We study the structural transition from B form of DNA to A form of DNA using group theoretic methods. The transition is not of the order-disorder type and hence to construct a Landau kind of theory for the transition we define a higher symmetry and relevant order parameters. We also discuss the issue of all the conformations, observed experimentally during the course of transition, being fundamentally different or not.

We study firm collaborations in the life sciences and the information and communication technology sectors. We propose an approach to characterize industrial leadership using $k$-shell decomposition, with top-ranking firms in terms of market value in higher $k$-shell layers. We find that the life sciences industry network consists of three distinct components: a “nucleus,” which is a small well-connected subgraph, “tendrils,” which are small subgraphs consisting of small degree nodes connected exclusively to the nucleus, and a “bulk body,” which consists of the majority of nodes. Industrial leaders, i.e., the largest companies in terms of market value, are in the highest $k$-shells of both networks. The nucleus of the life sciences sector is very stable: once a firm enters the nucleus, it is likely to stay there for a long time. At the same time we do not observe the above three components in the information and communication technology sector. We also conduct a systematic study of these three components in random scale-free networks. Our results suggest that the sizes of the nucleus and the tendrils in scale-free networks decrease as the exponent of the power-law degree distribution $\lambda$ increases, and disappear for $\lambda \ge 3$. We compare the $k$-shell structure of random scale-free model networks with two real-world business firm networks in the life sciences and in the information and communication technology sectors. We argue that the observed behavior of the $k$-shell structure in the two industries is consistent with the coexistence of both preferential and random agreements in the evolution of industrial networks.

This work is directed toward investigating the fate of three-dimensional long perturbation waves in a plane incompressible wake. The analysis is posed as an initial-value problem in space. More specifically, input is made at an initial location in the downstream direction and then tracing the resulting behavior further downstream subject to the restriction of finite kinetic energy. This presentation follows the outline given by Criminale and Drazin [W. O. Criminale and P. G. Drazin, Stud. Appl. Math. 83, 123 (1990)] that describes the system in terms of perturbation vorticity and velocity. The analysis is based on large scale waves and expansions using multiscales and multitimes for the partial differential equations. The multiscaling is based on an approach where the small parameter is linked to the perturbation property independently from the flow control parameter. Solutions of the perturbative equations are determined numerically after the introduction of a regular perturbation scheme analytically deduced up to the second order. Numerically, the complete linear system is also integrated. Since the results relevant to the complete problem are in very good agreement with the results of the first-order analysis, the numerical solution at the second order was deemed not necessary. The use for an arbitrary initial-value problem will be shown to contain a wealth of information for the different transient behaviors associated to the symmetry, angle of obliquity, and spatial decay of the long waves. The amplification factor of transversal perturbations never presents the trend—a growth followed by a long damping—usually seen in waves with wave number of order one or less. Asymptotical instability is always observed.

In this paper, at first, a lattice Boltzmann method for binary fluids, which is applicable at low viscosity values, is developed. The presented scheme is extension of the free-energy-based approach to a multi-relaxation-time collision model. Various benchmark problems such as the well-known Laplace law for stationary bubbles and capillary-wave test are conducted for validation. As an appealing application, instability of a rising bubble in an enclosed duct is studied and irregular behavior of the bubble is observed at very high Reynolds numbers. In order to highlight its capability to simulate high Reynolds number flows, which is a challenge for many other models, a typical wobbling bubble in the turbulent regime is simulated successfully. Then, in the context of phase-field modeling, a lattice Boltzmann method is proposed for multiphase flows with a density contrast. Unlike most of the previous models based on the phase-field theory, the proposed scheme not only tolerates very low viscosity values but also emerges as a promising method for investigation of two-phase flow problems with moderate density ratios. In addition to comparison to the kinetic-based model, the proposed approach is further verified by judging against the theoretical solutions and experimental data. Various case studies including the rising bubble, droplet splashing on a wet surface, and falling droplet are conducted to show the versatility of the presented lattice Boltzmann model.

In a system of noisy self-propelled particles with interactions that favor directional alignment, collective motion will appear if the density of particles increases beyond a certain threshold. In this paper, we argue that such a threshold may depend also on the profiles of the perturbation in the particle directions. Specifically, we perform mean-field, linear stability, perturbative, and numerical analyses on an approximated form of the Fokker-Planck equation describing the system. We find that if an angular perturbation to an initially homogeneous system is large in magnitude and highly localized in space, it will be amplified and thus serves as an indication of the onset of collective motion. Our results also demonstrate that high particle speed promotes collective motion.

