We develop a physical model to describe the kinetic behavior in cell-adhesion molecules. Unbinding of noncovalent biological bonds is assumed to occur by both bond dissociation and bond rupture. Such a decomposition of debonding processes is a space decomposition of the debonding events. Dissociation under thermal fluctuation is nondirectional in a three-dimensional space, and its energy barrier to escape is not influenced by a tensile force, but the microstates that could lead to dissociation are changed by the tensile force; rupture happens along the tensile force direction. An applied force effectively lowers the energy barrier to escape along the loading direction. The lifetime of the biological bond, due to the two concurrent off rates, may grow with increasing tensile force to a moderate amount and then decrease with further increasing load. We hypothesize that a catch-to-slip bond transition is a generic feature in biological bonds. The model also predicts that catch bonds in a more flexible molecular structure have longer lifetimes and need less force to be fully activated.

We study the structure of an interface in a three-dimensional Ising system created by an external nonuniform field $H\left(\mathbf{r},t\right)$. $H$ changes sign over a two-dimensional plane of arbitrary orientation. When the field is pulled with velocity ${\mathbf{v}}_e$, [i.e., $H\left(\mathbf{r},t\right)=H\left(\mathbf{r}-{\mathbf{v}}_{\mathbf{e}}t\right)$], the interface undergoes several dynamical transitions. For low velocities it is pinned by the field profile and moves along with it, the distribution of local slopes undergoing a series of commensurate-incommensurate transitions. For large ${\mathbf{v}}_e$ the interface depins and grows with Kardar-Parisi-Zhang exponents.

We propose a new measure of the communicability of a complex network, which is a broad generalization of the concept of the shortest path. According to the new measure, most of the real-world networks display the largest communicability between the most connected (popular) nodes of the network (assortative communicability). There are also several networks with the disassortative communicability, where the most “popular” nodes communicate very poorly to each other. Using this information we classify a diverse set of real-world complex systems into a small number of universality classes based on their structure-dynamic correlation. In addition, the new communicability measure is able to distinguish finer structures of networks, such as communities into which a network is divided. A community is unambiguously defined here as a set of nodes displaying larger communicability among them than to the rest of the nodes in the network.

We introduce the link-space formalism for analyzing network models with degree-degree correlations. The formalism is based on a statistical description of the fraction of links $l_{i,j}$ connecting nodes of degrees $i$ and $j$. To demonstrate its use, we apply the framework to some pedagogical network models, namely, random attachment, Barabási-Albert preferential attachment, and the classical Erdős and Rényi random graph. For these three models the link-space matrix can be solved analytically. We apply the formalism to a simple one-parameter growing network model whose numerical solution exemplifies the effect of degree-degree correlations for the resulting degree distribution. We also employ the formalism to derive the degree distributions of two very simple network decay models, more specifically, that of random link deletion and random node deletion. The formalism allows detailed analysis of the correlations within networks and we also employ it to derive the form of a perfectly nonassortative network for arbitrary degree distribution.

We demonstrate that the harmonic inversion technique is a powerful tool to analyze the spectral properties of optical microcavities. As an interesting example we study the statistical properties of complex frequencies of the fully chaotic microstadium. We show that the conjectured fractal Weyl law for open chaotic systems [Lu et al., Phys. Rev. Lett. 91, 154101 (2003)] is valid for dielectric microcavities only if the concept of the chaotic repeller is extended to a multifractal by incorporating Fresnel’s laws.

We evidenced a universal relaxation behavior of a droplet embedded in an immiscible fluid of the same density. After a large strain jump, the relaxation can be characterized by two related relaxation times ${\tau }_1=4.4{\tau }_2$ independently of the viscosity ratio and of the applied strain. The change in the kinetic process is driven by the drop geometry and happens invariably when the shape of the drop is an oblate ellipsoid of revolution where the relation between the major $\left(L\right)$ and the minor $\left(B\right)$ axis is given by $\ln (L∕B)\approx 0.5$. This universal behavior can be explained by considering the normal stress difference across the droplet interface, i.e., the curvature of the drop.

