We study the diffusion of heat in an aqueous suspension of disk-shaped nanoparticles of Laponite, which has finite elasticity and a pastelike consistency, by using the Mach-Zehnder interferometer. We estimate the thermal diffusivity of the suspension by comparing the experimentally obtained temperature distribution to that with an analytical solution. We observe that, despite the highly constrained Brownian diffusivity of particles owing to its soft glassy nature, suspensions at very small concentrations of Laponite demonstrate significant enhancement in thermal diffusivity. We correlate the observed enhancement with the possible microstructures of the Laponite suspension.

Optical Tweezers are employed to study the electrophoretic and the electroosmotic motion of a single colloid immersed in electrolyte solutions of ion concentrations between ${10}^{-5}$ and 1 mol/l and of different valencies (KCl, CaCl${}_2$, LaCl${}_3$). The measured particle mobility in monovalent salt is found to be in agreement with computations combining primitive model molecular dynamics simulations of the ionic double layer with the standard electrokinetic model. Mobility reversal of a single colloid—for the first time—is observed in the presence of trivalent ions (LaCl${}_3$) at ionic strengths larger than ${10}^{-2}$ mol/l. In this case, our numerical model is in a quantitative agreement with the experiment only when ion specific attractive forces are added to the primitive model, demonstrating that at low colloidal charge densities, ion correlation effects alone do not suffice to produce mobility reversal.

We performed a Brillouin scattering experiment on deeply supercooled water and compared the results with similar literature data obtained both at the same and at higher values of the exchanged wave vector. The whole set of available experimental data can be well reproduced with the use of the generalized hydrodynamic model where all the involved thermodynamic parameters are fixed to their literature values. On the contrary, the model based on the memory function approach generates the wrong estimates for measurables when the same values of the thermodynamic parameters are used. This result confirms our recent criticisms against the utilization of models originating from linear response theory [Phys. Rev. E 84, 051202 (2011)]. The inconsistency between models explains apparent discrepancies between the different conclusions on water acoustic behavior which may be found in the literature. We demonstrate that the observed behavior can be explained by assuming only a single relaxation process that is typical of any viscoelastic system. With all thermodynamics quantities fixed, the hydrodynamic description needs only two parameters to model the experimental data, namely, the relaxation time and the high-frequency limit of the sound velocity. The whole body of the experimental data can be well reproduced when the relaxation time behaves in an Arrhenian manner and the difference between the relaxed and not relaxed sound velocities is a constant. The high-frequency sound velocity is never higher than 2200 m/s. We conclude that, at least from experiments performed within the hydrodynamic regime, there is no indication for a fast sound close to the hypersonic velocity observed in ice.

In the context of Rosenfeld's fundamental measure theory, we show that the bending rigidity is not equal to zero for a hard-sphere fluid in contact with a curved hard wall. The implication is that the Hadwiger theorem does not hold in this case and the surface free energy is given by the Helfrich expansion instead. The value obtained for the bending rigidity (i) is an order of magnitude smaller than the bending constant associated with Gaussian curvature, (ii) changes sign as a function of the fluid volume fraction, and (iii) is independent of the choice of the location of the hard wall.

To investigate the role of the ribosomal exit tunnel on protein folding, we simulate the initial-stage folding behavior of the protein villin headpiece subdomain HP35 (PDB id: 1yrf) with and without prefolding in the exit tunnel by using an all-atom model and find that prefolding in the exit tunnel could effectively help the protein form native secondary structures. Furthermore, our results show that, after releasing from the exit tunnel, the prefolded chains may have a tendency to form more native contacts than those only in free space and this reduces the conformational space of sampling. Our results may provide an alternative way to explain the fast folding mechanism of proteins in vivo.

Mixing patterns in large self-organizing networks, such as the Internet, the World Wide Web, and social and biological networks, are often characterized by degree-degree dependencies between neighboring nodes. In this paper, we propose a new way of measuring degree-degree dependencies. One of the problems with the commonly used assortativity coefficient is that in disassortative networks its magnitude decreases with the network size. We mathematically explain this phenomenon and validate the results on synthetic graphs and real-world network data. As an alternative, we suggest to use rank correlation measures such as Spearman's $\rho$. Our experiments convincingly show that Spearman's $\rho$ produces consistent values in graphs of different sizes but similar structure, and it is able to reveal strong (positive or negative) dependencies in large graphs. In particular, we discover much stronger negative degree-degree dependencies in Web graphs than was previously thought. Rank correlations allow us to compare the assortativity of networks of different sizes, which is impossible with the assortativity coefficient due to its genuine dependence on the network size. We conclude that rank correlations provide a suitable and informative method for uncovering network mixing patterns.

