The free-volume hole relaxation in polycarbonate and poly(methyl methacrylate) with different levels of molecular orientation was studied by positron annihilation lifetime spectroscopy at variable pressures. The molecular orientation was achieved through a simple shear process performed at different temperatures and extrusion rates. It has been demonstrated that the β relaxation is largely responsible for the free-volume hole anisotropy after simple shear orientation. Upon the removal of mechanical force, the deformation of the free volume is mostly reversible at temperatures much lower than the glass transition. No strong correlation between macroscopic deformation and the free-volume hole deformation was found regardless of molecular orientation.

To unveil the electronic states of divalent metal ion incorporated M-DNAs, where M is Mg, Mn, Ni, Co, or Fe, optical absorption spectra have been studied in aqueous solutions of single-stranded (SS) 30mer DNA of poly(dA) (adenine), poly(dG) (guanine), poly(dT) (thymine), poly(dC) (cytosine), salmon-sperm DNA (B-DNA), and M-DNA. The absorption spectrum of the double-stranded (DS) B-DNA can be reproduced with the sum of the four absorption spectra of the SS oligo-DNAs in the ratio corresponding to the composition of B-DNA. This observation suggests that the interactions between complementary strands of DS DNA are negligibly weaker than the bandwidths of the optical spectra. In the metal-incorporated M-DNAs, except for Fe-DNA, the absorption spectra show no significant qualitative change from that of B-DNA. Quantitatively, however, the absorption intensity decreases by $\approx$15% uniquely in a DS poly(dA)-poly(dT) solution with adding ${\text{MCl}}_2$, while nothing happens quantitatively and qualitatively in any SS oligo-DNA and DS poly(dG)-poly(dC) solutions, suggesting some suppression of the electronic excitation only in the Adenine-M-Thymine complex. In contrast, remarkable differences have been observed in Fe-DNA, prepared with ${\text{FeCl}}_2$ and B-DNA. New absorption bands appear in the intragap energy of Fe-DNA, in addition to the suppression of the interband absorption peak of DNA at 4.8 eV. The intragap absorption is attributed to the appearance of Fe${}^{3+}$ species with the same spectral feature as that of ${\text{FeCl}}_3$, that is, purely ionic Fe${}^{3+}$ species. This observation suggests that ${\text{FeCl}}_2+\mathrm{B}$-DNA forms Fe-DNA with hydrated Fe${}^{3+}$ ions with ionic bonds. Thus, it is concluded that the charge transfer from Fe${}^{2+}$ to DNA has occurred in Fe-DNA and that the transferred charges are expected to be located in the nearby bases.

We develop a transition model to interpret single-molecule ricin-aptamer interactions with multiple unbinding pathways and energy barriers measured by atomic force microscopy dynamic force spectroscopy. Molecular simulations establish the relationship between binding conformations and the corresponding unbinding pathways. Each unbinding pathway follows a Bell-Evans multiple-barrier model. Markov-type transition matrices are developed to analyze the redistribution of unbinding events among the pathways under different loading rates. Our study provides detailed information about complex behaviors in ricin-aptamer unbinding events.

Although species longevity is subject to a diverse range of evolutionary forces, the mortality curves of a wide variety of organisms are rather similar. Here we argue that qualitative and quantitative features of aging can be reproduced by a simple model based on the interdependence of fault-prone agents on one other. In addition to fitting our theory to the empiric mortality curves of six very different organisms, we establish the dependence of lifetime and aging rate on initial conditions, damage and repair rate, and system size. We compare the size distributions of disease and death and see that they have qualitatively different properties. We show that aging patterns are independent of the details of interdependence network structure, which suggests that aging is a many-body effect, and that the qualitative and quantitative features of aging are not sensitively dependent on the details of dependency structure or its formation.

We give heuristic arguments and    computer results to support the hypothesis that, after appropriate rescaling, the statistics of spacings between adjacent prime numbers follows the Poisson distribution. The scaling transformation removes the oscillations in the nearest-neighbor-spacing distribution of primes. These oscillations have the very profound period of length six. We also calculate the spectral rigidity ${\Delta }_3$ for prime numbers by two methods. After suitable averaging one of these methods gives the Poisson dependence ${\Delta }_3\left(L\right)=L/15$.

Classical model reduction techniques approximate the solution of a physical model by a limited number of global modes. These modes are usually determined by variants of principal component analysis. Global modes can lead to reduced models that perform well in terms of stability and accuracy. However, when the physics of the model is mainly characterized by advection, the nonlocal representation of the solution by global modes essentially reduces to a Fourier expansion. In this paper we describe a method to determine a low-order representation of advection. This method is based on the solution of Monge-Kantorovich mass transfer problems. Examples of application to point vortex scattering, Korteweg–de Vries equation, and hurricane Dean advection are discussed.

