Conformational transitions of heteropolymers in dilute solutions

In this paper we extend the Gaussian self-consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are transformed to a form containing only the mean squared distances between pairs of monomers. These equations are further expressed in terms of instantaneous gradients of the variational free energy. The method allowed us to study exhaustively the stability and conformational structure of some periodic and random aperiodic sequences. A typical phase diagram of a fairly long amphiphilic heteropolymer chain is found to contain phases of the extended coil, the homogeneous globule, the micro-phase separated globule, and a large number of frustrated states, which result in conformational phases of the random coil and the frozen globule. We have also found that for a certain class of sequences the frustrated phases are suppressed. The kinetics of folding from the extended coil to the globule proceeds through non-equilibrium states possessing locally compacted, but partially misfolded and frustrated, structure. This results in a rather complicated multistep kinetic process typical of glassy systems.Comment: 15 pages, RevTeX, 20 ps figures, accepted for publication in Phys. Rev.

Fracture mechanics approach to design analysis of notches, steps and internal cut-outs in planar components

A new approach to the assessment and optimization of geometric stress-concentrating features is proposed on the basis of the correspondence between sharp crack or corner stressfield intensity factors and conventional elastic stress concentration factors (SCFs) for radiused transitions. This approach complements the application of finite element analysis (FEA) and the use of standard SCF data from the literature. The method makes it possible to develop closed-form solutions for SCFs in cases where corresponding solutions for the sharp crack geometries exist. This is helpful in the context of design optimization. The analytical basis of the correspondence is shown, together with the limits on applicability where stress-free boundaries near the stress concentrating feature are present or adjacent features interact. Examples are given which compare parametric results derived from FEA with closed-form solutions based on the proposed method. New information is given on the stress state at a 90° corner or width step, where the magnitude of the stress field intensity is related to that of the corresponding crack geometry. This correspondence enables the user to extend further the application of crack-tip stress-field intensity information to square-cornered steps, external U-grooves, and internal cut-outs

The partition function versus boundary conditions and confinement in the Yang-Mills theory

We analyse dependence of the partition function on the boundary condition for the longitudinal component of the electric field strength in gauge field theories. In a physical gauge the Gauss law constraint may be resolved explicitly expressing this component via an integral of the physical transversal variables. In particular, we study quantum electrodynamics with an external charge and SU(2) gluodynamics. We find that only a charge distribution slowly decreasing at spatial infinity can produce a nontrivial dependence in the Abelian theory. However, in gluodynamics for temperatures below some critical value the partition function acquires a delta-function like dependence on the boundary condition, which leads to colour confinement.Comment: 14 pages, RevTeX, submitted to Phys. Rev.

A node-based smoothed conforming point interpolation method (NS-CPIM) for elasticity problems

This paper formulates a node-based smoothed conforming point interpolation method (NS-CPIM) for solid mechanics. In the proposed NS-CPIM, the higher order conforming PIM shape functions (CPIM) have been constructed to produce a continuous and piecewise quadratic displacement field over the whole problem domain, whereby the smoothed strain field was obtained through smoothing operation over each smoothing domain associated with domain nodes. The smoothed Galerkin weak form was then developed to create the discretized system equations. Numerical studies have demonstrated the following good properties: NS-CPIM (1) can pass both standard and quadratic patch test; (2) provides an upper bound of strain energy; (3) avoid the volumetric locking; (4) provides the higher accuracy than those in the node-based smoothed schemes of the original PIMs

The cascade structure of linear instability in collapsible channel flows

This paper studies the unsteady behaviour and linear stability of the flow in a collapsible channel using a fluid–beam model. The solid mechanics is analysed in a plane strain configuration, in which the principal stretch is defined with a zero initial strain. Two approaches are employed: unsteady numerical simulations solving the nonlinear fully coupled fluid–structure interaction problem; and the corresponding linearized eigenvalue approach solving the Orr–Sommerfeld equations modified by the beam. The two approaches give good agreement with each other in predicting the frequencies and growth rates of the perturbation modes, close to the neutral curves. For a given Reynolds number in the range of 200–600, a cascade of instabilities is discovered as the wall stiffness (or effective tension) is reduced. Under small perturbation to steady solutions for the same Reynolds number, the system loses stability by passing through a succession of unstable zones, with mode number increasing as the wall stiffness is decreased. It is found that this cascade structure can, in principle, be extended to many modes, depending on the parameters. A puzzling ‘tongue’ shaped stable zone in the wall stiffness–Re space turns out to be the zone sandwiched by the mode-2 and mode-3 instabilities. Self-excited oscillations dominated by modes 2–4 are found near their corresponding neutral curves. These modes can also interact and form period-doubling oscillations. Extensive comparisons of the results with existing analytical models are made, and a physical explanation for the cascade structure is proposed

Aggregation number distributions and mesoglobules in dilute solutions of diblock and triblock copolymers

We investigate the aggregation number and size distributions for inter-molecular clusters of amphiphilic diblock and triblock copolymers in poor solvent at very low concentrations. Diblocks and triblocks with hydrophilic ends are shown to possess narrow distributions corresponding to formation of monodispersed mesoglobules. Diblocks with hydrophobic ends are found to produce inter-cluster multimers due to bridging by the hydrophilic middle blocks, resulting in polydisperse distributions. Implications of these observations for preparation of monodispersed nanoparticles and, potentially, understanding of the quaternary structure of proteins are discussed.Comment: 4 pages, 4 PS figures. Accepted for publication in EP

First-principles calculation of intrinsic defect formation volumes in silicon

We present an extensive first-principles study of the pressure dependence of the formation enthalpies of all the know vacancy and self-interstitial configurations in silicon, in each charge state from -2 through +2. The neutral vacancy is found to have a formation volume that varies markedly with pressure, leading to a remarkably large negative value (-0.68 atomic volumes) for the zero-pressure formation volume of a Frenkel pair (V + I). The interaction of volume and charge was examined, leading to pressure--Fermi level stability diagrams of the defects. Finally, we quantify the anisotropic nature of the lattice relaxation around the neutral defects.Comment: 9 pages, 9 figure

Wavelet treatment of the intra-chain correlation functions of homopolymers in dilute solutions

Discrete wavelets are applied to parametrization of the intra-chain two-point correlation functions of homopolymers in dilute solutions obtained from Monte Carlo simulation. Several orthogonal and biorthogonal basis sets have been investigated for use in the truncated wavelet approximation. Quality of the approximation has been assessed by calculation of the scaling exponents obtained from des Cloizeaux ansatz for the correlation functions of homopolymers with different connectivities in a good solvent. The resulting exponents are in a better agreement with those from the recent renormalisation group calculations as compared to the data without the wavelet denoising. We also discuss how the wavelet treatment improves the quality of data for correlation functions from simulations of homopolymers at varied solvent conditions and of heteropolymers.Comment: RevTeX, 19 pages, 7 PS figures. Accepted for publication in PR

Anti-corrosion ceramic coatings on the surface of Nd-Fe-B repelling magnets

The results of vacuum-arc deposition of thin ZrO₂coatings to protect the surface of Nd-Fe-B permanent magnets used as repelling devices in orthodontics are presented. The structure, phase composition and mechanical properties of zirconium dioxide films have been investigated by means of SEM, XRD, EDX, XRF and nanoindentation method. It was revealed the formation of polycrystalline ZrO₂ films of monoclinic modification with average grain size 25 nm. The influence of the ZrO₂ coating in terms of its barrier properties for corrosion in quasi-physiological 0.9 NaCl solution has been studied. Electrochemical measurements indicated good barrier properties of the coating on specimens in the physiological solution environment