Radiation magnetohydrodynamic modeling is used to study the plasma formed on the surface of a cylindrical metallic load, driven by megagauss magnetic field at the $1\mathrm{MA}$ Zebra generator (University of Nevada, Reno). An ionized aluminum plasma is used to represent the “core-corona” behavior in which a heterogeneous $Z$-pinch consists of a hot low-density corona surrounding a dense low-temperature core. The radiation dynamics model included simultaneously a self-consistent treatment of both the opaque and transparent plasma regions in a corona. For the parameters of this experiment, the boundary of the opaque plasma region emits the major radiation power with Planckian black-body spectrum in the extreme ultraviolet corresponding to an equilibrium temperature of $16\mathrm{eV}$. The radiation heat transport significantly exceeds the electron and ion kinetic heat transport in the outer layers of the opaque plasma. Electromagnetic field energy is partly radiated (13%) and partly deposited into inner corona and core regions (87%). Surface temperature estimates are sensitive to the radiation effects, but the surface motion in response to pressure and magnetic forces is not. The general results of the present investigation are applicable to the liner compression experiments at multi-MA long-pulse current accelerators such as Atlas and Shiva Star. Also the radiation magnetohydrodynamic model discussed in the paper may be useful for understanding key effects of wire array implosion dynamics.

We present a general method for obtaining multiple-mode waves (MMWs), which is introduced as a concept expressed in the form of nonlinear superpositions of single-mode waves (SMWs) with different wave speeds, for nonlinear evolution equations. The validity of the approach has been demonstrated using two wave equations. It is shown that MMWs may combine different types of SMWs such as periodic waves, kink waves, compactons, solitary waves, etc., to form more general solutions, which can be used to display the whole evolution process of interactions between different types of waves, especially to reveal the dynamic details of the wave patterns.

We suggest an approach to microrheology based on optical traps capable of measuring fluid fluxes around singular points of fluid flows. We experimentally demonstrate this technique, applying it to the characterization of controlled flows produced by a set of birefringent spheres spinning due to the transfer of light angular momentum. Unlike the previous techniques, this method is able to distinguish between a singular point in a complex flow and the absence of flow at all; furthermore it permits us to characterize the stability of the singular point.

We demonstrate that nonlinear decay of obliquely propagating Langmuir waves into Langmuir and Alfvén waves $\left(L\to L^{\prime }+A\right)$ is possible in a one-dimensional, highly relativistic, streaming pair plasma. Such a plasma may be in the magnetospheres of pulsars. It is shown that the characteristic frequency of generated Alfvén waves is much less than the frequency of Langmuir waves and may be consistent with the observational data on the radio emission of pulsars.

We perform molecular dynamics simulations to investigate the diffusive motion of TIP5P (the transferable intermolecular potential with five points) water in the direction perpendicular to the two hydrophobic confining walls. To calculate the diffusion constant, we use the concept of the characteristic residence time which is calculated from the exponential decay of the residence time probability density function. We find that a diffusion anomaly, increase of diffusion upon compression, is absent in the direction perpendicular to the confining walls down to the lowest temperature we simulate, $220\mathrm{K}$, whereas there is a diffusion anomaly, similar to that in bulk water, in the direction parallel to the walls. The absence of a diffusion anomaly in the direction perpendicular to the walls may arise mainly due to nanoconfinement, rather than due to the hydrophobic property of the confining walls. In addition, we find that the temperature dependence of the diffusion constant along the constant density path in the perpendicular direction shows a Vogel-Fulcher-Tammann form.

The dynamics of the expansion of a Lennard-Jones system, initially confined at high density and subsequently expanding freely in a vacuum, is compared with an expanding statistical ensemble derived in the diluted quasi-ideal Boltzmann approximation. The description proves to be fairly accurate at predicting average one-body global observables, but important deviations are observed in the configuration-space structure of the events. Possible implications for finite expanding physical systems are outlined.

The connection between the Maxwell-Cattaneo heat transport equation and a nonequilibrium entropy is examined through four different thermodynamic approaches, and it is shown that all of them lead to the same form of the nonequilibrium entropy. Furthermore, it is seen that this form is also consistent with three microscopic formalisms. This robustness underlines the consistency and relevance of the entropy.

We consider a periodic Ising chain with nearest-neighbor and $r$th neighbor interaction and quench it from infinite temperature to zero temperature. The persistence probability $P\left(t\right)$, measured as the probability that a spin remains unflipped up to time $t$, is studied by computer simulation for suitable values of $r$. We observe that as time progresses, $P\left(t\right)$ first decays as $t^{-0.22}$ (the first regime), then the $P\left(t\right)\text{−}t$ curve has a small slope (in log-log scale) for some time (the second regime) and at last it decays nearly as $t^{-3/8}$ (the third regime). We argue that in the first regime, the persistence behavior is the usual one for a two-dimensional system, in the second regime it is like that of a noninteracting (“zero-dimensional”) system, and in the third regime the persistence behavior is like that of a one-dimensional Ising model. We also provide explanations for such behavior.

