Highly specific spatiotemporal interactions between cognate molecular partners essentially sustain all biochemical transactions in living matter. That such an exquisite level of accuracy may result from encountering forces solely driven by thermal diffusive processes is unlikely. Here we propose a yet unexplored strategy to experimentally tackle the long-standing question of a possibly active recruitment at a distance of cognate partners of biomolecular reactions via the action of resonant electrodynamic interactions. We considered two simplified models for a preliminary feasibility investigation of the devised methodology. By taking advantage of advanced experimental techniques nowadays available, we propose to measure the characteristic encounter time scales of dually interacting biopartners and to compare them with theoretical predictions worked out in both the presence and absence of putative long-range electromagnetic forces.

Social networks are not static but, rather, constantly evolve in time. One of the elements thought to drive the evolution of social network structure is homophily—the need for individuals to connect with others who are similar to them. In this paper, we study how the spread of a new opinion, idea, or behavior on such a homophily-driven social network is affected by the changing network structure. In particular, using simulations, we study a variant of the Axelrod model on a network with a homophily-driven rewiring rule imposed. First, we find that the presence of rewiring within the network, in general, impedes the reaching of consensus in opinion, as the time to reach consensus diverges exponentially with network size $N$. We then investigate whether the introduction of committed individuals who are rigid in their opinion on a particular issue can speed up the convergence to consensus on that issue. We demonstrate that as committed agents are added, beyond a critical value of the committed fraction, the consensus time growth becomes logarithmic in network size $N$. Furthermore, we show that slight changes in the interaction rule can produce strikingly different results in the scaling behavior of consensus time, $T_c$. However, the benefit gained by introducing committed agents is qualitatively preserved across all the interaction rules we consider.

We introduce a generic model of a weakly nonlinear self-sustained oscillator as a simplified tool to study synchronization in a fluid at low Reynolds number. By averaging over the fast degrees of freedom, we examine the effect of hydrodynamic interactions on the slow dynamics of two oscillators and show that they can lead to synchronization. Furthermore, we find that synchronization is strongly enhanced when the oscillators are nonisochronous, which on the limit cycle means the oscillations have an amplitude-dependent frequency. Nonisochronity is determined by a nonlinear coupling $\alpha$ being nonzero. We find that its ($\alpha$) sign determines if they synchronize in phase or antiphase. We then study an infinite array of oscillators in the long-wavelength limit, in the presence of noise. For $\alpha >0$, hydrodynamic interactions can lead to a homogeneous synchronized state. Numerical simulations for a finite number of oscillators confirm this and, when $\alpha <0$, show the propagation of waves, reminiscent of metachronal coordination.

Population dynamics of individuals undergoing birth and death and diffusing by short- or long-range two-dimensional spatial excursions (Gaussian jumps or Lévy flights) is studied. Competitive interactions are considered in a global case, in which birth and death rates are influenced by all individuals in the system, and in a nonlocal but finite-range case in which interaction affects individuals in a neighborhood (we also address the noninteracting case). In the global case one single or few-cluster configurations are achieved with the spatial distribution of the bugs tied to the type of diffusion. In the Lévy case long tails appear for some properties characterizing the shape and dynamics of clusters. Under nonlocal finite-range interactions periodic patterns appear with periodicity set by the interaction range. This length acts as a cutoff limiting the influence of the long Lévy jumps, so that spatial configurations under the two types of diffusion become more similar. By dividing initially everyone into different families and following their descent it is possible to show that mixing of families and their competition is greatly influenced by the spatial dynamics.

Delayed responses to external drivers are ubiquitous in environmental, social, and biological processes. Delays may induce oscillations, Hopf bifurcations, and instabilities in deterministic systems even in the absence of nonlinearities. Despite recent advances in the study of delayed stochastic differential equations, the interaction of random drivers with delays remains poorly understood. In particular, it is unclear whether noise-induced behaviors may emerge from these interactions. Here we show that noise may enhance and sustain transient periodic oscillations inherent to deterministic delayed systems. We investigate the conditions conducive to the emergence and disappearance of these dynamics in a linear system in the presence of both additive and multiplicative noise.

We present a systematic overview of granular deposits composed of ellipsoidal particles with different particle shapes and size polydispersities. We study the density and anisotropy of such deposits as functions of small to moderate size polydispersity and two shape parameters that fully describe the shape of a general ellipsoid. Our results show that, while shape influences significantly the macroscopic properties of the deposits, polydispersity in the studied range plays apparently a secondary role. The density attains a maximum for a particular family of nonsymmetrical ellipsoids, larger than the density observed for prolate or oblate ellipsoids. As for anisotropy measures, the contact forces are increasingly preferred along the vertical direction as the shape of the particles deviates from a sphere. The deposits are constructed by means of a molecular dynamics method, where the contact forces are efficiently and accurately computed. The main results are discussed in the light of applications for porous media models and sedimentation processes.