A model for a three-component plasma consisting of two distinct ionic species and electrons is developed and applied to study x-ray Thomson scattering. Ions of a specific type are assumed to be identical and are treated in the average-atom approximation. Given the plasma temperature and density, the model predicts mass densities, effective ionic charges, and cell volumes for each ionic type, together with the plasma chemical potential and free-electron density. Additionally, the average-atom treatment of individual ions provides a quantum-mechanical description of bound and continuum electrons. The model is used to obtain parameters needed to determine the dynamic structure factors for x-ray Thomson scattering from a three-component plasma. The contribution from inelastic scattering by free electrons is evaluated in the random-phase approximation. The contribution from inelastic scattering by bound electrons is evaluated using the bound-state and scattering wave functions obtained from the average-atom calculations. Finally, the partial static structure factors for elastic scattering by ions are evaluated using a two-component version of the Ornstein-Zernike equations with hypernetted chain closure, in which electron-ion interactions are accounted for using screened ion-ion interaction potentials. The model is used to predict the x-ray Thomson scattering spectrum from a CH plasma and the resulting spectrum is compared with experimental results obtained by Feltcher et al. [Phys. Plasmas 20, 056316 (2013)].

We present calculations of x-ray scattering spectra based on ionic and electronic structure factors that are computed from a new model for warm dense matter. In this model, which has no free parameters, the ionic structure is determined consistently with the electronic structure of the bound and free states. The x-ray scattering spectrum is thus fully determined by the plasma temperature, density and nuclear charge, and the experimental parameters. The combined model of warm dense matter and of the x-ray scattering theory is validated against an experiment on room-temperature, solid beryllium. It is then applied to experiments on warm dense beryllium and aluminum. Generally good agreement is found with the experiments. However, some significant discrepancies are revealed and appraised. Based on the strength of our model, we discuss the current state of x-ray scattering experiments on warm dense matter and their potential to determine plasma parameters, to discriminate among models, and to reveal interesting and difficult to model physics in dense plasmas.

In the present paper, we verify the effectiveness of the two-relaxation-time (TRT) collision operator in reducing boundary slip computed by the immersed boundary–lattice Boltzmann method (IB-LBM). In the linear collision operator of the TRT, we decompose the distribution function into symmetric and antisymmetric components and define the relaxation parameters for each part. The Chapman-Enskog expansion indicates that one relaxation time for the symmetric component is related to the kinematic viscosity. Rigorous analysis of the symmetric shear flows reveals that the relaxation time for the antisymmetric part controls the velocity gradient, the boundary velocity, and the boundary slip velocity computed by the IB-LBM. Simulation of the symmetric shear flows, the symmetric Poiseuille flows, and the cylindrical Couette flows indicates that the profiles of the numerical velocity calculated by the TRT collision operator under the IB-LBM framework exactly agree with those of the multirelaxation time (MRT). The TRT is as effective in removing the boundary slip as the MRT. We demonstrate analytically and numerically that the error of the boundary velocity is caused by the smoothing technique using the $\delta$ function used in the interpolation method. In the simulation of the flow past a circular cylinder, the IB-LBM based on the implicit correction method with the TRT succeeds in preventing the flow penetration through the solid surface as well as unphysical velocity distortion. The drag coefficient, the wake length, and the separation points calculated by the present IB-LBM agree well with previous studies at Re = 10, 20, and 40.

Concentrated suspensions may shear thin when the suspended particles form planar sheets that slide over one another with less friction than if the particles are randomly distributed. In a naive model the suspension is described by a mean effective viscosity and particles that collide with each other redistribute the mean density in the shearing direction. This leads to a diffusion equation for the particle density. If the viscosity in the unthinned state is a steeply increasing function of particle density the effective diffusion coefficient is negative and the diffusion equation, meaningful only on scales larger than the particle separation, is ill posed. This singularity corresponds to the formation of planar sheets of particles and defines a critical particle density for the onset of shear thinning.

Nonequilibrium thermodynamics of a general second-order stochastic system is investigated. We prove that at steady state, under inversion of velocities, the condition of time reversibility over the phase space is equivalent to the antisymmetry of spatial flux and the symmetry of velocity flux. Then we show that the condition of time reversibility alone cannot always guarantee the Maxwell-Boltzmann distribution. Comparing the two conditions together, we find that the frictional force naturally emerges as the unique odd term of the total force at thermodynamic equilibrium, and is followed by the Einstein relation. The two conditions respectively correspond to two previously reported different entropy production rates. In the case where the external force is only position dependent, the two entropy production rates become one. We prove that such an entropy production rate can be decomposed into two non-negative terms, expressed respectively by the conditional mean and variance of the thermodynamic force associated with the irreversible velocity flux at any given spatial coordinate. In the small inertia limit, the former term becomes the entropy production rate of the corresponding overdamped dynamics, while the anomalous entropy production rate originates from the latter term. Furthermore, regarding the connection between the first law and second law, we find that in the steady state of such a limit, the anomalous entropy production rate is also the leading order of the Boltzmann-factor weighted difference between the spatial heat dissipation densities of the underdamped and overdamped dynamics, while their unweighted difference always tends to vanish.

