Silk cocoons are reconstituted into an aqueous suspension, and protein stability is investigated by comparing the protein's response to hydrochloric acid and sodium chloride. Aggregation occurs for systems mixed with hydrochloric acid, while sodium chloride over the same range of concentrations does not cause aggregation. We measure the structures present on the protein and aggregate length scales in these solutions using both optical and small-angle neutron scattering, while mass spectrometry techniques shed light on a possible mechanism for aggregate formation. We find that the introduction of acid modulates the aggregate size and pervaded volume of the protein, an effect that is not observed with salt.

We present the dynamics of overdamped Brownian self-propelled particles moving on the surface of a sphere. The effect of self-propulsion on the diffusion of these particles is elucidated by determining their angular (azimuthal and polar) mean-square displacement. Short- and long-times analytical expressions for their angular mean-square displacement are offered. Finally, the particles' steady marginal angular probability density functions are also elucidated.

We use a three-bead–spring model to investigate the dynamics of biflagellate microswimmers near a surface. While the primary dynamics and scattering are governed by geometric-dependent direct contact, the fluid flows generated by the swimmer locomotion are important in orienting it toward or away from the surface. Flagellar noise and in particular cell spinning about the main axis help a surface-trapped swimmer escape, whereas the time a swimmer spends at the surface depends on the incident angle. The dynamics results from a nuanced interplay of direct collisions, hydrodynamics, noise, and the swimmer geometry. We show that to correctly capture the dynamics of a biflagellate swimmer, minimal models need to resolve the shape asymmetry.

We study the response of Preisach models of hysteresis to stochastically fluctuating external fields. We perform numerical simulations, which indicate that analytical expressions derived previously for the autocorrelation functions and power spectral densities of the Preisach model with uncorrelated input, hold asymptotically also if the external field shows exponentially decaying correlations. As a consequence, the mechanisms causing long-term memory and $1/f$ noise in Preisach models with uncorrelated inputs still apply in the presence of fast decaying input correlations. We collect additional evidence for the importance of the effective Preisach density previously introduced even for Preisach models with correlated inputs. Additionally, we present some results for the output of the Preisach model with uncorrelated input using analytical methods. It is found, for instance, that in order to produce the same long-time tails in the output, the elementary hysteresis loops of large width need to have a higher weight for the generic Preisach model than for the symmetric Preisach model. Further, we find autocorrelation functions and power spectral densities to be monotonically decreasing independently of the choice of input and Preisach density.

We derive an extended fluctuation theorem for geometric pumping of a spin-boson system under periodic control of environmental temperatures by using a Markovian quantum master equation. We obtain the current distribution, the average current, and the fluctuation in terms of the Monte Carlo simulation. To explain the results of our simulation we derive an extended fluctuation theorem. This fluctuation theorem leads to the fluctuation dissipation relations but the absence of the conventional reciprocal relation.

The Curzon-Ahlborn efficiency has long served as the definite upper bound for the thermal efficiency at maximum output power, and has thus shaped the development of finite-time thermodynamics. In this paper, we repeal the ruling consensus according to which it has a genuine universal character that can be derived from linear irreversible thermodynamics. We demonstrate that the Curzon-Ahlborn efficiency should instead properly be associated with a particular case of nonlinear heat engines, and we derive a generalized expression for the efficiency at maximum power beyond the restrictive case of linear models.

Since its original formulation in 2000, transfer entropy has become an invaluable tool in the toolbox of nonlinear dynamicists working with empirical data. Transfer entropy and its generalizations provide a precise definition of uncertainty and information transfer that are central to the coupled systems studied in nonlinear science. However, a canonical definition of state-dependent transfer entropy has yet to be introduced. We introduce a candidate measure, the specific transfer entropy, and compare its properties to both total and local transfer entropy. Specific transfer entropy makes possible both state- and time-resolved analysis of the predictive impact of a candidate input system on a candidate output system. We also present principled methods for estimating total, local, and specific transfer entropies from empirical data. We demonstrate the utility of specific transfer entropy and our proposed estimation procedures with two model systems, and find that specific transfer entropy provides more, and more easily interpretable, information about an input-output system compared to currently existing methods.

We investigate the behavior of traveling waves in a defect turbulence regime with the periodic boundary conditions by using the lowest-order complex Ginzburg-Landau equation (CGLE), and we show the effect of the nonlinear gradient terms in the system. It is found that the nonlinear gradient terms which appear at the same order as the quintic term can change the behavior of the wave patterns. The presence of the nonlinear gradient terms can cause major changes in the behavior of the solution. They can be considered like the stabilizing terms. The system which was initially unstable or chaotic can become stable by including the nonlinear gradient terms.