Extinction of a long-lived isolated stochastic population can be described as an exponentially slow decay of quasistationary probability distribution of the population size. We address extinction of a population in a two-population system in the case when the population turnover—renewal and removal—is much slower than all other processes. In this case there is a time-scale separation in the system which enables one to introduce a short-time quasistationary extinction rate $W_1$ and a long-time quasistationary extinction rate $W_2$, and to develop a time-dependent theory of the transition between the two rates. It is shown that $W_1$ and $W_2$ coincide with the extinction rates when the population turnover is absent and present, but very slow, respectively. The exponentially large disparity between the two rates reflects fragility of the extinction rate in the population dynamics without turnover.

In this paper, we report an extensive experimental study of the configurations of a plastic wire injected into a two-dimensional planar cavity populated with fixed pins. The wire is not allowed to cross any pin, but it can move in a wormlike manner within the cavity until to become jammed in a crumpled state. The jammed packing fraction depends heavily on the topology of the cavity, which depends on the number of pins. The experiment reveals nontrivial entanglement effects and scaling laws which are largely independent of the details of the distribution of pins, the symmetry of the cavity or the type of the wire. A mean-field model for the process is presented and analogies with some basic aspects of statistical thermodynamics are discussed.

Vibrational density of states (VDOS) in a supercooled polydisperse liquid is computed by diagonalizing the Hessian matrix evaluated at the potential energy minima for systems with different values of polydispersity. An increase in polydispersity leads to an increase in the relative population of localized high-frequency modes. At low frequencies, the density of states shows an excess compared to the Debye squared-frequency law, which has been identified with the boson peak. The height of the boson peak increases with polydispersity and shows a rather narrow sensitivity to changes in temperature. While the modes comprising the boson peak appear to be largely delocalized, there is a sharp drop in the participation ratio of the modes that exist just below the boson peak indicative of the quasilocalized nature of the low-frequency vibrations. Study of the difference spectrum at two different polydispersity reveals that the increase in the height of boson peak is due to a population shift from modes with frequencies above the maximum in the VDOS to that below the maximum, indicating an increase in the fraction of the unstable modes in the system. The latter is further supported by the facilitation of the observed dynamics by polydispersity. Since the strength of the liquid increases with polydispersity, the present result provides an evidence that the intensity of boson peak correlates positively with the strength of the liquid, as observed earlier in many experimental systems.

Premelting describes the confluence of phenomena that are responsible for the stable existence of the liquid phase of matter in the solid region of its bulk phase diagram. Here we develop a theoretical description of the premelting of water ice contained in a porous matrix, made of a material with a melting temperature substantially larger than ice itself, to predict the amount of liquid water in the matrix at temperatures below its bulk freezing point. Our theory combines the interfacial premelting of ice in contact with the matrix, grain-boundary melting in the ice, and impurity and curvature induced premelting, with the latter occurring in regions which force the ice-liquid interface into a high curvature configuration. These regions are typically found at points where the matrix surface is concave, along contact lines of a grain boundary with the matrix, and in liquid veins. Both interfacial premelting and curvature induced premelting depend on the concentration of impurities in the liquid, which, due to the small segregation coefficient of impurities in ice are treated as homogeneously distributed in the premelted liquid. Our principal result is an equation for the fraction of liquid in the porous medium as a function of the undercooling, which embodies the combined effects of interfacial premelting, curvature induced premelting, and impurities. The result is analyzed in detail and applied to a range of experimentally relevant settings.

In this paper, we investigate the spectral characteristics of normal incident light reflected by a multilayered structure composed of an alternated sequence of single-pitch cholesteric liquid-crystal (ChLC) and anisotropic layers. Using the Berreman $4\times 4$ matrix formalism, we numerically obtain the reflection spectrum and the chromaticity diagram as a function of the anisotropic layers thickness $d$. For $d\to 0$, the structure behaves like a single ChLC layer, showing a single reflection band. As the anisotropic layer thickness increases, the reflection band shifts toward high-wavelength spectral regions, while new reflection bands appear. As a consequence, the reflection chromaticity continuously changes with $d$. It is observed that a suitable choice of the anisotropic layer thickness can produce a threefold reflection band with a red-green-blue associated color for both polarized and unpolarized incident lights.

