Recent experimental studies of molten metal droplets wetting high-temperature reactive substrates have established that the majority of triple-line motion occurs when inertial effects are dominant. In light of these studies, this paper investigates wetting and spreading on reactive substrates when inertial effects are dominant using a thermodynamically derived diffuse interface model of a binary three-phase material. The liquid-vapor transition is modeled using a van der Waals diffuse interface approach, while the solid-fluid transition is modeled using a phase field approach. The results from the simulations demonstrate an $O\left(t^{-1/2}\right)$ spreading rate during the inertial regime and oscillations in the triple-line position when the metal droplet transitions from inertial to diffusive spreading. It is found that the spreading extent is reduced by enhancing dissolution by manipulating the initial liquid composition. The results from the model exhibit good qualitative and quantitative agreement with a number of recent experimental studies of high-temperature droplet spreading, particularly experiments of copper droplets spreading on silicon substrates. Analysis of the numerical data from the model suggests that the extent and rate of spreading are regulated by the spreading coefficient calculated from a force balance based on a plausible definition of the instantaneous interface energies. A number of contemporary publications have discussed the likely dissipation mechanism in spreading droplets. Thus, we examine the dissipation mechanism using the entropy-production field and determine that dissipation primarily occurs in the locality of the triple-line region during the inertial stage but extends along the solid-liquid interface region during the diffusive stage.

We study shear-induced instabilities of lipid bilayers immersed in water using coarse-grained molecular dynamics simulations. The shear imposed by the flow of the water induces initially microscopic structural changes of the membrane, starting with tilting of the molecules in the direction of the shear. The tilting propagates in the spanwise direction when the shear rate exceeds a critical value and the membrane undergoes a bucklinglike deformation in the direction perpendicular to the shear. The bucklinglike undulation continues until a localized Kelvin-Helmholtz-like instability leads to membrane rupture. We study the different modes of membrane undulation using membranes of different geometries and quantify the relative importance of the bucklinglike bending and the Kelvin-Helmholtz-like instability of the membrane.

In many cell-signaling pathways information is transmitted via the diffusion of messenger molecules. In most cases, messengers react with other substances and diffuse at the same time. Effective diffusion coefficients may be introduced to characterize the net transport rate that results from the combined effect of these two processes. It was shown in [B. Pando et al., Proc. Natl. Acad. Sci. U.S.A. 103, 5338 (2006)] that even in the simplest scenario in which one bimolecular reaction is involved, two different effective coefficients are relevant. One gives the rate at which small perturbations spread out with time while the other relates the mean square displacement of a single particle to the time elapsed. They coincide in the absence of reactions but may be very different in other cases. Optical techniques provide a relatively noninvasive means by which transport rates can be estimated. In the above mentioned paper it was discussed why, under certain conditions, fluorescence recovery after photobleaching (FRAP), a technique commonly used to estimate diffusion rates in cells, provides information on one of the two effective coefficients. In the present paper we show that, under the same conditions, another commonly used optical technique, fluorescence correlation spectroscopy (FCS), gives information on the other one. This opens up the possibility of combining experiments to obtain information that goes beyond effective transport rates. In the present paper we discuss different ways to do so.

Since its inception by Kimura in 1955 [M. Kimura, Proc. Natl. Acad. Sci. U.S.A. 41, 144 (1955)], the diffusion equation has become a standard technique of population genetics. The diffusion equation is however only an approximation, valid in the limit of large populations and small selection. Moreover, useful quantities such as the fixation probabilities are not easily extracted from it and need the concomitant use of a forward and backward equation. We show here that the partial differential equation governing the probability generating function can be used as an alternative to the diffusion equation with none of its drawbacks: it does not involve any approximation, it has well-defined initial and boundary conditions, and its solutions are finite polynomials. We apply this technique to derive analytical results for the Moran process with selection, which encompasses the Kimura diffusion equation.