Spirals or scroll wave activities in cardiac tissues are the cause of lethal arrhythmias. The external control of these waves is thus of prime interest to scientists and physicians. In this article, we demonstrate the spatial control of scroll waves by using external electric fields and thermal gradients in experiments with the Belousov-Zhabotinsky reaction. We show that a scroll ring can be made to trace cyclic trajectories under a rotating electric field. Application of a thermal gradient in addition to the electric field deflects the motion and changes the nature of the trajectory. Our experimental results are analyzed and corroborated by numerical simulations based on an excitable reaction diffusion model.

In the present paper, an experimental feasibility study on the detection of long-range intermolecular interactions through three-dimensional molecular diffusion in solution is performed. This follows recent theoretical and numerical analyses reporting that long-range electrodynamic forces between biomolecules could be identified through deviations from Brownian diffusion. The suggested experimental technique was fluorescence correlation spectroscopy (FCS). By considering two oppositely charged molecular species in aqueous solution, namely, lysozymes and fluorescent dye molecules (Alexa488), the diffusion coefficient of the dyes has been measured for different values of the concentration of lysozyme, that is, for different average distances between the oppositely charged molecules. For our model, long-range interactions are of electrostatic origin, suggesting that their action radius can be varied by changing the ionic strength of the solution. The experimental outcomes clearly prove the detectability of long-range intermolecular interactions by means of the FCS technique. Molecular dynamics simulations provide a clear and unambiguous interpretation of the experimental results.

The Liouville and stochastic Liouville equations have been investigated with respect to the susceptible-infected-recovered (SIR) epidemic model, described in terms of extended Nambu mechanics. It has been shown that, along with the equilibrium distribution functions, the Kubo formula can be derived for the SIR model, although the theory undergoes a few restrictions imposed by the nonlinear nature of the model.

Results of broadband dielectric spectroscopy (BDS) studies of pure liquid crystalline (4-pentyloxy-4-biphenylcarbonitryle) 5OCB and its nanocolloids with ${\mathrm{BaTiO}}_3$ nanoparticles (NPs) under varying pressure and temperature are presented. The notable impact of NPs on phase transitions and dynamics was found. Particularly strong impact on pretransitional behavior was observed for relatively low concentrations of NPs, which can be related to the NPs-induced disorder. There are also notable differences between pressure and temperature paths of studies for nanocomposites, absent for the pure LC compound. For instance, tests focused on the translational orientational decoupling via the fractional Debye-Stokes-Einstein relation yielded $S=0.71$ and $S=0.3$ for the temperature and pressure paths, respectively: $S=1$ is for the complete coupling. The possible theoretical frame of observed phenomena is also proposed.

The quest for predictive indicators for the collapse of coal mines has led to a robust criterion from scale-model tests in the laboratory. Mechanical collapse under uniaxial stress forms avalanches with a power-law probability distribution function of radiated energy $P\sim {E^{-}}^{\varepsilon }$, with exponent $\varepsilon =1.5$. Impending major collapse is preceded by a reduction of the energy exponent to the mean-field value $\varepsilon =1.32$. Concurrently, the crackling noise increases in intensity and the waiting time between avalanches is reduced when the major collapse is approaching. These latter criteria were so-far deemed too unreliable for safety assessments in coal mines. We report a reassessment of previously collected extensive collapse data sets using “record-breaking analysis,” based on the statistical appearance of “superjerks” within a smaller spectrum of collapse events. Superjerks are defined as avalanche signals with energies that surpass those of all previous events. The final major collapse is one such superjerk but other “near collapse” events equally qualify. In this way a very large data set of events is reduced to a sparse sequence of superjerks (21 in our coal sample). The main collapse can be anticipated from the sequence of energies and waiting times of superjerks, ignoring all weaker events. Superjerks are excellent indicators for the temporal evolution, and reveal clear nonstationarity of the crackling noise at constant loading rate, as well as self-similarity in the energy distribution of superjerks as a function of the number of events so far in the sequence $E_{sj}\sim n^{\delta }$ with $\delta =1.79$. They are less robust in identifying the precise time of the final collapse, however, than the shift of the energy exponents in the whole data set which occurs only over a short time interval just before the major event. Nevertheless, they provide additional diagnostics that may increase the reliability of such forecasts.

We propose a simulation strategy which uses a classical device of linearly coupled chain of springs to simulate quantum dynamics, in particular quantum walks. Through this strategy, we obtain the quantum wave function from the classical evolution. Specially, this goal is achieved with the classical momenta of the particles on the chain and their Hilbert transform, from which we construct the many-body momentum and Hilbert transformed momentum pair correlation functions yielding the real and imaginary parts of the wave function, respectively. With such a wave function, we show that the classical chain's energy and heat spreading densities can be related to the wave function's modulus square. This relation provides a new perspective to understand ballistic heat transport. The results here may give a definite answer to Feynman's idea of using a classical device to simulate quantum physics.