Game theory is introduced to simulate the complicated interaction relations among the conflicting pedestrians in a pedestrian flow system, which is defined on a square lattice with the parallel update rule. Modified on the traditional lattice gas model, each pedestrian can move to not only an empty site, but also an occupied site. It is found that each individual chooses its neighbor randomly and occupies the site with the probability $W(x\to y)=\frac{1}{1+\exp [-(P_x-U_x)/\kappa ]}$, where $P_x$ is the $x$'s payoff representing his personal energy, and $U_x$ is the average payoff of its neighborhood indicating the potential well energy if he stays. Two types of pedestrians are considered, and they interact with their neighbors following the payoff matrix of snowdrift game theory. The cost-to-benefit ratio $r=c/(2b-c)$ (where $b$ is the perfect payoff and $c$ is the labor cost) represents the fear index of the pedestrians in this model. It is found that there exists a moderate value of $r$ leading to the shortest escape time, and the situation for large values of $r$ is better than that for small ones in general. In addition, the pedestrian flow system always arrives at a consistent state in which the two types of walkers have the same number and evolve by the same law irrespectively of the parameters, which can be interpreted as the self-organization effect of pedestrian flow. It is also proven that the time point of the onset of the steady state is unrelated to the scale of the pedestrians and the square lattice. Meanwhile, the system exhibits different dynamics before reaching the consistent state: the number of the two types of walkers oscillates when $P_C>0.5$ (i.e., probability to change the present strategy), while no oscillation happens for $P_C\le 0.5$. Finally, it is shown that a smaller density of pedestrians $\rho$ induces a shorter average escape time.

We report the pattern dynamics in the vicinity of an inverse homoclinic bifurcation in an extended dissipative system. We observe, in direct numerical simulations of three dimensional Rayleigh-Bénard convection with stress-free top and bottom plates, a spontaneous breaking of a competition of two mutually perpendicular sets of oscillating cross rolls to one of two possible sets of oscillating cross rolls as the Rayleigh number is raised above a critical value. The time period of the oscillating cross-roll patterns diverges and shows scaling behavior near the bifurcation point. This is an example of a transition from nonlocal to local pattern dynamics near an inverse homoclinic bifurcation. We also present a simple four-mode model that captures the pattern dynamics quite well.

Ponderomotive forces (PFs) induced in cold subwavelength plasmas by an externally applied electromagnetic wave are studied analytically. To this end, the plasma is modeled as a sphere with a radially varying permittivity, and the internal electric fields are calculated by solving the macroscopic Maxwell equations using an expansion in Debye potentials. It is found that the PF is directed opposite to the plasma density gradient, similarly to large-scale plasmas. In the case of a uniform density profile, a residual spherically symmetric compressive PF is found, suggesting possibilities for contactless ponderomotive manipulation of homogeneous subwavelength objects. The presence of a surface PF on discontinuous plasma boundaries is derived. This force is essential for a microscopic description of the radiation-plasma interaction consistent with momentum conservation. It is shown that the PF integrated over the plasma volume is equivalent to the radiation pressure exerted on the plasma by the incident wave. The concept of radiative acceleration of subwavelength plasmas, proposed earlier, is applied to ultracold plasmas. It is estimated that these plasmas may be accelerated to keV ion energies, resulting in a neutralized beam with a brightness comparable to that of current high-performance ion sources.

A simulated tempering method, which is referred to as simulated-tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated tempering were performed to study the intramolecular proton transfer reaction of malonaldehyde in an aqueous solution. Conformational sampling in reaction coordinate space can be easily enhanced with this method, and the free energy along a reaction coordinate can be calculated accurately. Moreover, the simulated-tempering umbrella sampling provides trajectory data more efficiently than the conventional umbrella sampling method.