Macromolecular crowding inside cells affects the thermodynamic and kinetic properties of proteins. The scaled particle theory (SPT) has played an important role toward establishing a qualitative picture for the effects of crowding. However, SPT-based modeling lacks molecular details. Molecular dynamics simulations overcome this limitation, but at great computational cost. Here, we present a theoretical method for modeling crowding at the atomic level. The method makes it possible to achieve exhaustive conformational sampling in modeling crowding effects and to tackle challenges posed by large protein oligomers and by complex mixtures of crowders.

We introduce a method to incorporate hydrodynamic interaction in a model of semiflexible filament dynamics. Hydrodynamic screening and other hydrodynamic interaction effects lead to nonuniform drag along even a rigid filament, and cause bending fluctuations in semiflexible filaments, in addition to the nonuniform Brownian forces. We develop our hydrodynamics model from a string-of-beads idealization of filaments, and capture hydrodynamic interaction by Stokes superposition of the solvent flow around beads. However, instead of the commonly used first-order Stokes superposition, we do an equivalent of infinite-order superposition by solving for the true relative velocity or hydrodynamic velocity of the beads implicitly. We also avoid the computational cost of the string-of-beads idealization by assuming a single normal, parallel and angular hydrodynamic velocity over sections of beads, excluding the beads at the filament ends. We do not include the end beads in the averaging and solve for them separately instead, in order to better resolve the drag profiles along the filament. A large part of the hydrodynamic drag is typically concentrated at the filament ends. The averaged implicit hydrodynamics methods can be easily incorporated into a string-of-rods idealization of semiflexible filaments that was developed earlier by the authors. The earlier model was used to solve the Brownian dynamics of semiflexible filaments, but without hydrodynamic interactions incorporated. We validate our current model at each stage of development, and reproduce experimental observations on the mean-squared displacement of fluctuating actin filaments . We also show how hydrodynamic interaction confines a fluctuating actin filament between two stationary lateral filaments. Finally, preliminary examinations suggest that a large part of the observed velocity in the interior segments of a fluctuating filament can be attributed to induced solvent flow or hydrodynamic screening.

Birds are endowed with a magnetic sense that allows them to detect Earth’s magnetic field and to use it for orientation. Physiological and behavioral experiments have shown the upper beak to host a magnetoreceptor. Putative magnetoreceptive structures in the beak are nerve terminals that each contain a dozen or so of micrometer-sized clusters of superparamagnetic nanocrystals made of magnetite/maghemite and numerous electron-opaque platelets filled with a so far unidentified, amorphous ferric iron compound. The platelets typically form chainlike structures, which have been proposed to function as magnetic flux focusers for detecting the intensity of the geomagnetic field. Here, we test that proposition from first principles and develop an unconstrained model to determine the equilibrium distribution of magnetization along a linear chain of platelets which we assume to behave magnetically soft and to have no magnetic remanence. Our analysis, which is valid for arbitrary values of the intrinsic magnetic susceptibility $\chi$, shows that $\chi$ needs to be much greater than unity to amplify the external field by two orders of magnitude in a chain of platelets. However, the high amplification is confined to the central region of the chain and subsides quadratically toward the ends of the chain. For large values of $\chi$, the possibility opens up of realizing magnetoreceptor mechanisms on the basis of attraction forces between adjacent platelets in a linear chain. The force in the central region of the chain may amount to several pN, which would be sufficient to convert magnetic input energy into mechanical output energy. The striking feature of an ensemble of platelets is its ability to organize into tightly spaced chains under the action of an external field of given strength. We discuss how this property can be exploited for a magnetoreception mechanism.

We present a model of $Z$-ring constriction in bacteria based on different experimental in vitro results. The forces produced by the $Z$ ring due to lateral attraction of its constituent parts, estimated in previous studies that were based on FtsZ filaments observed by atomic force microscopy, are in good agreement with an estimation of the force required for recently found deformations in liposomes caused by FtsZ. These forces are calculated within the usual Helfrich energy formalism. In this context, we also explain the apparent attraction of multiple $Z$ rings in the liposomes initially separated by small distances, as well as the stable distribution of rings separated by distances greater than approximately twice the diameter of the cylindrical liposomes. We adapted the model to the in vivo conditions imposed by the bacterial cell wall, concluding that the proposed mechanism gives a qualitative explanation for the force generation during bacterial division.

