We test a hypothesis that the closed form of the C2 domain of coagulation factor V is more stable than the open form in an aqueous environment using a two-dimensional free-energy calculation with a simple dielectric solvent model. Our result shows that while the free-energy difference between two forms is small, favoring the closed form, a two-dimensional free-energy surface (FES) reveals that a transition state (1.53 kcal/mol) exists between the two conformations. By mapping the one-dimensional order parameter $\Delta Q$ onto the two-dimensional FES, we search the conformational change path with the highest Boltzmann weighting factor between the closed and open form of the factor V C2 domain. The predicted transition path from the closed to open form is not that of simple side chain movements, but instead concerted movements of several loops. We also present a one-dimensional free-energy profile using a collective order parameter, which in a coarse manner locates the energy barriers found on the two-dimensional FES.

The wings of the moth Cacostatia ossa (Ctenuchinae) are covered on both sides by non-close-packed nipple arrays which are known to act as broadband antireflection coatings. Experimental evaluation of the antireflection property of these biological structures is problematic because of the lack of a proper reference for reflectance measurements, i.e., a smooth surface made of the same material as the wing. Theoretical evaluation, on the other hand, is much more reliable provided that optical simulations are carried out on a realistic structural model of the wing. Based on detailed morphological characterizations, we established a three-dimensional (3D) model of the wing and used 3D transfer-matrix optical simulations in order to demonstrate the broadband antireflection property of the wings of Cacostatia ossa. Differences between hemispherical and specular reflectance spectra revealed that diffraction effects were not negligible for this structure although they did not jeopardize the antireflection efficiency. The influences of the backside corrugation and of the material’s absorption on the reflectance spectrum were also studied. In addition, simulations based on an effective-medium model of the wing were carried out using a multilayer thin-film code. In comparison with the latter simulations, the 3D transfer-matrix simulations were found to be more accurate for evaluating the antireflection property.

We present a skewness measurement of the density fluctuations $\delta {\tilde{\rho }}_l$ on scales $l$ in a vertical turbulent soap film driven by a temperature gradient. Unlike the temperature difference $\delta T_l$ in Rayleigh-Bénard convection, the density difference in the film is strongly active because $\delta {\tilde{\rho }}_l∕\overline{\rho }⪢\delta T_l∕\overline{T}$, where the over-bar indicates the mean. Our results show persistent nonzero skewness $S_y\left(l\right)\equiv ⟨\delta {\tilde{\rho }}_l^3⟩∕{⟨\delta {\tilde{\rho }}_l^2⟩}^{3∕2}$ on different scales along the gravity direction $\widehat{y}$; $S_y\left(l\right)$ is positive for small $l$ and negative for large $l$. The sign switch occurs approximately at the Bolgiano length scale $l_B$. The simultaneous presence of positive and negative skewnesses is interpreted here as a result of the structures of rising and falling plumes in a strongly stratified medium.

We show that the topology and dynamics of a network of unsynchronized Kuramoto oscillators can be simultaneously controlled by means of a forcing mechanism which yields a phase locking of the oscillators to that of an external pacemaker in connection with the reshaping of the network’s degree distribution. The entrainment mechanism is based on the addition, at regular time intervals, of unidirectional links from oscillators that follow the dynamics of a pacemaker to oscillators in the pristine graph whose phases hold a prescribed phase relationship. Such a dynamically based rule in the attachment process leads to the emergence of a power-law shape in the final degree distribution of the graph whenever the network is entrained to the dynamics of the pacemaker. We show that the arousal of a scale-free distribution in connection with the success of the entrainment process is a robust feature, characterizing different networks’ initial configurations and parameters.

The Loschmidt echo (LE) (or fidelity) quantifies the sensitivity of the time evolution of a quantum system with respect to a perturbation of the Hamiltonian. In a typical chaotic system the LE has been previously argued to exhibit a long-time saturation at a value inversely proportional to the effective size of the Hilbert space of the system. However, until now no quantitative results have been known and, in particular, no explicit expression for the proportionality constant has been proposed. In this paper we perform a quantitative analysis of the phenomenon of the LE saturation and provide the analytical expression for its long-time saturation value for a semiclassical particle in a two-dimensional chaotic billiard. We further perform extensive (fully quantum mechanical) numerical calculations of the LE saturation value and find the numerical results to support the semiclassical theory.

A technique for the accurate computation of the electromagnetic fields radiated by a charged particle moving within a parallel-plate waveguide is presented. Based on a transformation of the time-varying current density of the particle into a time-harmonic current density, this technique allows the evaluation of the radiated electromagnetic fields both in the frequency and time domains, as well as in the near- and far-field regions. For this purpose, several accelerated versions of the parallel-plate Green’s function in the frequency domain have been considered. The theory has been successfully applied to the multipactor discharge occurring within a two metal-plates region. The proposed formulation has been tested with a particle-in-cell code based on the finite-difference time-domain method, obtaining good agreement.

