Dynamic steady‐state crack propagation in quasi‐crystals

The steady propagation of planar cracks in quasi‐crystalline bodies with velocity lower than the one of bulk elastic macroscopic waves is under scrutiny. Closed‐form solutions to the balance laws are provided. Unusual Mach number limits are determined. Numerical experiments describing peculiar aspects of the crack propagation in quasi‐crystals are performed by varying parametrically the coupling coefficient between macroscopic deformation and substructural events. In this way, classes of quasi‐crystals are then compared. Copyright © 2010 John Wiley & Sons, Ltd.     

采用不同疏水相互作用色谱柱从包涵体中快速制备重组人干细胞因子

为了提高重组人干细胞因子(rhSCF)的复性效率,改进了高效疏水相互作用色谱(HPHIC)纯化和复性rhSCF的方法。首先将目标蛋白溶解于8.0 mol/L脲中,然后将rhSCF包涵体的提取液直接进样到不同规格的HPHIC柱进行纯化和复性。优化了固定相配基结构和流动相组成等实验条件,结果表明,本方法可以快速地获得高质量回收率和高生物活性的rhSCF,rhSCF在40 min内即可完成复性与纯化,目标蛋白的纯度在95.5%以上,质量回收率高于49.6%。通过体积排阻色谱和基质辅助激光解吸离子化飞行时间质谱(MALDI-TOF-MS)的分析,确认rhSCF以单体存在。结果进一步证明HPHIC法是同时复性和纯化重组蛋白的有效工具。     

Accelerating molecular Monte Carlo simulations using distance and orientation-dependent energy tables: tuning from atomistic accuracy to smoothed "coarse-grained" models

Typically, the most time consuming part of any atomistic molecular simulation is the repeated calculation of distances, energies, and forces between pairs of atoms. However, many molecules contain nearly rigid multi-atom groups such as rings and other conjugated moieties, whose rigidity can be exploited to significantly speed-up computations. The availability of GB-scale random-access memory (RAM) offers the possibility of tabulation (precalculation) of distance- and orientation-dependent interactions among such rigid molecular bodies. Here, we perform an investigation of this energy tabulation approach for a fluid of atomistic-but rigid-benzene molecules at standard temperature and density. In particular, using O(1) GB of RAM, we construct an energy look-up table, which encompasses the full range of allowed relative positions and orientations between a pair of whole molecules. We obtain a hardware-dependent speed-up of a factor of 24-50 as compared to an ordinary ("exact") Monte Carlo simulation and find excellent agreement between energetic and structural properties. Second, we examine the somewhat reduced fidelity of results obtained using energy tables based on much less memory use. Third, the energy table serves as a convenient platform to explore potential energy smoothing techniques, akin to coarse-graining. Simulations with smoothed tables exhibit near atomistic accuracy while increasing diffusivity. The combined speed-up in sampling from tabulation and smoothing exceeds a factor of 100. For future applications, greater speed-ups can be expected for larger rigid groups, such as those found in biomolecules.     

High-Level Expression,Purification, and In Vitro Refolding of Soluble Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand (TRAIL)

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a new member of the TNF superfamily. In this paper, we report the expression, purification, and preparation of a recombinant form of the extracelluar domain of the TRAIL (sTRAIL) without posttranslational modifications, which may selectively induce apoptosis of tumor cells in vitro. To obtain recombinant nonfusion sTRAIL protein, the encoding region for sTRAIL was cloned between KpnI and BamHI in pET32a. The Trx (thioredoxin)/sTRAIL fusion proteins were expressed in the form of inclusion bodies in Escherichia coli host strain BL21 (DE3). The expression level was more than 35% of total cell lysate. Inclusion bodies were disrupted, washed, and isolated at pH 9.0, and were completely dissolved in a buffer containing 2 M urea at pH 9.0. After nickel ion metal affinity chromatography, gel filtration chromatography, and renaturation, the refolded fusion proteins with a purity of >98% were obtained. Trx/sTRAIL L proteins were digested by enterokinase to both Trx and sTRAIL fragments, which then were separated by cation exchange chromatography. Cell proliferation experiments proved that the rsTRAIL (98% purity) retains its cancer-selective apoptosis-inducing properties. This result suggested that the recombinant sTRAIL may have cancer therapeutic applications.     

