Physical Review E最新文献

Polymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combinatoric arguments to enumerate the emergent chromatin loop networks, both in the case where TUs are labeled and where they are unlabeled. We then combine these mathematical results with those of computer simulations aimed at finding the inter-TU energy required to form a target loop network. We show that different topologies are vastly different in terms of both their combinatorial weight and energy of formation. We explain the latter result qualitatively by computing the topological weight of a given network-i.e., its partition function in statistical mechanics language-in the approximation where excluded volume interactions are neglected. Our results show that networks featuring local loops are statistically more likely with respect to networks including more nonlocal contacts. We suggest our classification of loop networks, together with our estimate of the combinatorial and topological weight of each network, will be relevant to catalog three-dimensional structures of chromatin fibers around eukaryotic genes, and to estimate their relative frequency in both simulations and experiments.

In open water, social fish gather to form schools, in which fish generally align with each other. In this work, we study how this social behavior evolves when perturbed by artificial obstacles. We measure the behavior of a group of zebrafish in the presence of a periodic array of pillars. When the pillar density is low, the fish regroup with a typical interdistance and a well-polarized state with parallel orientations, similarly to their behavior in open-water conditions. Above a critical density of pillars, their social interactions, which are mostly based on vision, are screened and the fish spread randomly through the aquarium, orienting themselves along the free axes of the pillar lattice. The abrupt transition from natural to artificial orientation happens when the pillar interdistance is comparable to the social distance of the fish, i.e., their most probable interdistance. We develop a stochastic model of the relative orientation between fish pairs, taking into account alignment, antialignment, and tumbling, from a distribution biased by the environment. This model provides a good description of the experimental probability distribution of the relative orientation between the fish and captures the behavioral transition. Using the model to fit the experimental data provides qualitative information on the evolution of cognitive parameters, such as the alignment or the tumbling rates, as the pillar density increases. At high pillar density, we find that the artificial environment imposes its geometrical constraints to the fish school, drastically increasing the tumbling rate.

The spectral form factor (SFF) plays a crucial role in revealing the statistical properties of energy-level distributions in complex systems. It is one of the tools to diagnose quantum chaos and unravel the universal dynamics therein. The definition of SFF in most literature only encapsulates the two-level correlation. In this manuscript, we extend the definition of SSF to include the high-order correlation. Specifically, we introduce the standard deviation of energy levels to define correlation functions, from which the generalized spectral form factor (GSFF) can be obtained by Fourier transforms. GSFF provides a more comprehensive knowledge of the dynamics of chaotic systems. Using random matrices as examples, we demonstrate dynamics features that are encoded in GSFF. Remarkably, the GSFF is complex, and the real and imaginary parts exhibit universal dynamics. For instance, in the two-level correlated case, the real part of GSFF shows a dip-ramp-plateau structure akin to the conventional counterpart, and the imaginary part for different system sizes converges in the long-time limit. For the two-level GSFF, the analytical forms of the real part are obtained and consistent with numerical results. The results of the imaginary part are obtained by numerical calculation. Similar analyses are extended to three-level GSFF.

The analytical expression for the conditions of the solid-fluid phase transition, i.e., the melting curve, for two-dimensional (2D) Yukawa systems is derived theoretically from the isomorph theory. To demonstrate that the isomorph theory is applicable to 2D Yukawa systems, molecular dynamical simulations are performed under various conditions. Based on the isomorph theory, the analytical isomorphic curves of 2D Yukawa systems are derived using the local effective power-law exponent of the Yukawa potential. From the obtained analytical isomorphic curves, the melting curve of 2D Yukawa systems is directly determined using only two known melting points. The determined melting curve of 2D Yukawa systems well agrees with the previous obtained melting results using completely different approaches.

We describe experimentally observed collective dynamics in colloidal suspensions of model hard-sphere particles using a modified mode coupling theory (MCT). This rescaled MCT is capable of describing quantitatively the wave-vector and time-dependent diffusion in these systems. Intermediate scattering functions of liquidlike structured dispersions are determined by means of static and dynamic light-scattering experiments. The structure and short-time dynamics of the systems can be described quantitatively employing a multicomponent Percus-Yevick ansatz for the partial structure factors and an effective, one-component description of hydrodynamic interactions based on the semianalytical δγ expansion. Combined with a recently proposed empirical modification of MCT in which memory functions are calculated using effective structure factors at rescaled number densities, the scheme is able to model the collective dynamics over the entire accessible time and wave-vector range and predicts the volume-fraction-dependence of long-time self-diffusion coefficients and the zero-shear viscosity quantitatively. This highlights the potential of MCT as a practical tool for the quantitative analysis and prediction of experimental observations.

A binary mixture of two-different-size proliferating motile disks is studied. As growth is space limited, we focus on the conditions such that there is a coexistence of both large and small disks, or dominance of the larger disks. The study involves systematically varying some system parameters, such as diffusivities, growth rates, and self-propulsion velocities. In particular, we demonstrate that diffusing faster confers a competitive advantage, so that larger disks can in the long time coexist or even dominate the smaller ones. In the case of self-propelled disks, a coexistence regime is induced by the activity where the two types of disks show the same spatial distribution: both particles are phase separated or both are homogeneously distributed in the whole system.

Differential equations of the form R[over ̈]=-kR^{γ}, with a positive constant k and real parameter γ, are fundamental in describing phenomena such as the spherical gravitational collapse (γ=-2), the implosion of cavitation bubbles (γ=-4), and the orbital decay in binary black holes (γ=-7). While explicit elemental solutions exist for select integer values of γ, more comprehensive solutions encompassing larger subsets of γ have been independently developed in hydrostatics (see Lane-Emden equation) and hydrodynamics (see Rayleigh-Plesset equation). I here present a universal explicit solution for all real γ, invoking the beta distribution. Although standard numerical ordinary differential equation solvers can readily evaluate more general second-order differential equations, this explicit solution reveals a hidden connection between collapse motions and probability theory that enables further analytical manipulations, it conceptually unifies distinct fields, and it offers insights into symmetry properties, thereby enhancing our understanding of these pervasive differential equations.

The concept of soliton gas was introduced in 1971 by Zakharov as an infinite collection of weakly interacting solitons in the framework of Korteweg-de Vries (KdV) equation. In this theoretical construction of a diluted (rarefied) soliton gas, solitons with random amplitude and phase parameters are almost nonoverlapping. More recently, the concept has been extended to dense gases in which solitons strongly and continuously interact. The notion of soliton gas is inherently associated with integrable wave systems described by nonlinear partial differential equations like the KdV equation or the one-dimensional nonlinear Schrödinger equation that can be solved using the inverse scattering transform. Over the last few years, the field of soliton gases has received a rapidly growing interest from both the theoretical and experimental points of view. In particular, it has been realized that the soliton gas dynamics underlies some fundamental nonlinear wave phenomena such as spontaneous modulation instability and the formation of rogue waves. The recently discovered deep connections of soliton gas theory with generalized hydrodynamics have broadened the field and opened new fundamental questions related to the soliton gas statistics and thermodynamics. We review the main recent theoretical and experimental results in the field of soliton gas. The key conceptual tools of the field, such as the inverse scattering transform, the thermodynamic limit of finite-gap potentials, and generalized Gibbs ensembles are introduced and various open questions and future challenges are discussed.