In this Brief Report, the dynamical hysteresis is investigated in constant-density traffic system of scale-free, small-world, and lattice networks. With the local-searching strategy, hysteresis persists for scale-free networks, while it disappears for small-world networks and lattice grids when the handling ability of nodes is higher than a certain threshold. With the shortest-path-routing strategy, hysteresis persists for all three networks investigated. When using shortest-path strategy, the system is easy to congest and difficult to recover to free-flow state.

We discuss multidimensional generalizations of multicanonical algorithm, simulated tempering, and replica-exchange method. We generalize the original potential-energy function $E_0$ by adding any physical quantity $V$ of interest as a new energy term with a coupling constant $\lambda$. We then perform a multidimensional multicanonical simulation where a random walk in $E_0$ and $V$ spaces is realized. We can alternately perform a multidimensional simulated-tempering simulation where a random walk in temperature $T$ and parameter $\lambda$ is realized. The results of the multidimensional replica-exchange simulations can be used to determine the weight factors for these multidimensional multicanonical and simulated-tempering simulations.

Polymerized phantom membranes are revisited using a nonperturbative renormalization-group approach. This allows one to investigate both the crumpling transition and the low-temperature flat phase in any internal dimension $D$ and embedding dimension $d$ and to determine the lower critical dimension. The crumpling phase transition for physical membranes is found to be of second order within our approximation. A weak first-order behavior, as observed in recent Monte Carlo simulations, is however not excluded.

We study the dynamic susceptibility ${\chi }_T\left(Q,t\right)$ of deeply supercooled water by means of quasielastic neutron scattering and molecular dynamics simulations. Both techniques show an increase in the peak height of ${\chi }_T\left(Q,t\right)$ as the temperature is lowered toward the dynamic crossover temperature $T_L$. Below $T_L$, the peak height decreases steadily. We attribute this phenomenon to the change in slope of the Arrhenius plot of the translational relaxation time at $T_L$. In contrast, the peak height of the calculated four-point correlation function ${\chi }_4\left(Q,t\right)$, directly related to the size of dynamic heterogeneity, increases toward and below $T_L$.

We report the statistical properties of the fluctuations of the energy flux in an electronic $RC$ circuit driven with a stochastic voltage. The fluctuations of the power injected in the circuit are measured as a function of the damping rate and the forcing parameters. We show that its distribution exhibits a cusp close to zero and two asymmetric exponential tails, with the asymmetry being driven by the mean dissipation. This simple experiment allows one to capture the qualitative features of the energy flux distribution observed in more complex dissipative systems. We also show that the large fluctuations of injected power averaged on a time lag do not verify the fluctuation theorem even for long averaging time. This is in contrast to the findings of previous experiments due to their small range of explored fluctuation amplitude. The injected power in a system of $N$ components either correlated or not is also studied to mimic systems with large number of particles, such as in a dilute granular gas.

We present Monte Carlo simulations for a molecular motor system found in virtually all eukaryotic cells, the acto-myosin motor system, composed of a group of organic macromolecules. Cell motors were mapped to an Ising-like model, where the interaction field is transmitted through a tropomyosin polymer chain. The presence of ${\text{Ca}}^{2+}$ induces tropomyosin to block or unblock binding sites of the myosin motor leading to its activation or deactivation. We used the Metropolis algorithm to find the transient and the equilibrium states of the acto-myosin system composed of solvent, actin, tropomyosin, troponin, ${\text{Ca}}^{2+}$, and myosin-S1 at a given temperature, including the spatial configuration of tropomyosin on the actin filament surface. Our model describes the short- and long-range cooperativity during actin-myosin binding which emerges from the bending stiffness of the tropomyosin complex. We found all transition rates between the states only using the interaction energy of the constituents. The agreement between our model and experimental data also supports the recent theory of flexible tropomyosin.

An energy minimization formulation of electrostatics that allows computation of the electrostatic energy and forces to any desired accuracy in a system with arbitrary dielectric properties is presented. An integral equation for the scalar charge density is derived from an energy functional of the polarization vector field. This energy functional represents the true energy of the system even in nonequilibrium states. Arbitrary accuracy is achieved by solving the integral equation for the charge density via a series expansion in terms of the equation’s kernel, which depends only on the geometry of the dielectrics. The streamlined formalism operates with volume charge distributions only, not resorting to introducing surface charges by hand. Therefore, it can be applied to any spatial variation of the dielectric susceptibility, which is of particular importance in applications to biomolecular systems. The simplicity of application of the formalism to real problems is shown with analytical and numerical examples.