A Cartesian cut cell based two-way strong fluid–solid coupling algorithm for 2D floating bodies

In a recent paper Kelly et al. (2015) [PICIN: A Particle-In-Cell solver for incompressible free surface flows with two-way fluid–solid coupling. SIAM Journal on Scientific Computing 37 (3), B403–24.] detailed the PICIN full particle Particle-In-Cell (PIC) solver for incompressible free-surface flows. The model described in that paper employed a tailored version of the Distributed Lagrange Multiplier (DLM) method for the strong coupling of fluid–solid interaction. In this paper we propose an alternative strong fluid–solid coupling algorithm based on a modification to the cut cell methodology that is informed by the variational approach. The solid velocity flux/integral on the boundary is expressed purely in terms of pressure leading to a revised pressure Poisson equation that is discretised in a finite volume sense. This approach allows the PICIN model to simulate the motion of floating bodies of arbitrary configuration. 2D test cases involving floating bodies with one or more degrees of freedom (DoF) are used to validate the modified PICIN model. The results presented show that the modified PICIN model is able to both efficiently and robustly predict the motions of surface-piercing floating structures under either regular or extreme wave action.     

On the forward and backward in time problems in the Kelvin–Voigt thermoviscoelastic materials

This paper studies the uniqueness of solutions to the forward and backward in time boundary value problems associated with the Kelvin–Voigt viscoelastic model of the thermoelastic materials. For thermoviscoelastic materials with a center of symmetry, it is shown the uniqueness of solutions to the forward in time boundary value problems without any assumptions upon the thermoviscoelastic constitutive coefficients other than the symmetry properties and those induced by the dissipation inequality. While for the final boundary value problems two uniqueness theorems are presented: the first one is essentially based on the assumption that the specific heat is of negative definite sign, while the second is established in the class of displacement–temperature variation fields whose dissipation energy has a temporal behavior lower than an appropriate growing exponential.     

Simulation of forced deformable bodies interacting with two-dimensional incompressible flows: Application to fish-like swimming

We present an efficient algorithm for simulation of deformable bodies interacting with two-dimensional incompressible fluid flows. The temporal and spatial discretizations of the Navier–Stokes equations in vorticity stream-function formulation are based on classical fourth-order Runge–Kutta scheme and compact finite differences, respectively. Using a uniform Cartesian grid we benefit from the advantage of a new fourth-order direct solver for the Poisson equation to ensure the incompressibility constraint down to machine zero over an optimal grid. For introducing a deformable body in fluid flow, the volume penalization method is used. A Lagrangian structured grid with prescribed motion covers the deformable body which is interacting with the surrounding fluid due to the hydrodynamic forces and the torque calculated on the Eulerian reference grid. An efficient law for controlling the curvature of an anguilliform fish, swimming toward a prescribed goal, is proposed which is based on the geometrically exact theory of nonlinear beams and quaternions. Validation of the developed method shows the efficiency and expected accuracy of the algorithm for fish-like swimming and also for a variety of fluid/solid interaction problems.     

The application of a modified method of discrete sources for solving the problem of wave scattering by group of bodies

A new universal and effective algorithm for solving the problems of wave diffraction on complicated structures composed of bodies of revolution is presented. The method is applied to diffraction on a group made of two impedance bodies of revolution. The method permits to get the pattern and the field with high accuracy.     

Unsteady flow around impacting bluff bodies

The flow resulting from the collision without rebound of generic bluff bodies with a wall in a still viscous fluid is investigated both computationally and experimentally. Emphasis is on the case of a circular cylinder impact (two-dimensional geometry), but comparisons with the flow generated by the impact of a sphere (axisymmetric geometry) are included. For normal cylinder impacts, the two counter-rotating vortices forming behind the body during its motion continue their trajectory towards the wall after the collision, leading to the generation of opposite-signed secondary vorticity at the cylinder and wall surfaces. Secondary vortices forming from this vorticity at higher Reynolds numbers exhibit a short-wavelength three-dimensional instability. Comparison with the sphere impact reveals significant differences in the scales of the vortices after the collision, due to the additional vortex stretching acting in the axisymmetric geometry. This leads to a delay in the onset of three-dimensionality and to a different instability mechanism. Oblique cylinder impacts are also considered. For increasing impact angles, the wall effect is gradually reduced on one side of the cylinder, which favours the roll-up of the secondary vorticity and increases the rebound height of the vortex system.     

Pseudo-Rigid Bodies: A Geometric Lagrangian Approach

The pseudo-rigid body model is viewed within the context of continuum mechanics and elasticity theory. A Lagrangian reduction, based on variational principles, is developed for both anisotropic and isotropic pseudo-rigid bodies. For isotropic Lagrangians, the reduced equations of motion for the pseudo-rigid body are a system of two (coupled) Lax equations on so(3)×so(3) and a second-order differential equation on the set of diagonal matrices with a positive determinant. Several examples of pseudo-rigid bodies such as stretching bodies, spinning gas cloud and Riemann ellipsoids are presented.