We propose a unified framework for both Shannon–Khinchin and Shore–Johnson axiomatic systems. We do it by rephrasing Shannon–Khinchine axioms in terms of generalized arithmetics of Kolmogorov and Nagumo. We prove that the two axiomatic schemes yield identical classes of entropic functionals — the Uffink class of entropies. This allows to re-establish the entropic parallelism between information theory

The most widely used techniques for community detection in networks, including methods based on modularity, statistical inference, and information theoretic arguments, all work by optimizing objective functions that measure the quality of network partitions. There is a good case to be made, however, that one should not look solely at the single optimal community structure under such an objective function

In the classical susceptible-infected-susceptible (SIS) model, a disease or infection spreads over a given, mostly fixed graph. However, in many real complex networks, the topology of the underlying graph can change due to the influence of the dynamical process. In this paper, besides the spreading process, the network adaptively changes its topology based on the states of the nodes in the network

Electrostatic theory preserves charges, but allows dipolar excitations. Elasticity theory preserves dipoles, but allows quadrupolar (Eshelby like) plastic events. Charged amorphous granular systems are interesting in their own right; here we focus on their plastic instabilities and examine their mechanical response to external strain and to external electric field, to expose the competition between

This paper introduces improvements to the amplitude expansion of the phase field crystal model (APFC) that enable the simulation of grains within a full range of orientations. The unphysical grain boundary between grains, rotated by a crystal’s symmetry rotation, is removed using a combination of the auxiliary rotation field described in our previous work and an algorithm that correctly matches the

Nonadditive Tsallis q-statistics has successfully been applied for a plethora of systems in natural sciences and other branches of knowledge. Nevertheless, its foundations have been severely criticised by some authors based on the standard additive Boltzmann-Gibbs approach thereby remaining a quite controversial subject. In order to clarify some polemical concepts, the distribution function for an

In this paper, we present a novel finite-volume direct kinetic method, the so-called discrete unified gas kinetic scheme (DUGKS), for electrostatic plasma. One key feature of this method is the semi-implicit un-splitting treatment of particle transport and collision, thus the time step in current DUGKS is not limited by the particle collision time. In addition, a fourth order compact MUSCL scheme with

The properties of a wide range of two-dimensional network materials are investigated by developing a generalised network theory. The methods developed are shown to be applicable to a wide range of systems generated from both computation and experiment; incorporating atomistic materials, foams, fullerenes, colloidal monolayers and geopolitical regions. The ring structure in physical networks is described

It is a longstanding debate on the absence of threshold for SIS model on networks with finite second order moment of degree distribution. The eigenvector localization of the adjacency matrix for a network gives rise to the inactive Griffiths phase featuring slow decay of the activity localized around highly connected nodes due to the dynamical fluctuation. We show how it dramatically changes our understanding

Theory of direct scattering transform for nonlinear wave fields containing solitons is revisited to overcome fundamental difficulties hindering its stable numerical implementation. With the focusing one-dimensional nonlinear Schrdinger equation serving as a model, we study a crucial fundamental property of the scattering problem for multi-soliton potentials demonstrating that in many cases phase and

Iron is an essential requirement for the survival and virulence of most bacteria. The bacterial ferrous iron transporter protein FeoB functions as a major reduced iron transporter in prokaryotes, but its biochemical mechanism has not been fully elucidated. In the present study, we compared enzymatic properties of the cytosolic portions of pathogenic bacterial FeoBs to elucidate each bacterial strain-specific

Ion sound waves are studied in a plasma subject to gravitational field {giving rise to vertically inhomogeneous steady state plasma conditions}. Such systems are interesting by exhibiting a wave growth that is a result of energy flux conservation {for pulses propagating in an inhomogeneous system. The increase of the amplitude of a pulse as it propagates along the density gradient in the direction

At equilibrium, the structure and response of ordered phases are typically determined by the spontaneous breaking of spatial symmetries. Out of equilibrium, spatial order itself can become a dynamically emergent concept. In this article, we show that spatially anisotropic viscous coefficients and stresses can be designed in a far-from-equilibrium fluid by applying to its constituents a time-modulated

Computed tomography (CT) images of large core samples acquired by imaging equipment are insufficiently clear and ineffectively describe the tiny pore structure; conversely, images of small core samples are insufficiently globally representative. To alleviate these challenges, the idea of a super-resolution reconstruction algorithm is combined with that of a three-dimensional core reconstruction algorithm

We investigate the mechanisms of opening-mode fracture initiation in granular media. The study is based on simulation of grain-scale fluid-grain interactions through a coupled numerical approach in which the discrete element model (DEM) is used to solve for the mechanics of a solid granular medium and computational fluid dynamics (CFD) is used to model fluid flow and drag forces. We present benchmark

Modeling stochastic gene expression has long relied on Markovian hypothesis. In recent years, however, this hypothesis is challenged by the increasing availability of time-resolved data. Correspondingly, there is considerable interest in understanding how non-Markovian reaction kinetics of gene expression impact protein variations across a population of cells. Here, we analyze a stochastic model of

Uptake of liquid drops into capillary tubes has been experimentally studied and quantitatively analysed. In experiments, drops of water and aqueous glycerol (≤50~wt% ) were drawn into cylindrical borosilicate glass and quartz tubes of inner diameter 0.50 - 0.75~mm. The meniscus height rise was measured using high-speed images captured at 4000 frames per second, and results within a conservatively-defined

