A deformation model of the forced-induced dissociation of biological bonds is developed. A simple illustration shows that protein deformations can change the receptor-ligand interaction linearly with applied force at small forces, either increasing or decreasing the bond stability, and that a minor external work can lead to notable changes in the interaction energy. The deformation-induced increase of bond stability is illustrated with the remarkable catch-bond phenomenon in P and L selections. Additionally, the model rationalizes the frequently seen disparity between the bond dissociation rates of many free complexes and the zero-force asymptotic rates measured by force spectroscopy.

The onset of the “eye phase” (a phase consisting of configurations of eye-type conformations or bubbles in the double-stranded DNA) and its role during the DNA unzipping is studied when a force is applied to the interior of the chain. The directionality of the hydrogen bond introduced here shows oscillations in force-extension curve similar to a “sawtooth” kind of oscillations seen in the protein unfolding experiments. The effects of intermediates (hairpins) and stacking energies on the melting profile have also been discussed.

We study the effect of the bending potential on the stability of toroidal and rodlike globules which are typical collapsed conformations of a single stiff-chain macromolecule. We perform numerical calculations in the framework of the bead-stick model of a polymer chain. The intrinsic structure of globules is also analyzed. It was shown that the bending potential affects the packing geometry of bundles in a toroidal globule in the ground state. This potential also influences the bends at the ends of a rodlike globule: both the shape of the loops and the number of bonds in each loop have been investigated numerically as well as by Monte Carlo computer simulations performed for a separate loop. Our main results are (1) the shape of the bending potential could be possibly seen from the geometry of a globule; (2) toroidal globules are always more favorable than the rodlike ones.

We consider a simple dissipative system with spatial structure in contact with a heat bath. The system always exhibits correlations except in the cases of zero and maximal dissipation. We explicitly calculate the correlation function and the nonlocal response function of the system and show that they have the same spatial dependence.

Fully nonlinear motion of a circular interface in incompressible Richtmyer–Meshkov instability is investigated by treating it as a nonuniform vortex sheet between two different fluids. There are many features in cylindrical geometry such as the existence of two independent spatial scales, radius and wavelength, and the ingoing and outgoing growth of bubbles and spikes. Geometrical complexities lead to the results that nonlinear dynamics of the vortex sheet is determined from the inward and outward motion rather than bubbles and spikes, and that the nonlinear growth strongly depends on mode number.

The ion sphere model introduced long ago by Salpeter is placed in a rigorous theoretical setting. The leading corrections to this model for very highly charged but dilute ions in thermal equilibrium with a weakly coupled, one-component background plasma are explicitly computed, and the subleading corrections shown to be negligibly small. This is done using the effective field theory methods advocated by Brown and Yaffe. Thus, corrections to nuclear reaction rates that such highly charged ions may undergo can be computed precisely. Moreover, their contribution to the equation of state can also be computed with precision. Such analytic results for very strong coupling are rarely available, and they can serve as benchmarks for testing computer models in this limit.

We have performed molecular dynamics simulations to study the kinetics of crystal nucleation in the one-component plasma. We have monitored nucleation in the supercooled liquid phase by following the time evolution of the size distribution of crystal nuclei formed during the phase transition. Although several observations are consistent with classical nucleation theory such as transient effects and the existence of a free-energy barrier to crystallization, we could not unambiguously identify a critical size for the crystal nuclei formed within the metastable phase.

We propose a phenomenological description for the effect of a weak noise on the position of a front described by the Fisher-Kolmogorov-Petrovsky-Piscounov equation or any other traveling-wave equation in the same class. Our scenario is based on four hypotheses on the relevant mechanism for the diffusion of the front. Our parameter-free analytical predictions for the velocity of the front, its diffusion constant and higher cumulants of its position agree with numerical simulations.

Certain dynamical systems, such as the shift map and the logistic map, have an edge of chaos in their parameter spaces. On one side of this edge, the dynamics are chaotic for many parameter values, on the other side of the edge they are periodic. We find that discrete-time dynamical systems with wavelet filtered feedback from the dynamical variable to the parameters are attracted to a narrow parameter range near the edge of chaos, the periodic boundary regime. We show that the migration from the chaotic regime to the periodic boundary regime can be attributed to a conserved quantity, and find that such adaptation to the edge of chaos is accompanied by a depopulation of the chaotic regime. We use this conserved quantity to determine the location of the periodic boundary regime and show that its size is proportional to the size of the feedback. Further, we compute the dynamics of the probability density for the parameter for a specific example.

We present an experimental study of the azimuthal motion of the mean wind in turbulent thermal convection. The experiments were conducted with cylindrical convection cells of unity aspect ratio and over the range of the Rayleigh number from $1\times {10}^9$ to $1\times {10}^{10}$. The azimuthal angle of the circulation plane of the mean wind was measured using both the particle image velocimetry and flow-visualization techniques. It is found that the azimuthal motion consists of erratic fluctuations and a time-periodic oscillation. The orientation of the wind is found to be “locked,” i.e., it fluctuates about a preferred direction most of the time with all other orientations appearing as “transient states,” and large excursions of the azimuthal angle often result in a net rotation which takes the wind back to the preferred orientation. The rate of erratic rotation of the circulation plane is found to have a strong dependence on Ra. Our result suggests that the oscillatory motion of the wind in its vertically oriented circulation plane and the orientational oscillation of the circulation plane itself have the same dynamic origin.

When acoustic waves propagate in two-dimensional sonic crystals composed of parallel rigid cylinders in air, anisotropic band gaps, such as a partial gap and deaf band, forbid the waves within certain frequency regions from propagating along certain directions, thus forming a stable imaging focus effect. If the introduced disorder has not destroyed the original anisotropic band gap, this unique effect still exists, although the focused image becomes blurred. Once the sample reaches complete disorder, the anisotropic band gap is destroyed, and this effect also disappears.