We present an analytical study of the role of thermal fluctuations in shaping molecular elastic properties of semiflexible polymers. Our study interpolates between mechanics and statistical mechanics in a controlled way and shows how thermal fluctuations modify the elastic properties of biopolymers. We present a study of the minimum-energy configurations with explicit expressions for their energy and writhe and plots of the extension versus link for these configurations and a study of fluctuations around the local minima of energy and approximate analytical formulas for the free energy of stretched twisted polymers. The central result of our study is a closed-form expression for the leading thermal fluctuation correction to the free energy around the nonperturbative writhing family solution for the configuration of a biopolymer. From the derived formulas, the predictions of the wormlike chain model for molecular elasticity can be worked out for a comparison against numerical simulations and experiments.

Living cells must control the reading out or “expression” of information encoded in their genomes, and this regulation often is mediated by transcription factors—proteins that bind to DNA and either enhance or repress the expression of nearby genes. But the expression of transcription factor proteins is itself regulated, and many transcription factors regulate their own expression in addition to responding to other input signals. Here we analyze the simplest of such self-regulatory circuits, asking how parameters can be chosen to optimize information transmission from inputs to outputs in the steady state. Some nonzero level of self-regulation is almost always optimal, with self-activation dominant when transcription factor concentrations are low and self-repression dominant when concentrations are high. In steady state the optimal self-activation is never strong enough to induce bistability, although there is a limit in which the optimal parameters are very close to the critical point.

High-temperature and white-noise approximations are frequently invoked when deriving the quantum Brownian equation for an oscillator. Even if this white-noise approximation is avoided, it is shown that if the zero-point energies of the environment are neglected, as they often are, the resultant equation will violate not only the basic tenet of quantum mechanics that requires the density operator to be positive, but also the uncertainty principle. When the zero-point energies are included, asymptotic results describing the evolution of the oscillator are obtained that preserve positivity and, therefore, the uncertainty principle.

We interpret a generalized short-time expansion of stochastic hydrodynamic dispersion dynamics in the case of small Reynolds number flow through macroscopically homogenous permeable porous media to directly determine hydrodynamic permeability. The approach allows determination of hydrodynamic permeability from pulsed field gradient spin-echo nuclear magnetic resonance measurement of the short-time effective hydrodynamic dispersion coefficient. The analytical expansion of asymptotic dynamics agrees with experimental NMR data and lattice Boltzmann simulation of hydrodynamic dispersion in consolidated random sphere pack media.

Randomizing networks using a naive “accept-all” edge-swap algorithm is generally biased. Building on recent results for nondirected graphs, we construct an ergodic detailed balance Markov chain with nontrivial acceptance probabilities for directed graphs, which converges to a strictly uniform measure and is based on edge swaps that conserve all in and out degrees. The acceptance probabilities can also be generalized to define Markov chains that target any alternative desired measure on the space of directed graphs in order to generate graphs with more sophisticated topological features. This is demonstrated by defining a process tailored to the production of directed graphs with specified degree-degree correlation functions. The theory is implemented numerically and tested on synthetic and biological network examples.

A generalization of the Weyl law to systems with a sharply divided mixed phase space is proposed. The ansatz is composed of the usual Weyl term which counts the number of states in regular islands and a term associated with sticky regions in phase space. For a piecewise linear map, we numerically check the validity of our hypothesis, and find good agreement not only for the case with a sharply divided phase space but also for the case where tiny island chains surround the main regular island. For the latter case, a nontrivial power law exponent appears in the survival probability of classical escaping orbits, which may provide a clue to develop the Weyl law for more generic mixed systems.

We consider oscillators coupled with asymmetric time delays, namely, when the speed of information transfer is direction dependent. As the coupling parameter is varied, there is a regime of amplitude death within which there is a phase-flip transition. At this transition the frequency changes discontinuously, but unlike the equal delay case when the relative phase difference changes by $\pi$, here the phase difference changes by an arbitrary value that depends on the difference in delays. We consider asymmetric delays in coupled Landau-Stuart oscillators and Rössler oscillators. Analytical estimates of phase synchronization frequencies and phase differences are obtained by separating the evolution equations into phase and amplitude components. Eigenvalues and eigenvectors of the Jacobian matrix in the neighborhood of the transition also show an “avoided crossing,” as has been observed in previous studies with symmetric delays.