Microarray technology, in its simplest form, allows one to gather abundance data for target DNA molecules, associated with genomes or gene-expressions, and relies on hybridizing the target to many short probe oligonucleotides arrayed on a surface. While for such multiplexed reactions conditions are optimized to make the most of each individual probe-target interaction, subsequent analysis of these experiments is based on the implicit assumption that a given experiment yields the same result regardless of whether it was conducted in isolation or in parallel with many others. It has been discussed in the literature that this assumption is frequently false, and its validity depends on the types of probes and their interactions with each other. We present a detailed physical model of hybridization as a means of understanding probe interactions in a multiplexed reaction. Ultimately, the model can be derived from a system of ordinary differential equations (ODE’s) describing kinetic mass action with conservation-of-mass equations completing the system. We examine pairwise probe interactions in detail and present a model of “competition” between the probes for the target—especially, when the target is effectively in short supply. These effects are shown to be predictable from the affinity constants for each of the four probe sequences involved, namely, the match and mismatch sequences for both probes. These affinity constants are calculated from the thermodynamic parameters such as the free energy of hybridization, which are in turn computed according to the nearest neighbor (NN) model for each probe and target sequence. Simulations based on the competitive hybridization model explain the observed variability in the signal of a given probe when measured in parallel with different groupings of other probes or individually. The results of the simulations can be used for experiment design and pooling strategies, based on which probes have been shown to have a strong effect on each other’s signal in the in silico experiment. These results are aimed at better design of multiplexed reactions on arrays used in genotyping (e.g., HLA typing, SNP, or CNV detection, etc.) and mutation analysis (e.g., cystic fibrosis, cancer, autism, etc.).

The dry frictional contact between two solid surfaces is well known to obey Coulomb friction laws. In particular, the static friction force resisting the relative lateral (tangential) motion of solid surfaces, initially at rest, is known to be proportional to the normal force and independent of the area of the macroscopic surfaces in contact. Experimentally, the static friction force has been observed to slightly depend on time. Such an aging phenomenon has been accounted for either by the creep of the material or by the condensation of water bridges at the microscopic contact points. By studying a toy model, we show that the small uncontrolled temperature changes of the system can also lead to a significant increase of the static friction force.

In this work, we investigate gradient coupling effect on oscillation death in a ring of $N$ delay-coupled oscillators. We find that the gradient coupling monotonically reduces the domain of death island in the parameter space of the diffusive coupling and time delay, and thus the death island can be completely eliminated once the gradient coupling strength exceeds a certain threshold, whose value is found to be a constant if $N$ is sufficiently large. For two special cases, a ring with zero gradient coupling and a one-way ring for identical diffusive and gradient couplings, all previous results in the literature are recovered. In particular, for the one-way ring, a size effect of $N$ is discovered, which indicates that under this situation the death can always be eliminated if $N$ is above a critical $N_{max}$. All the described results are proved to hold generally in coupled oscillator systems.

The operator fidelity is a measure of the information-theoretic distinguishability between perturbed and unperturbed evolutions. The response of this measure to the perturbation may be formulated in terms of the operator fidelity susceptibility (OFS), a quantity which has been used to investigate the parameter spaces of quantum systems in order to discriminate their regular and chaotic regimes. In this work we numerically study the OFS for a pair of nonlinearly coupled two-dimensional harmonic oscillators, a model which is equivalent to that of a hydrogen atom in a uniform external magnetic field. We show how the two terms of the OFS, being linked to the main properties that differentiate regular from chaotic behavior, allow for the detection of this model’s transition between the two regimes. In addition, we find that the parameter interval where perturbation theory applies is delimited from above by a local minimum of one of the analyzed terms.

We consider the Riemann problem for relativistic flows of polytropic fluids and find relations for the flow characteristics. Evolution of physical quantities takes especially simple form for the case of cold magnetized plasmas. We find exact explicit analytical solutions for one-dimensional expansion of magnetized plasma into vacuum, valid for arbitrary magnetization. We also consider expansion into cold unmagnetized external medium both for stationary initial conditions and for initially moving plasma, as well as reflection of rarefaction wave from a wall. We also find self-similar structure of three-dimensional magnetized outflows into vacuum, valid close to the plasma-vacuum interface.

