The relaxation of initially straight semiflexible polymers has been discussed mainly with respect to the longest relaxation time. The biologically relevant nonequilibrium dynamics on shorter times is comparatively poorly understood, partly because “initially straight” can be realized in manifold ways. Combining Brownian dynamics simulations and systematic theory, we demonstrate how different experimental preparations give rise to specific short-time and universal long-time dynamics. We also discuss boundary effects and the onset of the stretch-coil transition.

We propose a density-functional theory for inhomogeneous polyatomic fluids with complex architecture by introducing a different representation for the polymers. This representation gives an efficient hierarchical algorithm to calculate the direct bonding connectivity integral for polymers with complex architecture, such as linear, star, branched, and dendritic structures. A comparison with the available simulated data for linear and star polymers confirms the accuracy of the present theory in reproducing the density profiles of the two types of polymer in the slits. By using the proposed algorithm, we also explore partitioning coefficients of polymers of different architectures in a slit, and find that the partitioning coefficients of branched, star, and dendrimer forms of 22-mers decrease to a minimum at extremely low packing fraction, and then increase monotonically with packing fraction. Moreover, it is found that it is more difficult for a linear polymer of 22-mers to enter the slit than for branched, star, and dendritic polymers. In addition, we also investigate the self-assembly of diblock copolymers with different tails in a slit. It is found that the linear copolymer self-assembles into a trilayer film structure, while copolymers with branched and dendritic tails self-assemble into a five-layer film structure. Interestingly, the copolymer with a star tail self-assembles into a trilayer film structure, and then the trilayer structure evolves into a five-layer structure with increase of the bulk packing fraction in the case studied.

A force field formulator for organic molecules (FF-FOM) was developed to assign bond, angle, and dihedral parameters to arbitrary organic molecules in a unified manner including proteins and nucleic acids. With the unified force field parametrization we performed massively parallel computations of absolute binding free energies for pharmaceutical target proteins and ligands. Compared with the previous calculation with the ff99 force field in the Amber simulation package (Amber99) and the ligand charges produced by the Austin Model 1 bond charge correction (AM1-BCC), the unified parametrization gave better absolute binding energies for the FK506 binding protein (FKBP) and ligand system. Our method is based on extensive work measurement between thermodynamic states to calculate the free energy difference and it is also the same as the traditional free energy perturbation. There are important requirements for accurate calculations. The first is a well-equilibrated bound structure including the conformational change of the protein induced by the binding of the ligand. The second requirement is the convergence of the work distribution with a sufficient number of trajectories and dense spacing of the coupling constant between the ligand and the rest of the system. Finally, the most important requirement is the force field parametrization.

We investigate numerically the stability of a model food web, introduced by Nunes Amaral and Meyer [Phys. Rev. Lett. 82, 652 (1999)]. The model describes a system of species located in niches at several levels. Upper level species are predating on those from a lower level. We show that the model web is more stable when it is larger, although the number of niches is more important than the number of levels. The food web is self-organizing itself, trying to reach a certain degree of complexity, i.e., number of species and links among them. If the system cannot achieve this state, it will go extinct. We demonstrate that the average number of links per species and the reduced number of species depend in the same way on the number of niches. We also determine how the stability of the food web depends on another parameter of the model, the killing probability. Despite keeping the ratio of the creation and killing probabilities constant, increasing the latter reduces significantly the stability of the model food web. We show that connectance dependence on the number of niches has a power-type character, which agrees with the field data, and that it decreases with the number of species also as a power-type function.

We present here a mechanics model for the force generation by actin polymerization. The possible adhesions between the actin filaments and the load surface, as well as the nucleation and capping of filament tips, are included in this model on top of the well-known elastic Brownian ratchet formulation. A closed form solution is provided from which the force-velocity relationship, summarizing the mechanics of polymerization, can be drawn. Model predictions on the velocity of moving beads driven by actin polymerization are consistent with experiment observations. This model also seems capable of explaining the enhanced actin-based motility of Listeria monocytogenes and beads by the presence of Vasodilator-stimulated phosphoprotein, as observed in recent experiments.

We report a method to measure the viscosity of $\mu \mathrm{L}$ volumes of biofluid obtained from threadlike structures (NTSs) on the surfaces of mammalian (rabbit) internal organs. The fluid was mechanically microextracted in situ from NTSs on the organ surfaces by a glass capillary connected to an extractor. From the Brownian motion of the $0.8\pm 0.1\mu \mathrm{m}$ diameter granules in the extracted fluid, the fluid viscosity was determined to be $1.4\pm 0.1\mathrm{mPa}\cdot \mathrm{s}$ at room temperature. This viscosity is comparable to the viscosity of rabbit blood plasma.