The Nikolaevskiy equation was originally proposed as a model for seismic waves and is also a model for a wide variety of systems incorporating a neutral “Goldstone” mode, including electroconvection and reaction-diffusion systems. It is known to exhibit chaotic dynamics at the onset of pattern formation, at least when the dispersive terms in the equation are suppressed, as is commonly the practice in previous analyses. In this paper, the effects of reinstating the dispersive terms are examined. It is shown that such terms can stabilize some of the spatially periodic traveling waves; this allows us to study the loss of stability and transition to chaos of the waves. The secondary stability diagram (“Busse balloon”) for the traveling waves can be remarkably complicated.

Concentrated particulate suspensions under vibrations can support stable, localized, vertically oriented free surfaces. The most robust of these structures are persistent holes: deep and stable depressions of the interface. Using a reduced model of the hydrodynamics we show that a rheology with hysteresis can lead to motion opposite to the time-averaged applied force. Moreover, we show experimentally that particulate suspensions of cornstarch in water exhibits hysteresis in the shear-rate response to an applied sinusoidal stress. The results of our model and our experiments suggest that hysteresis accounts for the outward force needed to support persistent holes.

Rayleigh-Bénard convection in a cylindrical container can take on many different spatial forms. Motivated by the results of Hof et al. [Phys. Fluids 11, 2815 (1999)], who observed coexistence of several stable states at a single set of parameter values, we have carried out simulations at the same Prandtl number, that of water, and a radius-to-height aspect ratio of two. We have used two kinds of thermal boundary conditions: perfectly insulating sidewalls and perfectly conducting sidewalls. In both cases we obtain a wide variety of coexisting steady and time-dependent flows.

A large number of flows with distinctive patterns have been observed in experiments and simulations of Rayleigh-Bénard convection in a water-filled cylinder whose radius is twice the height. We have adapted a time-dependent pseudospectral code, first, to carry out Newton’s method and branch continuation and, second, to carry out the exponential power method and Arnoldi iteration to calculate leading eigenpairs and determine the stability of the steady states. The resulting bifurcation diagram represents a compromise between the tendency in the bulk toward parallel rolls and the requirement imposed by the boundary conditions that primary bifurcations be toward states whose azimuthal dependence is trigonometric. The diagram contains 17 branches of stable and unstable steady states. These can be classified geometrically as roll states containing two, three, and four rolls; axisymmetric patterns with one or two tori; threefold-symmetric patterns called Mercedes, Mitsubishi, marigold, and cloverleaf; trigonometric patterns called dipole and pizza; and less symmetric patterns called CO and asymmetric three rolls. The convective branches are connected to the conductive state and to each other by 16 primary and secondary pitchfork bifurcations and turning points. In order to better understand this complicated bifurcation diagram, we have partitioned it according to azimuthal symmetry. We have been able to determine the bifurcation-theoretic origin from the conductive state of all the branches observed at high Rayleigh number.

The axisymmetric flow in an aspect-ratio-one cylinder whose upper and lower bounding disks are maintained at different temperatures and rotate at equal and opposite velocities is investigated. In this combined Rayleigh-Bénard/von Kármán problem, the imposed temperature gradient is measured by the Rayleigh number Ra and the angular velocity by the Reynolds number Re. Although fluid motion is present as soon as $\text{Re}\ne 0$, a symmetry-breaking transition analogous to the onset of convection takes place at a finite Rayleigh number higher than that for $\text{Re}=0$. For $\text{Re}<95$, the transition is a pitchfork bifurcation to a pair of steady states, while for $\text{Re}>95$, it is a Hopf bifurcation to a limit cycle. The steady states and limit cycle are connected via a pair of saddle-node infinite-period bifurcations except very near the Takens-Bogdanov codimension-two point, where the scenario includes global bifurcations. Detailed phase portraits and bifurcation diagrams are presented, as well as the evolution of the leading part of the spectrum, over the parameter ranges $0\le \text{Re}\le 120$ and $0\le \text{Ra}\le 30000$.

A reduced model to decrease the number of degrees of freedom of the discretized Navier-Stokes equations to a small set that nevertheless captures the essential dynamics of the flow is proposed. The Rayleigh-Bénard convection problem in a cylinder of aspect ratio one where the lower and upper disks, maintained at hot and cold temperatures, respectively, rotate at equal and opposite angular velocities has been chosen to test the technique. The nonlinear dynamics is rich and complex when the temperature difference between disks and their angular velocity is varied. Representatives states—stationary, periodic near sinusoidal, and near heteroclinic—are presented. In each case, the reduced model is compared with temporal integration, and we show that 41 degrees of freedom are sufficient to reproduce the signal. We discuss the strengths and weaknesses of the algorithm by which we build our reduced model.