We develop a nonlinear theory for self-modulation of a circularly polarized electromagnetic wave in a relativistic hot weakly magnetized electron-positron plasma. The case of parallel propagation along an ambient magnetic field is considered. A nonlinear Schrödinger equation is derived for the complex wave amplitude of a self-modulated wave packet. We show that the maximum growth rate of the modulational instability decreases as the temperature of the pair plasma increases. Depending on the initial conditions, the unstable wave envelope can evolve nonlinearly to either periodic wave trains or solitary waves. This theory has application to high-energy astrophysics and high-power laser physics.

In this work, we investigate the behavior of the microcanonical and canonical averages of the two-dimensional Ising model during the Wang-Landau simulation. The simulations were carried out using conventional Wang-Landau sampling and the $1/t$ scheme. Our findings reveal that the microcanonical average should not be accumulated during the initial modification factors $f$, and they outline a criterion to find this limit, which we define as $f_{\text{micro}}$. We show that updating the density of states only after every $L^2$ spin-flip trials leads to a much better precision. We present a mechanism to determine for the given model up to what final modification factor $f_{\text{final}}$ the simulations should be carried out. Altogether these small adjustments lead to an improved procedure for simulations with much more reliable results. We compare our results with $1/t$ simulations. We also present an application of the procedure to a self-avoiding homopolymer.

We investigate transport properties of one-dimensional fermionic tight binding models featuring nearest and next-nearest neighbor hopping, where the fermions are additionally subject to a weak short range mutual interaction. To this end we employ a pertinent approach which allows for a mapping of the underlying Schrödinger dynamics onto an adequate linear quantum Boltzmann equation. This approach is based on a suitable projection operator method. From this Boltzmann equation we are able to numerically obtain diffusion coefficients in the case of nonvanishing next-nearest neighbor hopping, i.e., the nonintegrable case, whereas the diffusion coefficient diverges without next-nearest neighbor hopping. For the latter case we analytically investigate the decay behavior of the current with the result that arbitrarily small parts of the current relax arbitrarily slowly which suggests anomalous diffusive transport behavior within the scope of our approach.

Spin systems with long-range interactions are “nonextensive” if the strength of the interactions falls off sufficiently slowly with distance. It has been conjectured for ferromagnets and, more recently, for spin glasses that, everywhere in the nonextensive regime, the free energy is exactly equal to that for the infinite range model in which the characteristic strength of the interaction is independent of distance. In this paper we present the results of Monte Carlo simulations of the one-dimensional long-range spin glasses in the nonextensive regime. Using finite-size scaling, our results for the transition temperatures are consistent with this prediction. We also propose and provide numerical evidence for an analogous result for diluted long-range spin glasses in which the coordination number is finite, namely, that the transition temperature throughout the nonextensive regime is equal to that of the infinite-range model known as the Viana-Bray model.

We suggest a theoretical description of the force-induced translocation dynamics of a polymer chain through a nanopore. Our consideration is based on the tensile (Pincus) blob picture of a pulled chain and the notion of a propagating front of tensile force along the chain backbone, suggested by Sakaue [Phys. Rev. E 76, 021803 (2007); Phys. Rev. E 81, 041808 (2010); Eur. Phys. J. E 34, 135 (2011)]. The driving force is associated with a chemical potential gradient that acts on each chain segment inside the pore. Depending on its strength, different regimes of polymer motion (named after the typical chain conformation: trumpet, stem-trumpet, etc.) occur. Assuming that the local driving and drag forces are equal (i.e., in a quasistatic approximation), we derive an equation of motion for the tensile front position $X\left(t\right)$. We show that the scaling law for the average translocation time $\langle \tau \rangle$ changes from $\langle \tau \rangle \sim N^{2\nu }/f^{1/\nu }$ to $\langle \tau \rangle \sim N^{1+\nu }/f$ (for the free-draining case) as the dimensionless force ${\tilde{f}}_R=a{N}^{\nu }f/T$ (where $a$, $N$, $\nu$, $f$, and $T$ are the Kuhn segment length, the chain length, the Flory exponent, the driving force, and the temperature, respectively) increases. These and other predictions are tested by molecular-dynamics simulation. Data from our computer experiment indicate indeed that the translocation scaling exponent $\alpha$ grows with the pulling force ${\tilde{f}}_R$, albeit the observed exponent $\alpha$ stays systematically smaller than the theoretically predicted value. This might be associated with fluctuations that are neglected in the quasistatic approximation.

In some recent papers, the use of random forces has been related to a systematic breakdown of the fluctuation theorem. In the framework of nonequilibrium molecular dynamics, we provide a derivation of this theorem for systems driven by both deterministic and stochastic forces. It turns out that it is still valid and describes the total dissipation, explicitly the sum of two dimensionless works for which fluctuation relations may fail. We numerically study their range of validity, comment on experimental results, and point out in which limit a noise can be neglected.