The normal form for codimension 1 border collision bifurcations of fixed points of discrete time piecewise smooth dynamical systems is considered in the unstable case. We show that in appropriate parameter regions there is a snap-back repeller immediately after the bifurcation, and hence that the bifurcation creates chaos. Although the chaotic solutions are repellers they may explain observations, and this is illustrated through an example.

The influence of a localized inhomogeneity (oscillatory or stationary) on spatiotemporal chaotic state in an excitable reaction-diffusion system is investigated. We find that various coherent wave patterns, such as spiral waves (including multiarmed) and target wave patterns are able to be created by the inhomogeneity from the chaotic state. Due to the growth of these coherent wave patterns, the previously existing turbulent waves in the absence of inhomogeneity are suppressed. At last, the whole system is entrained by the coherent wave patterns. Closer investigations indicate that the possible mechanisms underlying the inhomogeneity sustained coherent wave patterns seem quite different for oscillatory and stationary inhomogeneities.

For a nonrelativistic classical particle undergoing arbitrary oscillations in external fields, the generalized effective potential $\Psi$ is derived through calculating the nonlinear eigenfrequencies of the particle-field system. Specifically, the ponderomotive potential is extended to a nonlinear oscillator, resulting in multiple branches near the primary resonance. For a pair of particle natural frequencies in a beat resonance, $\Psi$ scales linearly with the internal actions and is analogous to the dipole potential for a two-level quantum system. Thus cold quantum particles and highly excited quasiclassical objects permit uniform manipulation tools, particularly, one-way walls.

The explicit determinations of the mean first-passage time (MFPT) for trapping problem are limited to some simple structure, e.g., regular lattices and regular geometrical fractals, and determining MFPT for random walks on other media, especially complex real networks, is a theoretical challenge. In this paper, we investigate a simple random walk on the the pseudofractal scale-free web (PSFW) with a perfect trap located at a node with the highest degree, which simultaneously exhibits the remarkable scale-free and small-world properties observed in real networks. We obtain the exact solution for the MFPT that is calculated through the recurrence relations derived from the structure of PSFW. The rigorous solution exhibits that the MFPT approximately increases as a power-law function of the number of nodes, with the exponent less than 1. We confirm the closed-form solution by direct numerical calculations. We show that the structure of PSFW can improve the efficiency of transport by diffusion, compared with some other structure, such as regular lattices, Sierpinski fractals, and T-graph. The analytical method can be applied to other deterministic networks, making the accurate computation of MFPT possible.

We discuss relativistic diffusion in proper time in the approach of Schay (Ph.D. thesis, Princeton University, Princeton, NJ, 1961) and Dudley [Ark. Mat. 6, 241 (1965)]. We derive (Langevin) stochastic differential equations in various coordinates. We show that in some coordinates the stochastic differential equations become linear. We obtain momentum probability distribution in an explicit form. We discuss a relativistic particle diffusing in an external electromagnetic field. We solve the Langevin equations in the case of parallel electric and magnetic fields. We derive a kinetic equation for the evolution of the probability distribution. We discuss drag terms leading to an equilibrium distribution. The relativistic analog of the Ornstein-Uhlenbeck process is not unique. We show that if the drag comes from a diffusion approximation to the master equation then its form is strongly restricted. The drag leading to the Tsallis equilibrium distribution satisfies this restriction whereas the one of the Jüttner distribution does not. We show that any function of the relativistic energy can be the equilibrium distribution for a particle in a static electric field. A preliminary study of the time evolution with friction is presented. It is shown that the problem is equivalent to quantum mechanics of a particle moving on a hyperboloid with a potential determined by the drag. A relation to diffusions appearing in heavy ion collisions is briefly discussed.

We present an analysis leading to precise locations of the multicritical points for spin glasses on regular lattices. The conventional technique for determination of the location of the multicritical point was previously derived using a hypothesis emerging from duality and the replica method. In the present study, we propose a systematic technique, by an improved technique, giving more precise locations of the multicritical points on the square, triangular, and hexagonal lattices by carefully examining the relationship between two partition functions related with each other by the duality. We can find that the multicritical points of the $\pm J$ Ising model are located at $p_c=0.890813$ on the square lattice, where $p_c$ means the probability of $J_{ij}=J(>0)$, at $p_c=0.835985$ on the triangular lattice, and at $p_c=0.932593$ on the hexagonal lattice. These results are in excellent agreement with recent numerical estimations.

Polymer nanocomposites offer the potential to create a new type of hybrid material with unique thermal, optical, or electrical properties. Understanding their structure, phase behavior, and dynamics is crucial for realizing such potentials. In this work we provide an experimental insight into the dynamics of such composites in terms of the temperature, wave vector, and volume fraction of nanoparticles, using multispeckle synchrotron x-ray photon correlation spectroscopy measurements on gold nanoparticles embedded in polymethylmethacrylate. Detailed analysis of the intermediate scattering functions reveals possible existence of an intrinsic length scale for dynamic heterogeneity in polymer nanocomposites similar to that seen in other soft materials like colloidal gels and glasses.