In this paper we introduce a three-dimensional Lattice-Boltzmann model that recovers in the continuous limit the Maxwell equations in materials. In order to build conservation equations with antisymmetric tensors, like the Faraday law, the model assigns four auxiliary vectors to each velocity vector. These auxiliary vectors, when combined with the distribution functions, give the electromagnetic fields. The evolution is driven by the usual Bhatnager-Gross-Krook (BGK) collision rule, but with a different form for the equilibrium distribution functions. This lattice Bhatnager-Gross-Krook (LBGK) model allows us to consider for both dielectrics and conductors with realistic parameters, and therefore it is adequate to simulate the most diverse electromagnetic problems, like the propagation of electromagnetic waves (both in dielectric media and in waveguides), the skin effect, the radiation pattern of a small dipole antenna and the natural frequencies of a resonant cavity, all with 2% accuracy. Actually, it shows to be one order of magnitude faster than the original Finite-difference time-domain (FDTD) formulation by Yee to reach the same accuracy. It is, therefore, a valuable alternative to simulate electromagnetic fields and opens lattice Boltzmann for a broad spectrum of new applications in electrodynamics.

We propose the modification of the complex wavelet transform adapted for an analysis of strong nonlinear oscillations with a shape far from sinusoidal. It is based on the rotation of transform modulus obtained via usage of the Morlet wavelet in such a way that higher harmonics are merged with a main one. The method is illustrated by application to the analysis of regular and chaotic oscillations generated by the Rössler system.

The tensor renormalization-group method, developed by Levin and Nave, brings systematic improvability to the position-space renormalization-group method and yields essentially exact results for phase diagrams and entire thermodynamic functions. The method, previously used on systems with no quenched randomness, is extended in this study to systems with quenched randomness. Local magnetizations and correlation functions as a function of spin separation are calculated as tensor products subject to renormalization-group transformation. Phase diagrams are extracted from the long-distance behavior of the correlation functions. The approach is illustrated with the quenched bond-diluted Ising model on the triangular lattice. An accurate phase diagram is obtained in temperature and bond-dilution probability for the entire temperature range down to the percolation threshold at zero temperature.

Two granular gases separated by an adiabatic piston and initially in the same macroscopic state are considered. It is found that a phase transition with an spontaneous symmetry breaking occurs. When the mass of the piston is increased beyond a critical value, the piston moves to a stationary position different from the middle of the system. The transition is accurately described by a simple kinetic model that takes into account the velocity fluctuations of the piston. Interestingly, the final state is not characterized by the equality of the temperatures of the subsystems but by the cooling rates being the same. Some relevant consequences of this feature are discussed.

Neuronal network behavior results from a combination of the dynamics of individual neurons and the connectivity of the network that links them together. We study a simplified model, based on the proposal of Feldman and Del Negro (FDN) [Nat. Rev. Neurosci. 7, 232 (2006)], of the preBötzinger Complex, a small neuronal network that participates in the control of the mammalian breathing rhythm through periodic firing bursts. The dynamics of this randomly connected network of identical excitatory neurons differ from those of a uniformly connected one. Specifically, network connectivity determines the identity of emergent leader neurons that trigger the firing bursts. When neuronal desensitization is controlled by the number of input signals to the neurons (as proposed by FDN), the network’s collective desensitization—required for successful burst termination—is mediated by $k$ -core clusters of neurons.

By defining “flow density” in a reversible ratchet, a kind of Brownian motor that runs four processes in a two-dimensional parameter space to complete a cycle, we analytically investigate the behavior of the motor’s integrated flow in terms of the magnitude and location of the density maximum. It turns out that flow density gives information that can serve as a guide for obtaining the most suitable integrated flow important in the design of reversible ratchets.