Cardiac tissue elastically deforms under an applied stress, permitting shear waves to propagate through the heart. Traditionally, this behavior has been modeled with a monodomain approach, in which the mechanical properties of the intracellular and extracellular spaces are averaged together. We consider a mechanical bidomain model of cardiac tissue in which the mechanics of the intracellular and extracellular spaces are considered individually with the two spaces coupled by a spring constant. We find two normal modes of oscillation: one in which the intracellular and extracellular spaces oscillate together (a monodomain mode) and the other in which they oscillate in opposition (a bidomain mode). These two modes have unique dispersion relationships. In the extreme approximation of equal shear moduli and mass densities of the intracellular and extracellular spaces, the dispersion in the bidomain mode depends on the spring constant, while it does not in the monodomain mode.

An approach to the coupling-parameter expansion in the liquid state theory of simple fluids is presented by combining the ideas of thermodynamic perturbation theory and integral equation theories. This hybrid scheme avoids the problems of the latter in the two phase region. A method to compute the perturbation series to any arbitrary order is developed and applied to square well fluids. Apart from the Helmholtz free energy, the method also gives the radial distribution function and the direct correlation function of the perturbed system. The theory is applied for square well fluids of variable ranges and compared with simulation data. While the convergence of perturbation series and the overall performance of the theory is good, improvements are needed for potentials with shorter ranges. Possible directions for further developments in the coupling-parameter expansion are indicated.

In the simple [hyper]cubic five-dimension, near-neighbor-interaction Ising ferromagnet, extensive simulation measurements are made of the link overlap and the spin overlap distributions. These “two replica” measurements are standard in the spin glass context but are not usually recorded in ferromagnet simulations. The moments and moment ratios of these distributions (the variance, the kurtosis, and the skewness) show clear critical behaviors at the known ordering temperature of the ferromagnet. Analogous overlap effects can be expected quite generally in Ising ferromagnets in any dimension. The link overlap results in particular, with peaks at criticality in the kurtosis and the skewness, also have implications for spin glasses.

A temperature wave method has been applied to observe the thermal diffusivity through the isotropic (Iso)–nematic (N)–smectic Sm-A–Sm-C–Sm-$B$–crystals VI-VII-VIII phase transitions of terephthal-bis-(4-$n$-butylaniline) (TBBA). Critical anomalies have been found in the N–Sm-A and Sm-C–Sm-$B$ phase transitions as diplike shaped, consistent with the predictions based on the dissipative couplings between the order parameter and the conserved free-energy density. Singular points with a gap have been observed at the Sm-$B$–crystal VI, crystals VI-VII, and crystals VII-VIII phase transitions, which show polymorphic behaviors on heating and cooling. The second-order Sm-A–Sm-C phase transition emerged as a singular temperature dependence. In all the phases thermal diffusivity decreases with increasing temperature except for Sm-C, where thermal diffusivity increases with increasing temperature. The origin of the anomaly in the thermal diffusivity in Sm-C is discussed based on the parametric analysis of dynamic critical behavior in the Sm-A–Sm-C phase transitions together with the tilt angle change obtained by use of simultaneous measurements of x-ray diffraction and differential scanning calorimetry.

The nonlinear dynamics of isolated flexible but rotating many-body atomic systems is theoretically investigated, following the dependence on initial conditions through Lyapunov exponents. The tangent-space equations of motion that rule the time evolution of such small perturbations are rewritten in the rotating reference frame, and the various contributions of the centrifugal, Coriolis, and Euler forces are determined. Evaluating the largest Lyapunov in the rotating frame under various approximations, we show on the example of Lennard-Jones clusters that the dynamics in phase space is qualitatively at variance with the effective dynamics on the centrifugal energy surface. Coupling terms between positions and momenta in phase space, especially arising from the Coriolis force, are essential to recover the measure of chaos in the fixed reference frame.

We experimentally examine dissolution-generated, density-driven convection with an inclined boundary in both a Hele-Shaw cell and in a porous medium. The convection, manifested by descending, dense fingers, is generated by a diffusive mixing of two liquids at the interface. We investigate the dynamics, widths, and wavelengths of the fingers and characterize the global convective transport for a wide range of permeabilities and tilt angles of the boundaries. Our results have implications for CO${}_2$ storage in a saline aquifer when brine saturated with CO${}_2$ produces a heavier mixture, which may result in an enhanced mass transfer by convection. Our measurements reveal a further enhancement of convection with inclined boundaries, which suggests that sloping formations provide improved sites for CO${}_2$ storage.