The characteristic time scales in ac ionic conduction near equilibrium are reassessed via consideration of a selection of one-dimensional model problems. It is observed that, in addition to the two basic electrodiffusion time scales, those of diffusion relaxation in the macroscopic- and Debye-scale domains, $T$ and $t_D$ (the latter identical with the bulk charge relaxation time), some intermediate time scales are present in each system. It is concluded that, due to insensitivity of the electric double layers to harmonic voltage disturbances, the short-time response on the $t_D$ scale is determined by the quasielectroneutral bulk.

The ground states of Lennard-Jones clusters for sizes up to $n=147$ are estimated as a function of the de Boer quantum delocalization length $\Lambda$, and the $n-\Lambda$ “phase diagram” is constructed. The increase in $\Lambda$ favors more disordered and diffuse structures over more symmetric and compact ones, eventually making the liquidlike motif most energetically favorable. The analogy between the quantum- and thermally-induced structural transitions is explored.

To investigate the role of information flow in group formation, we introduce a model of communication and social navigation. We let agents gather information in an idealized network society and demonstrate that heterogeneous groups can evolve without presuming that individuals have different interests. In our scenario, individuals’ access to global information is constrained by local communication with the nearest neighbors on a dynamic network. The result is reinforced interests among like-minded agents in modular networks; the flow of information works as a glue that keeps individuals together. The model explains group formation in terms of limited information access and highlights global broadcasting of information as a way to counterbalance this fragmentation. To illustrate how the information constraints imposed by the communication structure affects future development of real-world systems, we extrapolate dynamics from the topology of four social networks.

Random networks of coupled phase oscillators with phase shifts in the interaction functions are considered. In such systems, extensive chaos (turbulence) is observed in a wide range of parameters. We show that, by introducing global feedback, the turbulence can be suppressed and a transition to synchronous oscillations can be induced. Our attention is focused on the transition scenario and the properties of patterns, including intermittent turbulence, which are found at the edge of chaos. The emerging coherent patterns represent various self-organized active (sub)networks whose size and behavior can be controlled.

We investigate the mechanism of friction-induced fluid heating under the influence of surfaces. The temperature distributions of liquid argon and helium in nanoscale Poiseuille flows are studied through molecular dynamics simulations. It is found that the fluid heating is mainly caused by the viscous friction in the fluid when the external force is small and there is no slip at the fluid-solid interface. When the external force is larger than the fluid-surface binding force, the friction at the fluid-solid interface dominates over the internal friction of the fluid and is the major contribution to fluid heating. An asymmetric temperature gradient in the fluid is developed in the case of nonidentical walls and the general temperature gradient may change sign as the dominant heating factor changes from internal to interfacial friction with increasing external force. The effect of temperature on the fluid heating is also discussed.

We study numerically the influence of contact angle on slow evaporation in two-dimensional model porous media. For sufficiently low contact angles, the drying pattern is fractal and can be predicted by a simple model combining the invasion percolation model with the computation of the diffusive transport in the gas phase. The overall drying time is minimum in this regime and is independent of contact angle over a large range of contact angles up to the beginning of a transition zone. As the contact angle increases in the transition region, the cooperative smoothing mechanisms of the interface become important and the width of the liquid gas interface fingers that form during the evaporation process increases. The mean overall drying time increases in the transition region up to an upper bound which is reached at a critical contact angle ${\theta }_c$. The increase in the drying time in the transition region is explained in relation with the diffusional screening phenomenon associated with the Laplace equation governing the vapor transport in the gas phase. Above ${\theta }_c$ the drying pattern is characterized by a flat traveling front and the mean overall drying time becomes independent of the contact angle. Drying time fluctuations are studied and are found to be important below ${\theta }_c$, i.e., when the pattern is fractal. The fluctuations are of the same order of magnitude regardless of the value of contact angle in this range. The fluctuations are found to die out abruptly at ${\theta }_c$ as the liquid gas interface becomes a flat front.

We examine the effects of viscous damping in the boundary layers on the Bragg resonance of surface water waves by a two-dimensional array of vertical cylinders. For cylinders of small radius relative to the wavelength, we first derive an effective boundary condition for the radial derivative of the velocity potential to account for the viscous forces. Coupled-mode equations are then rederived by an asymptotic method for the envelopes of multiply resonated waves inside the array. Effects of viscosity on band gaps and scattering coefficients due to a plane incident wave are examined analytically for an infinitely long array of finite width surrounded by open water. For normal incidence the envelope physics is one dimensional. The transmission and reflection properties are studied first. Oblique incidence can in principle excite several wave trains in different directions. Explicit solutions are given and discussed when there are only two wave trains inside the array. Results are compared with recent theories where viscosity is not taken into account. The asymptotic theory can be modified for two-dimensional sound scattering by a cylinder array.