We solve analytically the model of gene expression induction which consists of three steps: gene activation, gene products synthesis, and product degradation. The solution is given as a time-dependent probability distribution for gene products. Following the distribution in time from the inactive state of the gene to the stationary state we observe binary or graded response depending solely on the ratio $r$ of the gene activation rate to the rate of the gene product degradation. If $r⪡1$ the response is binary and the continuous transition from binary to graded response occurs between $r=0.1$ and $r=1$. Therefore, if binary response is observed during relaxation to steady state, then the activation rate constant must be smaller than the degradation rate constant.

Determining the relative importance of nodes in directed networks is important in, for example, ranking websites, publications, and sports teams, and for understanding signal flows in systems biology. A prevailing centrality measure in this respect is the PageRank. In this work, we focus on another class of centrality derived from the Laplacian of the network. We extend the Laplacian-based centrality, which has mainly been applied to strongly connected networks, to the case of general directed networks such that we can quantitatively compare arbitrary nodes. Toward this end, we adopt the idea used in the PageRank to introduce global connectivity between all the pairs of nodes with a certain strength. Numerical simulations are carried out on some networks. We also offer interpretations of the Laplacian-based centrality for general directed networks in terms of various dynamical and structural properties of networks. Importantly, the Laplacian-based centrality defined as the stationary density of the continuous-time random walk with random jumps is shown to be equivalent to the absorption probability of the random walk with sinks at each node but without random jumps. Similarly, the proposed centrality represents the importance of nodes in dynamics on the original network supplied with sinks but not with random jumps.

The nonlinear propagation of electromagnetic (EM) electron-cyclotron waves (whistlers) along an external magnetic field, and their modulation by electrostatic small but finite amplitude ion-acoustic density perturbations are investigated in a uniform quantum plasma with intrinsic spin of electrons. The effects of the quantum force associated with the Bohm potential and the combined effects of the classical as well as the spin-induced ponderomotive forces (CPF and SPF, respectively) are taken into consideration. The latter modify the local plasma density in a self-consistent manner. The coupled modes of wave propagation is shown to be governed by a modified set of nonlinear Schrödinger-Boussinesq-like equations which admit exact solutions in form of stationary localized envelopes. Numerical simulation reveals the existence of large-scale density fluctuations that are self-consistently created by the localized whistlers in a strongly magnetized high density plasma. The conditions for the modulational instability (MI) and the value of its growth rate are obtained. Possible applications of our results, e.g., in strongly magnetized dense plasmas and in the next generation laser-solid density plasma interaction experiments are discussed.

We have considered linear kinetic theory, including the electron-spin properties in a magnetized plasma. The starting point is a mean-field Vlasov-like equation, derived from a fully quantum-mechanical treatment, where effects from the electron-spin precession and the magnetic dipole force are taken into account. The general conductivity tensor is derived, including both the free current contribution and the magnetization current associated with the spin contribution. We conclude the paper with an extensive discussion of the quantum-mechanical boundary where we list parameter conditions that must be satisfied for various quantum effects to be influential.

We present a systematic study of the existence and stability of discrete breathers that are spatially localized in the bulk of a one-dimensional chain of compressed elastic beads that interact via Hertzian contact. The chain is diatomic, consisting of a periodic arrangement of heavy and light spherical particles. We examine two families of discrete gap breathers: (1) an unstable discrete gap breather that is centered on a heavy particle and characterized by a symmetric spatial energy profile and (2) a potentially stable discrete gap breather that is centered on a light particle and is characterized by an asymmetric spatial energy profile. We investigate their existence, structure, and stability throughout the band gap of the linear spectrum and classify them into four regimes: a regime near the lower optical band edge of the linear spectrum, a moderately discrete regime, a strongly discrete regime that lies deep within the band gap of the linearized version of the system, and a regime near the upper acoustic band edge. We contrast discrete breathers in anharmonic Fermi-Pasta-Ulam (FPU)-type diatomic chains with those in diatomic granular crystals, which have a tensionless interaction potential between adjacent particles, and note that the asymmetric nature of the tensionless interaction potential can lead to hybrid bulk-surface localized solutions.