We study effective colloidal interactions in de-ionized colloidal mixtures through sedimentation-diffusion equilibrium. We derive a coarse-grained effective model (EM) and compare its density profiles with those of the computationally much more expensive primitive model (PM) of colloids and counterions in gravity. The EM, which contains not only standard pairwise screened-Coulomb interactions, but also explicit many-body effects by means of a so-called volume term, can quantitatively account for all observed sedimentation phenomena such as lifting of colloids to high altitudes, segregation into layers in mixtures, and floating of heavy colloids on top of lighter ones. Without the volume term there is no quantitative agreement between the PM and EM, even in the present high-temperature limit of interest, showing that de-ionized colloidal suspensions cannot be described by a pairwise Yukawa model.

Process of stripe formation is analyzed numerically in a binary mixture. The system consists of particles of two sizes, without any direct mutual interactions. Overlapping of large particles, surrounded by a dense system of small particles, induces indirect entropy driven interactions between large particles. Under an influence of an external driving force the system orders and stripes are formed. Mean width of stripes grows logarithmically with time, in contrast to a typical power law temporal increase observed for driven interacting lattice gas systems. We describe the mechanism responsible for this behavior and attribute the logarithmic growth to a random walk of large particles in a random potential created by the site blocking due to the small ones.

We investigate the morphological transitions of surface patterns induced in a soft elastic film in the presence of an applied electric field by the linear stability analysis and simulations. The surface patterns emerge beyond a critical strength of the electric field and the pattern length scale is always nearly three times the film thickness, regardless of the precise pattern morphology and other physical parameters. Interestingly, the simulations show that the precise pattern morphology depends strongly on the film and the field parameters and can be classified into three broad morphological phases: columns, stripes, and cavities. By tuning the electric field and the gap distance, we show that transitions from one morphological phase to another can be induced as described by a morphological phase diagram for this phenomenon. We also study the conditions under which the transitions can be “glassy” or “hysteretic.” In addition to uncovering the rich physics underlying these nearly two-dimensional morphological phase transitions, our simulations also suggest experiments and applications of this phenomenon in mesopatterning. In particular, simulations demonstrate the possibility of controlling the pattern morphology and alignment by using the electric-field induced instability in soft elastic films. Unlike the short range adhesive interactions which cannot be varied, the use of an electric field allows far greater flexibility in modulation and control of the pattern morphology and its height.

We propose a single molecule experiment that could be carried out in order to measure a solitonic wave speed in DNA. In addition, we discuss possible values of the speed according to the Peyrard-Bishop-Dauxois model of DNA dynamics.

The dynamics of a genetically labeled cell population may be used to infer the laws of cell division in mammalian tissue. Recently, we showed that in mouse tail skin, where proliferating cells are confined to a two-dimensional layer, cells proliferate and differentiate according to a simple stochastic model of cell division involving just one type of proliferating cell that may divide both symmetrically and asymmetrically. Curiously, these simple rules provide excellent predictions of the cell population dynamics without having to address the cells’ spatial distribution. Yet, if the spatial behavior of cells is addressed by allowing cells to diffuse at random, one deduces that density fluctuations destroy tissue confluence, implying some hidden degree of spatial regulation of cell division. To infer the mechanism of spatial regulation, we consider a two-dimensional model of cell fate that preserves the overall population dynamics. By identifying the resulting behavior with a three-species variation of the voter model, we predict that proliferating cells in the basal layer should cluster. Analysis of empirical correlations of cells stained for proliferation activity confirms that the expected clustering behavior is indeed seen in nature. As well as explaining how cells maintain a uniform two-dimensional density, these findings present an interesting experimental example of voter-model statistics in biology.

By covering a much wider concentration range than previous studies we find a very unusual exponential dependence of the rate of helix formation on concentration of gelatin in water and ethylene glycol solutions. By applying a procedure of concentration-temperature superposition we build a master curve describing the initial renaturation rates in both solvents. The growth of the normalized helical fraction $\chi \left(t\right)$ is a first-order process, with a rate constant consistent with cis-trans isomerization, in most situations. We propose that association of three separate chains to form a triple helical nucleus occurs rapidly and contributes less to the helical onset than previously thought. The measured helix content is a result of lengthening of the triple helix after nucleation, by zipping from the associated nuclei.