Chiral condensed matter systems, such as liquid crystals and magnets, exhibit a host of spatially localized topological structures that emerge from the medium’s tendency to twist and its competition with confinement and field coupling effects. We show that the strength of perpendicular surface boundary conditions can be used to control the structure and topology of solitonic and other localized field

We study the energy landscapes of particles with short-range attractive interactions as the range of the interactions increases. Starting with the set of local minima for 6≤N≤12 hard spheres that are "sticky", i.e. they interact only when their surfaces are exactly in contact, we use numerical continuation to evolve the local minima (clusters) as the range of the potential increases, using both the

An important question in turbulent Rayleigh-B'{e}nard convection (RBC) is the effectiveness of convective heat transport, which is conveniently described via the scaling of the Nusselt number (${\rm{Nu}}$) with the Rayleigh (${\rm{Ra}}$) and Prandtl (${\rm{Pr}}$) numbers. In RBC experiments, the heat supplied to the bottom plate is also partly transferred by thermal radiation. This heat transport channel

Plasticity in amorphous solids is mediated by localized quadrupolar instabilities, but the mechanism by which an amorphous solid eventually fails or melts is debated. In this work {we argue that these phenomena can be investigated in the model problem of an elastic continuum with quadrupolar defects, at finite temperature. This problem is posed and the collective behavior of the defects is analytically

When a water drop impinges on a flat superhydrophobic surface, it bounces off the surface after certain dwelling time, which is determined by Rayleigh inertia-capillary timescale. Recent works have demonstrated that this dwelling time (i.e., contact time) is modified on curved superhydrophobic surfaces, as the drop asymmetrically spreads over the surface. However, the contact time on the curved surfaces

The information theoretic measure known as mutual information is widely used as a way to quantify the similarity of two different labelings or divisions of the same set of objects, such as arises for instance in clustering and classification problems in machine learning or community detection problems in network science. Here we argue that the standard mutual information, as commonly defined, omits

Mobility properties of spatially localized structures arising from chaotic but deterministic forcing of the bistable Swift-Hohenberg equation are studied and compared with the corresponding results when the chaotic forcing is replaced by white noise. Short structures are shown to possess greater mobility, resulting in larger r.m.s. speeds but shorter displacements than longer structures. Averaged over

To investigate the evolution of cooperation in spatial public goods games, this paper establishes a bi-random geometric graph, in which two types of nodes, representing players and public goods respectively, are placed at random locations in the unit square. Each public good has a limit influence range and the individuals that fall into the same range engage in a public good game. In contrast to the

We discuss a thermodynamic process with information and justify a general form of fluctuation relation. It shows that the fluctuation relation is valid whatever it is the temperature or Hamiltonian that drives the system out of equilibrium state. Based on the stochastic equation we obtain a non-equilibrium equality that involves both information and time-varying temperature. Through the processing

Hydrogen absorption by Pd exhibits hysteresis loops (provided the temperature is not too hight) and represents one of the classical examples of the first-order phase transitions in metals. The experiments indicate that addition of even small amount of Au is able to suppress hysteresis. From this perspective, we analyze the energetic of hydrogen in a Pd-Au alloy by using extensive density-functional-theory

Recent years have seen an increasing interest in quantum chaos and related aspects of spatially extended systems, such as spin chains. However, the results are strongly system dependent, generic approaches suggest the presence of many-body localization while analytical calculations for certain system classes, here referred to as the "self-dual case", prove adherence to universal (chaotic) spectral

Origami-based mechanical metamaterials and metastructure have been demonstrated to exhibit unique properties originating from their intricate geometries of folding. This research aims to extend the current investigation level from quasi-statics to dynamics. In detail, this research focuses on the wave dynamics of a metastructure composed of stacked Miura-ori (SMO) units. The SMO unit could possess

Pioneer transcription factors are a recently defined class of transcription factors which can bind directly to nucleosomal DNA; they play a key role in gene activation in certain pathways. Here we quantify their role in the initiation of nucleosome displacement within the kinetic proofreading scenario of chromatin remodeling. The model allows to perform remodeling efficiency comparisons for scenarios

Slender elastic objects such as a column tend to buckle under loads. While static buckling is well understood as a bifurcation problem, the evolution of shapes during dynamic buckling is much harder to study. Elastic rings under normal pressure have emerged as a theoretical and experimental paradigm for the study of dynamic buckling with controlled loads. Experimentally, an elastic ring is placed within

We find novel site-dependent Lax operators in terms of which we demonstrate exact solvability of a dissipatively driven XYZ spin-1/2 chain in the Zeno limit of strong dissipation, with jump operators polarizing the boundary spins in arbitrary directions. We write the corresponding nonequilibrium steady state using an inhomogeneous MPA, where the constituent matrices satisfy a simple set of linear recurrence

We investigate the collective dynamics of self-propelled droplets, confined in a one dimensional micro-fluidic channel. On one hand, neighboring droplets align and form large trains of droplets moving in the same direction. On the other hand, the droplets condensates, leaving large regions with very low density. A careful examination of the interactions between two “colliding” droplets demonstrates