeling instrumented indentation measurements. Specifically, we examine conical and pyramidal indentation in elastic-plastic solids with power-law work-hardening, in power-law creep solids, and in linear viscoelastic materials. We show that the scaling approach to indentation modeling provides new insights into several basic questions in instrumented indentation, including, what information is contained in the indentation load-displacement curves? How does hardness depend on the mechanical properties and indenter geometry? What are the factors determining piling-up and sinking-in of surface profiles around indents? Can stress-strain relationships be obtained from indentation load-displacement curves? How to measure time dependent mechanical properties from indentation? How to detect or confirm indentation size effects? The scaling approach also helps organize knowledge and provides a framework for bridging micro- and macroscales. We hope that this review will accomplish two purposes: (1) introducing the basic concepts of scaling and dimensional analysis to materials scientists and engineers, and (2) providing a better understanding of instrumented indentation measurements.

Mode I crack tip field with strain gradient effects

A plane strain mode I crack tip field with strain gradient effects is investigated. A new strain gradient theory is used. An elastic-power law hardening strain gradient material is considered and two hardening laws, i.e. a separation law and an integration Law are used respectively. As for the material with the separation law hardening, the angular distributions of stresses are consistent with the HRR field, which differs from the stress results([19]); the angular distributions of couple stresses are the same as the couple stress results([19]). For the material with the integration law hardening, the stress field and the couple stress field can not exist simultaneously, which is the same as the conclusion([19]), but for the stress dominated field, the angular distributions of stresses are consistent with the HRR field; for the couple stress dominated field, the angular distributions of couple stresses are consistent with those in Ref. [19]. However, the increase in stresses is not observed in strain gradient plasticity because the present theory is based on the rotation gradient of the deformation only, while the crack tip field of mode I is dominated by the tension gradient, which will be shown in another paper.

Avalanche behavior and statistical properties in a microcrack coalescence process

Fracture owing to the coalescence of numerous microcracks can be described by a simple statistical model, where a coalescence event stochastically occurs as the number density of nucleated microcracks increases. Both numerical simulation and statistical analysis reveal that a microcrack coalescence process may display avalanche behavior and that the final failure is catastrophic. The cumulative distribution of coalescence events in the vicinity of critical fracture follows a power law and the fracture profile has self-affine fractal characteristic. Some macromechanical quantities may be traced back and extracted from the mesoscopic process based on the statistical analysis of coalescence events.

Sediment incipience in turbulence generated in a square tank by a vertically oscillating grid

The failure of hydraulic structures in many estuaries and coastal regions around the world has been attributed to sediment transport and local scour. The sediment incipience in homogenous turbulence generated by oscillating grid is studied in this paper. The turbulent flow is measured by particle tracer velocimetry (PTV) technique. The integral length scale and time scale of turbulence are obtained. The turbulent flow near the wall is measured by local optical magnification. The sediment incipience is described by static theory. The relationship of probability of sediment incipience and the turbulent kinetic energy were obtained experimentally and theoretically. The distribution of the turbulent kinetic energy near the wall is found to obey the power law and the turbulent energy is further identified as the dynamic mechanism of sediment incipience.