Connecting the macroscopic world of continuous fields to the microscopic world of discrete molecular events is important for understanding several phenomena occurring at physical boundaries of systems. An important example is heterogeneous catalysis, where reactions take place at active surfaces, but the effective reaction rates are determined by transport limitations in the bulk fluid and reaction limitations on the catalyst surface. In this work we study the macro-micro connection in a model heterogeneous catalytic reactor by means of stochastic rotation dynamics. The model is able to resolve the convective and diffusive interplay between participating species, while including adsorption, desorption, and reaction processes on the catalytic surface. Here we apply the simulation methodology to a simple straight microchannel with a catalytic strip. Dimensionless Damkohler numbers are used to comment on the spatial concentration profiles of reactants and products near the catalyst strip and in the bulk. We end the discussion with an outlook on more complicated geometries and increasingly complex reactions.

As is well known, solitons can be excited in nonlinear lattice systems; however, whether, and if so, how, this kind of nonlinear excitation can affect the energy transport behavior is not yet fully understood. Here we study both the scattering dynamics of solitons and heat transport properties in the Fermi-Pasta-Ulam-$\alpha \text{−}\beta$ model with an asymmetric interparticle interaction. By varying the asymmetry degree of the interaction (characterized by $\alpha )$, we find that (i) for each $\alpha$ there exists a momentum threshold for exciting solitons from which one may infer an $\alpha$-dependent feature of probability of presentation of solitons at a finite-temperature equilibrium state and (ii) the scattering rate of solitons is sensitively dependent on $\alpha$. Based on these findings, we conjecture that the scattering between solitons will cause the nonmonotonic $\alpha$-dependent feature of heat conduction. Fortunately, such a conjecture is indeed verified by our detailed examination of the time decay behavior of the heat current correlation function, but it is only valid for an early time stage. Thus, this result may suggest that solitons can have only a relatively short survival time when exposed in a thermal environment, eventually affecting the heat transport in a short time.

Devising strategies for economic development in a globally competitive landscape requires a solid and unbiased understanding of countries' technological advancements and similarities among export products. Both can be addressed through the bipartite representation of the International Trade Network. In this paper, we apply the recently proposed grand canonical projection algorithm to uncover country and product communities. Contrary to past endeavors, our methodology, based on information theory, creates monopartite projections in an unbiased and analytically tractable way. Single links between countries or products represent statistically significant signals, which are not accounted for by null models such as the bipartite configuration model. We find stable country communities reflecting the socioeconomic distinction in developed, newly industrialized, and developing countries. Furthermore, we observe product clusters based on the aforementioned country groups. Our analysis reveals the existence of a complicated structure in the bipartite International Trade Network: apart from the diversification of export baskets from the most basic to the most exclusive products, we observe a statistically significant signal of an export specialization mechanism towards more sophisticated products.

The study of fungal cells is of great interest due to their importance as pathogens and as fermenting fungi and for their appropriateness as model organisms. The differential pressure between the hyphal cytoplasm and the bordering medium is essential for the growth process, because the pressure is correlated with the growth rate. Notably, during the invasion of tissues, the external pressure at the tip of the hypha may be different from the pressure in the surrounding medium. We report the use of a method, based on the micropipette-aspiration technique, to study the influence of this external pressure at the hyphal tip. Moreover, this technique makes it possible to study hyphal growth mechanics in the case of very thin hyphae, not accessible to turgor pressure probes. We found a correlation between the local pressure at the tip and the growth rate for the species Arpergillus nidulans. Importantly, the proposed method allows one to measure the pressure at the tip required to arrest the hyphal growth. Determining that pressure could be useful to develop new medical treatments for fungal infections. Finally, we provide a mechanical model for these experiments, taking into account the cytoplasm flow and the wall deformation.

When rough grains in loose packing conditions are discharged from a silo, a conical depression with a single slope is formed at the surface. We observed that the increase of volume fraction generates a more complex depression, characterized by two angles of discharge: one at the bottom similar to the angle of repose and a considerably larger upper angle. The change in slope appears at the boundary between a dense stagnant region at the periphery and the central flowing channel formed over the aperture. Since the material in the latter zone is always fluidized, the flow rate is unaffected by the initial packing of the bed. On the other hand, the contrast between both angles is markedly smaller when smooth particles of the same size and density are used, which reveals that high packing fraction and friction must combine to produce the observed geometry. Our results show that the surface profile helps to identify by simple visual inspection the packing conditions of a granular bed, being useful to prevent undesirable collapses during silo discharge in industry.