The ionic and electronic structures of warm dense silane at the densities of 1.795, 2.260, 3.382, and 3.844 g/cm${}^3$ have been studied with temperatures from 1000 K to 3 eV using quantum molecular dynamics simulations. At all densities, the structures are melted above 1000 K. The matter states are characterized as polymeric from 1000 to 4000 K and become dense plasma states with further increasing temperature to 1 eV. At two lower densities of 1.795 and 2.260 g/cm${}^3$, silane first dissociates and then becomes the polymeric state via a chain state from the initial crystalline structure. At higher densities, however, no dissociation stage was found. These findings can help us understand how the warm dense matter forms. A rise is found for the direct current electric conductivity at $T\sim 1000$ K, indicating the nonmetal-to-metal transition. The conductivity decreases slightly with the increase of temperature, which is due to the more disordered structures at higher temperatures.

The thermal conductivity of rare gases in liquid and dense fluid states has been evaluated using molecular dynamics simulation with the Lennard-Jones (LJ) potentials and the Green-Kubo (GK) formula. All the calculated thermal conductivities are in very good agreement with experimental results for a wide range of temperature and density. Special attention was paid to temperature and packing-fraction dependence which is nontrivial from dimensional analysis on the LJ potentials and the GK formula. First, the temperature dependence of $T^{1/4}$ was determined from the calculations at constant densities. Secondly, in order to obtain the dependence on packing fraction from that on number density separately, a scaling method of particle and/or cell size was introduced. The number density dependence of ${(N/V)}^{2/3}$ which is expected from the dimensional analysis of the GK formulas was confirmed and the packing-fraction dependence of ${\eta }^{3/2}$ was determined by using the scaling method. It turned out that the summarized functional form of $m^{-1/2}$${(N/V)}^{2/3}$${\eta }^{3/2}$$T^{1/4}$ can well express both the calculated and experimental thermal conductivities for Ar, Kr, and Xe, where $m$ is the atomic mass. The scaling method has also been applied to molten NaCl and KCl so that it has been found that the thermal conductivity has the packing-fraction dependence of ${\eta }^{2/3}$ which is much weaker than that of the simple LJ liquids.

In the thermodynamic limit, systems with long-range interactions do not relax to equilibrium, but become trapped in quasistationary states (qSS), the life time of which diverges with the number of particles. In this paper we will explore the relaxation of the Hamiltonian Mean-Field model to qSS for a class of initial conditions of the multilevel water-bag form. We will show that if the initial distribution satisfies the virial condition, thereby reducing mean field changes, the final distribution in the qSS can be predicted very accurately using a reduced exactly integrable model. The calculated distribution functions obtained using this approach are found to be more accurate than the ones predicted by the Lynden-Bell theory.

We use boundary layer analysis for an open system consisting of two parallel totally asymmetric simple exclusion processes with Langmuir kinetics under a biased lane-changing rule. The two kinds of phase transitions—bulk transitions and surface transitions—have been examined. The dynamics of shock and their dependence on the system parameters have been investigated. We find a reduction in the number of steady-state phases with increase in lane-changing rate.

Using a combination of experimental results and discrete particle method simulations, the role of buoyancy-driven convection in the segregative behavior of a three-dimensional, binary granular system is investigated. A relationship between convective motion and segregation intensity is presented, and a qualitative explanation for this behavior is proposed. This study also provides an insight into the role of diffusive behavior in the segregation of a granular bed in the convective regime. The results of this work strongly imply the possibility that, for an adequately fluidized granular bed, the degree of segregation may be indirectly controlled through the adjustment of the system's driving parameters, or the dissipative properties of the system's side-boundaries.

Janus particles present an important class of building blocks for directional assembly. These are compartmentalized colloids with two different hemispheres. Here, we consider a two-dimensional model of Janus disks consisting of a hydrophobic semicircle and an electro-negatively charged one. Placed in a solution, the hydrophobic sides will attract each other while the charged sides will give rise to a repulsive force. Using molecular dynamics simulations, we study the morphology of these particles when confined in a channel-like environment using a one dimensional harmonic confinement potential. The interest to this system is first of all due to the fact that it could serve as a simple model for membrane formation. Indeed, the recently synthesized new class of artificial amphiphiles, known as Janus dendrimers, were shown to self-assemble in bilayer structures mimicking biological membranes. In turn, Janus particles that combine the amphiphilicity and colloidal rigidity serve as a good model for Janus dendrimers. A variety of ordered membrane-like morphologies are found consisting of single and multiple chain configurations with different orientations of the particles with respect to each other that we summarize in a phase diagram.

Cluster growth in a coagulating system of active particles (such as microswimmers in a solvent) is studied by theory and simulation. In contrast to passive systems, the net velocity of a cluster can have various scalings dependent on the propulsion mechanism and alignment of individual particles. Additionally, the persistence length of the cluster trajectory typically increases with size. As a consequence, a growing cluster collects neighboring particles in a very efficient way and thus amplifies its growth further. This results in unusual large growth exponents for the scaling of the cluster size with time and, for certain conditions, even leads to “explosive” cluster growth where the cluster becomes macroscopic in a finite amount of time.