We explore the quantum version of the Brayton cycle with a composite system as the working substance. The actual Brayton cycle consists of two adiabatic and two isobaric processes. Two pressures can be defined in our isobaric process; one corresponds to the external magnetic field (characterized by $F_x$) exerted on the system, while the other corresponds to the coupling constant between the subsystems (characterized by $F_y$). As a consequence, we can define two types of quantum Brayton cycle for the composite system. We find that the subsystem experiences a quantum Brayton cycle in one quantum Brayton cycle (characterized by $F_x$), whereas the subsystem's cycle is quantum Otto cycle in another Brayton cycle (characterized by $F_y$). The efficiency for the composite system equals to that for the subsystem in both cases, but the work done by the total system is usually larger than the sum of the work done by the two subsystems. The other interesting finding is that for the cycle characterized by $F_y$, the subsystem can be a refrigerator, while the total system is a heat engine. The result in this paper can be generalized to a quantum Brayton cycle with a general coupled system as the working substance.

We investigate the critical line separating isotropic from polar phases in an amphiphilic bulk fluid by means of density functional theory (DFT) and Monte Carlo (MC) simulations in the isothermal-isobaric ensemble. The intermolecular interactions are described by a Lennard-Jones potential in which the attractive contribution is modified by an orientation-dependent function. The latter consists of two terms: The first one has the orientation dependence of a classical three-dimensional Heisenberg interaction, whereas, the second one has the orientation dependence of a classical dipole-dipole interaction. However, both contributions are short range. Employing DFT together with a modified mean-field (MMF) approximation for the orientation-dependent pair correlation function, we derive an analytical expression for the critical line separating isotropic from polar liquidlike phases. In parallel MC simulations, we locate the line of critical points through an analysis of Binder's second-order cumulant of the polar-order parameter. Comparison with DFT shows that the dipolelike contribution is irrelevant for the isotropic-polar phase transition. As far as the Heisenberg contribution is concerned, the MC data are in semiquantitative agreement with the DFT predictions for sufficiently strong coupling between molecular orientations. For weaker coupling, the variation in the ratio of critical density and temperature ${\rho }_{\mathrm{c}}/T_{\mathrm{c}}$ with the Heisenberg coupling constant ${\varepsilon }_{\mathrm{H}}$ is underestimated by the MMF treatment. The MC results suggest that this is because ${\rho }_{\mathrm{c}}$ increases with decreasing ${\varepsilon }_{\mathrm{H}}$ such that the assumption on which the MMF approach rests becomes less applicable in the weaker-coupling limit.

We investigate the sedimentation of knotted polymers by means of stochastic rotation dynamics, a molecular dynamics algorithm that takes hydrodynamics fully into account. We show that the sedimentation coefficient $s$, related to the terminal velocity of the knotted polymers, increases linearly with the average crossing number $n_c$ of the corresponding ideal knot. This provides direct computational confirmation of this relation, postulated on the basis of sedimentation experiments by Rybenkov et al. [J. Mol. Biol. 267, 299 (1997)]. Such a relation was previously shown to hold with simulations for knot electrophoresis. We also show that there is an accurate linear dependence of $s$ on the inverse of the radius of gyration $R_g^{-1}$, more specifically with the inverse of the $R_g$ component that is perpendicular to the direction along which the polymer sediments. When the polymer sediments in a slab, the walls affect the results appreciably. However, $R_g^{-1}$ remains to a good precision linearly dependent on $n_c$. Therefore, $R_g^{-1}$ is a good measure of a knot's complexity.

The study of the kinematic and dynamic features of human arm movements provides insights into the computational strategies underlying human motor control. In this paper a differential geometric approach to movement control is taken by endowing arm configuration space with different non-Euclidean metric structures to study the predictions of the generalized minimum-jerk (MJ) model in the resulting Riemannian manifold for different types of human arm movements. For each metric space the solution of the generalized MJ model is given by reparametrized geodesic paths. This geodesic model is applied to a variety of motor tasks ranging from three-dimensional unconstrained movements of a four degree of freedom arm between pointlike targets to constrained movements where the hand location is confined to a surface (e.g., a sphere) or a curve (e.g., an ellipse). For the latter speed-curvature relations are derived depending on the boundary conditions imposed (periodic or nonperiodic) and the compatibility with the empirical one-third power law is shown. Based on these theoretical studies and recent experimental findings, I argue that geodesics may be an emergent property of the motor system and that the sensorimotor system may shape arm configuration space by learning metric structures through sensorimotor feedback.