While entropy per unit time is a meaningful index to quantify the dynamic features of experimental time series, its estimation is often hampered in practice by the finite length of the data. We here investigate the performance of entropy estimation procedures, relying either on block entropies or Lempel-Ziv complexity, when only very short symbolic sequences are available. Heuristic analytical arguments point at the influence of temporal correlations on the bias and statistical fluctuations, and put forward a reduced effective sequence length suitable for error estimation. Numerical studies are conducted using, as benchmarks, the wealth of different dynamic regimes generated by the family of logistic maps and stochastic evolutions generated by a Markov chain of tunable correlation time. Practical guidelines and validity criteria are proposed. For instance, block entropy leads to a dramatic overestimation for sequences of low entropy, whereas it outperforms Lempel-Ziv complexity at high entropy. As a general result, the quality of entropy estimation is sensitive to the sequence temporal correlation hence self-consistently depends on the entropy value itself, thus promoting a two-step procedure. Lempel-Ziv complexity is to be preferred in the first step and remains the best estimator for highly correlated sequences.

We study synchronous behavior in ensembles of locally coupled nonidentical Bonhoeffer–van der Pol oscillators. We show that, in a chain of $N$ elements not less than $2^{N-1}$, different coexisting regimes of global synchronization are possible, and we investigate wave-induced synchronous regimes in a chain and in a lattice of coupled nonidentical Bonhoeffer–van der Pol oscillators.

A system of two coupled ensembles of phase oscillators can follow different routes to interensemble synchronization. Following a short report of our preliminary results [Phys. Rev. E 78, 025201(R) (2008)], we present a more detailed study of the effects of coupling, noise, and phase asymmetries in coupled phase-oscillator ensembles. We identify five distinct synchronization regions and routes to synchronization that are characteristic of the coupling asymmetry. We show that noise asymmetry induces effects similar to that of coupling asymmetry when the latter is absent. We also find that phase asymmetry controls the probability of occurrence of particular routes to synchronization. Our results suggest that asymmetry plays a crucial role in controlling synchronization within and between oscillator ensembles, and hence that its consideration is vital for modeling real life problems.

In this paper we investigate intrinsic thermally excited nonequilibrium velocity fluctuations in laminar planar Couette flow. For this purpose we have complemented the solution of the stochastic Orr-Sommerfeld equation for the intensity of the fluctuations of the wall-normal velocity, presented in a previous publication, with a solution of the stochastic Squire equation for the intensity of the fluctuations of the wall-normal vorticity. We have obtained exact solutions of these equations without boundary conditions and solutions in a Galerkin approximation when appropriate boundary conditions are included. These results enable us to make a quantitative assessment of the intensity of these nonequilibrium fluctuations, as well as of the related energy amplification, which are always present, even in the absence of any externally imposed noise.

In this paper we present an interactive numerical method that can predict ac electro-osmotic flows around completely polarized electrodes. In this method the slip velocity on the electrode surface is calculated by numerically solving the Laplace equation for the potential in the bulk coupled with the dynamical equation for the surface charge density on the electrodes; here the dynamical equation has been derived from the asymptotic solutions of the Poisson-Nernst-Planck equation for the potential drop across the electrical thin layer near the electrode. A unique feature of this study is that the effect of nonspecific ion adsorption is considered. The numerical code was applied to the two-dimensional ac electro-osmotic flow above a pair of coplanar electrodes, and the solutions compared well with the experimental data reported in the literature. We investigated the effect of various parameters on the slip velocity distribution, such as the ac frequency, the electrode length, the effective Stern-layer thickness, and the adsorption coefficients.

A thorough study of shear stress within the lattice Boltzmann method is provided. Via standard multiscale Chapman-Enskog expansion we investigate the dependence of the error in shear stress on grid resolution showing that the shear stress obtained by the lattice Boltzmann method is second-order accurate. This convergence, however, is usually spoiled by the boundary conditions. It is also investigated which value of the relaxation parameter minimizes the error. Furthermore, for simulations using velocity boundary conditions, an artificial mass increase is often observed. This is a consequence of the compressibility of the lattice Boltzmann fluid. We investigate this issue and derive an analytic expression for the time dependence of the fluid density in terms of the Reynolds number, Mach number, and a geometric factor for the case of a Poiseuille flow through a rectangular channel in three dimensions. Comparison of the analytic expression with results of lattice Boltzmann simulations shows excellent agreement.

We generate two-dimensional Lennard-Jones networks with random topology by preparing a perfect four-functional network of identical harmonic springs and randomly cutting some of the springs. Using molecular-dynamics simulations we find that the fraction $p$ of active springs affects both the temperature of phase separation and the type of structures observed below this temperature, from networklike high-density patterns at $p>0.5$ (“gel”) to dropletlike structures at $p<0.5$ (“sol”). In the gel domain, these patterns are determined by the interplay between free energy and network topology, with the former dominant as $p\to 1$ and the latter as $p\to 0.5$.