The simulation of multicomponent fluids at low Reynolds number and low capillary number is of interest in a variety of applications such as the modeling of venule scale blood flow and microfluidics; however, such simulations are computationally demanding. An improved multicomponent lattice Boltzmann scheme, designed to represent interfaces in the continuum approximation, is presented and shown (i) significantly to reduce common algorithmic artifacts and (ii) to recover full Galilean invariance. The method is used to model drop dynamics in shear flow in two dimensions where it recovers correct results over a range of Reynolds and capillary number greater than that which may be addressed with previous methods.

Following the recent proposal by Van den Broeck for a heat engine [Phys. Rev. Lett. 95, 190602 (2005)], we analyze the coefficient of performance of a refrigerator in two working regimes using the tools of linear irreversible thermodynamics. In particular, one of the analyzed regimes gives a coefficient of performance which could be considered as the equivalent to the Curzon-Ahlborn efficiency. Also we consider the relation with the Clausius inequality, and some results for the relevant thermodynamic magnitudes in this formalism are confronted with those obtained using the finite-time thermodynamics framework.

We report a demonstration of a generation of sub-Mbar pressure on the axis of the implosion wave produced by an underwater electrical explosion of a cylindrical wire array. The array was exploded by microsecond time scale discharge of a capacitor bank having a stored energy of $4.5\mathrm{kJ}$ and discharge current amplitude of up to $90\mathrm{kA}$. Optical diagnostics were used to determine the time of flight and the trajectory of the converging shock wave. This data were applied for a calculation of the water flow parameters using one-dimensional (1D) and 2D hydrodynamic calculations and the Whitham method. All three methods have shown that the shock wave pressure at $0.1\mathrm{mm}$ from the axis reaches $200\mathrm{kbar}$.

Depletion forces can be accounted for by a contraction of the description in the framework of the integral equations theory of simple liquids. This approach includes, in a natural way, the effects of the concentration on the depletion forces, as well as energetic contributions. In this paper we systematically study this approach in a large variety of dilute colloidal systems composed of spherical and nonspherical hard particles, in two and in three dimensions, in the bulk and in front of a hard wall with a relief pattern. We show by this way the form in which concentration and geometry determine the entropic interaction between colloidal particles. The accuracy of our results is corroborated by comparison with computer simulations.

We consider a dissipative variant of the stochastic-Abelian sandpile model on a two-dimensional lattice. The boundaries are closed and the dissipation is due to the fact that each toppled grain is removed from the lattice with probability $ϵ$. It is shown that the scaling properties of this model are in the universality class of the stochastic-Abelian models with conservative dynamics and open boundaries. In particular, the dissipation rate $ϵ$ can be adjusted according to a suitable function $ϵ=f\left(L\right)$, such that the avalanche size distribution will coincide with that of the conservative model on a finite lattice of size $L$.

We investigate Turing pattern formation in the presence of additive dichotomous fluctuations in the context of an extended system with diffusive coupling and FitzHugh-Nagumo kinetics. The fluctuations vary in space and/or time. Depending on the realization of the dichotomous switching the system is, at a given time (for spatial disorder at a given position) in one of two possible excitable dynamical regimes. Each of the two excitable dynamics for itself does not support pattern formation. With proper dichotomous fluctuations, however, the homogeneous steady state is destabilized via a Turing instability. We investigate the influence of different switching rates (different correlation length of the spatial disorder) on pattern formation. We find three distinct mechanisms: For slow switching existing boundaries become unstable, for high rates the system exhibits “effective bistability” which allows for a Turing instability. For medium rates the fluctuations create spatial structures via a new mechanism where the influence of the fluctuations is twofold. First they produce local inhomogeneities, which then grow (again caused by fluctuations) until the whole space is covered. Utilizing a nonlinear map approach we show bistability of a period-one and a period-two orbit being associated with the steady homogeneous and the Turing pattern state, respectively. Finally, for purely static dichotomous disorder we find destabilization of homogeneous steady states for finite nonzero correlation length of the disorder resulting again in Turing patterns.

The propagation of transverse-longitudinal acoustic pulses through a strained cubic crystal containing resonant paramagnetic impurities with effective spin $S=1$ is investigated. It is supposed that the pulses propagate under arbitrary angle with respect to the direction of the external static deformation parallel to the fourth-order symmetry axis. In this geometry, both the transverse and longitudinal components of the acoustic field have high-frequency and zero-frequency spectral components. We show that a pulse can propagate in modes different from the acoustic self-induced transparency. In particular, a pulse propagating in the mode of an acoustic self-induced supertransparency substantially changes the populations of the spin sublevels, but its group velocity remains almost equal to the linear velocity of the sound. If a pulse propagates in the acoustic extraordinary transparency mode, then its group velocity is substantially lower while the sublevel populations remain virtually invariant. Also, the modes of propagation under conditions of weakly excited spin transitions and large detuning of the pulse high-frequency components are identified.

We study the front characteristics of the $A+B\to C$ reaction-diffusion system with initially separated reactants in disordered media, exemplified by two-dimensional (2D) percolation. We investigate the front characteristics as a function of the disorder degree in this system, in particular close to criticality. We show that the front width exponent is larger than the mean-field (MF) exponent of $1∕6$, and at criticality it approaches $1∕4$, which is the one-dimensional (1D) exponent. We show that previous predictions in the literature for the 2D percolation cluster at criticality are wrong. The results are discussed in the context of other systems with attenuated transport where the front width exponent is smaller than the MF exponent. We also study the short-time behavior of the front width exponent, and discuss the validity of the scaling relations between the relevant exponents.